Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae.

Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana.

Sources of bias in the detection and reporting of p53 mutations in human cancer: analysis of the IARC p53 mutation database.
Hernandez-Boussard T, Montesano R, Hainaut P

Finding a mouse: the International Mouse Strain Resource (IMSR).

IRIS: Integrated Risk Information System database.

Combining sensitive database searches with multiple intermediates to detect distant homologues.
Salamov AA, Suwa M, Orengo CA, Swindells MB

Genome analysis: Assigning protein coding regions to three-dimensional structures.

TOXLINE: evolution of an online interactive bibliographic database.

Splicing-independent processing of plant box C/D and box H/ACA small nucleolar RNAs.
Leader DJ, Clark GP, Watters J, Beven AF, Shaw PJ, Brown JW

IARC p53 mutation database: a relational database to compile and analyze p53 mutations in human tumors and cell lines. International Agency for Research on Cancer.
Hernandez-Boussard T, Rodriguez-Tome P, Montesano R, Hainaut P

The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes.
Spradling AC, Stern D, Beaton A, Rhem EJ, Laverty T, Mozden N, Misra S, Rubin GM

A handful of intron-containing genes produces the lion's share of yeast mRNA.

SWEET - WWW-based rapid 3D construction of oligo- and polysaccharides.

Barker WC, Garavelli JS, Huang H, McGarvey PB, Orcutt BC, Srinivasarao GY, Xiao C, Yeh LS, Ledley RS, Janda JF, Pfeiffer F, Mewes HW, Tsugita A, Wu C

Karp PD, Riley M, Saier M, Paulsen IT, Paley SM, Pellegrini-Toole A

EMGLib: the enhanced microbial genomes library (update 2000).

CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000.

INE: a rice genome database with an integrated map view.
Sakata K, Antonio BA, Mukai Y, Nagasaki H, Sakai Y, Makino K, Sasaki T

The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse. The Mouse Genome Database Group.
Blake JA, Eppig JT, Richardson JE, Davisson MT

Maglott DR, Katz KS, Sicotte H, Pruitt KD

MAGEST: MAboya gene expression patterns and sequence tags.
Kawashima T, Kawashima S, Kanehisa M, Nishida H, Makabe KW

BodyMap: a human and mouse gene expression database.
Hishiki T, Kawamoto S, Morishita S, Okubo K

The TIGR gene indices: reconstruction and representation of expressed gene sequences.
Quackenbush J, Liang F, Holt I, Pertea G, Upton J

Szymanski M, Barciszewska MZ, Barciszewski J, Erdmann VA

The RDP (Ribosomal Database Project) continues.
Maidak BL, Cole JR, Lilburn TG, Parker CT, Saxman PR, Stredwick JM, Garrity GM, Li B, Olsen GJ, Pramanik S, Schmidt TM, Tiedje JM

UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs.
Pesole G, Liuni S, Grillo G, Licciulli F, Larizza A, Makalowski W, Saccone C

The prostate expression database (PEDB): status and enhancements in 2000.
Nelson PS, Clegg N, Eroglu B, Hawkins V, Bumgarner R, Smith T, Hood L

IMGT, the international ImMunoGeneTics database.
Ruiz M, Giudicelli V, Ginestoux C, Stoehr P, Robinson J, Bodmer J, Marsh SG, Bontrop R, Lemaitre M, Lefranc G, Chaume D, Lefranc MP

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE

The IMB Jena Image Library of biological macromolecules.
Reichert J, Jabs A, Slickers P, Sühnel J

ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons.

ProTherm, version 2.0: thermodynamic database for proteins and mutants.
Gromiha MM, An J, Kono H, Oobatake M, Uedaira H, Prabakaran P, Sarai A

Hoogland C, Sanchez JC, Tonella L, Binz PA, Bairoch A, Hochstrasser DF, Appel RD

DIP: the database of interacting proteins.
Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D

Codon usage tabulated from international DNA sequence databases: status for the year 2000.

Périer RC, Praz V, Junier T, Bonnard C, Bucher P

HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project.
Kikuno R, Nagase T, Suyama M, Waki M, Hirosawa M, Ohara O

Atlas of genetics and cytogenetics in oncology and haematology, an interactive database.
Huret JL, Minor SL, Dorkeld F, Dessen P, Bernheim A

dbSNP: a database of single nucleotide polymorphisms.
Smigielski EM, Sirotkin K, Ward M, Sherry ST

HGBASE: a database of SNPs and other variations in and around human genes.
Brookes AJ, Lehväslaiho H, Siegfried M, Boehm JG, Yuan YP, Sarkar CM, Bork P, Ortigao F

Keio Mutation Database (KMDB) for human disease gene mutations.
Minoshima S, Mitsuyama S, Ohno S, Kawamura T, Shimizu N

A linkage map of 243 DNA markers in an intercross of Göttingen miniature and Meishan pigs.
Mikawa S, Akita T, Hisamatsu N, Inage Y, Ito Y, Kobayashi E, Kusumoto H, Matsumoto T, Mikami H, Minezawa M, Miyake M, Shimanuki S, Sugiyama C, Uchida Y, Wada Y, Yanai S, Yasue H

Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins.
Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, Sakaki Y

Construction and evaluation of a porcine bacterial artificial chromosome library.
Suzuki K, Asakawa S, Iida M, Shimanuki S, Fujishima N, Hiraiwa H, Murakami Y, Shimizu N, Yasue H

Chromosome of the enterohemorrhagic Escherichia coli O157:H7; comparative analysis with K-12 MG1655 revealed the acquisition of a large amount of foreign DNAs.
Ohnishi M, Tanaka C, Kuhara S, Ishii K, Hattori M, Kurokawa K, Yasunaga T, Makino K, Shinagawa H, Murata T, Nakayama K, Terawaki Y, Hayashi T

A large scale structural analysis of cDNAs in a unicellular green alga, Chlamydomonas reinhardtii. I. Generation of 3433 non-redundant expressed sequence tags.
Asamizu E, Nakamura Y, Sato S, Fukuzawa H, Tabata S

Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development.
Ko MS, Kitchen JR, Wang X, Threat TA, Wang X, Hasegawa A, Sun T, Grahovac MJ, Kargul GJ, Lim MK, Cui Y, Sano Y, Tanaka T, Liang Y, Mason S, Paonessa PD, Sauls AD, DePalma GE, Sharara R, Rowe LB, Eppig J, Morrell C, Doi H

Gottlieb B, Pinsky L, Beitel LK, Trifiro M

Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast.

Complete nucleotide sequence of the prophage VT2-Sakai carrying the verotoxin 2 genes of the enterohemorrhagic Escherichia coli O157:H7 derived from the Sakai outbreak.
Makino K, Yokoyama K, Kubota Y, Yutsudo CH, Kimura S, Kurokawa K, Ishii K, Hattori M, Tatsuno I, Abe H, Iida T, Yamamoto K, Onishi M, Hayashi T, Yasunaga T, Honda T, Sasakawa C, Shinagawa H

Statistical analysis of the 5' untranslated region of human mRNA using "Oligo-Capped" cDNA libraries.
Suzuki Y, Ishihara D, Sasaki M, Nakagawa H, Hata H, Tsunoda T, Watanabe M, Komatsu T, Ota T, Isogai T, Suyama A, Sugano S

Large-scale screening of intracellular protein localization in living fission yeast cells by the use of a GFP-fusion genomic DNA library.
Ding DQ, Tomita Y, Yamamoto A, Chikashige Y, Haraguchi T, Hiraoka Y

Generation of 7137 non-redundant expressed sequence tags from a legume, Lotus japonicus.

Fibrillarin genes encode both a conserved nucleolar protein and a novel small nucleolar RNA involved in ribosomal RNA methylation in Arabidopsis thaliana.

A filamentous phage associated with recent pandemic Vibrio parahaemolyticus O3:K6 strains.
Nasu H, Iida T, Sugahara T, Yamaichi Y, Park KS, Yokoyama K, Makino K, Shinagawa H, Honda T

Cn3D: sequence and structure views for Entrez.
Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH

McGarvey PB, Huang H, Barker WC, Orcutt BC, Garavelli JS, Srinivasarao GY, Yeh LS, Xiao C, Wu CH

Genome-wide analysis of oral cancer--early results from the Cancer Genome Anatomy Project.
Shillitoe EJ, May M, Patel V, Lethanakul C, Ensley JF, Strausberg RL, Gutkind JS

SAGEmap: a public gene expression resource.
Lash AE, Tolstoshev CM, Wagner L, Schuler GD, Strausberg RL, Riggins GJ, Altschul SF

A large scale analysis of cDNA in Arabidopsis thaliana: generation of 12,028 non-redundant expressed sequence tags from normalized and size-selected cDNA libraries.

Analysis of expressed sequence tags of flower buds in Lotus japonicus.
Endo M, Kokubun T, Takahata Y, Higashitani A, Tabata S, Watanabe M

Generation of 10,154 expressed sequence tags from a leafy gametophyte of a marine red alga, Porphyra yezoensis.
Nikaido I, Asamizu E, Nakajima M, Nakamura Y, Saga N, Tabata S

The Cancer Genome Anatomy Project: EST sequencing and the genetics of cancer progression.
Krizman DB, Wagner L, Lash A, Strausberg RL, Emmert-Buck MR

The "Atlas of genetics and cytogenetics in oncology and haematology" on the internet and a review on infant leukemias.
Huret JL, Dessen P, Le Minor S, Bernheim A

Pig cloning by microinjection of fetal fibroblast nuclei.
Onishi A, Iwamoto M, Akita T, Mikawa S, Takeda K, Awata T, Hanada H, Perry AC

Repbase update: a database and an electronic journal of repetitive elements.

STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.

An automatic homology modeling method consisting of database searches and simulated annealing.

Better access to information about clinical trials.

BodyMap: a collection of 3' ESTs for analysis of human gene expression information.
Kawamoto S, Yoshii J, Mizuno K, Ito K, Miyamoto Y, Ohnishi T, Matoba R, Hori N, Matsumoto Y, Okumura T, Nakao Y, Yoshii H, Arimoto J, Ohashi H, Nakanishi H, Ohno I, Hashimoto J, Shimizu K, Maeda K, Kuriyama H, Nishida K, Shimizu-Matsumoto A, Adachi W, Ito R, Kawasaki S, Chae KS

Precise estimation of allele frequencies of single-nucleotide polymorphisms by a quantitative SSCP analysis of pooled DNA.
Sasaki T, Tahira T, Suzuki A, Higasa K, Kukita Y, Baba S, Hayashi K

Generation of expressed sequence tags from low-CO2 and high-CO2 adapted cells of Chlamydomonas reinhardtii.
Asamizu E, Miura K, Kucho K, Inoue Y, Fukuzawa H, Ohyama K, Nakamura Y, Tabata S

Comparative analysis of the whole set of rRNA operons between an enterohemorrhagic Escherichia coli O157:H7 Sakai strain and an Escherichia coli K-12 strain MG1655.
Ohnishi M, Murata T, Nakayama K, Kuhara S, Hattori M, Kurokawa K, Yasunaga T, Yokoyama K, Makino K, Shinagawa H, Hayashi T

Complete nucleotide sequence of the prophage VT1-Sakai carrying the Shiga toxin 1 genes of the enterohemorrhagic Escherichia coli O157:H7 strain derived from the Sakai outbreak.
Yokoyama K, Makino K, Kubota Y, Watanabe M, Kimura S, Yutsudo CH, Kurokawa K, Ishii K, Hattori M, Tatsuno I, Abe H, Yoh M, Iida T, Ohnishi M, Hayashi T, Yasunaga T, Honda T, Sasakawa C, Shinagawa H

Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ, Ghandehari D, Sherman BK, Yu G

Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium.
Kawashima T, Amano N, Koike H, Makino S, Higuchi S, Kawashima-Ohya Y, Watanabe K, Yamazaki M, Kanehori K, Kawamoto T, Nunoshiba T, Yamamoto Y, Aramaki H, Makino K, Suzuki M

Protein Information Resource: a community resource for expert annotation of protein data.
Barker WC, Garavelli JS, Hou Z, Huang H, Ledley RS, McGarvey PB, Mewes HW, Orcutt BC, Pfeiffer F, Tsugita A, Vinayaka CR, Xiao C, Yeh LS, Wu C

CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins.
Kriventseva EV, Fleischmann W, Zdobnov EM, Apweiler R

TIGRFAMs: a protein family resource for the functional identification of proteins.
Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, White O

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.
Apweiler R, Biswas M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Phan I, Zdobnov E

iProClass: an integrated, comprehensive and annotated protein classification database.
Wu CH, Xiao C, Hou Z, Huang H, Barker WC

FULL-malaria: a database for a full-length enriched cDNA library from human malaria parasite, Plasmodium falciparum.
Watanabe J, Sasaki M, Suzuki Y, Sugano S

WormBase: network access to the genome and biology of Caenorhabditis elegans.
Stein L, Sternberg P, Durbin R, Thierry-Mieg J, Spieth J

The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research.
Sprague J, Doerry E, Douglas S, Westerfield M

The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant.
Huala E, Dickerman AW, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, Hanley D, Kiphart D, Zhuang M, Huang W, Mueller LA, Bhattacharyya D, Bhaya D, Sobral BW, Beavis W, Meinke DW, Town CD, Somerville C, Rhee SY

The ARKdb: genome databases for farmed and other animals.
Hu J, Mungall C, Law A, Papworth R, Nelson JP, Brown A, Simpson I, Leckie S, Burt DW, Hillyard AL, Archibald AL

GenMapDB: a database of mapped human BAC clones.
Morley M, Arcaro M, Burdick J, Yonescu R, Reid T, Kirsch IR, Cheung VG

Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM

The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species.
Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J

The RDP-II (Ribosomal Database Project).
Maidak BL, Cole JR, Lilburn TG, Parker CT, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB).

PDBsum: summaries and analyses of PDB structures.

DIP: The Database of Interacting Proteins: 2001 update.
Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D

Szymanski M, Deniziak MA, Barciszewski J

Atlas of Genetics and Cytogenetics in Oncology and Haematology, updated.

dbSNP: the NCBI database of genetic variation.
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K

STRBase: a short tandem repeat DNA database for the human identity testing community.

The KMDB/MutationView: a mutation database for human disease genes.
Minoshima S, Mitsuyama S, Ohtsubo M, Kawamura T, Ito S, Shibamoto S, Ito F, Shimizu N

ICB database: the gyrB database for identification and classification of bacteria.
Watanabe K, Nelson J, Harayama S, Kasai H

Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems.

Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database searches.

TOXNET: an evolving web resource for toxicology and environmental health information.

Quantitative trait loci (QTL) analysis in a Meishan x Göttingen cross population.
Wada Y, Akita T, Awata T, Furukawa T, Sugai N, Inage Y, Ishii K, Ito Y, Kobayashi E, Kusumoto H, Matsumoto T, Mikawa S, Miyake M, Murase A, Shimanuki S, Sugiyama T, Uchida Y, Yanai S, Yasue H

Embarking on rice functional genomics via cDNA microarray: use of 3' UTR probes for specific gene expression analysis.
Yazaki J, Kishimoto N, Nakamura K, Fujii F, Shimbo K, Otsuka Y, Wu J, Yamamoto K, Sakata K, Sasaki T, Kikuchi S

Functional and structural genomics using PEDANT.
Frishman D, Albermann K, Hani J, Heumann K, Metanomski A, Zollner A, Mewes HW

Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays.
Miki R, Kadota K, Bono H, Mizuno Y, Tomaru Y, Carninci P, Itoh M, Shibata K, Kawai J, Konno H, Watanabe S, Sato K, Tokusumi Y, Kikuchi N, Ishii Y, Hamaguchi Y, Nishizuka I, Goto H, Nitanda H, Satomi S, Yoshiki A, Kusakabe M, DeRisi JL, Eisen MB, Iyer VR, Brown PO, Muramatsu M, Shimada H, Okazaki Y, Hayashizaki Y

Contribution of the Tos17 retrotransposon to rice functional genomics.

Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi.
Maeda I, Kohara Y, Yamamoto M, Sugimoto A

Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans.
Reboul J, Vaglio P, Tzellas N, Thierry-Mieg N, Moore T, Jackson C, Shin-i T, Kohara Y, Thierry-Mieg D, Thierry-Mieg J, Lee H, Hitti J, Doucette-Stamm L, Hartley JL, Temple GF, Brasch MA, Vandenhaute J, Lamesch PE, Hill DE, Vidal M

SSCP analysis of point mutations by multicolor capillary electrophoresis.
Hayashi K, Wenz HM, Inazuka M, Tahira T, Sasaki T, Atha DH

Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12.
Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T, Tanaka M, Tobe T, Iida T, Takami H, Honda T, Sasakawa C, Ogasawara N, Yasunaga T, Kuhara S, Shiba T, Hattori M, Shinagawa H

Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana.
Qu LH, Meng Q, Zhou H, Chen YQ, Liang-Hu Q, Qing M, Hui Z, Yue-Qin C

A new cancer genome anatomy project web resource for the community.
Schaefer C, Grouse L, Buetow K, Strausberg RL

A comprehensive two-hybrid analysis to explore the yeast protein interactome.
Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y

Identification and characterization of the potential promoter regions of 1031 kinds of human genes.
Suzuki Y, Tsunoda T, Sese J, Taira H, Mizushima-Sugano J, Hata H, Ota T, Isogai T, Tanaka T, Nakamura Y, Suyama A, Sakaki Y, Morishita S, Okubo K, Sugano S

Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites.
Suzuki Y, Taira H, Tsunoda T, Mizushima-Sugano J, Sese J, Hata H, Ota T, Isogai T, Tanaka T, Morishita S, Okubo K, Sakaki Y, Nakamura Y, Suyama A, Sugano S

A systematic analysis of human disease-associated gene sequences in Drosophila melanogaster.
Reiter LT, Potocki L, Chien S, Gribskov M, Bier E

Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm.

yMGV: a database for visualization and data mining of published genome-wide yeast expression data.

Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive gene duplications generated multiple isoforms predicting new ribosomal RNA 2'-O-methylation sites.
Barneche F, Gaspin C, Guyot R, Echeverría M

MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products.

GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles.
Friedman C, Kra P, Yu H, Krauthammer M, Rzhetsky A

Cell-free translation reconstituted with purified components.
Shimizu Y, Inoue A, Tomari Y, Suzuki T, Yokogawa T, Nishikawa K, Ueda T

PicSNP: a browsable catalog of nonsynonymous single nucleotide polymorphisms in the human genome.

The Cancer Genome Anatomy Project: new resources for reading the molecular signatures of cancer.

Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites.
Omura S, Ikeda H, Ishikawa J, Hanamoto A, Takahashi C, Shinose M, Takahashi Y, Horikawa H, Nakazawa H, Osonoe T, Kikuchi H, Shiba T, Sakaki Y, Hattori M

A functional update of the Escherichia coli K-12 genome.
Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M

Knowledge representation of signal transduction pathways.

Structural and functional features of eukaryotic mRNA untranslated regions.
Pesole G, Mignone F, Gissi C, Grillo G, Licciulli F, Liuni S

Diversification of Escherichia coli genomes: are bacteriophages the major contributors?

LINUCS: linear notation for unique description of carbohydrate sequences.
Bohne-Lang A, Lang E, Förster T, von der Lieth CW

A comparative genomics approach for studying ancestral proteins and evolution.

In silico analysis of cancer through the Cancer Genome Anatomy Project.
Strausberg RL, Greenhut SF, Grouse LH, Schaefer CF, Buetow KH

An integrated analysis and database system for full-length cDNA.
Genome Inform Ser Workshop Genome Inform
Nishikawa T, Murakami K, Harada N, Ota T, Sugiyama T, Nagai K, Irie R, Matui H, Suwa M, Isogai T

Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs.

Thermodynamic database for protein-nucleic acid interactions (ProNIT).
Prabakaran P, An J, Gromiha MM, Selvaraj S, Uedaira H, Kono H, Sarai A

DNA Data Bank of Japan (DDBJ) for genome scale research in life science.
Tateno Y, Imanishi T, Miyazaki S, Fukami-Kobayashi K, Saitou N, Sugawara H, Gojobori T

The Protein Information Resource: an integrated public resource of functional annotation of proteins.
Wu CH, Huang H, Arminski L, Castro-Alvear J, Chen Y, Hu ZZ, Ledley RS, Lewis KC, Mewes HW, Orcutt BC, Suzek BE, Tsugita A, Vinayaka CR, Yeh LS, Zhang J, Barker WC

Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M

BRENDA, enzyme data and metabolic information.

Karp PD, Riley M, Paley SM, Pellegrini-Toole A

Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more.

yMGV: helping biologists with yeast microarray data mining.

Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags.
Kawashima T, Kawashima S, Kohara Y, Kanehisa M, Makabe KW

Homophila: human disease gene cognates in Drosophila.

HOWDY: an integrated database system for human genome research.

JSNP: a database of common gene variations in the Japanese population.
Hirakawa M, Tanaka T, Hashimoto Y, Kuroda M, Takagi T, Nakamura Y

PharmGKB: the Pharmacogenetics Knowledge Base.
Hewett M, Oliver DE, Rubin DL, Easton KL, Stuart JM, Altman RB, Klein TE

The tmRNA Website: invasion by an intron.

HERVd: database of human endogenous retroviruses.

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.

Bono H, Kasukawa T, Hayashizaki Y, Okazaki Y

The human (PEDB) and mouse (mPEDB) Prostate Expression Databases.
Nelson PS, Pritchard C, Abbott D, Clegg N

The IMB Jena Image Library of Biological Macromolecules: 2002 update.

SCOP database in 2002: refinements accommodate structural genomics.
Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG

GTOP: a database of protein structures predicted from genome sequences.
Kawabata T, Fukuchi S, Homma K, Ota M, Araki J, Ito T, Ichiyoshi N, Nishikawa K

[The secondary amenorrhoea -- may be treated by regulation menstruation in our conditions (author's transl)].

ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0.
Gromiha MM, Uedaira H, An J, Selvaraj S, Prabakaran P, Sarai A

The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data.

DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs.
Suzuki Y, Yamashita R, Nakai K, Sugano S

UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002.
Pesole G, Liuni S, Grillo G, Licciulli F, Mignone F, Gissi C, Saccone C

S/MARt DB: a database on scaffold/matrix attached regions.
Liebich I, Bode J, Frisch M, Wingender E

MDB: the Metalloprotein Database and Browser at The Scripps Research Institute.
Castagnetto JM, Hennessy SW, Roberts VA, Getzoff ED, Tainer JA, Pique ME

HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources.
Fredman D, Siegfried M, Yuan YP, Bork P, Lehväslaiho H, Brookes AJ

SWEET-DB: an attempt to create annotated data collections for carbohydrates.
Loss A, Bunsmann P, Bohne A, Loss A, Schwarzer E, Lang E, von der Lieth CW

Multiple snoRNA gene clusters from Arabidopsis.
Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T

BRENDA: a resource for enzyme data and metabolic information.
Schomburg I, Chang A, Hofmann O, Ebeling C, Ehrentreich F, Schomburg D

[GTOP: database for protein 3D structure prediction].

Database and analysis system for cDNA clones obtained from full-length enriched cDNA libraries.
Nishikawa T, Ota T, Kawai Y, Ishii S, Saito K, Yamamoto J, Wakamatsu A, Ozawa M, Suzuki Y, Sugano S, Isogai T

The EBI SRS server--recent developments.
Zdobnov EM, Lopez R, Apweiler R, Etzold T

Comparison of sequences of cDNA clones obtained from oligo-capping cDNA libraries with those from unigene.
Nishikawa T, Ota T, Kawai Y, Ishii S, Saito K, Yamamoto JI, Wakamatsu A, Ozawa M, Suzuki Y, Sugano S, Isocal T

Genome-wide transcriptional orchestration of circadian rhythms in Drosophila.
Ueda HR, Matsumoto A, Kawamura M, Iino M, Tanimura T, Hashimoto S

The Mouse Tumor Biology Database: a public resource for cancer genetics and pathology of the mouse.
Näf D, Krupke DM, Sundberg JP, Eppig JT, Bult CJ

Functional annotation of a full-length Arabidopsis cDNA collection.
Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y, Muramatsu M, Hayashizaki Y, Kawai J, Carninci P, Itoh M, Ishii Y, Arakawa T, Shibata K, Shinagawa A, Shinozaki K

Functional genomics of the social amoebae, Dictyostelium discoideum.

Physiological genomics of Escherichia coli protein families.

cDNA microarray analysis of gene expression during Fe-deficiency stress in barley suggests that polar transport of vesicles is implicated in phytosiderophore secretion in Fe-deficient barley roots.
Negishi T, Nakanishi H, Yazaki J, Kishimoto N, Fujii F, Shimbo K, Yamamoto K, Sakata K, Sasaki T, Kikuchi S, Mori S, Nishizawa NK

Thermodynamic databases for proteins and protein-nucleic acid interactions.
Sarai A, Gromiha MM, An J, Prabakaran P, Selvaraj S, Kono H, Oobatake M, Uedaira H

Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays.

The IARC TP53 database: new online mutation analysis and recommendations to users.
Olivier M, Eeles R, Hollstein M, Khan MA, Harris CC, Hainaut P

[LIPIDBANK for Web, the newly developed lipid database].

Searching yeast intron data at Ares lab Web site.

An international database and integrated analysis tools for the study of cancer gene expression.
Strausberg RL, Camargo AA, Riggins GJ, Schaefer CF, de Souza SJ, Grouse LH, Lal A, Buetow KH, Boon K, Greenhut SF, Simpson AJ

An anatomy of normal and malignant gene expression.
Boon K, Osorio EC, Greenhut SF, Schaefer CF, Shoemaker J, Polyak K, Morin PJ, Buetow KH, Strausberg RL, De Souza SJ, Riggins GJ

A novel gene organization: intronic snoRNA gene clusters from Oryza sativa.
Liang D, Zhou H, Zhang P, Chen YQ, Chen X, Chen CL, Qu LH

Comparison of genome structures of vibrios, bacteria possessing two chromosomes.

Intercellular coupling mechanism for synchronized and noise-resistant circadian oscillators.

A transcription factor response element for gene expression during circadian night.
Ueda HR, Chen W, Adachi A, Wakamatsu H, Hayashi S, Takasugi T, Nagano M, Nakahama K, Suzuki Y, Sugano S, Iino M, Shigeyoshi Y, Hashimoto S

Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray.
Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Taji T, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K

Filamentous bacteriophages of vibrios are integrated into the dif-like site of the host chromosome.
Iida T, Makino K, Nasu H, Yokoyama K, Tagomori K, Hattori A, Okuno T, Shinagawa H, Honda T

A new resource of locally transposed Dissociation elements for screening gene-knockout lines in silico on the Arabidopsis genome.
Ito T, Motohashi R, Kuromori T, Mizukado S, Sakurai T, Kanahara H, Seki M, Shinozaki K

Oligosaccharide specificity of galectins: a search by frontal affinity chromatography.
Hirabayashi J, Hashidate T, Arata Y, Nishi N, Nakamura T, Hirashima M, Urashima T, Oka T, Futai M, Muller WE, Yagi F, Kasai K

ProDom: automated clustering of homologous domains.
Servant F, Bru C, Carrère S, Courcelle E, Gouzy J, Peyruc D, Kahn D

PROSITE: a documented database using patterns and profiles as motif descriptors.
Sigrist CJ, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P

A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome.
Homma K, Fukuchi S, Kawabata T, Ota M, Nishikawa K

GETDB, a database compiling expression patterns and molecular locations of a collection of Gal4 enhancer traps.
Hayashi S, Ito K, Sado Y, Taniguchi M, Akimoto A, Takeuchi H, Aigaki T, Matsuzaki F, Nakagoshi H, Tanimura T, Ueda R, Uemura T, Yoshihara M, Goto S

Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12.
Oshima T, Aiba H, Masuda Y, Kanaya S, Sugiura M, Wanner BL, Mori H, Mizuno T

CDART: protein homology by domain architecture.
Geer LY, Domrachev M, Lipman DJ, Bryant SH

Annotating regulatory DNA based on man-mouse genomic comparison.
Dieterich C, Cusack B, Wang H, Rateitschak K, Krause A, Vingron M

GeneCards 2002: towards a complete, object-oriented, human gene compendium.
Safran M, Solomon I, Shmueli O, Lapidot M, Shen-Orr S, Adato A, Ben-Dor U, Esterman N, Rosen N, Peter I, Olender T, Chalifa-Caspi V, Lancet D

Functional SNPs in the lymphotoxin-alpha gene that are associated with susceptibility to myocardial infarction.
Ozaki K, Ohnishi Y, Iida A, Sekine A, Yamada R, Tsunoda T, Sato H, Sato H, Hori M, Nakamura Y, Tanaka T

Gene-based SNP discovery as part of the Japanese Millennium Genome Project: identification of 190,562 genetic variations in the human genome. Single-nucleotide polymorphism.
Haga H, Yamada R, Ohnishi Y, Nakamura Y, Tanaka T

Visualization by comprehensive microarray analysis of gene expression programs during transdifferentiation of mesophyll cells into xylem cells.
Demura T, Tashiro G, Horiguchi G, Kishimoto N, Kubo M, Matsuoka N, Minami A, Nagata-Hiwatashi M, Nakamura K, Okamura Y, Sassa N, Suzuki S, Yazaki J, Kikuchi S, Fukuda H

TAIR: a resource for integrated Arabidopsis data.
Garcia-Hernandez M, Berardini TZ, Chen G, Crist D, Doyle A, Huala E, Knee E, Lambrecht M, Miller N, Mueller LA, Mundodi S, Reiser L, Rhee SY, Scholl R, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P

Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray.
Seki M, Ishida J, Narusaka M, Fujita M, Nanjo T, Umezawa T, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K

Hemi-stranded SSCP analysis of SNPs in short sequence-tagged sites.

The cancer genome anatomy project: online resources to reveal the molecular signatures of cancer.
Strausberg RL, Buetow KH, Greenhut SF, Grouse LH, Schaefer CF

Prediction of the coding sequences of mouse homologues of KIAA gene: I. The complete nucleotide sequences of 100 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries.
Okazaki N, Kikuno R, Ohara R, Inamoto S, Hara Y, Nagase T, Ohara O, Koga H

The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans.
Sasaki Y, Ishikawa J, Yamashita A, Oshima K, Kenri T, Furuya K, Yoshino C, Horino A, Shiba T, Sasaki T, Hattori M

The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants.
Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, Nakazono M, Hirai A, Kadowaki K

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.
['Strausberg RL', 'Feingold EA', 'Grouse LH', 'Derge JG', 'Klausner RD', 'Collins FS', 'Wagner L', 'Shenmen CM', 'Schuler GD', 'Altschul SF', 'Zeeberg B', 'Buetow KH', 'Schaefer CF', 'Bhat NK', 'Hopkins RF', 'Jordan H', 'Moore T', 'Max SI', 'Wang J', 'Hsieh F', 'Diatchenko L', 'Marusina K', 'Farmer AA', 'Rubin GM', 'Hong L', 'Stapleton M', 'Soares MB', 'Bonaldo MF', 'Casavant TL', 'Scheetz TE', 'Brownstein MJ', 'Usdin TB', 'Toshiyuki S', 'Carninci P', 'Prange C', 'Raha SS', 'Loquellano NA', 'Peters GJ', 'Abramson RD', 'Mullahy SJ', 'Bosak SA', 'McEwan PJ', 'McKernan KJ', 'Malek JA', 'Gunaratne PH', 'Richards S', 'Worley KC', 'Hale S', 'Garcia AM', 'Gay LJ', 'Hulyk SW', 'Villalon DK', 'Muzny DM', 'Sodergren EJ', 'Lu X', 'Gibbs RA', 'Fahey J', 'Helton E', 'Ketteman M', 'Madan A', 'Rodrigues S', 'Sanchez A', 'Whiting M', 'Madan A', 'Young AC', 'Shevchenko Y', 'Bouffard GG', 'Blakesley RW', 'Touchman JW', 'Green ED', 'Dickson MC', 'Rodriguez AC', 'Grimwood J', 'Schmutz J', 'Myers RM', 'Butterfield YS', 'Krzywinski MI', 'Skalska U', 'Smailus DE', 'Schnerch A', 'Schein JE', 'Jones SJ', 'Marra MA']

Genomic diversity of enterohemorrhagic Escherichia coli O157 revealed by whole genome PCR scanning.
Ohnishi M, Terajima J, Kurokawa K, Nakayama K, Murata T, Tamura K, Ogura Y, Watanabe H, Hayashi T

Multiple promoter inversions generate surface antigenic variation in Mycoplasma penetrans.

Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae.

SNP detection and allele frequency determination by SSCP.

CORG: a database for COmparative Regulatory Genomics.
Dieterich C, Wang H, Rateitschak K, Luz H, Vingron M

MBGD: microbial genome database for comparative analysis.

ArrayExpress--a public repository for microarray gene expression data at the EBI.
Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA

MEPD: a Medaka gene expression pattern database.
['Henrich T', 'Ramialison M', 'Quiring R', 'Wittbrodt B', 'Furutani-Seiki M', 'Wittbrodt J', 'Kondoh H']

The Stanford Microarray Database: data access and quality assessment tools.
Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, Hebert JM, Hernandez-Boussard T, Jin H, Kaloper M, Matese JC, Schroeder M, Brown PO, Botstein D, Sherlock G

ASAP: the Alternative Splicing Annotation Project.

WormBase: a cross-species database for comparative genomics.
Harris TW, Lee R, Schwarz E, Bradnam K, Lawson D, Chen W, Blasier D, Kenny E, Cunningham F, Kishore R, Chan J, Muller HM, Petcherski A, Thorisson G, Day A, Bieri T, Rogers A, Chen CK, Spieth J, Sternberg P, Durbin R, Stein LD

GrainGenes, the genome database for small-grain crops.
Matthews DE, Carollo VL, Lazo GR, Anderson OD

Frishman D, Mokrejs M, Kosykh D, Kastenmüller G, Kolesov G, Zubrzycki I, Gruber C, Geier B, Kaps A, Albermann K, Volz A, Wagner C, Fellenberg M, Heumann K, Mewes HW

The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.
Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P

WorfDB: the Caenorhabditis elegans ORFeome Database.
Vaglio P, Lamesch P, Reboul J, Rual JF, Martinez M, Hill D, Vidal M

STRING: a database of predicted functional associations between proteins.
von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B

Studies on energy-linked reactions: isolation, characterisation and genetic analysis of trialkyl-tin-resistant mutants of Saccharomyces cerevisiae.

Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003.

Online Mendelian Inheritance in Animals (OMIA): a comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals.

Wu CH, Yeh LS, Huang H, Arminski L, Castro-Alvear J, Chen Y, Hu Z, Kourtesis P, Ledley RS, Suzek BE, Vinayaka CR, Zhang J, Barker WC

The TIGRFAMs database of protein families.

Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters.

iProClass: an integrated database of protein family, function and structure information.

TMPDB: a database of experimentally-characterized transmembrane topologies.

Brown JW, Echeverria M, Qu LH, Lowe TM, Bachellerie JP, Hüttenhofer A, Kastenmayer JP, Green PJ, Shaw P, Marshall DF

Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR

The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy.
['Cole JR', 'Chai B', 'Marsh TL', 'Farris RJ', 'Wang Q', 'Kulam SA', 'Chandra S', 'McGarrell DM', 'Schmidt TM', 'Garrity GM', 'Tiedje JM']

Zwieb C, Gorodkin J, Knudsen B, Burks J, Wower J

Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species.
Yamaguchi A, Iwadate M, Suzuki E, Yura K, Kawakita S, Umeyama H, Go M

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003.

RNABase: an annotated database of RNA structures.

Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins.
Fukami-Kobayashi K, Tateno Y, Nishikawa K

Gene discovery in oral squamous cell carcinoma through the Head and Neck Cancer Genome Anatomy Project: confirmation by microarray analysis.
['Leethanakul C', 'Knezevic V', 'Patel V', 'Amornphimoltham P', 'Gillespie J', 'Shillitoe EJ', 'Emko P', 'Park MH', 'Emmert-Buck MR', 'Strausberg RL', 'Krizman DB', 'Gutkind JS']

Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae.
Makino K, Oshima K, Kurokawa K, Yokoyama K, Uda T, Tagomori K, Iijima Y, Najima M, Nakano M, Yamashita A, Kubota Y, Kimura S, Yasunaga T, Honda T, Shinagawa H, Hattori M, Iida T

Unique amino acid composition of proteins in halophilic bacteria.
Fukuchi S, Yoshimune K, Wakayama M, Moriguchi M, Nishikawa K

Development of 50 gene-associated microsatellite markers using BAC clones and the construction of a linkage map of swine chromosome 4.
Fujishima-Kanaya N, Toki D, Suzuki K, Sawazaki T, Hiraiwa H, Iida M, Hayashi T, Uenishi H, Wada Y, Ito Y, Awata T

[Orphanet, an information site on rare diseases].

C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression.
Reboul J, Vaglio P, Rual JF, Lamesch P, Martinez M, Armstrong CM, Li S, Jacotot L, Bertin N, Janky R, Moore T, Hudson JR, Hartley JL, Brasch MA, Vandenhaute J, Boulton S, Endress GA, Jenna S, Chevet E, Papasotiropoulos V, Tolias PP, Ptacek J, Snyder M, Huang R, Chance MR, Lee H, Doucette-Stamm L, Hill DE, Vidal M

Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis J, Christiansen LC, Danchin A, Débarbouille M, Dervyn E, Deuerling E, Devine K, Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R, Eschevins C, Fukushima T, Haga K, Harwood CR, Hecker M, Hosoya D, Hullo MF, Kakeshita H, Karamata D, Kasahara Y, Kawamura F, Koga K, Koski P, Kuwana R, Imamura D, Ishimaru M, Ishikawa S, Ishio I, Le Coq D, Masson A, Mauël C, Meima R, Mellado RP, Moir A, Moriya S, Nagakawa E, Nanamiya H, Nakai S, Nygaard P, Ogura M, Ohanan T, O'Reilly M, O'Rourke M, Pragai Z, Pooley HM, Rapoport G, Rawlins JP, Rivas LA, Rivolta C, Sadaie A, Sadaie Y, Sarvas M, Sato T, Saxild HH, Scanlan E, Schumann W, Seegers JF, Sekiguchi J, Sekowska A, Séror SJ, Simon M, Stragier P, Studer R, Takamatsu H, Tanaka T, Takeuchi M, Thomaides HB, Vagner V, van Dijl JM, Watabe K, Wipat A, Yamamoto H, Yamamoto M, Yamamoto Y, Yamane K, Yata K, Yoshida K, Yoshikawa H, Zuber U, Ogasawara N

Human chromosome 7: DNA sequence and biology.
Scherer SW, Cheung J, MacDonald JR, Osborne LR, Nakabayashi K, Herbrick JA, Carson AR, Parker-Katiraee L, Skaug J, Khaja R, Zhang J, Hudek AK, Li M, Haddad M, Duggan GE, Fernandez BA, Kanematsu E, Gentles S, Christopoulos CC, Choufani S, Kwasnicka D, Zheng XH, Lai Z, Nusskern D, Zhang Q, Gu Z, Lu F, Zeesman S, Nowaczyk MJ, Teshima I, Chitayat D, Shuman C, Weksberg R, Zackai EH, Grebe TA, Cox SR, Kirkpatrick SJ, Rahman N, Friedman JM, Heng HH, Pelicci PG, Lo-Coco F, Belloni E, Shaffer LG, Pober B, Morton CC, Gusella JF, Bruns GA, Korf BR, Quade BJ, Ligon AH, Ferguson H, Higgins AW, Leach NT, Herrick SR, Lemyre E, Farra CG, Kim HG, Summers AM, Gripp KW, Roberts W, Szatmari P, Winsor EJ, Grzeschik KH, Teebi A, Minassian BA, Kere J, Armengol L, Pujana MA, Estivill X, Wilson MD, Koop BF, Tosi S, Moore GE, Boright AP, Zlotorynski E, Kerem B, Kroisel PM, Petek E, Oscier DG, Mould SJ, Döhner H, Döhner K, Rommens JM, Vincent JB, Venter JC, Li PW, Mural RJ, Adams MD, Tsui LC

Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis.
Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, Omura S

Prediction of the coding sequences of mouse homologues of KIAA gene: II. The complete nucleotide sequences of 400 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries.
Okazaki N, Kikuno R, Ohara R, Inamoto S, Aizawa H, Yuasa S, Nakajima D, Nagase T, Ohara O, Koga H

Construction of a full-length enriched and a 5'-end enriched cDNA library using the oligo-capping method.

Analysis of 5'-end sequences of chimpanzee cDNAs.
Sakate R, Osada N, Hida M, Sugano S, Hayasaka I, Shimohira N, Yanagi S, Suto Y, Hashimoto K, Hirai M

Novel gene encoding a Ca2+-binding protein and under hexokinase-dependent sugar regulation.
Otsuki S, Ikeda A, Sunako T, Muto S, Yazaki J, Nakamura K, Fujii F, Shimbo K, Otsuka Y, Yamamoto K, Sakata K, Sasaki T, Kishimoto N, Kikuchi S, Yamaguchi J

The Cancer Genome Anatomy Project: power tools for cancer biologists.

New allele frequency database: http://www.allelefrequencies.net.
Middleton D, Menchaca L, Rood H, Komerofsky R

Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins.
Kaji H, Saito H, Yamauchi Y, Shinkawa T, Taoka M, Hirabayashi J, Kasai K, Takahashi N, Isobe T

Construction of a new porcine whole-genome framework map using a radiation hybrid panel.
Hamasima N, Suzuki H, Mikawa A, Morozumi T, Plastow G, Mitsuhashi T

Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures.

[The integrated database for mutations in disease-causing genes: Mutation View/KMDB].

Changing patterns of gene expression in dictyostelium prestalk cell subtypes recognized by in situ hybridization with genes from microarray analyses.
Maeda M, Sakamoto H, Iranfar N, Fuller D, Maruo T, Ogihara S, Morio T, Urushihara H, Tanaka Y, Loomis WF

Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution.
Nakagawa I, Kurokawa K, Yamashita A, Nakata M, Tomiyasu Y, Okahashi N, Kawabata S, Yamazaki K, Shiba T, Yasunaga T, Hayashi H, Hattori M, Hamada S

Kinase pathway database: an integrated protein-kinase and NLP-based protein-interaction resource.

Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution.
Nishiyama T, Fujita T, Shin-I T, Seki M, Nishide H, Uchiyama I, Kamiya A, Carninci P, Hayashizaki Y, Shinozaki K, Kohara Y, Hasebe M

IMGT/PhyloGene: an on-line tool for comparative analysis of immunoglobulin and T cell receptor genes.

Inferring higher functional information for RIKEN mouse full-length cDNA clones with FACTS.
Nagashima T, Silva DG, Petrovsky N, Socha LA, Suzuki H, Saito R, Kasukawa T, Kurochkin IV, Konagaya A, Schönbach C

AHMII: Agent to Help Microbial Information Integration.

ExPASy: The proteomics server for in-depth protein knowledge and analysis.
Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A

Microarray analysis of embryonic retinoic acid target genes in the ascidian Ciona intestinalis.
Ishibashi T, Nakazawa M, Ono H, Satoh N, Gojobori T, Fujiwara S

Protein informatics towards function identification.

Identification of protein functions from a molecular surface database, eF-site.

GeneLoc: exon-based integration of human genome maps.
Rosen N, Chalifa-Caspi V, Shmueli O, Adato A, Lapidot M, Stampnitzky J, Safran M, Lancet D

Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.

Genomic structure around joining segments and constant regions of swine T-cell receptor alpha/delta (TRA/TRD) locus.
Uenishi H, Hiraiwa H, Yamamoto R, Yasue H, Takagaki Y, Shiina T, Kikkawa E, Inoko H, Awata T

Conservation of the syntenies between porcine chromosome 7 and human chromosomes 6, 14 and 15 demonstrated by radiation hybrid mapping and linkage analysis.
Tanaka M, Matsumoto T, Yanai S, Domukai M, Toki D, Hayashi T, Kiuchi S, Yasue H, Uenishi H, Kobayashi E, Awata T

Identification of protein biochemical functions by similarity search using the molecular surface database eF-site.

Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8.
Handa N, Terada T, Kamewari Y, Hamana H, Tame JR, Park SY, Kinoshita K, Ota M, Nakamura H, Kuramitsu S, Shirouzu M, Yokoyama S

Cytochrome p450 complement (CYPome) of the avermectin-producer Streptomyces avermitilis and comparison to that of Streptomyces coelicolor A3(2).
Lamb DC, Ikeda H, Nelson DR, Ishikawa J, Skaug T, Jackson C, Omura S, Waterman MR, Kelly SL

Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome.
Miyao A, Tanaka K, Murata K, Sawaki H, Takeda S, Abe K, Shinozuka Y, Onosato K, Hirochika H

Dynamic molecules: molecular dynamics for everyone. An internet-based access to molecular dynamic simulations: basic concepts.
Frank M, Gutbrod P, Hassayoun C, von Der Lieth CW

Rice gene expression in response to N-acetylchitooligosaccharide elicitor: comprehensive analysis by DNA microarray with randomly selected ESTs.
Akimoto-Tomiyama C, Sakata K, Yazaki J, Nakamura K, Fujii F, Shimbo K, Yamamoto K, Sasaki T, Kishimoto N, Kikuchi S, Shibuya N, Minami E

Frontal affinity chromatography as a tool for elucidation of sugar recognition properties of lectins.

The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA

First RFLP linkage map of red clover ( Trifolium pratense L.) based on cDNA probes and its transferability to other red clover germplasm.
Isobe S, Klimenko I, Ivashuta S, Gau M, Kozlov NN

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids.
Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, Demeny T, Hsieh SH, Srinivasan AR, Schneider B

Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways.

An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.
Zeller KI, Jegga AG, Aronow BJ, O'Donnell KA, Dang CV

The novel MYB protein EARLY-PHYTOCHROME-RESPONSIVE1 is a component of a slave circadian oscillator in Arabidopsis.
Kuno N, Møller SG, Shinomura T, Xu X, Chua NH, Furuya M

Activation of a plant gene by T-DNA tagging: auxin-independent growth in vitro.
Hayashi H, Czaja I, Lubenow H, Schell J, Walden R

Comparative analysis of the genomes of cyanobacteria and plants.

Quantitative metabolome analysis using capillary electrophoresis mass spectrometry.
Soga T, Ohashi Y, Ueno Y, Naraoka H, Tomita M, Nishioka T

A gene expression atlas of the central nervous system based on bacterial artificial chromosomes.
Gong S, Zheng C, Doughty ML, Losos K, Didkovsky N, Schambra UB, Nowak NJ, Joyner A, Leblanc G, Hatten ME, Heintz N

The yeast mitochondrial proteome, a study of fermentative and respiratory growth.
Ohlmeier S, Kastaniotis AJ, Hiltunen JK, Bergmann U

The construction of an EST database for Bombyx mori and its application.
Mita K, Morimyo M, Okano K, Koike Y, Nohata J, Kawasaki H, Kadono-Okuda K, Yamamoto K, Suzuki MG, Shimada T, Goldsmith MR, Maeda S

Prediction of the coding sequences of mouse homologues of KIAA gene: III. the complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries.
Okazaki N, Kikuno R, Ohara R, Inamoto S, Koseki H, Hiraoka S, Saga Y, Nagase T, Ohara O, Koga H

Announcing the worldwide Protein Data Bank.

High-resolution yeast phenomics resolves different physiological features in the saline response.
Warringer J, Ericson E, Fernandez L, Nerman O, Blomberg A

ACLAME: a CLAssification of Mobile genetic Elements.
Leplae R, Hebrant A, Wodak SJ, Toussaint A

HERVd: the Human Endogenous RetroViruses Database: update.
Paces J, Pavlícek A, Zika R, Kapitonov VV, Jurka J, Paces V

Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities.

Xpro: database of eukaryotic protein-encoding genes.
Gopalan V, Tan TW, Lee BT, Ranganathan S

DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics.

The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.
Schmid CD, Praz V, Delorenzi M, Périer R, Bucher P

HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development.

The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts.

ProTherm, version 4.0: thermodynamic database for proteins and mutants.
Bava KA, Gromiha MM, Uedaira H, Kitajima K, Sarai A

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.

ESTHER, the database of the alpha/beta-hydrolase fold superfamily of proteins.
Hotelier T, Renault L, Cousin X, Negre V, Marchot P, Chatonnet A

RPG: the Ribosomal Protein Gene database.

SCOP database in 2004: refinements integrate structure and sequence family data.
Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG

The KEGG resource for deciphering the genome.
Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M

GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins.

SCMD: Saccharomyces cerevisiae Morphological Database.
Saito TL, Ohtani M, Sawai H, Sano F, Saka A, Watanabe D, Yukawa M, Ohya Y, Morishita S

dictyBase: a new Dictyostelium discoideum genome database.
Kreppel L, Fey P, Gaudet P, Just E, Kibbe WA, Chisholm RL, Kimmel AR

Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species.
Watanabe J, Suzuki Y, Sasaki M, Sugano S

The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants.

The Rice PIPELINE: a unification tool for plant functional genomics.
Yazaki J, Kojima K, Suzuki K, Kishimoto N, Kikuchi S

Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003.
Komatsu S, Kojima K, Suzuki K, Ozaki K, Higo K

MaizeGDB, the community database for maize genetics and genomics.
Lawrence CJ, Dong Q, Polacco ML, Seigfried TE, Brendel V

WormBase: a multi-species resource for nematode biology and genomics.
Harris TW, Chen N, Cunningham F, Tello-Ruiz M, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Chan J, Chen CK, Chen WJ, Davis P, Kenny E, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Ozersky P, Petcherski A, Rogers A, Sabo A, Schwarz EM, Van Auken K, Wang Q, Durbin R, Spieth J, Sternberg PW, Stein LD

BRENDA, the enzyme database: updates and major new developments.
Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D

IntEnz, the integrated relational enzyme database.
Fleischmann A, Darsow M, Degtyarenko K, Fleischmann W, Boyce S, Axelsen KB, Bairoch A, Schomburg D, Tipton KF, Apweiler R

MetaCyc: a multiorganism database of metabolic pathways and enzymes.
Krieger CJ, Zhang P, Mueller LA, Wang A, Paley S, Arnaud M, Pick J, Rhee SY, Karp PD

The Database of Interacting Proteins: 2004 update.
Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D

FREP: a database of functional repeats in mouse cDNAs.
['Nagashima T', 'Matsuda H', 'Silva DG', 'Petrovsky N', 'Konagaya A', 'Schönbach C', 'Kasukawa T', 'Arakawa T', 'Carninci P', 'Kawai J', 'Hayashizaki Y']

The Mouse SAGE Site: database of public mouse SAGE libraries.

PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries.
Uenishi H, Eguchi T, Suzuki K, Sawazaki T, Toki D, Shinkai H, Okumura N, Hamasima N, Awata T

HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE.
Kikuno R, Nagase T, Nakayama M, Koga H, Okazaki N, Nakajima D, Ohara O

RTCGD: retroviral tagged cancer gene database.
Akagi K, Suzuki T, Stephens RM, Jenkins NA, Copeland NG

CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature.

EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes.
Nikaido I, Saito C, Wakamoto A, Tomaru Y, Arakawa T, Hayashizaki Y, Okazaki Y

GermOnline, a cross-species community knowledgebase on germ cell differentiation.
Wiederkehr C, Basavaraj R, Sarrauste de Menthière C, Hermida L, Koch R, Schlecht U, Amon A, Brachat S, Breitenbach M, Briza P, Caburet S, Cherry M, Davis R, Deutschbauer A, Dickinson HG, Dumitrescu T, Fellous M, Goldman A, Grootegoed JA, Hawley R, Ishii R, Jégou B, Kaufman RJ, Klein F, Lamb N, Maro B, Nasmyth K, Nicolas A, Orr-Weaver T, Philippsen P, Pineau C, Rabitsch KP, Reinke V, Roest H, Saunders W, Schröder M, Schedl T, Siep M, Villeneuve A, Wolgemuth DJ, Yamamoto M, Zickler D, Esposito RE, Primig M

Complete sequencing and characterization of 21,243 full-length human cDNAs.
Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, Kimura K, Makita H, Sekine M, Obayashi M, Nishi T, Shibahara T, Tanaka T, Ishii S, Yamamoto J, Saito K, Kawai Y, Isono Y, Nakamura Y, Nagahari K, Murakami K, Yasuda T, Iwayanagi T, Wagatsuma M, Shiratori A, Sudo H, Hosoiri T, Kaku Y, Kodaira H, Kondo H, Sugawara M, Takahashi M, Kanda K, Yokoi T, Furuya T, Kikkawa E, Omura Y, Abe K, Kamihara K, Katsuta N, Sato K, Tanikawa M, Yamazaki M, Ninomiya K, Ishibashi T, Yamashita H, Murakawa K, Fujimori K, Tanai H, Kimata M, Watanabe M, Hiraoka S, Chiba Y, Ishida S, Ono Y, Takiguchi S, Watanabe S, Yosida M, Hotuta T, Kusano J, Kanehori K, Takahashi-Fujii A, Hara H, Tanase TO, Nomura Y, Togiya S, Komai F, Hara R, Takeuchi K, Arita M, Imose N, Musashino K, Yuuki H, Oshima A, Sasaki N, Aotsuka S, Yoshikawa Y, Matsunawa H, Ichihara T, Shiohata N, Sano S, Moriya S, Momiyama H, Satoh N, Takami S, Terashima Y, Suzuki O, Nakagawa S, Senoh A, Mizoguchi H, Goto Y, Shimizu F, Wakebe H, Hishigaki H, Watanabe T, Sugiyama A, Takemoto M, Kawakami B, Yamazaki M, Watanabe K, Kumagai A, Itakura S, Fukuzumi Y, Fujimori Y, Komiyama M, Tashiro H, Tanigami A, Fujiwara T, Ono T, Yamada K, Fujii Y, Ozaki K, Hirao M, Ohmori Y, Kawabata A, Hikiji T, Kobatake N, Inagaki H, Ikema Y, Okamoto S, Okitani R, Kawakami T, Noguchi S, Itoh T, Shigeta K, Senba T, Matsumura K, Nakajima Y, Mizuno T, Morinaga M, Sasaki M, Togashi T, Oyama M, Hata H, Watanabe M, Komatsu T, Mizushima-Sugano J, Satoh T, Shirai Y, Takahashi Y, Nakagawa K, Okumura K, Nagase T, Nomura N, Kikuchi H, Masuho Y, Yamashita R, Nakai K, Yada T, Nakamura Y, Ohara O, Isogai T, Sugano S

GeneAnnot: interfacing GeneCards with high-throughput gene expression compendia.
Chalifa-Caspi V, Shmueli O, Benjamin-Rodrig H, Rosen N, Shmoish M, Yanai I, Ophir R, Kats P, Safran M, Lancet D

Automated indexing of the Hazardous Substances Data Bank (HSDB).

ArrayExpress: a public database of gene expression data at EBI.
Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA

CIBEX: center for information biology gene expression database.
Ikeo K, Ishi-i J, Tamura T, Gojobori T, Tateno Y

Gene Unscrambler for detangling scrambled genes in ciliates.

GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures.

A reference ontology for biomedical informatics: the Foundational Model of Anatomy.

OQAFMA Querying agent for the Foundational Model of Anatomy: a prototype for providing flexible and efficient access to large semantic networks.

eF-site and PDBjViewer: database and viewer for protein functional sites.

GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes.
Chalifa-Caspi V, Yanai I, Ophir R, Rosen N, Shmoish M, Benjamin-Rodrig H, Shklar M, Stein TI, Shmueli O, Safran M, Lancet D

Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis.
Yazaki J, Shimatani Z, Hashimoto A, Nagata Y, Fujii F, Kojima K, Suzuki K, Taya T, Tonouchi M, Nelson C, Nakagawa A, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S

Toxoplasma gondii genomics: shedding light on pathogenesis and chemotherapy.

A collection of 11 800 single-copy Ds transposon insertion lines in Arabidopsis.
Kuromori T, Hirayama T, Kiyosue Y, Takabe H, Mizukado S, Sakurai T, Akiyama K, Kamiya A, Ito T, Shinozaki K

Het-PDB Navi.: a database for protein-small molecule interactions.
Yamaguchi A, Iida K, Matsui N, Tomoda S, Yura K, Go M

Data mining the protein data bank: automatic detection and assignment of carbohydrate structures.

Expression profiling with arrays of randomly disrupted genes in mouse embryonic stem cells leads to in vivo functional analysis.
Matsuda E, Shigeoka T, Iida R, Yamanaka S, Kawaichi M, Ishida Y

Investigation of differentially expressed genes during the development of mouse cerebellum.

The iProClass integrated database for protein functional analysis.
Wu CH, Huang H, Nikolskaya A, Hu Z, Barker WC

Genomics approach to abscisic acid- and gibberellin-responsive genes in rice.
Yazaki J, Kishimoto N, Nagata Y, Ishikawa M, Fujii F, Hashimoto A, Shimbo K, Shimatani Z, Kojima K, Suzuki K, Yamamoto M, Honda S, Endo A, Yoshida Y, Sato Y, Takeuchi K, Toyoshima K, Miyamoto C, Wu J, Sasaki T, Sakata K, Yamamoto K, Iba K, Oda T, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S

Differential profiles of genes expressed in neonatal brain of 129X1/SvJ and C57BL/6J mice: A database to aid in analyzing DNA microarrays using nonisogenic gene-targeted mice.

Development of Ciona intestinalis juveniles (through 2nd ascidian stage).
Chiba S, Sasaki A, Nakayama A, Takamura K, Satoh N

ProMode: a database of normal mode analyses on protein molecules with a full-atom model.

ONCOMINE: a cancer microarray database and integrated data-mining platform.
Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM

Development and evaluation of an Arabidopsis whole genome Affymetrix probe array.

Large-scale RT-PCR recovery of full-length cDNA clones.
Wu JQ, Garcia AM, Hulyk S, Sneed A, Kowis C, Yuan Y, Steffen D, McPherson JD, Gunaratne PH, Gibbs RA

FREX: a query interface for biological processes with hierarchical and recursive structures.

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S

Colourful history of Japan's rat resources.

The androgen receptor gene mutations database (ARDB): 2004 update.

Update of mouse microsatellite database of Japan (MMDBJ).
Sakai T, Miura I, Yamada-Ishibashi S, Wakita Y, Kohara Y, Yamazaki Y, Inoue T, Kominami R, Moriwaki K, Shiroishi T, Yonekawa H, Kikkawa Y

pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files.

A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins: generation and evaluation of anti-mKIAA antibodies.
Koga H, Shimada K, Hara Y, Nagano M, Kohga H, Yokoyama R, Kimura Y, Yuasa S, Magae J, Inamoto S, Okazaki N, Ohara O

Large-scale isolation of ESTs from medaka embryos and its application to medaka developmental genetics.
Kimura T, Jindo T, Narita T, Naruse K, Kobayashi D, Shin-I T, Kitagawa T, Sakaguchi T, Mitani H, Shima A, Kohara Y, Takeda H

Public web-based services from the European Bioinformatics Institute.
['Harte N', 'Silventoinen V', 'Quevillon E', 'Robinson S', 'Kallio K', 'Fustero X', 'Patel P', 'Jokinen P', 'Lopez R']

GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates.

KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains.
Aoki KF, Yamaguchi A, Ueda N, Akutsu T, Mamitsuka H, Goto S, Kanehisa M

CD-Search: protein domain annotations on the fly.

The International Protein Index: an integrated database for proteomics experiments.
Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R

Nuclear receptors and disease: androgen receptor.
Gottlieb B, Beitel LK, Wu J, Elhaji YA, Trifiro M

Comparative genomic hybridization (CGH)-arrays pave the way for identification of novel cancer-related genes.

CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data.

Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project.
Cavalcanti AR, Stover NA, Orecchia L, Doak TG, Landweber LF

Bioinformatics for glycomics: status, methods, requirements and perspectives.
von der Lieth CW, Bohne-Lang A, Lohmann KK, Frank M

TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks.
Heida N, Hasegawa Y, Mochizuki Y, Hirosawa K, Konagaya A, Toyoda T

Hoogland C, Mostaguir K, Sanchez JC, Hochstrasser DF, Appel RD

Rice mutant resources for gene discovery.
Hirochika H, Guiderdoni E, An G, Hsing YI, Eun MY, Han CD, Upadhyaya N, Ramachandran S, Zhang Q, Pereira A, Sundaresan V, Leung H

Characteristics of the Lotus japonicus gene repertoire deduced from large-scale expressed sequence tag (EST) analysis.

Detection of large-scale variation in the human genome.
Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C

5'-end SAGE for the analysis of transcriptional start sites.
Hashimoto S, Suzuki Y, Kasai Y, Morohoshi K, Yamada T, Sese J, Morishita S, Sugano S, Matsushima K

A genome-wide and nonredundant mouse transcription factor database.
Kanamori M, Konno H, Osato N, Kawai J, Hayashizaki Y, Suzuki H

Developments of geriatric autopsy database and Internet-based database of Japanese single nucleotide polymorphisms for geriatric research (JG-SNP).
['Sawabe M', 'Arai T', 'Kasahara I', 'Esaki Y', 'Nakahara K', 'Hosoi T', 'Orimo H', 'Takubo K', 'Murayama S', 'Tanaka N']

Stable isotope labeling of Arabidopsis thaliana for an NMR-based metabolomics approach.

The MeSH translation maintenance system: structure, interface design, and implementation.
Nelson SJ, Schopen M, Savage AG, Schulman JL, Arluk N

Prediction of the coding sequences of mouse homologues of KIAA gene: IV. The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries.
Okazaki N, F-Kikuno R, Ohara R, Inamoto S, Koseki H, Hiraoka S, Saga Y, Seino S, Nishimura M, Kaisho T, Hoshino K, Kitamura H, Nagase T, Ohara O, Koga H

Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism.
Ueda K, Yamashita A, Ishikawa J, Shimada M, Watsuji TO, Morimura K, Ikeda H, Hattori M, Beppu T

Prediction of the coding sequences of mouse homologues of FLJ genes: the complete nucleotide sequences of 110 mouse FLJ-homologous cDnas identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries.
Okazaki N, Kikuno R, Ohara R, Inamoto S, Koseki H, Hiraoka S, Saga Y, Kitamura H, Nakagawa T, Nagase T, Ohara O, Koga H

Mitochondrial genome variation in eastern Asia and the peopling of Japan.
Tanaka M, Cabrera VM, González AM, Larruga JM, Takeyasu T, Fuku N, Guo LJ, Hirose R, Fujita Y, Kurata M, Shinoda K, Umetsu K, Yamada Y, Oshida Y, Sato Y, Hattori N, Mizuno Y, Arai Y, Hirose N, Ohta S, Ogawa O, Tanaka Y, Kawamori R, Shamoto-Nagai M, Maruyama W, Shimokata H, Suzuki R, Shimodaira H

The complete genomic sequence of Nocardia farcinica IFM 10152.
Ishikawa J, Yamashita A, Mikami Y, Hoshino Y, Kurita H, Hotta K, Shiba T, Hattori M

Construction of a human glycogene library and comprehensive functional analysis.

Control of cell type proportioning in Dictyostelium discoideum by differentiation-inducing factor as determined by in situ hybridization.
Maruo T, Sakamoto H, Iranfar N, Fuller D, Morio T, Urushihara H, Tanaka Y, Maeda M, Loomis WF

C. elegans ORFeome version 3.1: increasing the coverage of ORFeome resources with improved gene predictions.
Lamesch P, Milstein S, Hao T, Rosenberg J, Li N, Sequerra R, Bosak S, Doucette-Stamm L, Vandenhaute J, Hill DE, Vidal M

Systematic recovery and analysis of full-ORF human cDNA clones.
Baross A, Butterfield YS, Coughlin SM, Zeng T, Griffith M, Griffith OL, Petrescu AS, Smailus DE, Khattra J, McDonald HL, McKay SJ, Moksa M, Holt RA, Marra MA

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
['Gerhard DS', 'Wagner L', 'Feingold EA', 'Shenmen CM', 'Grouse LH', 'Schuler G', 'Klein SL', 'Old S', 'Rasooly R', 'Good P', 'Guyer M', 'Peck AM', 'Derge JG', 'Lipman D', 'Collins FS', 'Jang W', 'Sherry S', 'Feolo M', 'Misquitta L', 'Lee E', 'Rotmistrovsky K', 'Greenhut SF', 'Schaefer CF', 'Buetow K', 'Bonner TI', 'Haussler D', 'Kent J', 'Kiekhaus M', 'Furey T', 'Brent M', 'Prange C', 'Schreiber K', 'Shapiro N', 'Bhat NK', 'Hopkins RF', 'Hsie F', 'Driscoll T', 'Soares MB', 'Casavant TL', 'Scheetz TE', 'Brown-stein MJ', 'Usdin TB', 'Toshiyuki S', 'Carninci P', 'Piao Y', 'Dudekula DB', 'Ko MS', 'Kawakami K', 'Suzuki Y', 'Sugano S', 'Gruber CE', 'Smith MR', 'Simmons B', 'Moore T', 'Waterman R', 'Johnson SL', 'Ruan Y', 'Wei CL', 'Mathavan S', 'Gunaratne PH', 'Wu J', 'Garcia AM', 'Hulyk SW', 'Fuh E', 'Yuan Y', 'Sneed A', 'Kowis C', 'Hodgson A', 'Muzny DM', 'McPherson J', 'Gibbs RA', 'Fahey J', 'Helton E', 'Ketteman M', 'Madan A', 'Rodrigues S', 'Sanchez A', 'Whiting M', 'Madari A', 'Young AC', 'Wetherby KD', 'Granite SJ', 'Kwong PN', 'Brinkley CP', 'Pearson RL', 'Bouffard GG', 'Blakesly RW', 'Green ED', 'Dickson MC', 'Rodriguez AC', 'Grimwood J', 'Schmutz J', 'Myers RM', 'Butterfield YS', 'Griffith M', 'Griffith OL', 'Krzywinski MI', 'Liao N', 'Morin R', 'Morrin R', 'Palmquist D', 'Petrescu AS', 'Skalska U', 'Smailus DE', 'Stott JM', 'Schnerch A', 'Schein JE', 'Jones SJ', 'Holt RA', 'Baross A', 'Marra MA', 'Clifton S', 'Makowski KA', 'Bosak S', 'Malek J']

WormBase as an integrated platform for the C. elegans ORFeome.
Chen N, Lawson D, Bradnam K, Harris TW, Stein LD

A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins II: public release of inaugural version of InGaP database containing gene/protein expression profiles for 127 mouse KIAA genes/proteins.
Koga H, Yuasa S, Nagase T, Shimada K, Nagano M, Imai K, Ohara R, Nakajima D, Murakami M, Kawai M, Miki F, Magae J, Inamoto S, Okazaki N, Ohara O

A comprehensive gene expression analysis toward the understanding of growth and differentiation of tobacco BY-2 cells.
Matsuoka K, Demura T, Galis I, Horiguchi T, Sasaki M, Tashiro G, Fukuda H

Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1.
Warren R, Hsiao WW, Kudo H, Myhre M, Dosanjh M, Petrescu A, Kobayashi H, Shimizu S, Miyauchi K, Masai E, Yang G, Stott JM, Schein JE, Shin H, Khattra J, Smailus D, Butterfield YS, Siddiqui A, Holt R, Marra MA, Jones SJ, Mohn WW, Brinkman FS, Fukuda M, Davies J, Eltis LD

A simple statistical method for discriminating outer membrane proteins with better accuracy.

Sequence features of Oxytricha trifallax (class Spirotrichea) macronuclear telomeric and subtelomeric sequences.
Cavalcanti AR, Dunn DM, Weiss R, Herrick G, Landweber LF, Doak TG

Contribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC-end sequence-SNP analysis.
Abe K, Noguchi H, Tagawa K, Yuzuriha M, Toyoda A, Kojima T, Ezawa K, Saitou N, Hattori M, Sakaki Y, Moriwaki K, Shiroishi T

Transporter database, TP-Search: a web-accessible comprehensive database for research in pharmacokinetics of drugs.
Ozawa N, Shimizu T, Morita R, Yokono Y, Ochiai T, Munesada K, Ohashi A, Aida Y, Hama Y, Taki K, Maeda K, Kusuhara H, Sugiyama Y

Rat Phenome Project: the untapped potential of existing rat strains.
Mashimo T, Voigt B, Kuramoto T, Serikawa T

Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions.
Kotera M, Okuno Y, Hattori M, Goto S, Kanehisa M

Current status of medaka genetics and genomics. The Medaka Genome Initiative (MGI).
Schartl M, Nanda I, Kondo M, Schmid M, Asakawa S, Sasaki T, Shimizu N, Henrich T, Wittbrodt J, Furutani-Seiki M, Kondoh H, Himmelbauer H, Hong Y, Koga A, Nonaka M, Mitani H, Shima A

NONCODE: an integrated knowledge database of non-coding RNAs.
Liu C, Bai B, Skogerbø G, Cai L, Deng W, Zhang Y, Bu D, Zhao Y, Chen R

Rfam: annotating non-coding RNAs in complete genomes.
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A

UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.
Mignone F, Grillo G, Licciulli F, Iacono M, Liuni S, Kersey PJ, Duarte J, Saccone C, Pesole G

The ProDom database of protein domain families: more emphasis on 3D.
Bru C, Courcelle E, Carrère S, Beausse Y, Dalmar S, Kahn D

Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB.

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids.
Laskowski RA, Chistyakov VV, Thornton JM

The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis.
Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM

Riley ML, Schmidt T, Wagner C, Mewes HW, Frishman D

Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation.
Winsor GL, Lo R, Ho Sui SJ, Ung KS, Huang S, Cheng D, Ching WK, Hancock RE, Brinkman FS

The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information.
Arnaud MB, Costanzo MC, Skrzypek MS, Binkley G, Lane C, Miyasato SR, Sherlock G

WormBase: a comprehensive data resource for Caenorhabditis biology and genomics.
Chen N, Harris TW, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Canaran P, Chan J, Chen CK, Chen WJ, Cunningham F, Davis P, Kenny E, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Pai S, Ozersky P, Petcherski A, Rogers A, Sabo A, Schwarz EM, Van Auken K, Wang Q, Durbin R, Spieth J, Sternberg PW, Stein LD

EzCatDB: the Enzyme Catalytic-mechanism Database.

Reactome: a knowledgebase of biological pathways.
Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, Lewis S, Birney E, Stein L

STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P

DED: Database of Evolutionary Distances.

L1Base: from functional annotation to prediction of active LINE-1 elements.

Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues.
Kato K, Yamashita R, Matoba R, Monden M, Noguchi S, Takagi T, Nakai K

5'SAGE: 5'-end Serial Analysis of Gene Expression database.
Kasai Y, Hashimoto S, Yamada T, Sese J, Sugano S, Matsushima K, Morishita S

Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, Sharma A, Sansone S, Brazma A

NCBI GEO: mining millions of expression profiles--database and tools.
Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R

The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms.
Tanino M, Debily MA, Tamura T, Hishiki T, Ogasawara O, Murakawa K, Kawamoto S, Itoh K, Watanabe S, de Souza SJ, Imbeaud S, Graudens E, Eveno E, Hilton P, Sudo Y, Kelso J, Ikeo K, Imanishi T, Gojobori T, Auffray C, Hide W, Okubo K

The Stanford Microarray Database accommodates additional microarray platforms and data formats.
Ball CA, Awad IA, Demeter J, Gollub J, Hebert JM, Hernandez-Boussard T, Jin H, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G

HOPPSIGEN: a database of human and mouse processed pseudogenes.
Khelifi A, Adel K, Duret L, Laurent D, Mouchiroud D, Dominique M

IMGT, the international ImMunoGeneTics information system.
Lefranc MP, Giudicelli V, Kaas Q, Duprat E, Jabado-Michaloud J, Scaviner D, Ginestoux C, Clément O, Chaume D, Lefranc G

RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome.
Sakurai T, Satou M, Akiyama K, Iida K, Seki M, Kuromori T, Ito T, Konagaya A, Toyoda T, Shinozaki K

Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.
Ito Y, Arikawa K, Antonio BA, Ohta I, Naito S, Mukai Y, Shimano A, Masukawa M, Shibata M, Yamamoto M, Ito Y, Yokoyama J, Sakai Y, Sakata K, Nagamura Y, Namiki N, Matsumoto T, Higo K, Sasaki T

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.
Lee Y, Tsai J, Sunkara S, Karamycheva S, Pertea G, Sultana R, Antonescu V, Chan A, Cheung F, Quackenbush J

Visualizing the laboratory mouse: capturing phenotype information.

Identification of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-inducible and -suppressive genes in the rat placenta: induction of interferon-regulated genes with possible inhibitory roles for angiogenesis in the placenta.
Mizutani T, Yoshino M, Satake T, Nakagawa M, Ishimura R, Tohyama C, Kokame K, Kangawa K, Miyamoto K

Characterization of full-length enriched expressed sequence tags of stress-treated poplar leaves.
Nanjo T, Futamura N, Nishiguchi M, Igasaki T, Shinozaki K, Shinohara K

System-level identification of transcriptional circuits underlying mammalian circadian clocks.
Ueda HR, Hayashi S, Chen W, Sano M, Machida M, Shigeyoshi Y, Iino M, Hashimoto S

[International public gene expression database (CIBEX) and data submission].

Inferring the mode of speciation from genomic data: a study of the great apes.

Identification of the ligand binding sites on the molecular surface of proteins.

Identification of ciliated sensory neuron-expressed genes in Caenorhabditis elegans using targeted pull-down of poly(A) tails.

Molecular pathology of the androgen receptor in male (in)fertility.
Gottlieb B, Lombroso R, Beitel LK, Trifiro MA

Efficient tree-matching methods for accurate carbohydrate database queries.
Aoki KF, Yamaguchi A, Okuno Y, Akutsu T, Ueda N, Kanehisa M, Mamitsuka H

Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.
Dufayard JF, Duret L, Penel S, Gouy M, Rechenmann F, Perrière G

Comparative promoter region analysis powered by CORG.
Dieterich C, Grossmann S, Tanzer A, Röpcke S, Arndt PF, Stadler PF, Vingron M

Effects of dioxin on gene expression in female reproductive system in the rat.

Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues.
Zhang X, Odom DT, Koo SH, Conkright MD, Canettieri G, Best J, Chen H, Jenner R, Herbolsheimer E, Jacobsen E, Kadam S, Ecker JR, Emerson B, Hogenesch JB, Unterman T, Young RA, Montminy M

Genomic structure of eight porcine chemokine receptors and intergene sharing of an exon between CCR1 and XCR1.
Shinkai H, Morozumi T, Toki D, Eguchi-Ogawa T, Muneta Y, Awata T, Uenishi H

Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas.
Watahiki A, Waki K, Hayatsu N, Shiraki T, Kondo S, Nakamura M, Sasaki D, Arakawa T, Kawai J, Harbers M, Hayashizaki Y, Carninci P

A gene expression map of Arabidopsis thaliana development.
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Schölkopf B, Weigel D, Lohmann JU

Filtering high-throughput protein-protein interaction data using a combination of genomic features.

Application of residue distribution along the sequence for discriminating outer membrane proteins.

A resource of 5,814 dissociation transposon-tagged and sequence-indexed lines of Arabidopsis transposed from start loci on chromosome 5.
Ito T, Motohashi R, Kuromori T, Noutoshi Y, Seki M, Kamiya A, Mizukado S, Sakurai T, Shinozaki K

Application of InChI to curate, index, and query 3-D structures.
Prasanna MD, Vondrasek J, Wlodawer A, Bhat TN

Comparison of the transcript profiles from the root and the nodulating root of the model legume Lotus japonicus by serial analysis of gene expression.

Analysis of expressed sequence tags in prothallia of Adiantum capillus-veneris.
Yamauchi D, Sutoh K, Kanegae H, Horiguchi T, Matsuoka K, Fukuda H, Wada M

Comparative analysis of carbohydrate-binding properties of two tandem repeat-type Jacalin-related lectins, Castanea crenata agglutinin and Cycas revoluta leaf lectin.
Nakamura S, Yagi F, Totani K, Ito Y, Hirabayashi J

The predictive power of the CluSTr database.
Petryszak R, Kretschmann E, Wieser D, Apweiler R

IMGT-Choreography for immunogenetics and immunoinformatics.
Lefranc MP, Clement O, Kaas Q, Duprat E, Chastellan P, Coelho I, Combres K, Ginestoux C, Giudicelli V, Chaume D, Lefranc G

Expressed sequence tags from the laboratory-grown miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom and mining for single nucleotide polymorphisms and insertions/deletions in tomato cultivars.
Yamamoto N, Tsugane T, Watanabe M, Yano K, Maeda F, Kuwata C, Torki M, Ban Y, Nishimura S, Shibata D

dbQSNP: a database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods.
Tahira T, Baba S, Higasa K, Kukita Y, Suzuki Y, Sugano S, Hayashi K

InterProScan: protein domains identifier.
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R

TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins.

GlyProt: in silico glycosylation of proteins.

Data mining tools for the Saccharomyces cerevisiae morphological database.
Saito TL, Sese J, Nakatani Y, Sano F, Yukawa M, Ohya Y, Morishita S

Olsen GJ, Overbeek R, Larsen N, Marsh TL, McCaughey MJ, Maciukenas MA, Kuan WM, Macke TJ, Xing Y, Woese CR

Whole genome association study of rheumatoid arthritis using 27 039 microsatellites.
Tamiya G, Shinya M, Imanishi T, Ikuta T, Makino S, Okamoto K, Furugaki K, Matsumoto T, Mano S, Ando S, Nozaki Y, Yukawa W, Nakashige R, Yamaguchi D, Ishibashi H, Yonekura M, Nakami Y, Takayama S, Endo T, Saruwatari T, Yagura M, Yoshikawa Y, Fujimoto K, Oka A, Chiku S, Linsen SE, Giphart MJ, Kulski JK, Fukazawa T, Hashimoto H, Kimura M, Hoshina Y, Suzuki Y, Hotta T, Mochida J, Minezaki T, Komai K, Shiozawa S, Taniguchi A, Yamanaka H, Kamatani N, Gojobori T, Bahram S, Inoko H

A novel method for development of malaria vaccines using full-length cDNA libraries.
Shibui A, Shiibashi T, Nogami S, Sugano S, Watanabe J

KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps.
Tokimatsu T, Sakurai N, Suzuki H, Ohta H, Nishitani K, Koyama T, Umezawa T, Misawa N, Saito K, Shibata D

Hashimoto K, Goto S, Kawano S, Aoki-Kinoshita KF, Ueda N, Hamajima M, Kawasaki T, Kanehisa M

Plasma Proteome Database as a resource for proteomics research.
Muthusamy B, Hanumanthu G, Suresh S, Rekha B, Srinivas D, Karthick L, Vrushabendra BM, Sharma S, Mishra G, Chatterjee P, Mangala KS, Shivashankar HN, Chandrika KN, Deshpande N, Suresh M, Kannabiran N, Niranjan V, Nalli A, Prasad TS, Arun KS, Reddy R, Chandran S, Jadhav T, Julie D, Mahesh M, John SL, Palvankar K, Sudhir D, Bala P, Rashmi NS, Vishnupriya G, Dhar K, Reshma S, Chaerkady R, Gandhi TK, Harsha HC, Mohan SS, Deshpande KS, Sarker M, Pandey A

A strategy for identification of oligosaccharide structures using observational multistage mass spectral library.
Kameyama A, Kikuchi N, Nakaya S, Ito H, Sato T, Shikanai T, Takahashi Y, Takahashi K, Narimatsu H

ProRule: a new database containing functional and structural information on PROSITE profiles.
Sigrist CJ, De Castro E, Langendijk-Genevaux PS, Le Saux V, Bairoch A, Hulo N

Repbase Update, a database of eukaryotic repetitive elements.
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J

Analysis of expressed sequence tags of the water flea Daphnia magna.
Watanabe H, Tatarazako N, Oda S, Nishide H, Uchiyama I, Morita M, Iguchi T

Tiling array-driven elucidation of transcriptional structures based on maximum-likelihood and Markov models.

The map-based sequence of the rice genome.

Automatic gene collection system for genome-scale overview of G-protein coupled receptors in eukaryotes.

A human protein atlas for normal and cancer tissues based on antibody proteomics.
Uhlén M, Björling E, Agaton C, Szigyarto CA, Amini B, Andersen E, Andersson AC, Angelidou P, Asplund A, Asplund C, Berglund L, Bergström K, Brumer H, Cerjan D, Ekström M, Elobeid A, Eriksson C, Fagerberg L, Falk R, Fall J, Forsberg M, Björklund MG, Gumbel K, Halimi A, Hallin I, Hamsten C, Hansson M, Hedhammar M, Hercules G, Kampf C, Larsson K, Lindskog M, Lodewyckx W, Lund J, Lundeberg J, Magnusson K, Malm E, Nilsson P, Odling J, Oksvold P, Olsson I, Oster E, Ottosson J, Paavilainen L, Persson A, Rimini R, Rockberg J, Runeson M, Sivertsson A, Sköllermo A, Steen J, Stenvall M, Sterky F, Strömberg S, Sundberg M, Tegel H, Tourle S, Wahlund E, Waldén A, Wan J, Wernérus H, Westberg J, Wester K, Wrethagen U, Xu LL, Hober S, Pontén F

Heavy-atom Database System: a tool for the preparation of heavy-atom derivatives of protein crystals based on amino-acid sequence and crystallization conditions.
Sugahara M, Asada Y, Ayama H, Ukawa H, Taka H, Kunishima N

Molecular characterization of ENU mouse mutagenesis and archives.
Sakuraba Y, Sezutsu H, Takahasi KR, Tsuchihashi K, Ichikawa R, Fujimoto N, Kaneko S, Nakai Y, Uchiyama M, Goda N, Motoi R, Ikeda A, Karashima Y, Inoue M, Kaneda H, Masuya H, Minowa O, Noguchi H, Toyoda A, Sakaki Y, Wakana S, Noda T, Shiroishi T, Gondo Y

The transcriptional landscape of the mammalian genome.
['Carninci P', 'Kasukawa T', 'Katayama S', 'Gough J', 'Frith MC', 'Maeda N', 'Oyama R', 'Ravasi T', 'Lenhard B', 'Wells C', 'Kodzius R', 'Shimokawa K', 'Bajic VB', 'Brenner SE', 'Batalov S', 'Forrest AR', 'Zavolan M', 'Davis MJ', 'Wilming LG', 'Aidinis V', 'Allen JE', 'Ambesi-Impiombato A', 'Apweiler R', 'Aturaliya RN', 'Bailey TL', 'Bansal M', 'Baxter L', 'Beisel KW', 'Bersano T', 'Bono H', 'Chalk AM', 'Chiu KP', 'Choudhary V', 'Christoffels A', 'Clutterbuck DR', 'Crowe ML', 'Dalla E', 'Dalrymple BP', 'de Bono B', 'Della Gatta G', 'di Bernardo D', 'Down T', 'Engstrom P', 'Fagiolini M', 'Faulkner G', 'Fletcher CF', 'Fukushima T', 'Furuno M', 'Futaki S', 'Gariboldi M', 'Georgii-Hemming P', 'Gingeras TR', 'Gojobori T', 'Green RE', 'Gustincich S', 'Harbers M', 'Hayashi Y', 'Hensch TK', 'Hirokawa N', 'Hill D', 'Huminiecki L', 'Iacono M', 'Ikeo K', 'Iwama A', 'Ishikawa T', 'Jakt M', 'Kanapin A', 'Katoh M', 'Kawasawa Y', 'Kelso J', 'Kitamura H', 'Kitano H', 'Kollias G', 'Krishnan SP', 'Kruger A', 'Kummerfeld SK', 'Kurochkin IV', 'Lareau LF', 'Lazarevic D', 'Lipovich L', 'Liu J', 'Liuni S', 'McWilliam S', 'Madan Babu M', 'Madera M', 'Marchionni L', 'Matsuda H', 'Matsuzawa S', 'Miki H', 'Mignone F', 'Miyake S', 'Morris K', 'Mottagui-Tabar S', 'Mulder N', 'Nakano N', 'Nakauchi H', 'Ng P', 'Nilsson R', 'Nishiguchi S', 'Nishikawa S', 'Nori F', 'Ohara O', 'Okazaki Y', 'Orlando V', 'Pang KC', 'Pavan WJ', 'Pavesi G', 'Pesole G', 'Petrovsky N', 'Piazza S', 'Reed J', 'Reid JF', 'Ring BZ', 'Ringwald M', 'Rost B', 'Ruan Y', 'Salzberg SL', 'Sandelin A', 'Schneider C', 'Schönbach C', 'Sekiguchi K', 'Semple CA', 'Seno S', 'Sessa L', 'Sheng Y', 'Shibata Y', 'Shimada H', 'Shimada K', 'Silva D', 'Sinclair B', 'Sperling S', 'Stupka E', 'Sugiura K', 'Sultana R', 'Takenaka Y', 'Taki K', 'Tammoja K', 'Tan SL', 'Tang S', 'Taylor MS', 'Tegner J', 'Teichmann SA', 'Ueda HR', 'van Nimwegen E', 'Verardo R', 'Wei CL', 'Yagi K', 'Yamanishi H', 'Zabarovsky E', 'Zhu S', 'Zimmer A', 'Hide W', 'Bult C', 'Grimmond SM', 'Teasdale RD', 'Liu ET', 'Brusic V', 'Quackenbush J', 'Wahlestedt C', 'Mattick JS', 'Hume DA', 'Kai C', 'Sasaki D', 'Tomaru Y', 'Fukuda S', 'Kanamori-Katayama M', 'Suzuki M', 'Aoki J', 'Arakawa T', 'Iida J', 'Imamura K', 'Itoh M', 'Kato T', 'Kawaji H', 'Kawagashira N', 'Kawashima T', 'Kojima M', 'Kondo S', 'Konno H', 'Nakano K', 'Ninomiya N', 'Nishio T', 'Okada M', 'Plessy C', 'Shibata K', 'Shiraki T', 'Suzuki S', 'Tagami M', 'Waki K', 'Watahiki A', 'Okamura-Oho Y', 'Suzuki H', 'Kawai J', 'Hayashizaki Y']

Antisense transcription in the mammalian transcriptome.
['Katayama S', 'Tomaru Y', 'Kasukawa T', 'Waki K', 'Nakanishi M', 'Nakamura M', 'Nishida H', 'Yap CC', 'Suzuki M', 'Kawai J', 'Suzuki H', 'Carninci P', 'Hayashizaki Y', 'Wells C', 'Frith M', 'Ravasi T', 'Pang KC', 'Hallinan J', 'Mattick J', 'Hume DA', 'Lipovich L', 'Batalov S', 'Engström PG', 'Mizuno Y', 'Faghihi MA', 'Sandelin A', 'Chalk AM', 'Mottagui-Tabar S', 'Liang Z', 'Lenhard B', 'Wahlestedt C']

An integrated database of the ascidian, Ciona intestinalis: towards functional genomics.
Satou Y, Kawashima T, Shoguchi E, Nakayama A, Satoh N

Prediction of glycan structures from gene expression data based on glycosyltransferase reactions.
Kawano S, Hashimoto K, Miyama T, Goto S, Kanehisa M

A web tool for comparative genomics: G-compass.
Fujii Y, Itoh T, Sakate R, Koyanagi KO, Matsuya A, Habara T, Yamaguchi K, Kaneko Y, Gojobori T, Imanishi T

Region-specific saturation germline mutagenesis in mice using the Sleeping Beauty transposon system.
Keng VW, Yae K, Hayakawa T, Mizuno S, Uno Y, Yusa K, Kokubu C, Kinoshita T, Akagi K, Jenkins NA, Copeland NG, Horie K, Takeda J

Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB).
Yamasaki C, Koyanagi KO, Fujii Y, Itoh T, Barrero R, Tamura T, Yamaguchi-Kabata Y, Tanino M, Takeda J, Fukuchi S, Miyazaki S, Nomura N, Sugano S, Imanishi T, Gojobori T

Protein structure prediction in CASP6 using CHIMERA and FAMS.
Takeda-Shitaka M, Terashi G, Takaya D, Kanou K, Iwadate M, Umeyama H

Development of dense microsatellite markers in the entire SLA region and evaluation of their polymorphisms in porcine breeds.
Tanaka M, Ando A, Renard C, Chardon P, Domukai M, Okumura N, Awata T, Uenishi H

Discrimination of outer membrane proteins using support vector machines.

STEM: a software tool for large-scale proteomic data analyses.
Shinkawa T, Taoka M, Yamauchi Y, Ichimura T, Kaji H, Takahashi N, Isobe T

Rice proteome database: a step toward functional analysis of the rice genome.

Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes.
Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O

GrainGenes 2.0. an improved resource for the small-grains community.
Carollo V, Matthews DE, Lazo GR, Blake TK, Hummel DD, Lui N, Hane DL, Anderson OD

Towards a human proteome atlas: high-throughput generation of mono-specific antibodies for tissue profiling.
Nilsson P, Paavilainen L, Larsson K, Odling J, Sundberg M, Andersson AC, Kampf C, Persson A, Al-Khalili Szigyarto C, Ottosson J, Björling E, Hober S, Wernérus H, Wester K, Pontén F, Uhlen M

GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research.
Lütteke T, Bohne-Lang A, Loss A, Goetz T, Frank M, von der Lieth CW

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.
Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahrén D, Tsoka S, Darzentas N, Kunin V, López-Bigas N

Genome-wide definitive haplotypes determined using a collection of complete hydatidiform moles.
Kukita Y, Miyatake K, Stokowski R, Hinds D, Higasa K, Wake N, Hirakawa T, Kato H, Matsuda T, Pant K, Cox D, Tahira T, Hayashi K

Cataloging transcription factor and major signaling molecule genes for functional genomic studies in Ciona intestinalis.

Porcine Toll-like receptor 1, 6, and 10 genes: complete sequencing of genomic region and expression analysis.
Shinkai H, Muneta Y, Suzuki K, Eguchi-Ogawa T, Awata T, Uenishi H

Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries.
Otsuki T, Ota T, Nishikawa T, Hayashi K, Suzuki Y, Yamamoto J, Wakamatsu A, Kimura K, Sakamoto K, Hatano N, Kawai Y, Ishii S, Saito K, Kojima S, Sugiyama T, Ono T, Okano K, Yoshikawa Y, Aotsuka S, Sasaki N, Hattori A, Okumura K, Nagai K, Sugano S, Isogai T

[Human mitochondrial genome polymorphism database (mtSNP)].

Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes.
Kimura K, Wakamatsu A, Suzuki Y, Ota T, Nishikawa T, Yamashita R, Yamamoto J, Sekine M, Tsuritani K, Wakaguri H, Ishii S, Sugiyama T, Saito K, Isono Y, Irie R, Kushida N, Yoneyama T, Otsuka R, Kanda K, Yokoi T, Kondo H, Wagatsuma M, Murakawa K, Ishida S, Ishibashi T, Takahashi-Fujii A, Tanase T, Nagai K, Kikuchi H, Nakai K, Isogai T, Sugano S

Terminology model discovery using natural language processing and visualization techniques.
Zhou L, Tao Y, Cimino JJ, Chen ES, Liu H, Lussier YA, Hripcsak G, Friedman C

A global representation of the carbohydrate structures: a tool for the analysis of glycan.
Hashimoto K, Kawano S, Goto S, Aoki-Kinoshita KF, Kawashima M, Kanehisa M

miRBase: microRNA sequences, targets and gene nomenclature.
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ

snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs.

Andersen ES, Rosenblad MA, Larsen N, Westergaard JC, Burks J, Wower IK, Wower J, Gorodkin J, Samuelsson T, Zwieb C

PINT: Protein-protein Interactions Thermodynamic Database.

ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions.
Kumar MD, Bava KA, Gromiha MM, Prabakaran P, Kitajima K, Uedaira H, Sarai A

ChimerDB--a knowledgebase for fusion sequences.

LOCATE: a mouse protein subcellular localization database.
Fink JL, Aturaliya RN, Davis MJ, Zhang F, Hanson K, Teasdale MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Teasdale RD

Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A

HUMHOT: a database of human meiotic recombination hot spots.

SMART 5: domains in the context of genomes and networks.
Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P

Zamyatnin AA, Borchikov AS, Vladimirov MG, Voronina OL

ISfinder: the reference centre for bacterial insertion sequences.
Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M

PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees.
Whelan S, de Bakker PI, Quevillon E, Rodriguez N, Goldman N

From genomics to chemical genomics: new developments in KEGG.
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M

ODB: a database of operons accumulating known operons across multiple genomes.
Okuda S, Katayama T, Kawashima S, Goto S, Kanehisa M

dictyBase, the model organism database for Dictyostelium discoideum.
Chisholm RL, Gaudet P, Just EM, Pilcher KE, Fey P, Merchant SN, Kibbe WA

WormBase: better software, richer content.
Schwarz EM, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Canaran P, Chan J, Chen N, Chen WJ, Davis P, Fiedler TJ, Girard L, Harris TW, Kenny EE, Kishore R, Lawson D, Lee R, Müller HM, Nakamura C, Ozersky P, Petcherski A, Rogers A, Spooner W, Tuli MA, Van Auken K, Wang D, Durbin R, Spieth J, Stein LD, Sternberg PW

Caspi R, Foerster H, Fulcher CA, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee SY, Tissier C, Zhang P, Karp PD

AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB.
Block P, Sotriffer CA, Dramburg I, Klebe G

DBTGR: a database of tunicate promoters and their regulatory elements.
Sierro N, Kusakabe T, Park KJ, Yamashita R, Kinoshita K, Nakai K

TreeFam: a curated database of phylogenetic trees of animal gene families.
Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R

BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression.
Ogasawara O, Otsuji M, Watanabe K, Iizuka T, Tamura T, Hishiki T, Kawamoto S, Okubo K

The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.
Nord AS, Chang PJ, Conklin BR, Cox AV, Harper CA, Hicks GG, Huang CC, Johns SJ, Kawamoto M, Liu S, Meng EC, Morris JH, Rossant J, Ruiz P, Skarnes WC, Soriano P, Stanford WL, Stryke D, von Melchner H, Wurst W, Yamamura K, Young SG, Babbitt PC, Ferrin TE

DrugBank: a comprehensive resource for in silico drug discovery and exploration.
Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J

GLIDA: GPCR-ligand database for chemical genomic drug discovery.
Okuno Y, Yang J, Taneishi K, Yabuuchi H, Tsujimoto G

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.
Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M

The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information.
Ohyanagi H, Tanaka T, Sakai H, Shigemoto Y, Yamaguchi K, Habara T, Fujii Y, Antonio BA, Nagamura Y, Imanishi T, Ikeo K, Itoh T, Gojobori T, Sasaki T

IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences.
Giudicelli V, Duroux P, Ginestoux C, Folch G, Jabado-Michaloud J, Chaume D, Lefranc MP

EPD in its twentieth year: towards complete promoter coverage of selected model organisms.

Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study.

Genomic structure and gene order of swine chromosome 7q1.1-->q1.2.
Tanaka M, Suzuki K, Morozumi T, Kobayashi E, Matsumoto T, Domukai M, Eguchi-Ogawa T, Shinkai H, Awata T, Uenishi H

Biomedical ontologies: what part-of is and isn't.

Identification and classification of genes required for tolerance to high-sucrose stress revealed by genome-wide screening of Saccharomyces cerevisiae.
Ando A, Tanaka F, Murata Y, Takagi H, Shima J

Minimotif Miner: a tool for investigating protein function.
Balla S, Thapar V, Verma S, Luong T, Faghri T, Huang CH, Rajasekaran S, del Campo JJ, Shinn JH, Mohler WA, Maciejewski MW, Gryk MR, Piccirillo B, Schiller SR, Schiller MR

Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns.

Chemical compound navigator: a web-based chem-BLAST, chemical taxonomy-based search engine for browsing compounds.
Prasanna MD, Vondrasek J, Wlodawer A, Rodriguez H, Bhat TN

2DDB - a bioinformatics solution for analysis of quantitative proteomics data.
Malmström L, Marko-Varga G, Westergren-Thorsson G, Laurell T, Malmström J

Beyond the data deluge: data integration and bio-ontologies.

Contribution of rpoB2 RNA polymerase beta subunit gene to rifampin resistance in Nocardia species.

"Per cell" normalization method for mRNA measurement by quantitative PCR and microarrays.
Kanno J, Aisaki K, Igarashi K, Nakatsu N, Ono A, Kodama Y, Nagao T

A set of highly informative rat simple sequence length polymorphism (SSLP) markers and genetically defined rat strains.
Mashimo T, Voigt B, Tsurumi T, Naoi K, Nakanishi S, Yamasaki K, Kuramoto T, Serikawa T

Large-scale identification of protein-protein interaction of Escherichia coli K-12.
Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H

Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumption.
Soga T, Baran R, Suematsu M, Ueno Y, Ikeda S, Sakurakawa T, Kakazu Y, Ishikawa T, Robert M, Nishioka T, Tomita M

Genome-wide analysis of mammalian promoter architecture and evolution.
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engström PG, Frith MC, Forrest AR, Alkema WB, Tan SL, Plessy C, Kodzius R, Ravasi T, Kasukawa T, Fukuda S, Kanamori-Katayama M, Kitazume Y, Kawaji H, Kai C, Nakamura M, Konno H, Nakano K, Mottagui-Tabar S, Arner P, Chesi A, Gustincich S, Persichetti F, Suzuki H, Grimmond SM, Wells CA, Orlando V, Wahlestedt C, Liu ET, Harbers M, Kawai J, Bajic VB, Hume DA, Hayashizaki Y

Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.
Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engström PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, Fletcher CF, Forrest AR, Furuno M, Hill D, Itoh M, Kanamori-Katayama M, Katayama S, Katoh M, Kawashima T, Quackenbush J, Ravasi T, Ring BZ, Shibata K, Sugiura K, Takenaka Y, Teasdale RD, Wells CA, Zhu Y, Kai C, Kawai J, Hume DA, Carninci P, Hayashizaki Y

The genomic structure and a novel alternatively spliced form of porcine pTalpha chain.
Yamamoto R, Uenishi H, Yasue H, Takagaki Y, Sato E

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.
Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H

Kazusa mammalian cDNA resources: towards functional characterization of KIAA gene products.

RARTF: database and tools for complete sets of Arabidopsis transcription factors.
Iida K, Seki M, Sakurai T, Satou M, Akiyama K, Toyoda T, Konagaya A, Shinozaki K

Preparation of a set of expression-ready clones of mammalian long cDNAs encoding large proteins by the ORF trap cloning method.
Nakajima D, Saito K, Yamakawa H, Kikuno RF, Nakayama M, Ohara R, Okazaki N, Koga H, Nagase T, Ohara O

Comprehensive structural analysis of the genome of red clover (Trifolium pratense L.).
Sato S, Isobe S, Asamizu E, Ohmido N, Kataoka R, Nakamura Y, Kaneko T, Sakurai N, Okumura K, Klimenko I, Sasamoto S, Wada T, Watanabe A, Kohara M, Fujishiro T, Tabata S

InCeP: intracellular pathway based on mKIAA protein-protein interactions.

Systematic analysis of the visual projection neurons of Drosophila melanogaster. I. Lobula-specific pathways.

ET viewer: an application for predicting and visualizing functional sites in protein structures.
Morgan DH, Kristensen DM, Mittelman D, Lichtarge O

A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis.
Kuromori T, Wada T, Kamiya A, Yuguchi M, Yokouchi T, Imura Y, Takabe H, Sakurai T, Akiyama K, Hirayama T, Okada K, Shinozaki K

Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance.
Li YY, Yu H, Guo ZM, Guo TQ, Tu K, Li YX

TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB.
Yamasaki C, Kawashima H, Todokoro F, Imamizu Y, Ogawa M, Tanino M, Itoh T, Gojobori T, Imanishi T

ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins.
de Castro E, Sigrist CJ, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E, Bairoch A, Hulo N

ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.
Castrignanò T, Rizzi R, Talamo IG, De Meo PD, Anselmo A, Bonizzoni P, Pesole G

GlyNest and CASPER: two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interface.
Loss A, Stenutz R, Schwarzer E, von der Lieth CW

Alternative splicing in human transcriptome: functional and structural influence on proteins.
Yura K, Shionyu M, Hagino K, Hijikata A, Hirashima Y, Nakahara T, Eguchi T, Shinoda K, Yamaguchi A, Takahashi K, Itoh T, Imanishi T, Gojobori T, Go M

The Candida Genome Database: facilitating research on Candida albicans molecular biology.
Costanzo MC, Arnaud MB, Skrzypek MS, Binkley G, Lane C, Miyasato SR, Sherlock G

Comparative promoter analysis in vertebrate genomes with the CORG workbench.

Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*.

Mass identification of chloroplast proteins of endosymbiont origin by phylogenetic profiling based on organism-optimized homologous protein groups.
Sato N, Ishikawa M, Fujiwara M, Sonoike K

Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii.
Khan A, Böhme U, Kelly KA, Adlem E, Brooks K, Simmonds M, Mungall K, Quail MA, Arrowsmith C, Chillingworth T, Churcher C, Harris D, Collins M, Fosker N, Fraser A, Hance Z, Jagels K, Moule S, Murphy L, O'Neil S, Rajandream MA, Saunders D, Seeger K, Whitehead S, Mayr T, Xuan X, Watanabe J, Suzuki Y, Wakaguri H, Sugano S, Sugimoto C, Paulsen I, Mackey AJ, Roos DS, Hall N, Berriman M, Barrell B, Sibley LD, Ajioka JW

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.
Takeda J, Suzuki Y, Nakao M, Barrero RA, Koyanagi KO, Jin L, Motono C, Hata H, Isogai T, Nagai K, Otsuki T, Kuryshev V, Shionyu M, Yura K, Go M, Thierry-Mieg J, Thierry-Mieg D, Wiemann S, Nomura N, Sugano S, Gojobori T, Imanishi T

Gene expression omnibus: microarray data storage, submission, retrieval, and analysis.

Data storage and analysis in ArrayExpress.
Brazma A, Kapushesky M, Parkinson H, Sarkans U, Shojatalab M

Functional genomic analysis of commercial baker's yeast during initial stages of model dough-fermentation.
Tanaka F, Ando A, Nakamura T, Takagi H, Shima J

Fey P, Gaudet P, Pilcher KE, Franke J, Chisholm RL

The semantics of procedures and diseases in SNOMED CT.

WormBase: methods for data mining and comparative genomics.

Identification and classification of genes required for tolerance to freeze-thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains.
Ando A, Nakamura T, Murata Y, Takagi H, Shima J

Biomedical knowledge navigation by literature clustering.

The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse.
McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE, Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJ, Holt R, Brinkman FS, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD

Rate and polarity of gene fusion and fission in Oryza sativa and Arabidopsis thaliana.

Practical aspects of uniform stable isotope labeling of higher plants for heteronuclear NMR-based metabolomics.

Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the EzCatDB database.

A first global analysis of plasmid encoded proteins in the ACLAME database.

OriDB: a DNA replication origin database.
Nieduszynski CA, Hiraga S, Ak P, Benham CJ, Donaldson AD

OmicBrowse: a browser of multidimensional omics annotations.
Toyoda T, Mochizuki Y, Player K, Heida N, Kobayashi N, Sakaki Y

InSatDb: a microsatellite database of fully sequenced insect genomes.
Archak S, Meduri E, Kumar PS, Nagaraju J

TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences.
Gromiha MM, Yabuki Y, Kundu S, Suharnan S, Suwa M

The TIGR Plant Transcript Assemblies database.
Childs KL, Hamilton JP, Zhu W, Ly E, Cheung F, Wu H, Rabinowicz PD, Town CD, Buell CR, Chan AP

CancerGenes: a gene selection resource for cancer genome projects.
Higgins ME, Claremont M, Major JE, Sander C, Lash AE

ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes.

Sequence resources at the Candida Genome Database.
Arnaud MB, Costanzo MC, Skrzypek MS, Shah P, Binkley G, Lane C, Miyasato SR, Sherlock G

The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data.
Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM

Ruan J, Guo Y, Li H, Hu Y, Song F, Huang X, Kristiensen K, Bolund L, Wang J

Event ontology: a pathway-centric ontology for biological processes.

STRING 7--recent developments in the integration and prediction of protein interactions.
von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P

NCBI GEO: mining tens of millions of expression profiles--database and tools update.
Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.
Karro JE, Yan Y, Zheng D, Zhang Z, Carriero N, Cayting P, Harrrison P, Gerstein M

fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences.
Kin T, Yamada K, Terai G, Okida H, Yoshinari Y, Ono Y, Kojima A, Kimura Y, Komori T, Asai K

WormBase: new content and better access.
Bieri T, Blasiar D, Ozersky P, Antoshechkin I, Bastiani C, Canaran P, Chan J, Chen N, Chen WJ, Davis P, Fiedler TJ, Girard L, Han M, Harris TW, Kishore R, Lee R, McKay S, Müller HM, Nakamura C, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Spooner W, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Durbin R, Stein LD, Sternberg PW, Spieth J

PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits.
Bao L, Zhou M, Wu L, Lu L, Goldowitz D, Williams RW, Cui Y

A large-scale full-length cDNA analysis to explore the budding yeast transcriptome.
Miura F, Kawaguchi N, Sese J, Toyoda A, Hattori M, Morishita S, Ito T

The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

Analysis of the genomic structure of the porcine CD1 gene cluster.
Eguchi-Ogawa T, Morozumi T, Tanaka M, Shinkai H, Okumura N, Suzuki K, Awata T, Uenishi H

Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome.
Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW

H-DBAS: alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational.
Takeda J, Suzuki Y, Nakao M, Kuroda T, Sugano S, Gojobori T, Imanishi T

VISTA Enhancer Browser--a database of tissue-specific human enhancers.
Visel A, Minovitsky S, Dubchak I, Pennacchio LA

ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis.
Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H

ArrayExpress--a public database of microarray experiments and gene expression profiles.
Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A

MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups.

Developments in CORG: a gene-centric comparative genomics resource.

MMDB: annotating protein sequences with Entrez's 3D-structure database.
Wang Y, Addess KJ, Chen J, Geer LY, He J, He S, Lu S, Madej T, Marchler-Bauer A, Thiessen PA, Zhang N, Bryant SH

CDD: a conserved domain database for interactive domain family analysis.
Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH

Computational design and experimental evaluation of glycosyltransferase mutants: engineering of a blood type B galactosyltransferase with enhanced glucosyltransferase activity.
Nakahara T, Hindsgaul O, Palcic MM, Nishimura S

RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes.
Kazakov AE, Cipriano MJ, Novichkov PS, Minovitsky S, Vinogradov DV, Arkin A, Mironov AA, Gelfand MS, Dubchak I

TassDB: a database of alternative tandem splice sites.
Hiller M, Nikolajewa S, Huse K, Szafranski K, Rosenstiel P, Schuster S, Backofen R, Platzer M

The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction.
Gattiker A, Niederhauser-Wiederkehr C, Moore J, Hermida L, Primig M

PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences.
Uenishi H, Eguchi-Ogawa T, Shinkai H, Okumura N, Suzuki K, Toki D, Hamasima N, Awata T

RNAdb 2.0--an expanded database of mammalian non-coding RNAs.
Pang KC, Stephen S, Dinger ME, Engström PG, Lenhard B, Mattick JS

PROPHECY--a yeast phenome database, update 2006.
Fernandez-Ricaud L, Warringer J, Ericson E, Glaab K, Davidsson P, Nilsson F, Kemp GJ, Nerman O, Blomberg A

PEDANT genome database: 10 years online.
Riley ML, Schmidt T, Artamonova II, Wagner C, Volz A, Heumann K, Mewes HW, Frishman D

The Rat Genome Database, update 2007--easing the path from disease to data and back again.
['Twigger SN', 'Shimoyama M', 'Bromberg S', 'Kwitek AE', 'Jacob HJ']

Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs.
Watanabe J, Wakaguri H, Sasaki M, Suzuki Y, Sugano S

NCBI GEO standards and services for microarray data.

Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS).
Kosuge T, Abe T, Okido T, Tanaka N, Hirahata M, Maruyama Y, Mashima J, Tomiki A, Kurokawa M, Himeno R, Fukuchi S, Miyazaki S, Gojobori T, Tateno Y, Sugawara H

D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples.
Higasa K, Miyatake K, Kukita Y, Tahira T, Hayashi K

A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes.
Miyao A, Iwasaki Y, Kitano H, Itoh J, Maekawa M, Murata K, Yatou O, Nagato Y, Hirochika H

The Stanford Microarray Database: implementation of new analysis tools and open source release of software.
Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, Maier D, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G, Ball CA

Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de.
Toukach P, Joshi HJ, Ranzinger R, Knirel Y, von der Lieth CW

BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.
Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D

SNPSTR: a database of compound microsatellite-SNP markers.

MaizeGDB's new data types, resources and activities.
Lawrence CJ, Schaeffer ML, Seigfried TE, Campbell DA, Harper LC

GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages.

Birth and death of genes promoted by transposable elements in Oryza sativa.

LactMed-new NLM database on drugs and lactation.

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization.
Sugita C, Ogata K, Shikata M, Jikuya H, Takano J, Furumichi M, Kanehisa M, Omata T, Sugiura M, Sugita M

MutationView/KMcancerDB: a database for cancer gene mutations.

AphidBase: a database for aphid genomic resources.
Gauthier JP, Legeai F, Zasadzinski A, Rispe C, Tagu D

New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA.
Piekna-Przybylska D, Decatur WA, Fournier MJ

Large-scale analysis of chlorophyll fluorescence kinetics in Synechocystis sp. PCC 6803: identification of the factors involved in the modulation of photosystem stoichiometry.
Ozaki H, Ikeuchi M, Ogawa T, Fukuzawa H, Sonoike K

Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database.
Petitjean A, Mathe E, Kato S, Ishioka C, Tavtigian SV, Hainaut P, Olivier M

Construction of a pair of practical Nocardia-Escherichia coli shuttle vectors.
Chiba K, Hoshino Y, Ishino K, Kogure T, Mikami Y, Uehara Y, Ishikawa J

Ontological foundations for biomedical sciences.

Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles.
Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, Barrette TR, Anstet MJ, Kincead-Beal C, Kulkarni P, Varambally S, Ghosh D, Chinnaiyan AM

The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses.
Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C, Bornberg-Bauer E, Kudla J, Harter K

Multiple high-throughput analyses monitor the response of E. coli to perturbations.
Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, Kakazu Y, Sugawara K, Igarashi S, Harada S, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, Yugi K, Arakawa K, Iwata N, Toya Y, Nakayama Y, Nishioka T, Shimizu K, Mori H, Tomita M

Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature.

Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes.

Mass spectrometric identification of N-linked glycopeptides using lectin-mediated affinity capture and glycosylation site-specific stable isotope tagging.
Kaji H, Yamauchi Y, Takahashi N, Isobe T

The Dugesia ryukyuensis database as a molecular resource for studying switching of the reproductive system.
Ishizuka H, Maezawa T, Kawauchi J, Nodono H, Hirao Y, Nishimura O, Nakagawa H, Sekii K, Tasaka K, Tarui H, Agata K, Hoshi M, Kobayashi K, Sakakibara Y, Matsumoto M

Histone methylation controls telomerase-independent telomere lengthening in cells undergoing dedifferentiation.
Grafi G, Ben-Meir H, Avivi Y, Moshe M, Dahan Y, Zemach A

A new partner for the international knockout mouse consortium.
Collins FS, Finnell RH, Rossant J, Wurst W

Analysis of the phage sequence space: the benefit of structured information.

ChromatinDB: a database of genome-wide histone modification patterns for Saccharomyces cerevisiae.

Progressive activation of Delta-Notch signaling from around the blastopore is required to set up a functional caudal lobe in the spider Achaearanea tepidariorum.
Oda H, Nishimura O, Hirao Y, Tarui H, Agata K, Akiyama-Oda Y

Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways.
Oh M, Yamada T, Hattori M, Goto S, Kanehisa M

A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer.
Hunter DJ, Kraft P, Jacobs KB, Cox DG, Yeager M, Hankinson SE, Wacholder S, Wang Z, Welch R, Hutchinson A, Wang J, Yu K, Chatterjee N, Orr N, Willett WC, Colditz GA, Ziegler RG, Berg CD, Buys SS, McCarty CA, Feigelson HS, Calle EE, Thun MJ, Hayes RB, Tucker M, Gerhard DS, Fraumeni JF, Hoover RN, Thomas G, Chanock SJ

Analysis of expressed sequence tags from the fungus Aspergillus oryzae cultured under different conditions.
Akao T, Sano M, Yamada O, Akeno T, Fujii K, Goto K, Ohashi-Kunihiro S, Takase K, Yasukawa-Watanabe M, Yamaguchi K, Kurihara Y, Maruyama J, Juvvadi PR, Tanaka A, Hata Y, Koyama Y, Yamaguchi S, Kitamoto N, Gomi K, Abe K, Takeuchi M, Kobayashi T, Horiuchi H, Kitamoto K, Kashiwagi Y, Machida M, Akita O

The medaka draft genome and insights into vertebrate genome evolution.
Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B, Yamada T, Nagayasu Y, Doi K, Kasai Y, Jindo T, Kobayashi D, Shimada A, Toyoda A, Kuroki Y, Fujiyama A, Sasaki T, Shimizu A, Asakawa S, Shimizu N, Hashimoto S, Yang J, Lee Y, Matsushima K, Sugano S, Sakaizumi M, Narita T, Ohishi K, Haga S, Ohta F, Nomoto H, Nogata K, Morishita T, Endo T, Shin-I T, Takeda H, Morishita S, Kohara Y

A web-based interactive developmental table for the ascidian Ciona intestinalis, including 3D real-image embryo reconstructions: I. From fertilized egg to hatching larva.
Hotta K, Mitsuhara K, Takahashi H, Inaba K, Oka K, Gojobori T, Ikeo K

Reconstruction of dopaminergic neural network and locomotion function in planarian regenerates.
Nishimura K, Kitamura Y, Inoue T, Umesono Y, Sano S, Yoshimoto K, Inden M, Takata K, Taniguchi T, Shimohama S, Agata K

Integration of bioinformatics resources for functional analysis of gene expression and proteomic data.

Mapping of chimpanzee full-length cDNAs onto the human genome unveils large potential divergence of the transcriptome.
Sakate R, Suto Y, Imanishi T, Tanoue T, Hida M, Hayasaka I, Kusuda J, Gojobori T, Hashimoto K, Hirai M

Mutational pattern and frequency of induced nucleotide changes in mouse ENU mutagenesis.

PhiGO, a phage ontology associated with the ACLAME database.

Identification and distribution of tryptophan hydroxylase (TPH)-positive neurons in the planarian Dugesia japonica.
Nishimura K, Kitamura Y, Inoue T, Umesono Y, Yoshimoto K, Takeuchi K, Taniguchi T, Agata K

OReFiL: an online resource finder for life sciences.

In-depth proteomic profiling of the normal human kidney glomerulus using two-dimensional protein prefractionation in combination with liquid chromatography-tandem mass spectrometry.
Miyamoto M, Yoshida Y, Taguchi I, Nagasaka Y, Tasaki M, Zhang Y, Xu B, Nameta M, Sezaki H, Cuellar LM, Osawa T, Morishita H, Sekiyama S, Yaoita E, Kimura K, Yamamoto T

Functional genomics of commercial baker's yeasts that have different abilities for sugar utilization and high-sucrose tolerance under different sugar conditions.
Tanaka-Tsuno F, Mizukami-Murata S, Murata Y, Nakamura T, Ando A, Takagi H, Shima J

Proteomics reveals N-linked glycoprotein diversity in Caenorhabditis elegans and suggests an atypical translocation mechanism for integral membrane proteins.
Kaji H, Kamiie J, Kawakami H, Kido K, Yamauchi Y, Shinkawa T, Taoka M, Takahashi N, Isobe T

Development and public release of a comprehensive hepatitis virus database.
Shin-I T, Tanaka Y, Tateno Y, Mizokami M

Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells.
Hijikata A, Kitamura H, Kimura Y, Yokoyama R, Aiba Y, Bao Y, Fujita S, Hase K, Hori S, Ishii Y, Kanagawa O, Kawamoto H, Kawano K, Koseki H, Kubo M, Kurita-Miki A, Kurosaki T, Masuda K, Nakata M, Oboki K, Ohno H, Okamoto M, Okayama Y, O-Wang J, Saito H, Saito T, Sakuma M, Sato K, Sato K, Seino K, Setoguchi R, Tamura Y, Tanaka M, Taniguchi M, Taniuchi I, Teng A, Watanabe T, Watarai H, Yamasaki S, Ohara O

CellMontage: similar expression profile search server.
Fujibuchi W, Kiseleva L, Taniguchi T, Harada H, Horton P

PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation.
Portales-Casamar E, Kirov S, Lim J, Lithwick S, Swanson MI, Ticoll A, Snoddy J, Wasserman WW

The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes.
Hashimoto K, Yoshizawa AC, Okuda S, Kuma K, Goto S, Kanehisa M

ChEBI: a database and ontology for chemical entities of biological interest.
Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M

The plant organelles database (PODB): a collection of visualized plant organelles and protocols for plant organelle research.
Mano S, Miwa T, Nishikawa S, Mimura T, Nishimura M

PubMeth: a cancer methylation database combining text-mining and expert annotation.
Ongenaert M, Van Neste L, De Meyer T, Menschaert G, Bekaert S, Van Criekinge W

COXPRESdb: a database of coexpressed gene networks in mammals.
Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H, Kinoshita K

UTGB/medaka: genomic resource database for medaka biology.
Ahsan B, Kobayashi D, Yamada T, Kasahara M, Sasaki S, Saito TL, Nagayasu Y, Doi K, Nakatani Y, Qu W, Jindo T, Shimada A, Naruse K, Toyoda A, Kuroki Y, Fujiyama A, Sasaki T, Shimizu A, Asakawa S, Shimizu N, Hashimoto S, Yang J, Lee Y, Matsushima K, Sugano S, Sakaizumi M, Narita T, Ohishi K, Haga S, Ohta F, Nomoto H, Nogata K, Morishita T, Endo T, Shin-I T, Takeda H, Kohara Y, Morishita S

Glycoconjugate Data Bank: Structures--an annotated glycan structure database and N-glycan primary structure verification service.
Nakahara T, Hashimoto R, Nakagawa H, Monde K, Miura N, Nishimura S

DBTSS: database of transcription start sites, progress report 2008.
Wakaguri H, Yamashita R, Suzuki Y, Sugano S, Nakai K

Frontal affinity chromatography: sugar-protein interactions.
Tateno H, Nakamura-Tsuruta S, Hirabayashi J

DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information.

Visualization of human prenatal development by magnetic resonance imaging (MRI).
Shiota K, Yamada S, Nakatsu-Komatsu T, Uwabe C, Kose K, Matsuda Y, Haishi T, Mizuta S, Matsuda T

Exonization of active mouse L1s: a driver of transcriptome evolution?
Zemojtel T, Penzkofer T, Schultz J, Dandekar T, Badge R, Vingron M

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, Karp PD

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.
Matsuya A, Sakate R, Kawahara Y, Koyanagi KO, Sato Y, Fujii Y, Yamasaki C, Habara T, Nakaoka H, Todokoro F, Yamaguchi K, Endo T, Oota S, Makalowski W, Ikeo K, Suzuki Y, Hanada K, Hashimoto K, Hirai M, Iwama H, Saitou N, Hiraki AT, Jin L, Kaneko Y, Kanno M, Murakami K, Noda AO, Saichi N, Sanbonmatsu R, Suzuki M, Takeda J, Tanaka M, Gojobori T, Imanishi T, Itoh T

Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL

The Arabidopsis Information Resource (TAIR): gene structure and function annotation.
Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E

LOCATE: a mammalian protein subcellular localization database.
Sprenger J, Lynn Fink J, Karunaratne S, Hanson K, Hamilton NA, Teasdale RD

TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates.

GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.
Okuno Y, Tamon A, Yabuuchi H, Niijima S, Minowa Y, Tonomura K, Kunimoto R, Feng C

UTRome.org: a platform for 3'UTR biology in C. elegans.
Mangone M, Macmenamin P, Zegar C, Piano F, Gunsalus KC

Rogers A, Antoshechkin I, Bieri T, Blasiar D, Bastiani C, Canaran P, Chan J, Chen WJ, Davis P, Fernandes J, Fiedler TJ, Han M, Harris TW, Kishore R, Lee R, McKay S, Müller HM, Nakamura C, Ozersky P, Petcherski A, Schindelman G, Schwarz EM, Spooner W, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Yook K, Durbin R, Stein LD, Spieth J, Sternberg PW

The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes.
Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, Mani P, Moxon SA, Pich C, Ramachandran S, Schaper K, Segerdell E, Shao X, Singer A, Song P, Sprunger B, Van Slyke CE, Westerfield M

Rawlings ND, Morton FR, Kok CY, Kong J, Barrett AJ

Comparative genomic analysis using the UCSC genome browser.
Karolchik D, Bejerano G, Hinrichs AS, Kuhn RM, Miller W, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ

AAindex: amino acid index database, progress report 2008.
Kawashima S, Pokarowski P, Pokarowska M, Kolinski A, Katayama T, Kanehisa M

He S, Liu C, Skogerbø G, Zhao H, Wang J, Liu T, Bai B, Zhao Y, Chen R

Data growth and its impact on the SCOP database: new developments.
Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG

Novel definition files for human GeneChips based on GeneAnnot.
Ferrari F, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli GA, Bicciato S

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.
Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A

Imaging of a large collection of human embryo using a super-parallel MR microscope.
Matsuda Y, Ono S, Otake Y, Handa S, Kose K, Haishi T, Yamada S, Uwabe C, Shiota K

Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray.
Satoh K, Doi K, Nagata T, Kishimoto N, Suzuki K, Otomo Y, Kawai J, Nakamura M, Hirozane-Kishikawa T, Kanagawa S, Arakawa T, Takahashi-Iida J, Murata M, Ninomiya N, Sasaki D, Fukuda S, Tagami M, Yamagata H, Kurita K, Kamiya K, Yamamoto M, Kikuta A, Bito T, Fujitsuka N, Ito K, Kanamori H, Choi IR, Nagamura Y, Matsumoto T, Murakami K, Matsubara K, Carninci P, Hayashizaki Y, Kikuchi S

Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets.
Chelala C, Hahn SA, Whiteman HJ, Barry S, Hariharan D, Radon TP, Lemoine NR, Crnogorac-Jurcevic T

DrugBank: a knowledgebase for drugs, drug actions and drug targets.
Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M

Functional annotation of 19,841 Populus nigra full-length enriched cDNA clones.
Nanjo T, Sakurai T, Totoki Y, Toyoda A, Nishiguchi M, Kado T, Igasaki T, Futamura N, Seki M, Sakaki Y, Shinozaki K, Shinohara K

Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, Hériché JK, Hu Y, Kristiansen K, Li R, Liu T, Moses A, Qin J, Vang S, Vilella AJ, Ureta-Vidal A, Bolund L, Wang J, Durbin R

The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.
Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

The Rice Annotation Project Database (RAP-DB): 2008 update.

Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response.
Sakurai T, Plata G, Rodríguez-Zapata F, Seki M, Salcedo A, Toyoda A, Ishiwata A, Tohme J, Sakaki Y, Shinozaki K, Ishitani M

The microRNA.org resource: targets and expression.
Betel D, Wilson M, Gabow A, Marks DS, Sander C

Characterization of the soybean genome using EST-derived microsatellite markers.
Hisano H, Sato S, Isobe S, Sasamoto S, Wada T, Matsuno A, Fujishiro T, Yamada M, Nakayama S, Nakamura Y, Watanabe S, Harada K, Tabata S

Possible roles of vacuolar H+-ATPase and mitochondrial function in tolerance to air-drying stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains.

Reticulate representation of evolutionary and functional relationships between phage genomes.
Lima-Mendez G, Van Helden J, Toussaint A, Leplae R

Prophinder: a computational tool for prophage prediction in prokaryotic genomes.

Comparative analysis of expressed sequence tag (EST) libraries in the seagrass Zostera marina subjected to temperature stress.
Reusch TB, Veron AS, Preuss C, Weiner J, Wissler L, Beck A, Klages S, Kube M, Reinhardt R, Bornberg-Bauer E

Mouse inter-subspecific consomic strains for genetic dissection of quantitative complex traits.
Takada T, Mita A, Maeno A, Sakai T, Shitara H, Kikkawa Y, Moriwaki K, Yonekawa H, Shiroishi T

Metabolite annotations based on the integration of mass spectral information.
Iijima Y, Nakamura Y, Ogata Y, Tanaka K, Sakurai N, Suda K, Suzuki T, Suzuki H, Okazaki K, Kitayama M, Kanaya S, Aoki K, Shibata D

SPIKE--a database, visualization and analysis tool of cellular signaling pathways.
Elkon R, Vesterman R, Amit N, Ulitsky I, Zohar I, Weisz M, Mass G, Orlev N, Sternberg G, Blekhman R, Assa J, Shiloh Y, Shamir R

Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS).

Exploration of human ORFeome: high-throughput preparation of ORF clones and efficient characterization of their protein products.
Nagase T, Yamakawa H, Tadokoro S, Nakajima D, Inoue S, Yamaguchi K, Itokawa Y, Kikuno RF, Koga H, Ohara O

Analysis of expressed sequence tags (ESTs) from Lentinula edodes.
Suizu T, Zhou GL, Oowatari Y, Kawamukai M

Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350.
Ohnishi Y, Ishikawa J, Hara H, Suzuki H, Ikenoya M, Ikeda H, Yamashita A, Hattori M, Horinouchi S

ASPicDB: a database resource for alternative splicing analysis.
Castrignanò T, D'Antonio M, Anselmo A, Carrabino D, D'Onorio De Meo A, D'Erchia AM, Licciulli F, Mangiulli M, Mignone F, Pavesi G, Picardi E, Riva A, Rizzi R, Bonizzoni P, Pesole G

Profiling of Escherichia coli Chromosome database.

The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access.
Goda H, Sasaki E, Akiyama K, Maruyama-Nakashita A, Nakabayashi K, Li W, Ogawa M, Yamauchi Y, Preston J, Aoki K, Kiba T, Takatsuto S, Fujioka S, Asami T, Nakano T, Kato H, Mizuno T, Sakakibara H, Yamaguchi S, Nambara E, Kamiya Y, Takahashi H, Hirai MY, Sakurai T, Shinozaki K, Saito K, Yoshida S, Shimada Y

FAMS and FAMSBASE for protein structure.

BioCompass: a novel functional inference tool that utilizes MeSH hierarchy to analyze groups of genes.
Nakazato T, Takinaka T, Mizuguchi H, Matsuda H, Bono H, Asogawa M

TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles.

Software.ncrna.org: web servers for analyses of RNA sequences.
Asai K, Kiryu H, Hamada M, Tabei Y, Sato K, Matsui H, Sakakibara Y, Terai G, Mituyama T

Aspergillus oryzae atfB encodes a transcription factor required for stress tolerance in conidia.
Sakamoto K, Arima TH, Iwashita K, Yamada O, Gomi K, Akita O

The RAS/MAPK syndromes: novel roles of the RAS pathway in human genetic disorders.
Aoki Y, Niihori T, Narumi Y, Kure S, Matsubara Y

Structural classification of CDR-H3 revisited: a lesson in antibody modeling.
Kuroda D, Shirai H, Kobori M, Nakamura H

Efficient production of monoclonal antibodies recognizing specific structures in Caenorhabditis elegans embryos using an antigen subtraction method.
Takeda K, Watanabe C, Qadota H, Hanazawa M, Sugimoto A

Genome structure of the legume, Lotus japonicus.
Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M, Sasamoto S, Watanabe A, Ono A, Kawashima K, Fujishiro T, Katoh M, Kohara M, Kishida Y, Minami C, Nakayama S, Nakazaki N, Shimizu Y, Shinpo S, Takahashi C, Wada T, Yamada M, Ohmido N, Hayashi M, Fukui K, Baba T, Nakamichi T, Mori H, Tabata S

Soybean seed extracts preferentially express genomic loci of Bradyrhizobium japonicum in the initial interaction with soybean, Glycine max (L.) Merr.
Wei M, Yokoyama T, Minamisawa K, Mitsui H, Itakura M, Kaneko T, Tabata S, Saeki K, Omori H, Tajima S, Uchiumi T, Abe M, Ohwada T

An improved scoring scheme for predicting glycan structures from gene expression data.
Suga A, Yamanishi Y, Hashimoto K, Goto S, Kanehisa M

TriMEDB: a database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae.
Mochida K, Saisho D, Yoshida T, Sakurai T, Shinozaki K

Cerebellar development transcriptome database (CDT-DB): profiling of spatio-temporal gene expression during the postnatal development of mouse cerebellum.
Sato A, Sekine Y, Saruta C, Nishibe H, Morita N, Sato Y, Sadakata T, Shinoda Y, Kojima T, Furuichi T

Establishment and evaluation of the Japanese edition of the Weekly Epidemiological Record (WER) website by the Faculty of Health Sciences of Kobe University School of Medicine.
Southeast Asian J. Trop. Med. Public Health

A gene wiki for community annotation of gene function.
Huss JW, Orozco C, Goodale J, Wu C, Batalov S, Vickers TJ, Valafar F, Su AI

The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server.
Hoogland C, Mostaguir K, Appel RD, Lisacek F

The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature.
Yamamoto S, Asanuma T, Takagi T, Fukuda KI

Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles.

Resources for global risk assessment: the International Toxicity Estimates for Risk (ITER) and Risk Information Exchange (RiskIE) databases.
Wullenweber A, Kroner O, Kohrman M, Maier A, Dourson M, Rak A, Wexler P, Tomljanovic C

Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules.
Hodis E, Prilusky J, Martz E, Silman I, Moult J, Sussman JL

Trends in large-scale mouse mutagenesis: from genetics to functional genomics.

bold: The Barcode of Life Data System (http://www.barcodinglife.org).

Systematic classification of CDR-L3 in antibodies: implications of the light chain subtypes and the VL-VH interface.

GlycomeDB - integration of open-access carbohydrate structure databases.
Ranzinger R, Herget S, Wetter T, von der Lieth CW

DiProDB: a database for dinucleotide properties.
Friedel M, Nikolajewa S, Sühnel J, Wilhelm T

Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock.
Kumaki Y, Ukai-Tadenuma M, Uno KD, Nishio J, Masumoto KH, Nagano M, Komori T, Shigeyoshi Y, Hogenesch JB, Ueda HR

Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database.

Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH

BodyParts3D: 3D structure database for anatomical concepts.
Mitsuhashi N, Fujieda K, Tamura T, Kawamoto S, Takagi T, Okubo K

The Universal Protein Resource (UniProt) 2009.

PiSite: a database of protein interaction sites using multiple binding states in the PDB.

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.
Takeda J, Suzuki Y, Sakate R, Sato Y, Seki M, Irie T, Takeuchi N, Ueda T, Nakao M, Sugano S, Gojobori T, Imanishi T

MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database.
Ahsan B, Saito TL, Hashimoto S, Muramatsu K, Tsuda M, Sasaki A, Matsushima K, Aigaki T, Morishita S

McKusick's Online Mendelian Inheritance in Man (OMIM).
Amberger J, Bocchini CA, Scott AF, Hamosh A

tRNADB-CE: tRNA gene database curated manually by experts.
Abe T, Ikemura T, Ohara Y, Uehara H, Kinouchi M, Kanaya S, Yamada Y, Muto A, Inokuchi H

RAPID: Resource of Asian Primary Immunodeficiency Diseases.
Keerthikumar S, Raju R, Kandasamy K, Hijikata A, Ramabadran S, Balakrishnan L, Ahmed M, Rani S, Selvan LD, Somanathan DS, Ray S, Bhattacharjee M, Gollapudi S, Ramachandra YL, Bhadra S, Bhattacharyya C, Imai K, Nonoyama S, Kanegane H, Miyawaki T, Pandey A, Ohara O, Mohan S

TMFunction: database for functional residues in membrane proteins.
Gromiha MM, Yabuki Y, Suresh MX, Thangakani AM, Suwa M, Fukui K

Distribution and effects of nonsense polymorphisms in human genes.
Yamaguchi-Kabata Y, Shimada MK, Hayakawa Y, Minoshima S, Chakraborty R, Gojobori T, Imanishi T

The Human Protein Atlas--a tool for pathology.

BioCaster: detecting public health rumors with a Web-based text mining system.
Collier N, Doan S, Kawazoe A, Goodwin RM, Conway M, Tateno Y, Ngo QH, Dien D, Kawtrakul A, Takeuchi K, Shigematsu M, Taniguchi K

PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes.

Human immunodeficiency virus type 1, human protein interaction database at NCBI.
Fu W, Sanders-Beer BE, Katz KS, Maglott DR, Pruitt KD, Ptak RG

DDBJ dealing with mass data produced by the second generation sequencer.
Sugawara H, Ikeo K, Fukuchi S, Gojobori T, Tateno Y

NCBI Reference Sequences: current status, policy and new initiatives.
Pruitt KD, Tatusova T, Klimke W, Maglott DR

Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library.
Umezawa T, Sakurai T, Totoki Y, Toyoda A, Seki M, Ishiwata A, Akiyama K, Kurotani A, Yoshida T, Mochida K, Kasuga M, Todaka D, Maruyama K, Nakashima K, Enju A, Mizukado S, Ahmed S, Yoshiwara K, Harada K, Tsubokura Y, Hayashi M, Sato S, Anai T, Ishimoto M, Funatsuki H, Teraishi M, Osaki M, Shinano T, Akashi R, Sakaki Y, Yamaguchi-Shinozaki K, Shinozaki K

ProSeg: a database of local structures of protein segments.

NCBI GEO: archive for high-throughput functional genomic data.
Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Edgar R

STRING 8--a global view on proteins and their functional interactions in 630 organisms.
Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C

PEDANT covers all complete RefSeq genomes.
Walter MC, Rattei T, Arnold R, Güldener U, Münsterkötter M, Nenova K, Kastenmüller G, Tischler P, Wölling A, Volz A, Pongratz N, Jost R, Mewes HW, Frishman D

Database resources of the National Center for Biotechnology Information.
Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J

The National Center for Biotechnology Information's Protein Clusters Database.
Klimke W, Agarwala R, Badretdin A, Chetvernin S, Ciufo S, Fedorov B, Kiryutin B, O'Neill K, Resch W, Resenchuk S, Schafer S, Tolstoy I, Tatusova T

The RNA WikiProject: community annotation of RNA families.
Daub J, Gardner PP, Tate J, Ramsköld D, Manske M, Scott WG, Weinberg Z, Griffiths-Jones S, Bateman A

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.
Mituyama T, Yamada K, Hattori E, Okida H, Ono Y, Terai G, Yoshizawa A, Komori T, Asai K

HGVbaseG2P: a central genetic association database.
Thorisson GA, Lancaster O, Free RC, Hastings RK, Sarmah P, Dash D, Brahmachari SK, Brookes AJ

PharmGKB: understanding the effects of individual genetic variants.
Sangkuhl K, Berlin DS, Altman RB, Klein TE

HMDB: a knowledgebase for the human metabolome.
Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, Lim E, Sobsey CA, Shrivastava S, Huang P, Liu P, Fang L, Peng J, Fradette R, Cheng D, Tzur D, Clements M, Lewis A, De Souza A, Zuniga A, Dawe M, Xiong Y, Clive D, Greiner R, Nazyrova A, Shaykhutdinov R, Li L, Vogel HJ, Forsythe I

ATTED-II provides coexpressed gene networks for Arabidopsis.
Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K

Rfam: updates to the RNA families database.
Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A

Implementation of GenePattern within the Stanford Microarray Database.
Hubble J, Demeter J, Jin H, Mao M, Nitzberg M, Reddy TB, Wymore F, Zachariah ZK, Sherlock G, Ball CA

VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts.
Shimada MK, Matsumoto R, Hayakawa Y, Sanbonmatsu R, Gough C, Yamaguchi-Kabata Y, Yamasaki C, Imanishi T, Gojobori T

tRNAdb 2009: compilation of tRNA sequences and tRNA genes.
Jühling F, Mörl M, Hartmann RK, Sprinzl M, Stadler PF, Pütz J

The GOA database in 2009--an integrated Gene Ontology Annotation resource.
Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences.
Portales-Casamar E, Arenillas D, Lim J, Swanson MI, Jiang S, McCallum A, Kirov S, Wasserman WW

dictyBase--a Dictyostelium bioinformatics resource update.
Fey P, Gaudet P, Curk T, Zupan B, Just EM, Basu S, Merchant SN, Bushmanova YA, Shaulsky G, Kibbe WA, Chisholm RL

Petabyte-scale innovations at the European Nucleotide Archive.
Cochrane G, Akhtar R, Bonfield J, Bower L, Demiralp F, Faruque N, Gibson R, Hoad G, Hubbard T, Hunter C, Jang M, Juhos S, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Plaister S, Radhakrishnan R, Robinson S, Sobhany S, Hoopen PT, Vaughan R, Zalunin V, Birney E

SMART 6: recent updates and new developments.

Lefranc MP, Giudicelli V, Ginestoux C, Jabado-Michaloud J, Folch G, Bellahcene F, Wu Y, Gemrot E, Brochet X, Lane J, Regnier L, Ehrenmann F, Lefranc G, Duroux P

Minimotif miner 2nd release: a database and web system for motif search.
Rajasekaran S, Balla S, Gradie P, Gryk MR, Kadaveru K, Kundeti V, Maciejewski MW, Mi T, Rubino N, Vyas J, Schiller MR

Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes.
Winsor GL, Van Rossum T, Lo R, Khaira B, Whiteside MD, Hancock RE, Brinkman FS

VIPERdb2: an enhanced and web API enabled relational database for structural virology.
Carrillo-Tripp M, Shepherd CM, Borelli IA, Venkataraman S, Lander G, Natarajan P, Johnson JE, Brooks CL, Reddy VS

GtRNAdb: a database of transfer RNA genes detected in genomic sequence.

BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009.
Chang A, Scheer M, Grote A, Schomburg I, Schomburg D

CDD: specific functional annotation with the Conserved Domain Database.
Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH

Transterm: a database to aid the analysis of regulatory sequences in mRNAs.
Jacobs GH, Chen A, Stevens SG, Stockwell PA, Black MA, Tate WP, Brown CM

Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009.
Wakaguri H, Suzuki Y, Katayama T, Kawashima S, Kibukawa E, Hiranuka K, Sasaki M, Sugano S, Watanabe J

The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions.
Fukuchi S, Homma K, Sakamoto S, Sugawara H, Tateno Y, Gojobori T, Nishikawa K

Human Protein Reference Database--2009 update.
Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A

Changes in gene expression of commercial baker's yeast during an air-drying process that simulates dried yeast production.
Nakamura T, Mizukami-Murata S, Ando A, Murata Y, Takagi H, Shima J

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM

SpBase: the sea urchin genome database and web site.
Cameron RA, Samanta M, Yuan A, He D, Davidson E

AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse.
Shionyu M, Yamaguchi A, Shinoda K, Takahashi K, Go M

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.
Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A

Cataloguing the HIV type 1 human protein interaction network.
Ptak RG, Fu W, Sanders-Beer BE, Dickerson JE, Pinney JW, Robertson DL, Rozanov MN, Katz KS, Maglott DR, Pruitt KD, Dieffenbach CW

Systematic NMR analysis of stable isotope labeled metabolite mixtures in plant and animal systems: coarse grained views of metabolic pathways.
Chikayama E, Suto M, Nishihara T, Shinozaki K, Hirayama T, Kikuchi J

PRIMe: a Web site that assembles tools for metabolomics and transcriptomics.
Akiyama K, Chikayama E, Yuasa H, Shimada Y, Tohge T, Shinozaki K, Hirai MY, Sakurai T, Kikuchi J, Saito K

Human protein factory for converting the transcriptome into an in vitro-expressed proteome,.
Goshima N, Kawamura Y, Fukumoto A, Miura A, Honma R, Satoh R, Wakamatsu A, Yamamoto J, Kimura K, Nishikawa T, Andoh T, Iida Y, Ishikawa K, Ito E, Kagawa N, Kaminaga C, Kanehori K, Kawakami B, Kenmochi K, Kimura R, Kobayashi M, Kuroita T, Kuwayama H, Maruyama Y, Matsuo K, Minami K, Mitsubori M, Mori M, Morishita R, Murase A, Nishikawa A, Nishikawa S, Okamoto T, Sakagami N, Sakamoto Y, Sasaki Y, Seki T, Sono S, Sugiyama A, Sumiya T, Takayama T, Takayama Y, Takeda H, Togashi T, Yahata K, Yamada H, Yanagisawa Y, Endo Y, Imamoto F, Kisu Y, Tanaka S, Isogai T, Imai J, Watanabe S, Nomura N

Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics.
Maruyama Y, Wakamatsu A, Kawamura Y, Kimura K, Yamamoto J, Nishikawa T, Kisu Y, Sugano S, Goshima N, Isogai T, Nomura N

DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins.

MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions.
Chautard E, Ballut L, Thierry-Mieg N, Ricard-Blum S

Gclust: trans-kingdom classification of proteins using automatic individual threshold setting.

Analysis and validation of carbohydrate three-dimensional structures.

Genome-wide validation of Magnaporthe grisea gene structures based on transcription evidence.
Numa H, Nishimura M, Tanaka T, Kanamori H, Yang CC, Matsumoto T, Nagamura Y, Itoh T

International Gene Trap Project: towards gene-driven saturation mutagenesis in mice.

Massive transcriptional start site analysis of human genes in hypoxia cells.
Tsuchihara K, Suzuki Y, Wakaguri H, Irie T, Tanimoto K, Hashimoto S, Matsushima K, Mizushima-Sugano J, Yamashita R, Nakai K, Bentley D, Esumi H, Sugano S

Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins.
Niwa T, Ying BW, Saito K, Jin W, Takada S, Ueda T, Taguchi H

HIV-host interactions: a map of viral perturbation of the host system.
Pinney JW, Dickerson JE, Fu W, Sanders-Beer BE, Ptak RG, Robertson DL

Searching the Mouse Genome Informatics (MGI) resources for information on mouse biology from genotype to phenotype.

Data mining the PDB for glyco-related data.

Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans.
Hashimoto K, Tokimatsu T, Kawano S, Yoshizawa AC, Okuda S, Goto S, Kanehisa M

Newly discovered breast cancer susceptibility loci on 3p24 and 17q23.2.
['Ahmed S', 'Thomas G', 'Ghoussaini M', 'Healey CS', 'Humphreys MK', 'Platte R', 'Morrison J', 'Maranian M', 'Pooley KA', 'Luben R', 'Eccles D', 'Evans DG', 'Fletcher O', 'Johnson N', 'dos Santos Silva I', 'Peto J', 'Stratton MR', 'Rahman N', 'Jacobs K', 'Prentice R', 'Anderson GL', 'Rajkovic A', 'Curb JD', 'Ziegler RG', 'Berg CD', 'Buys SS', 'McCarty CA', 'Feigelson HS', 'Calle EE', 'Thun MJ', 'Diver WR', 'Bojesen S', 'Nordestgaard BG', 'Flyger H', 'Dörk T', 'Schürmann P', 'Hillemanns P', 'Karstens JH', 'Bogdanova NV', 'Antonenkova NN', 'Zalutsky IV', 'Bermisheva M', 'Fedorova S', 'Khusnutdinova E']

A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1).
Thomas G, Jacobs KB, Kraft P, Yeager M, Wacholder S, Cox DG, Hankinson SE, Hutchinson A, Wang Z, Yu K, Chatterjee N, Garcia-Closas M, Gonzalez-Bosquet J, Prokunina-Olsson L, Orr N, Willett WC, Colditz GA, Ziegler RG, Berg CD, Buys SS, McCarty CA, Feigelson HS, Calle EE, Thun MJ, Diver R, Prentice R, Jackson R, Kooperberg C, Chlebowski R, Lissowska J, Peplonska B, Brinton LA, Sigurdson A, Doody M, Bhatti P, Alexander BH, Buring J, Lee IM, Vatten LJ, Hveem K, Kumle M, Hayes RB, Tucker M, Gerhard DS, Fraumeni JF, Hoover RN, Chanock SJ, Hunter DJ

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

The regulated retrotransposon transcriptome of mammalian cells.
Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest AR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P

Tiny RNAs associated with transcription start sites in animals.
Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest AR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, Kawazu C, Murata M, Nishiyori H, Fukuda S, Kawai J, Daub CO, Hume DA, Suzuki H, Orlando V, Carninci P, Hayashizaki Y, Mattick JS

PrognoScan: a new database for meta-analysis of the prognostic value of genes.

Fast linear feature detection using multiple directional non-maximum suppression.

Web API for biology with a workflow navigation system.
Kwon Y, Shigemoto Y, Kuwana Y, Sugawara H

Evaluation of haplotype inference using definitive haplotype data obtained from complete hydatidiform moles, and its significance for the analyses of positively selected regions.
Higasa K, Kukita Y, Kato K, Wake N, Tahira T, Hayashi K

TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics.
Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K

Unique inbred strain MSM/Ms established from the Japanese wild mouse.
Moriwaki K, Miyashita N, Mita A, Gotoh H, Tsuchiya K, Kato H, Mekada K, Noro C, Oota S, Yoshiki A, Obata Y, Yonekawa H, Shiroishi T

MIMAS 3.0 is a Multiomics Information Management and Annotation System.
Gattiker A, Hermida L, Liechti R, Xenarios I, Collin O, Rougemont J, Primig M

Evolution of pathogenicity and sexual reproduction in eight Candida genomes.
Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M, Cuomo CA

PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning.
Yoshida Y, Makita Y, Heida N, Asano S, Matsushima A, Ishii M, Mochizuki Y, Masuya H, Wakana S, Kobayashi N, Toyoda T

Functional and evolutionary insights into human brain development through global transcriptome analysis.
Johnson MB, Kawasawa YI, Mason CE, Krsnik Z, Coppola G, Bogdanović D, Geschwind DH, Mane SM, State MW, Sestan N

E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs.
Yamanishi Y, Hattori M, Kotera M, Goto S, Kanehisa M

From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations.
Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM

Soybean proteome database: a data resource for plant differential omics.
Sakata K, Ohyanagi H, Nobori H, Nakamura T, Hashiguchi A, Nanjo Y, Mikami Y, Yunokawa H, Komatsu S

ChEBI: an open bioinformatics and cheminformatics resource.
Degtyarenko K, Hastings J, de Matos P, Ennis M

Gendoo: functional profiling of gene and disease features using MeSH vocabulary.

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.
Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, Maidak BL, Mudge J, Murphy MR, Murphy T, Rajan J, Rajput B, Riddick LD, Snow C, Steward C, Webb D, Weber JA, Wilming L, Wu W, Birney E, Haussler D, Hubbard T, Ostell J, Durbin R, Lipman D

[Genome-wide association study of gastric cancer and GeMDBJ database].

Agouti C57BL/6N embryonic stem cells for mouse genetic resources.
Pettitt SJ, Liang Q, Rairdan XY, Moran JL, Prosser HM, Beier DR, Lloyd KC, Bradley A, Skarnes WC

['Celniker SE', 'Dillon LA', 'Gerstein MB', 'Gunsalus KC', 'Henikoff S', 'Karpen GH', 'Kellis M', 'Lai EC', 'Lieb JD', 'MacAlpine DM', 'Micklem G', 'Piano F', 'Snyder M', 'Stein L', 'White KP', 'Waterston RH']

Next-generation gene targeting in the mouse for functional genomics.

Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans.
Arnaud MB, Costanzo MC, Shah P, Skrzypek MS, Sherlock G

The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.

Annotating the human genome with Disease Ontology.
Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, Chisholm RL

Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis.

Genome-wide association database developed in the Japanese Integrated Database Project.
Koike A, Nishida N, Inoue I, Tsuji S, Tokunaga K

National BioResource Project-Rat and related activities.
Serikawa T, Mashimo T, Takizawa A, Okajima R, Maedomari N, Kumafuji K, Tagami F, Neoda Y, Otsuki M, Nakanishi S, Yamasaki K, Voigt B, Kuramoto T

ArachnoServer: a database of protein toxins from spiders.
Wood DL, Miljenović T, Cai S, Raven RJ, Kaas Q, Escoubas P, Herzig V, Wilson D, King GF

IL-10 is a negative regulatory factor of CAWS-vasculitis in CBA/J mice as assessed by comparison with Bruton's tyrosine kinase-deficient CBA/N mice.
Miura NN, Komai M, Adachi Y, Osada N, Kameoka Y, Suzuki K, Ohno N

An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow.

Computational overview of GPCR gene universe to support reverse chemical genomics study.

QuickGO: a web-based tool for Gene Ontology searching.
Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R

The Gene Wiki: community intelligence applied to human gene annotation.
Huss JW, Lindenbaum P, Martone M, Roberts D, Pizarro A, Valafar F, Hogenesch JB, Su AI

Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences.
Ranzinger R, Frank M, von der Lieth CW, Herget S

The completion of the Mammalian Gene Collection (MGC).

Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression.

The University of Minnesota Biocatalysis/Biodegradation Database: improving public access.

Recode-2: new design, new search tools, and many more genes.
Bekaert M, Firth AE, Zhang Y, Gladyshev VN, Atkins JF, Baranov PV

Collection of Macaca fascicularis cDNAs derived from bone marrow, kidney, liver, pancreas, spleen, and thymus.
Osada N, Hirata M, Tanuma R, Suzuki Y, Sugano S, Terao K, Kusuda J, Kameoka Y, Hashimoto K, Takahashi I

SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.
Duan J, Li R, Cheng D, Fan W, Zha X, Cheng T, Wu Y, Wang J, Mita K, Xiang Z, Xia Q

RESOPS: a database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures.
Yura K, Sulaiman S, Hatta Y, Shionyu M, Go M

New tools at the Candida Genome Database: biochemical pathways and full-text literature search.
Skrzypek MS, Arnaud MB, Costanzo MC, Inglis DO, Shah P, Binkley G, Miyasato SR, Sherlock G

Non-susceptibility genes to Bombyx densovirus type 1, Nid-1 and nsd-1, affect distinct steps of the viral infection pathway.
Kidokoro K, Ito K, Ogoyi DO, Abe H, Mita K, Kadono-Okuda K

KAIKObase: an integrated silkworm genome database and data mining tool.
Shimomura M, Minami H, Suetsugu Y, Ohyanagi H, Satoh C, Antonio B, Nagamura Y, Kadono-Okuda K, Kajiwara H, Sezutsu H, Nagaraju J, Goldsmith MR, Xia Q, Yamamoto K, Mita K

G-compass: a web-based comparative genome browser between human and other vertebrate genomes.
Kawahara Y, Sakate R, Matsuya A, Murakami K, Sato Y, Zhang H, Gojobori T, Itoh T, Imanishi T

REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.
Roberts RJ, Vincze T, Posfai J, Macelis D

The IntAct molecular interaction database in 2010.
Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H

DDBJ launches a new archive database with analytical tools for next-generation sequence data.
Kaminuma E, Mashima J, Kodama Y, Gojobori T, Ogasawara O, Okubo K, Takagi T, Nakamura Y

SALAD database: a motif-based database of protein annotations for plant comparative genomics.

Geer LY, Marchler-Bauer A, Geer RC, Han L, He J, He S, Liu C, Shi W, Bryant SH

Chemical Entities of Biological Interest: an update.
de Matos P, Alcántara R, Dekker A, Ennis M, Hastings J, Haug K, Spiteri I, Turner S, Steinbeck C

PROSITE, a protein domain database for functional characterization and annotation.
Sigrist CJ, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.
Grillo G, Turi A, Licciulli F, Mignone F, Liuni S, Banfi S, Gennarino VA, Horner DS, Pavesi G, Picardi E, Pesole G

PepX: a structural database of non-redundant protein-peptide complexes.
Vanhee P, Reumers J, Stricher F, Baeten L, Serrano L, Schymkowitz J, Rousseau F

CyanoBase: the cyanobacteria genome database update 2010.
Nakao M, Okamoto S, Kohara M, Fujishiro T, Fujisawa T, Sato S, Tabata S, Kaneko T, Nakamura Y

Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing.
Wakamatsu A, Kimura K, Yamamoto J, Nishikawa T, Nomura N, Sugano S, Isogai T

Genome-wide analysis of host gene expression in the silkworm cells infected with Bombyx mori nucleopolyhedrovirus.
Sagisaka A, Fujita K, Nakamura Y, Ishibashi J, Noda H, Imanishi S, Mita K, Yamakawa M, Tanaka H

Ensembl Genomes: extending Ensembl across the taxonomic space.
Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kähäri A, Kinsella RJ, Kulesha E, Maheswari U, Megy K, Nuhn M, Proctor G, Staines D, Valentin F, Vilella AJ, Yates A

In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean.
Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS

Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B

ChimerDB 2.0--a knowledgebase for fusion genes updated.
Kim P, Yoon S, Kim N, Lee S, Ko M, Lee H, Kang H, Kim J, Lee S

The Proteomics Identifications database: 2010 update.
Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L

MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

WormBase: a comprehensive resource for nematode research.
Harris TW, Antoshechkin I, Bieri T, Blasiar D, Chan J, Chen WJ, De La Cruz N, Davis P, Duesbury M, Fang R, Fernandes J, Han M, Kishore R, Lee R, Müller HM, Nakamura C, Ozersky P, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Yook K, Durbin R, Stein LD, Spieth J, Sternberg PW

DBTSS provides a tissue specific dynamic view of Transcription Start Sites.
Yamashita R, Wakaguri H, Sugano S, Suzuki Y, Nakai K

The Chloroplast Function Database: a large-scale collection of Arabidopsis Ds/Spm- or T-DNA-tagged homozygous lines for nuclear-encoded chloroplast proteins, and their systematic phenotype analysis.
Myouga F, Akiyama K, Motohashi R, Kuromori T, Ito T, Iizumi H, Ryusui R, Sakurai T, Shinozaki K

EuPathDB: a portal to eukaryotic pathogen databases.
Aurrecoechea C, Brestelli J, Brunk BP, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer ET, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Srinivasamoorthy G, Stoeckert CJ, Thibodeau R, Treatman C, Wang H

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.
Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW, Su AI

LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors.

H-InvDB in 2009: extended database and data mining resources for human genes and transcripts.
Yamasaki C, Murakami K, Takeda J, Sato Y, Noda A, Sakate R, Habara T, Nakaoka H, Todokoro F, Matsuya A, Imanishi T, Gojobori T

ACLAME: a CLAssification of Mobile genetic Elements, update 2010.

The European Bioinformatics Institute's data resources.

NCBI Peptidome: a new repository for mass spectrometry proteomics data.
Ji L, Barrett T, Ayanbule O, Troup DB, Rudnev D, Muertter RN, Tomashevsky M, Soboleva A, Slotta DJ

Monooxygenation of rifampicin catalyzed by the rox gene product of Nocardia farcinica: structure elucidation, gene identification and role in drug resistance.
Hoshino Y, Fujii S, Shinonaga H, Arai K, Saito F, Fukai T, Satoh H, Miyazaki Y, Ishikawa J

SMPDB: The Small Molecule Pathway Database.
Frolkis A, Knox C, Lim E, Jewison T, Law V, Hau DD, Liu P, Gautam B, Ly S, Guo AC, Xia J, Liang Y, Shrivastava S, Wishart DS

Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis.
Lammers CR, Flórez LA, Schmeisky AG, Roppel SF, Mäder U, Hamoen L, Stülke J

Archiving next generation sequencing data.

Planarians maintain a constant ratio of different cell types during changes in body size by using the stem cell system.

H-DBAS: human-transcriptome database for alternative splicing: update 2010.
Takeda J, Suzuki Y, Sakate R, Sato Y, Gojobori T, Imanishi T, Sugano S

Yellow-e determines the color pattern of larval head and tail spots of the silkworm Bombyx mori.
Ito K, Katsuma S, Yamamoto K, Kadono-Okuda K, Mita K, Shimada T

AtMetExpress development: a phytochemical atlas of Arabidopsis development.
Matsuda F, Hirai MY, Sasaki E, Akiyama K, Yonekura-Sakakibara K, Provart NJ, Sakurai T, Shimada Y, Saito K

A CD36-related transmembrane protein is coordinated with an intracellular lipid-binding protein in selective carotenoid transport for cocoon coloration.
Sakudoh T, Iizuka T, Narukawa J, Sezutsu H, Kobayashi I, Kuwazaki S, Banno Y, Kitamura A, Sugiyama H, Takada N, Fujimoto H, Kadono-Okuda K, Mita K, Tamura T, Yamamoto K, Tsuchida K

Howdy, partner! How your practice can team up with hospitals to recruit physicians.

A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58.
Yokoyama S, Ito Y, Ueno-Kudoh H, Shimizu H, Uchibe K, Albini S, Mitsuoka K, Miyaki S, Kiso M, Nagai A, Hikata T, Osada T, Fukuda N, Yamashita S, Harada D, Mezzano V, Kasai M, Puri PL, Hayashizaki Y, Okado H, Hashimoto M, Asahara H

Molecular characterization and functional analysis of novel carboxyl/cholinesterases with GQSAG motif in the silkworm Bombyx mori.
Tsubota T, Shimomura M, Ogura T, Seino A, Nakakura T, Mita K, Shinoda T, Shiotsuki T

Expression profiling of novel bacteria-induced genes from the silkworm, Bombyx mori.
Tanaka H, Suzuki N, Nakajima Y, Sato M, Sagisaka A, Fujita K, Ishibashi J, Imanishi S, Mita K, Yamakawa M

Single-cell gene profiling of planarian stem cells using fluorescent activated cell sorting and its "index sorting" function for stem cell research.
Hayashi T, Shibata N, Okumura R, Kudome T, Nishimura O, Tarui H, Agata K

Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information.
Zhang Y, De S, Garner JR, Smith K, Wang SA, Becker KG

Profiling polar and semipolar plant metabolites throughout extraction processes using a combined solution-state and high-resolution magic angle spinning NMR approach.

Cancer proteome-expression database: Genome Medicine Database of Japan Proteomics.

Identification and molecular characterization of a sex chromosome rearrangement causing a soft and pliable (spli) larval body phenotype in the silkworm, Bombyx mori.
Fujii T, Kuwazaki S, Yamamoto K, Abe H, Ohnuma A, Katsuma S, Mita K, Shimada T

Analysis of CASP8 targets, predictions and assessment methods.
Shi S, Pei J, Sadreyev RI, Kinch LN, Majumdar I, Tong J, Cheng H, Kim BH, Grishin NV

The Homeodomain Resource: a comprehensive collection of sequence, structure, interaction, genomic and functional information on the homeodomain protein family.
Moreland RT, Ryan JF, Pan C, Baxevanis AD

Laganà A, Forte S, Giudice A, Arena MR, Puglisi PL, Giugno R, Pulvirenti A, Shasha D, Ferro A

Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs.
Wissler L, Dattolo E, Moore AD, Reusch TB, Olsen JL, Migliaccio M, Bornberg-Bauer E, Procaccini G

The Prion Disease Database: a comprehensive transcriptome resource for systems biology research in prion diseases.
Gehlenborg N, Hwang D, Lee IY, Yoo H, Baxter D, Petritis B, Pitstick R, Marzolf B, Dearmond SJ, Carlson GA, Hood L

A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki.
Flórez LA, Roppel SF, Schmeisky AG, Lammers CR, Stülke J

SDOP-DB: a comparative standardized-protocol database for mouse phenotypic analyses.
Tanaka N, Waki K, Kaneda H, Suzuki T, Yamada I, Furuse T, Kobayashi K, Motegi H, Toki H, Inoue M, Minowa O, Noda T, Takao K, Miyakawa T, Takahashi A, Koide T, Wakana S, Masuya H

An atlas of combinatorial transcriptional regulation in mouse and man.
Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y

Interaction networks as a tool to investigate the mechanisms of aging.
Chautard E, Thierry-Mieg N, Ricard-Blum S

KMeyeDB: a graphical database of mutations in genes that cause eye diseases.
Kawamura T, Ohtsubo M, Mitsuyama S, Ohno-Nakamura S, Shimizu N, Minoshima S

Performance of common genetic variants in breast-cancer risk models.
Wacholder S, Hartge P, Prentice R, Garcia-Closas M, Feigelson HS, Diver WR, Thun MJ, Cox DG, Hankinson SE, Kraft P, Rosner B, Berg CD, Brinton LA, Lissowska J, Sherman ME, Chlebowski R, Kooperberg C, Jackson RD, Buckman DW, Hui P, Pfeiffer R, Jacobs KB, Thomas GD, Hoover RN, Gail MH, Chanock SJ, Hunter DJ

CaMPDB: a resource for calpain and modulatory proteolysis.
duVerle D, Takigawa I, Ono Y, Sorimachi H, Mamitsuka H

Cell migration that orients the dorsoventral axis is coordinated with anteroposterior patterning mediated by Hedgehog signaling in the early spider embryo.

Analysis of motor function modulated by cholinergic neurons in planarian Dugesia japonica.
Nishimura K, Kitamura Y, Taniguchi T, Agata K

Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics.
Aoki K, Yano K, Suzuki A, Kawamura S, Sakurai N, Suda K, Kurabayashi A, Suzuki T, Tsugane T, Watanabe M, Ooga K, Torii M, Narita T, Shin-I T, Kohara Y, Yamamoto N, Takahashi H, Watanabe Y, Egusa M, Kodama M, Ichinose Y, Kikuchi M, Fukushima S, Okabe A, Arie T, Sato Y, Yazawa K, Satoh S, Omura T, Ezura H, Shibata D

Myosin-dependent endoplasmic reticulum motility and F-actin organization in plant cells.
Ueda H, Yokota E, Kutsuna N, Shimada T, Tamura K, Shimmen T, Hasezawa S, Dolja VV, Hara-Nishimura I

A full-length enriched cDNA library and expressed sequence tag analysis of the parasitic weed, Striga hermonthica.
Yoshida S, Ishida JK, Kamal NM, Ali AM, Namba S, Shirasu K

Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases.
Hijikata A, Raju R, Keerthikumar S, Ramabadran S, Balakrishnan L, Ramadoss SK, Pandey A, Mohan S, Ohara O

Bioinformatics and molecular modeling in glycobiology.

Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways.

Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.
d'Alençon E, Sezutsu H, Legeai F, Permal E, Bernard-Samain S, Gimenez S, Gagneur C, Cousserans F, Shimomura M, Brun-Barale A, Flutre T, Couloux A, East P, Gordon K, Mita K, Quesneville H, Fournier P, Feyereisen R

Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms.
Yamamoto T, Nagasaki H, Yonemaru J, Ebana K, Nakajima M, Shibaya T, Yano M

CyanoClust: comparative genome resources of cyanobacteria and plastids.

TassDB2 - A comprehensive database of subtle alternative splicing events.
Sinha R, Lenser T, Jahn N, Gausmann U, Friedel S, Szafranski K, Huse K, Rosenstiel P, Hampe J, Schuster S, Hiller M, Backofen R, Platzer M

An interspecific linkage map of SSR and intronic polymorphism markers in tomato.
Shirasawa K, Asamizu E, Fukuoka H, Ohyama A, Sato S, Nakamura Y, Tabata S, Sasamoto S, Wada T, Kishida Y, Tsuruoka H, Fujishiro T, Yamada M, Isobe S

A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing.
Shimada MK, Hayakawa Y, Takeda J, Gojobori T, Imanishi T

PathPred: an enzyme-catalyzed metabolic pathway prediction server.
Moriya Y, Shigemizu D, Hattori M, Tokimatsu T, Kotera M, Goto S, Kanehisa M

Molecular evolution of lepidopteran silk proteins: insights from the ghost moth, Hepialus californicus.

SIMCOMP/SUBCOMP: chemical structure search servers for network analyses.

AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome.
Legeai F, Shigenobu S, Gauthier JP, Colbourne J, Rispe C, Collin O, Richards S, Wilson AC, Murphy T, Tagu D

Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice.
Yan H, Kikuchi S, Neumann P, Zhang W, Wu Y, Chen F, Jiang J

Developmental atlas of the early first trimester human embryo.
Yamada S, Samtani RR, Lee ES, Lockett E, Uwabe C, Shiota K, Anderson SA, Lo CW

Genome-wide germline analyses on cancer susceptibility and GeMDBJ database: Gastric cancer as an example.
Yoshida T, Ono H, Kuchiba A, Saeki N, Sakamoto H

Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants.
Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, Caspi R, Karp P, Kirkup V, Latendresse M, Lee C, Mueller LA, Muller R, Rhee SY

Mangone M, Manoharan AP, Thierry-Mieg D, Thierry-Mieg J, Han T, Mackowiak SD, Mis E, Zegar C, Gutwein MR, Khivansara V, Attie O, Chen K, Salehi-Ashtiani K, Vidal M, Harkins TT, Bouffard P, Suzuki Y, Sugano S, Kohara Y, Rajewsky N, Piano F, Gunsalus KC, Kim JK

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.
Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM

A definitive haplotype map as determined by genotyping duplicated haploid genomes finds a predominant haplotype preference at copy-number variation events.
Kukita Y, Yahara K, Tahira T, Higasa K, Sonoda M, Yamamoto K, Kato K, Wake N, Hayashi K

A mutation database for amyotrophic lateral sclerosis.
Yoshida M, Takahashi Y, Koike A, Fukuda Y, Goto J, Tsuji S

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C

Extended morphological processing: a practical method for automatic spot detection of biological markers from microscopic images.

MassBank: a public repository for sharing mass spectral data for life sciences.
Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K, Ojima Y, Tanaka K, Tanaka S, Aoshima K, Oda Y, Kakazu Y, Kusano M, Tohge T, Matsuda F, Sawada Y, Hirai MY, Nakanishi H, Ikeda K, Akimoto N, Maoka T, Takahashi H, Ara T, Sakurai N, Suzuki H, Shibata D, Neumann S, Iida T, Tanaka K, Funatsu K, Matsuura F, Soga T, Taguchi R, Saito K, Nishioka T

The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program.
Tassy O, Dauga D, Daian F, Sobral D, Robin F, Khoueiry P, Salgado D, Fox V, Caillol D, Schiappa R, Laporte B, Rios A, Luxardi G, Kusakabe T, Joly JS, Darras S, Christiaen L, Contensin M, Auger H, Lamy C, Hudson C, Rothbächer U, Gilchrist MJ, Makabe KW, Hotta K, Fujiwara S, Satoh N, Satou Y, Lemaire P

Efficient plant gene identification based on interspecies mapping of full-length cDNAs.
Amano N, Tanaka T, Numa H, Sakai H, Itoh T

GeneCards Version 3: the human gene integrator.
Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, Shmoish M, Nativ N, Bahir I, Doniger T, Krug H, Sirota-Madi A, Olender T, Golan Y, Stelzer G, Harel A, Lancet D

PmiRKB: a plant microRNA knowledge base.
Meng Y, Gou L, Chen D, Mao C, Jin Y, Wu P, Chen M

The RINGS resource for glycome informatics analysis and data mining on the Web.
Akune Y, Hosoda M, Kaiya S, Shinmachi D, Aoki-Kinoshita KF

Alternative splicing of genes during neuronal differentiation of NT2 pluripotential human embryonal carcinoma cells.
Wakamatsu A, Imai J, Watanabe S, Isogai T

MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis.

TRIP Database: a manually curated database of protein-protein interactions for mammalian TRP channels.

MatrixDB, the extracellular matrix interaction database.
Chautard E, Fatoux-Ardore M, Ballut L, Thierry-Mieg N, Ricard-Blum S

Biological databases at DNA Data Bank of Japan in the era of next-generation sequencing technologies.
Kodama Y, Kaminuma E, Saruhashi S, Ikeo K, Sugawara H, Tateno Y, Nakamura Y

DAnCER: disease-annotated chromatin epigenetics resource.
Turinsky AL, Turner B, Borja RC, Gleeson JA, Heath M, Pu S, Switzer T, Dong D, Gong Y, On T, Xiong X, Emili A, Greenblatt J, Parkinson J, Zhang Z, Wodak SJ

DDPC: Dragon Database of Genes associated with Prostate Cancer.
Maqungo M, Kaur M, Kwofie SK, Radovanovic A, Schaefer U, Schmeier S, Oppon E, Christoffels A, Bajic VB

DBASS3 and DBASS5: databases of aberrant 3'- and 5'-splice sites.
Buratti E, Chivers M, Hwang G, Vorechovsky I

TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea.
Shao Y, Harrison EM, Bi D, Tai C, He X, Ou HY, Rajakumar K, Deng Z

BSDB: the biomolecule stretching database.
Sikora M, Sulkowska JI, Witkowski BS, Cieplak M

Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes.
Winsor GL, Lam DK, Fleming L, Lo R, Whiteside MD, Yu NY, Hancock RE, Brinkman FS

ChemProt: a disease chemical biology database.
Taboureau O, Nielsen SK, Audouze K, Weinhold N, Edsgärd D, Roque FS, Kouskoumvekaki I, Bora A, Curpan R, Jensen TS, Brunak S, Oprea TI

The Protein Ontology: a structured representation of protein forms and complexes.
Natale DA, Arighi CN, Barker WC, Blake JA, Bult CJ, Caudy M, Drabkin HJ, D'Eustachio P, Evsikov AV, Huang H, Nchoutmboube J, Roberts NV, Smith B, Zhang J, Wu CH

The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish.
Lu J, Peatman E, Yang Q, Wang S, Hu Z, Reecy J, Kucuktas H, Liu Z

EMDataBank.org: unified data resource for CryoEM.
Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W

The NIH Roadmap Epigenomics Mapping Consortium.
Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA

HitPredict: a database of quality assessed protein-protein interactions in nine species.

CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge.
Ahmed J, Meinel T, Dunkel M, Murgueitio MS, Adams R, Blasse C, Eckert A, Preissner S, Preissner R

SuperSweet--a resource on natural and artificial sweetening agents.
Ahmed J, Preissner S, Dunkel M, Worth CL, Eckert A, Preissner R

The Pancreatic Expression database: 2011 update.
Cutts RJ, Gadaleta E, Hahn SA, Crnogorac-Jurcevic T, Lemoine NR, Chelala C

FragmentStore--a comprehensive database of fragments linking metabolites, toxic molecules and drugs.
Ahmed J, Worth CL, Thaben P, Matzig C, Blasse C, Dunkel M, Preissner R

NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data.

Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics.
Fei Z, Joung JG, Tang X, Zheng Y, Huang M, Lee JM, McQuinn R, Tieman DM, Alba R, Klee HJ, Giovannoni JJ

BriX: a database of protein building blocks for structural analysis, modeling and design.
Vanhee P, Verschueren E, Baeten L, Stricher F, Serrano L, Rousseau F, Schymkowitz J

WebGeSTer DB--a transcription terminator database.
Mitra A, Kesarwani AK, Pal D, Nagaraja V

The Autophagy Database: an all-inclusive information resource on autophagy that provides nourishment for research.

Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, Hoad G, Jang M, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Sobhany S, Ten Hoopen P, Vaughan R, Zalunin V, Cochrane G

AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species.
Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Caler EV, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Iodice J, Kissinger JC, Kraemer ET, Li W, Nayak V, Pennington C, Pinney DF, Pitts B, Roos DS, Srinivasamoorthy G, Stoeckert CJ, Treatman C, Wang H

The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources.
Gremse M, Chang A, Schomburg I, Grote A, Scheer M, Ebeling C, Schomburg D

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0.
Llorens C, Futami R, Covelli L, Domínguez-Escribá L, Viu JM, Tamarit D, Aguilar-Rodríguez J, Vicente-Ripolles M, Fuster G, Bernet GP, Maumus F, Munoz-Pomer A, Sempere JM, Latorre A, Moya A

ZFIN: enhancements and updates to the Zebrafish Model Organism Database.
Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Howe DG, Knight J, Mani P, Martin R, Moxon SA, Paddock H, Pich C, Ramachandran S, Ruef BJ, Ruzicka L, Bauer Schaper H, Schaper K, Shao X, Singer A, Sprague J, Sprunger B, Van Slyke C, Westerfield M

RBPDB: a database of RNA-binding specificities.
Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR

RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans.
Lee TY, Bo-Kai Hsu J, Chang WC, Huang HD

SNP discovery and linkage map construction in cultivated tomato.
Shirasawa K, Isobe S, Hirakawa H, Asamizu E, Fukuoka H, Just D, Rothan C, Sasamoto S, Fujishiro T, Kishida Y, Kohara M, Tsuruoka H, Wada T, Nakamura Y, Sato S, Tabata S

GPCRDB: information system for G protein-coupled receptors.
Vroling B, Sanders M, Baakman C, Borrmann A, Verhoeven S, Klomp J, Oliveira L, de Vlieg J, Vriend G

YPA: an integrated repository of promoter features in Saccharomyces cerevisiae.

GlycomeDB--a unified database for carbohydrate structures.
Ranzinger R, Herget S, von der Lieth CW, Frank M

ThYme: a database for thioester-active enzymes.

RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions.
Sato Y, Antonio BA, Namiki N, Takehisa H, Minami H, Kamatsuki K, Sugimoto K, Shimizu Y, Hirochika H, Nagamura Y

CADgene: a comprehensive database for coronary artery disease genes.
Liu H, Liu W, Liao Y, Cheng L, Liu Q, Ren X, Shi L, Tu X, Wang QK, Guo AY

CCDB: a curated database of genes involved in cervix cancer.
Agarwal SM, Raghav D, Singh H, Raghava GP

TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology.
Hong D, Park SS, Ju YS, Kim S, Shin JY, Kim S, Yu SB, Lee WC, Lee S, Park H, Kim JI, Seo JS

ODB: a database for operon organizations, 2011 update.

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.
Martelli PL, D'Antonio M, Bonizzoni P, Castrignanò T, D'Erchia AM, D'Onorio De Meo P, Fariselli P, Finelli M, Licciulli F, Mangiulli M, Mignone F, Pavesi G, Picardi E, Rizzi R, Rossi I, Valletti A, Zauli A, Zambelli F, Casadio R, Pesole G

ASD: a comprehensive database of allosteric proteins and modulators.
Huang Z, Zhu L, Cao Y, Wu G, Liu X, Chen Y, Wang Q, Shi T, Zhao Y, Wang Y, Li W, Li Y, Chen H, Chen G, Zhang J

VnD: a structure-centric database of disease-related SNPs and drugs.
Yang JO, Oh S, Ko G, Park SJ, Kim WY, Lee B, Lee S

REPAIRtoire--a database of DNA repair pathways.
Milanowska K, Krwawicz J, Papaj G, Kosinski J, Poleszak K, Lesiak J, Osinska E, Rother K, Bujnicki JM

SAHG, a comprehensive database of predicted structures of all human proteins.
Motono C, Nakata J, Koike R, Shimizu K, Shirota M, Amemiya T, Tomii K, Nagano N, Sakaya N, Misoo K, Sato M, Kidera A, Hiroaki H, Shirai T, Kinoshita K, Noguchi T, Ota M

The UCSC Cancer Genomics Browser: update 2011.
Sanborn JZ, Benz SC, Craft B, Szeto C, Kober KM, Meyer L, Vaske CJ, Goldman M, Smith KE, Kuhn RM, Karolchik D, Kent WJ, Stuart JM, Haussler D, Zhu J

Rfam: Wikipedia, clans and the "decimal" release.
Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A

The mouse Gene Expression Database (GXD): 2011 update.
Finger JH, Smith CM, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA, Richardson JE, Ringwald M

Kaminuma E, Kosuge T, Kodama Y, Aono H, Mashima J, Gojobori T, Sugawara H, Ogasawara O, Takagi T, Okubo K, Nakamura Y

['Leinonen R', 'Sugawara H', 'Shumway M']

BRENDA, the enzyme information system in 2011.
Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Söhngen C, Stelzer M, Thiele J, Schomburg D

Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations.
Gonzalez-Galarza FF, Christmas S, Middleton D, Jones AR

CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality.
Endo T, Ueno K, Yonezawa K, Mineta K, Hotta K, Satou Y, Yamada L, Ogasawara M, Takahashi H, Nakajima A, Nakachi M, Nomura M, Yaguchi J, Sasakura Y, Yamasaki C, Sera M, Yoshizawa AC, Imanishi T, Taniguchi H, Inaba K

Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera.
Munoz-Torres MC, Reese JT, Childers CP, Bennett AK, Sundaram JP, Childs KL, Anzola JM, Milshina N, Elsik CG

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments.
Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A

miRTarBase: a database curates experimentally validated microRNA-target interactions.
Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, Tsai WT, Chen GZ, Lee CJ, Chiu CM, Chien CH, Wu MC, Huang CY, Tsou AP, Huang HD

tRNADB-CE 2011: tRNA gene database curated manually by experts.
Abe T, Ikemura T, Sugahara J, Kanai A, Ohara Y, Uehara H, Kinouchi M, Kanaya S, Yamada Y, Muto A, Inokuchi H

Effective--a database of predicted secreted bacterial proteins.

PCDDB: the Protein Circular Dichroism Data Bank, a repository for circular dichroism spectral and metadata.
Whitmore L, Woollett B, Miles AJ, Klose DP, Janes RW, Wallace BA

LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana.

AREsite: a database for the comprehensive investigation of AU-rich elements.
Gruber AR, Fallmann J, Kratochvill F, Kovarik P, Hofacker IL

NCBI Epigenomics: a new public resource for exploring epigenomic data sets.
Fingerman IM, McDaniel L, Zhang X, Ratzat W, Hassan T, Jiang Z, Cohen RF, Schuler GD

The RIKEN integrated database of mammals.
Masuya H, Makita Y, Kobayashi N, Nishikata K, Yoshida Y, Mochizuki Y, Doi K, Takatsuki T, Waki K, Tanaka N, Ishii M, Matsushima A, Takahashi S, Hijikata A, Kozaki K, Furuichi T, Kawaji H, Wakana S, Nakamura Y, Yoshiki A, Murata T, Fukami-Kobayashi K, Mohan S, Ohara O, Hayashizaki Y, Mizoguchi R, Obata Y, Toyoda T

Gramene database in 2010: updates and extensions.
Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D

BISC: binary subcomplexes in proteins database.

dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa.
Gaudet P, Fey P, Basu S, Bushmanova YA, Dodson R, Sheppard KA, Just EM, Kibbe WA, Chisholm RL

Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome.
Reese JT, Childers CP, Sundaram JP, Dickens CM, Childs KL, Vile DC, Elsik CG

Liu X, Li Z, Jiang Z, Zhao Y, Peng J, Jin J, Guo H, Luo J

Identification of nocobactin NA biosynthetic gene clusters in Nocardia farcinica.
Hoshino Y, Chiba K, Ishino K, Fukai T, Igarashi Y, Yazawa K, Mikami Y, Ishikawa J

SPIKE: a database of highly curated human signaling pathways.
Paz A, Brownstein Z, Ber Y, Bialik S, David E, Sagir D, Ulitsky I, Elkon R, Kimchi A, Avraham KB, Shiloh Y, Shamir R

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system.
Zhu LJ, Christensen RG, Kazemian M, Hull CJ, Enuameh MS, Basciotta MD, Brasefield JA, Zhu C, Asriyan Y, Lapointe DS, Sinha S, Wolfe SA, Brodsky MH

KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data.
Sakurai N, Ara T, Ogata Y, Sano R, Ohno T, Sugiyama K, Hiruta A, Yamazaki K, Yano K, Aoki K, Aharoni A, Hamada K, Yokoyama K, Kawamura S, Otsuka H, Tokimatsu T, Kanehisa M, Suzuki H, Saito K, Shibata D

EcoCyc: a comprehensive database of Escherichia coli biology.
Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD

dbDNV: a resource of duplicated gene nucleotide variants in human genome.

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.
Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, Pokrzywa RM, Choi HP, Faller LL, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick MG, Osmani L, Swaminathan R, Tao KR, Letovsky S, Vitkup D, Segrè D, Salzberg SL, Delisi C, Steffen M, Kasif S

NCBI GEO: archive for functional genomics data sets--10 years on.
Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A

CDD: a Conserved Domain Database for the functional annotation of proteins.
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH

lncRNAdb: a reference database for long noncoding RNAs.
Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS

PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes.

Entrez Gene: gene-centered information at NCBI.
Maglott D, Ostell J, Pruitt KD, Tatusova T

The Plant Organelles Database 2 (PODB2): an updated resource containing movie data of plant organelle dynamics.

Bovine Genome Database: integrated tools for genome annotation and discovery.
Childers CP, Reese JT, Sundaram JP, Vile DC, Dickens CM, Childs KL, Salih H, Bennett AK, Hagen DE, Adelson DL, Elsik CG

iCOD: an integrated clinical omics database based on the systems-pathology view of disease.
Shimokawa K, Mogushi K, Shoji S, Hiraishi A, Ido K, Mizushima H, Tanaka H

GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle.
Lardenois A, Gattiker A, Collin O, Chalmel F, Primig M

Bacterial carbohydrate structure database 3: principles and realization.

IsoBase: a database of functionally related proteins across PPI networks.
Park D, Singh R, Baym M, Liao CS, Berger B

TMPad: an integrated structural database for helix-packing folds in transmembrane proteins.
Lo A, Cheng CW, Chiu YY, Sung TY, Hsu WL

OryzaExpress: an integrated database of gene expression networks and omics annotations in rice.
Hamada K, Hongo K, Suwabe K, Shimizu A, Nagayama T, Abe R, Kikuchi S, Yamamoto N, Fujii T, Yokoyama K, Tsuchida H, Sano K, Mochizuki T, Oki N, Horiuchi Y, Fujita M, Watanabe M, Matsuoka M, Kurata N, Yano K

ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants.
Obayashi T, Nishida K, Kasahara K, Kinoshita K

Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life.
Wissler L, Codoñer FM, Gu J, Reusch TB, Olsen JL, Procaccini G, Bornberg-Bauer E

Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice.
Sato Y, Antonio B, Namiki N, Motoyama R, Sugimoto K, Takehisa H, Minami H, Kamatsuki K, Kusaba M, Hirochika H, Nagamura Y

ARTADE2DB: improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses.
Iida K, Kawaguchi S, Kobayashi N, Yoshida Y, Ishii M, Harada E, Hanada K, Matsui A, Okamoto M, Ishida J, Tanaka M, Morosawa T, Seki M, Toyoda T

Systematizing and cloning of genes involved in the cerebellar cortex circuit development.
Furuichi T, Shiraishi-Yamaguchi Y, Sato A, Sadakata T, Huang J, Shinoda Y, Hayashi K, Mishima Y, Tomomura M, Nishibe H, Yoshikawa F

TOMATOMA: a novel tomato mutant database distributing Micro-Tom mutant collections.
Saito T, Ariizumi T, Okabe Y, Asamizu E, Hiwasa-Tanase K, Fukuda N, Mizoguchi T, Yamazaki Y, Aoki K, Ezura H

Flybrain neuron database: a comprehensive database system of the Drosophila brain neurons.
Shinomiya K, Matsuda K, Oishi T, Otsuna H, Ito K

The Mouse Tumor Biology Database (MTB): a central electronic resource for locating and integrating mouse tumor pathology data.
Begley DA, Krupke DM, Neuhauser SB, Richardson JE, Bult CJ, Eppig JT, Sundberg JP

Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis.
Sakai H, Ikawa H, Tanaka T, Numa H, Minami H, Fujisawa M, Shibata M, Kurita K, Kikuta A, Hamada M, Kanamori H, Namiki N, Wu J, Itoh T, Matsumoto T, Sasaki T

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis.
Yamashita R, Sathira NP, Kanai A, Tanimoto K, Arauchi T, Tanaka Y, Hashimoto S, Sugano S, Nakai K, Suzuki Y

Classification and annotation of the relationship between protein structural change and ligand binding.
Amemiya T, Koike R, Fuchigami S, Ikeguchi M, Kidera A

Gene orders in the upstream of 16S rRNA genes divide genera of the family Halobacteriaceae into two groups.
Minegishi H, Kamekura M, Kitajima-Ihara T, Nakasone K, Echigo A, Shimane Y, Usami R, Itoh T, Ihara K

GRIPDB - G protein coupled Receptor Interaction Partners DataBase.

Fabry-database.org: database of the clinical phenotypes, genotypes and mutant α-galactosidase A structures in Fabry disease.

['Petri V', 'Shimoyama M', 'Hayman GT', 'Smith JR', 'Tutaj M', 'de Pons J', 'Dwinell MR', 'Munzenmaier DH', 'Twigger SN', 'Jacob HJ']

OryzaPG-DB: rice proteome database based on shotgun proteogenomics.

Allie: a database and a search service of abbreviations and long forms.
Yamamoto Y, Yamaguchi A, Bono H, Takagi T

Methods and strategies for gene structure curation in WormBase.
Williams GW, Davis PA, Rogers AS, Bieri T, Ozersky P, Spieth J

The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video.
Harper LC, Schaeffer ML, Thistle J, Gardiner JM, Andorf CM, Campbell DA, Cannon EK, Braun BL, Birkett SM, Lawrence CJ, Sen TZ

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases.
Kobayashi N, Ishii M, Takahashi S, Mochizuki Y, Matsushima A, Toyoda T

On determining firing delay time of transitions for petri net based signaling pathways by introducing stochastic decision rules.
Miwa Y, Li C, Ge QW, Matsuno H, Miyano S

Bacteroides stercorirosoris sp. nov. and Bacteroides faecichinchillae sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces.
Kitahara M, Sakamoto M, Tsuchida S, Kawasumi K, Amao H, Benno Y, Ohkuma M

Lactobacillus nasuensis sp. nov., a lactic acid bacterium isolated from silage, and emended description of the genus Lactobacillus.

Bacteroides sartorii is an earlier heterotypic synonym of Bacteroides chinchillae and has priority.

The InterPro BioMart: federated query and web service access to the InterPro Resource.
Jones P, Binns D, McMenamin C, McAnulla C, Hunter S

Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV.

Development of a classification scheme for disease-related enzyme information.

Enzymatic activity and protein interactions in alpha/beta hydrolase fold proteins: moonlighting versus promiscuity.

Network-based analysis and characterization of adverse drug-drug interactions.
Takarabe M, Shigemizu D, Kotera M, Goto S, Kanehisa M

Adult onset cardiac dilatation in a transgenic mouse line with Galβ1,3GalNAc α2,3-sialyltransferase II (ST3Gal-II) transgenes: a new model for dilated cardiomyopathy.
Proc. Jpn. Acad., Ser. B, Phys. Biol. Sci.
Suzuki O, Kanai T, Nishikawa T, Yamamoto Y, Noguchi A, Takimoto K, Koura M, Noguchi Y, Uchio-Yamada K, Tsuji S, Matsuda J

Travelling and splitting of a wave of hedgehog expression involved in spider-head segmentation.
Kanayama M, Akiyama-Oda Y, Nishimura O, Tarui H, Agata K, Oda H

The Sequence Read Archive: explosive growth of sequencing data.

Comparison of RNA expression profiles on generations of Porphyra yezoensis (Rhodophyta), based on suppression subtractive hybridization (SSH).
Shen S, Zhang G, Li Y, Wang L, Xu P, Yi L

A potent inhibitor of SIK2, 3, 3', 7-trihydroxy-4'-methoxyflavon (4'-O-methylfisetin), promotes melanogenesis in B16F10 melanoma cells.
Kumagai A, Horike N, Satoh Y, Uebi T, Sasaki T, Itoh Y, Hirata Y, Uchio-Yamada K, Kitagawa K, Uesato S, Kawahara H, Takemori H, Nagaoka Y

The Histone Database: an integrated resource for histones and histone fold-containing proteins.
Mariño-Ramírez L, Levine KM, Morales M, Zhang S, Moreland RT, Baxevanis AD, Landsman D

Spatio-temporal transcriptome of the human brain.
Kang HJ, Kawasawa YI, Cheng F, Zhu Y, Xu X, Li M, Sousa AM, Pletikos M, Meyer KA, Sedmak G, Guennel T, Shin Y, Johnson MB, Krsnik Z, Mayer S, Fertuzinhos S, Umlauf S, Lisgo SN, Vortmeyer A, Weinberger DR, Mane S, Hyde TM, Huttner A, Reimers M, Kleinman JE, Sestan N

PomBase: a comprehensive online resource for fission yeast.
Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG

Crystal structure of the predicted phospholipase LYPLAL1 reveals unexpected functional plasticity despite close relationship to acyl protein thioesterases.
Bürger M, Zimmermann TJ, Kondoh Y, Stege P, Watanabe N, Osada H, Waldmann H, Vetter IR

SMART 7: recent updates to the protein domain annotation resource.

The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata.
Inglis DO, Arnaud MB, Binkley J, Shah P, Skrzypek MS, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G

IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature.
Fukuchi S, Sakamoto S, Nobe Y, Murakami SD, Amemiya T, Hosoda K, Koike R, Hiroaki H, Ota M

WormBase 2012: more genomes, more data, new website.
Yook K, Harris TW, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, de la Cruz N, Duong A, Fang R, Ganesan U, Grove C, Howe K, Kadam S, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Nash B, Ozersky P, Paulini M, Raciti D, Rangarajan A, Schindelman G, Shi X, Schwarz EM, Ann Tuli M, Van Auken K, Wang D, Wang X, Williams G, Hodgkin J, Berriman M, Durbin R, Kersey P, Spieth J, Stein L, Sternberg PW

The Gene Wiki in 2011: community intelligence applied to human gene annotation.

PSCDB: a database for protein structural change upon ligand binding.

PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits.
Ziebarth JD, Bhattacharya A, Chen A, Cui Y

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.

SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis.
Mäder U, Schmeisky AG, Flórez LA, Stülke J

InterPro in 2011: new developments in the family and domain prediction database.
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY

The Gene Ontology: enhancements for 2011.

Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins.
Shoemaker BA, Zhang D, Tyagi M, Thangudu RR, Fong JH, Marchler-Bauer A, Bryant SH, Madej T, Panchenko AR

From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource.
McDonagh EM, Whirl-Carrillo M, Garten Y, Altman RB, Klein TE

Two new species of the genus Candida in the Zygoascus clade, Candida lundiana sp. nov. and Candida suthepensis sp. nov., isolated from raw honey in Thailand.
Saksinchai S, Suzuki M, Lumyong S, Ohkuma M, Chantawannakul P

The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments.
Kodama Y, Mashima J, Kaminuma E, Gojobori T, Ogasawara O, Takagi T, Okubo K, Nakamura Y

Saccharomyces Genome Database: the genomics resource of budding yeast.
Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures.
Culhane AC, Schröder MS, Sultana R, Picard SC, Martinelli EN, Kelly C, Haibe-Kains B, Kapushesky M, St Pierre AA, Flahive W, Picard KC, Gusenleitner D, Papenhausen G, O'Connor N, Correll M, Quackenbush J

GeneDB--an annotation database for pathogens.
Logan-Klumpler FJ, De Silva N, Boehme U, Rogers MB, Velarde G, McQuillan JA, Carver T, Aslett M, Olsen C, Subramanian S, Phan I, Farris C, Mitra S, Ramasamy G, Wang H, Tivey A, Jackson A, Houston R, Parkhill J, Holden M, Harb OS, Brunk BP, Myler PJ, Roos D, Carrington M, Smith DF, Hertz-Fowler C, Berriman M

INOH: ontology-based highly structured database of signal transduction pathways.
Yamamoto S, Sakai N, Nakamura H, Fukagawa H, Fukuda K, Takagi T

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy.
Pruitt KD, Tatusova T, Brown GR, Maglott DR

OriDB, the DNA replication origin database updated and extended.
Siow CC, Nieduszynska SR, Müller CA, Nieduszynski CA

The IntAct molecular interaction database in 2012.
Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H

The UniProt-GO Annotation database in 2011.
Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra H, Auchincloss A, Axelsen K, Blatter MC, Boutet E, Braconi-Quintaje S, Breuza L, Bridge A, Coudert E, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Masson P, Moinat M, Pedruzzi I, Poux S, Rivoire C, Roechert B, Schneider M, Stutz A, Sundaram S, Tognolli M, Bougueleret L, Argoud-Puy G, Cusin I, Duek-Roggli P, Xenarios I, Apweiler R

KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research.
Afendi FM, Okada T, Yamazaki M, Hirai-Morita A, Nakamura Y, Nakamura K, Ikeda S, Takahashi H, Altaf-Ul-Amin M, Darusman LK, Saito K, Kanaya S

Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD

MMDB: 3D structures and macromolecular interactions.
Madej T, Addess KJ, Fong JH, Geer LY, Geer RC, Lanczycki CJ, Liu C, Lu S, Marchler-Bauer A, Panchenko AR, Chen J, Thiessen PA, Wang Y, Zhang D, Bryant SH

PoSSuM: a database of similar protein-ligand binding and putative pockets.
Ito J, Tabei Y, Shimizu K, Tsuda K, Tomii K

NONCODE v3.0: integrative annotation of long noncoding RNAs.
Bu D, Yu K, Sun S, Xie C, Skogerbø G, Miao R, Xiao H, Liao Q, Luo H, Zhao G, Zhao H, Liu Z, Liu C, Chen R, Zhao Y

BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.
Barrett T, Clark K, Gevorgyan R, Gorelenkov V, Gribov E, Karsch-Mizrachi I, Kimelman M, Pruitt KD, Resenchuk S, Tatusova T, Yaschenko E, Ostell J

RecountDB: a database of mapped and count corrected transcribed sequences.

HGPD: Human Gene and Protein Database, 2012 update.
Maruyama Y, Kawamura Y, Nishikawa T, Isogai T, Nomura N, Goshima N

Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Fingerman IM, Geer LY, Helmberg W, Kapustin Y, Krasnov S, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Karsch-Mizrachi I, Ostell J, Panchenko A, Phan L, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, Wilbur WJ, Yaschenko E, Ye J

SNPedia: a wiki supporting personal genome annotation, interpretation and analysis.

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools.
Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E

Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Zhou Z, Han L, Karapetyan K, Dracheva S, Shoemaker BA, Bolton E, Gindulyte A, Bryant SH

Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J, Sayers EW

Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences.
Mi T, Merlin JC, Deverasetty S, Gryk MR, Bill TJ, Brooks AW, Lee LY, Rathnayake V, Ross CA, Sargeant DP, Strong CL, Watts P, Rajasekaran S, Schiller MR

Mining the Gene Wiki for functional genomic knowledge.
Good BM, Howe DG, Lin SM, Kibbe WA, Su AI

Spirotoamides A and B, novel 6,6-spiroacetal polyketides isolated from a microbial metabolite fraction library.
Nogawa T, Takahashi S, Okano A, Kawatani M, Uramoto M, Saito T, Osada H

Database for crude drugs and Kampo medicine.
Arita M, Yoshimoto M, Suwa K, Hirai A, Kanaya S, Shibahara N, Tanaka K

Towards understanding how molecular networks evolve in plants.

Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation.
Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C, Mitchell A, Sangrador-Vegas A, Yong SY, Mulder N, Hunter S

The androgen receptor gene mutations database: 2012 update.
Gottlieb B, Beitel LK, Nadarajah A, Paliouras M, Trifiro M

Genotypic and phenotypic characterization of lactic acid bacteria isolated from Italian ryegrass silage.
Tohno M, Kobayashi H, Nomura M, Kitahara M, Ohkuma M, Uegaki R, Cai Y

Xanthohumol impairs autophagosome maturation through direct inhibition of valosin-containing protein.
Sasazawa Y, Kanagaki S, Tashiro E, Nogawa T, Muroi M, Kondoh Y, Osada H, Imoto M

Studies on the methylation of cytoplasmic ribosomal RNA from cultured higher plant cells.

Protein disulfide isomerase-mediated disulfide bonds regulate the gelatinolytic activity and secretion of matrix metalloproteinase-9.
Khan MM, Simizu S, Suzuki T, Masuda A, Kawatani M, Muroi M, Dohmae N, Osada H

Therapeutic chaperone effect of N-octyl 4-epi-β-valienamine on murine G(M1)-gangliosidosis.
Suzuki Y, Ichinomiya S, Kurosawa M, Matsuda J, Ogawa S, Iida M, Kubo T, Tabe M, Itoh M, Higaki K, Nanba E, Ohno K

Ovarian Kaleidoscope database: ten years and beyond.

The structure of the nervous system of the nematode Caenorhabditis elegans.
Philos. Trans. R. Soc. Lond., B, Biol. Sci.
White JG, Southgate E, Thomson JN, Brenner S

Dual-Specificity Phosphatase CDC25A/B Inhibitor Identified from a Focused Library with Nonelectrophilic Core Structure.
Tsuchiya A, Hirai G, Koyama Y, Oonuma K, Otani Y, Osada H, Sodeoka M

Statistical organelle dissection of Arabidopsis guard cells using image database LIPS.
Higaki T, Kutsuna N, Hosokawa Y, Akita K, Ebine K, Ueda T, Kondo N, Hasezawa S

IRView: a database and viewer for protein interacting regions.
Fujimori S, Hirai N, Masuoka K, Oshikubo T, Yamashita T, Washio T, Saito A, Nagasaki M, Miyano S, Miyamoto-Sato E

Protuboxepin A, a marine fungal metabolite, inducing metaphase arrest and chromosomal misalignment in tumor cells.
Asami Y, Jang JH, Soung NK, He L, Moon DO, Kim JW, Oh H, Muroi M, Osada H, Kim BY, Ahn JS

Global analysis of chaperone effects using a reconstituted cell-free translation system.

The Rice Proteogenomics Database OryzaPG-DB: Development, Expansion, and New Features.
Helmy M, Sugiyama N, Tomita M, Ishihama Y

GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.

TP Atlas: integration and dissemination of advances in Targeted Proteins Research Program (TPRP)-structural biology project phase II in Japan.
Iwayanagi T, Miyamoto S, Konno T, Mizutani H, Hirai T, Shigemoto Y, Gojobori T, Sugawara H

CancerProView: a graphical image database of cancer-related genes and proteins.

Soybean Proteome Database 2012: update on the comprehensive data repository for soybean proteomics.

Infectious endogenous retroviruses in cats and emergence of recombinant viruses.
Anai Y, Ochi H, Watanabe S, Nakagawa S, Kawamura M, Gojobori T, Nishigaki K

Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns.
Qu W, Hashimoto S, Shimada A, Nakatani Y, Ichikawa K, Saito TL, Ogoshi K, Matsushima K, Suzuki Y, Sugano S, Takeda H, Morishita S

Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome.
Higashino A, Sakate R, Kameoka Y, Takahashi I, Hirata M, Tanuma R, Masui T, Yasutomi Y, Osada N

Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, González VM, Hénaff E, Câmara F, Cozzuto L, Lowy E, Alioto T, Capella-Gutiérrez S, Blanca J, Cañizares J, Ziarsolo P, Gonzalez-Ibeas D, Rodríguez-Moreno L, Droege M, Du L, Alvarez-Tejado M, Lorente-Galdos B, Melé M, Yang L, Weng Y, Navarro A, Marques-Bonet T, Aranda MA, Nuez F, Picó B, Gabaldón T, Roma G, Guigó R, Casacuberta JM, Arús P, Puigdomènech P

RIKEN tandem mass spectral database (ReSpect) for phytochemicals: a plant-specific MS/MS-based data resource and database.
Sawada Y, Nakabayashi R, Yamada Y, Suzuki M, Sato M, Sakata A, Akiyama K, Sakurai T, Matsuda F, Aoki T, Hirai MY, Saito K

Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of Theileria-induced leukocyte transformation.
Hayashida K, Hara Y, Abe T, Yamasaki C, Toyoda A, Kosuge T, Suzuki Y, Sato Y, Kawashima S, Katayama T, Wakaguri H, Inoue N, Homma K, Tada-Umezaki M, Yagi Y, Fujii Y, Habara T, Kanehisa M, Watanabe H, Ito K, Gojobori T, Sugawara H, Imanishi T, Weir W, Gardner M, Pain A, Shiels B, Hattori M, Nene V, Sugimoto C

Transcriptome tomography for brain analysis in the web-accessible anatomical space.
Okamura-Oho Y, Shimokawa K, Takemoto S, Hirakiyama A, Nakamura S, Tsujimura Y, Nishimura M, Kasukawa T, Masumoto KH, Nikaido I, Shigeyoshi Y, Ueda HR, Song G, Gee J, Himeno R, Yokota H

TRIP database 2.0: a manually curated information hub for accessing TRP channel interaction network.
Shin YC, Shin SY, Chun JN, Cho HS, Lim JM, Kim HG, So I, Kwon D, Jeon JH

The UCSC Cancer Genomics Browser: update 2013.
Goldman M, Craft B, Swatloski T, Ellrott K, Cline M, Diekhans M, Ma S, Wilks C, Stuart J, Haussler D, Zhu J

Sagace: a web-based search engine for biomedical databases in Japan.
Morita M, Igarashi Y, Ito M, Chen YA, Nagao C, Sakaguchi Y, Sakate R, Masui T, Mizuguchi K

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.
Uchiyama I, Mihara M, Nishide H, Chiba H

DaizuBase, an integrated soybean genome database including BAC-based physical maps.
Katayose Y, Kanamori H, Shimomura M, Ohyanagi H, Ikawa H, Minami H, Shibata M, Ito T, Kurita K, Ito K, Tsubokura Y, Kaga A, Wu J, Matsumoto T, Harada K, Sasaki T

Virtual metagenome reconstruction from 16S rRNA gene sequences.
Okuda S, Tsuchiya Y, Kiriyama C, Itoh M, Morisaki H

Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR.
['Van Auken K', 'Fey P', 'Berardini TZ', 'Dodson R', 'Cooper L', 'Li D', 'Chan J', 'Li Y', 'Basu S', 'Muller HM', 'Chisholm R', 'Huala E', 'Sternberg PW']

An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values.
Sakurai N, Ara T, Kanaya S, Nakamura Y, Iijima Y, Enomoto M, Motegi T, Aoki K, Suzuki H, Shibata D

WDDD: Worm Developmental Dynamics Database.
Kyoda K, Adachi E, Masuda E, Nagai Y, Suzuki Y, Oguro T, Urai M, Arai R, Furukawa M, Shimada K, Kuramochi J, Nagai E, Onami S

Development of a gene expression database and related analysis programs for evaluation of anticancer compounds.
Ushijima M, Mashima T, Tomida A, Dan S, Saito S, Furuno A, Tsukahara S, Seimiya H, Yamori T, Matsuura M

ChemProt-2.0: visual navigation in a disease chemical biology database.
Kim Kjærulff S, Wich L, Kringelum J, Jacobsen UP, Kouskoumvekaki I, Audouze K, Lund O, Brunak S, Oprea TI, Taboureau O

DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters.
Ichikawa N, Sasagawa M, Yamamoto M, Komaki H, Yoshida Y, Yamazaki S, Fujita N

Dfam: a database of repetitive DNA based on profile hidden Markov models.
Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AF, Finn RD

A simple sequence repeat- and single-nucleotide polymorphism-based genetic linkage map of the brown planthopper, Nilaparvata lugens.
Jairin J, Kobayashi T, Yamagata Y, Sanada-Morimura S, Mori K, Tashiro K, Kuhara S, Kuwazaki S, Urio M, Suetsugu Y, Yamamoto K, Matsumura M, Yasui H

Deciphering and prediction of transcriptome dynamics under fluctuating field conditions.
Nagano AJ, Sato Y, Mihara M, Antonio BA, Motoyama R, Itoh H, Nagamura Y, Izawa T

The Chloroplast Function Database II: a comprehensive collection of homozygous mutants and their phenotypic/genotypic traits for nuclear-encoded chloroplast proteins.
Myouga F, Akiyama K, Tomonaga Y, Kato A, Sato Y, Kobayashi M, Nagata N, Sakurai T, Shinozaki K

Full-length transcriptome-based H-InvDB throws a new light on chromosome-centric proteomics.
Imanishi T, Nagai Y, Habara T, Yamasaki C, Takeda J, Mikami S, Bando Y, Tojo H, Nishimura T

PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset.
Kikugawa S, Nishikata K, Murakami K, Sato Y, Suzuki M, Altaf-Ul-Amin M, Kanaya S, Imanishi T

PRIMe Update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation.
Sakurai T, Yamada Y, Sawada Y, Matsuda F, Akiyama K, Shinozaki K, Hirai MY, Saito K

KNApSAcK-3D: a three-dimensional structure database of plant metabolites.
Nakamura K, Shimura N, Otabe Y, Hirai-Morita A, Nakamura Y, Ono N, Ul-Amin MA, Kanaya S

Construction of validated, non-redundant composite protein sequence databases.

Combination of liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry with 13C-labeling for chemical assignment of sulfur-containing metabolites in onion bulbs.
Nakabayashi R, Sawada Y, Yamada Y, Suzuki M, Hirai MY, Sakurai T, Saito K

Dynamic evolution of endogenous retrovirus-derived genes expressed in bovine conceptuses during the period of placentation.
Nakagawa S, Bai H, Sakurai T, Nakaya Y, Konno T, Miyazawa T, Gojobori T, Imakawa K

Modular architecture of metabolic pathways revealed by conserved sequences of reactions.
Muto A, Kotera M, Tokimatsu T, Nakagawa Z, Goto S, Kanehisa M

Discrimination of mammalian GPI-anchored proteins by hydropathy and amino acid propensities.
Mukai Y, Ikeda M, Tanaka H, Konishi T, Oura O, Sasaki T

Systematization of the protein sequence diversity in enzymes related to secondary metabolic pathways in plants, in the context of big data biology inspired by the KNApSAcK motorcycle database.
Ikeda S, Abe T, Nakamura Y, Kibinge N, Hirai Morita A, Nakatani A, Ono N, Ikemura T, Nakamura K, Altaf-Ul-Amin M, Kanaya S

Hong D, Lee J, Bleazard T, Jung H, Ju YS, Yu SB, Kim S, Park SS, Kim JI, Seo JS

The transcription start site landscape of C. elegans.
Saito TL, Hashimoto S, Gu SG, Morton JJ, Stadler M, Blumenthal T, Fire A, Morishita S

DNA marker applications to molecular genetics and genomics in tomato.

Protein co-migration database (PCoM -DB) for Arabidopsis thylakoids and Synechocystis cells.
Takabayashi A, Kadoya R, Kuwano M, Kurihara K, Ito H, Tanaka R, Tanaka A

KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella.
Jouraku A, Yamamoto K, Kuwazaki S, Urio M, Suetsugu Y, Narukawa J, Miyamoto K, Kurita K, Kanamori H, Katayose Y, Matsumoto T, Noda H

CoDNaS: a database of conformational diversity in the native state of proteins.
Monzon AM, Juritz E, Fornasari MS, Parisi G

Fematrin-1 is involved in fetomaternal cell-to-cell fusion in Bovinae placenta and has contributed to diversity of ruminant placentation.
Nakaya Y, Koshi K, Nakagawa S, Hashizume K, Miyazawa T

Coelacanth genomes reveal signatures for evolutionary transition from water to land.
Nikaido M, Noguchi H, Nishihara H, Toyoda A, Suzuki Y, Kajitani R, Suzuki H, Okuno M, Aibara M, Ngatunga BP, Mzighani SI, Kalombo HW, Masengi KW, Tuda J, Nogami S, Maeda R, Iwata M, Abe Y, Fujimura K, Okabe M, Amano T, Maeno A, Shiroishi T, Itoh T, Sugano S, Kohara Y, Fujiyama A, Okada N

Genome-wide discovery and information resource development of DNA polymorphisms in cassava.
Sakurai T, Mochida K, Yoshida T, Akiyama K, Ishitani M, Seki M, Shinozaki K

WormBase: Annotating many nematode genomes.
Howe K, Davis P, Paulini M, Tuli MA, Williams G, Yook K, Durbin R, Kersey P, Sternberg PW

Identification and characterization of cancer mutations in Japanese lung adenocarcinoma without sequencing of normal tissue counterparts.
Suzuki A, Mimaki S, Yamane Y, Kawase A, Matsushima K, Suzuki M, Goto K, Sugano S, Esumi H, Suzuki Y, Tsuchihara K

Next-generation survey sequencing and the molecular organization of wheat chromosome 6B.
Tanaka T, Kobayashi F, Joshi GP, Onuki R, Sakai H, Kanamori H, Wu J, Simkova H, Nasuda S, Endo TR, Hayakawa K, Doležel J, Ogihara Y, Itoh T, Matsumoto T, Handa H

Simple and direct assembly of kymographs from movies using KYMOMAKER.
Chiba K, Shimada Y, Kinjo M, Suzuki T, Uchida S

Large-scale collection and analysis of full-length cDNAs from Brachypodium distachyon and integration with Pooideae sequence resources.
Mochida K, Uehara-Yamaguchi Y, Takahashi F, Yoshida T, Sakurai T, Shinozaki K

RAvariome: a genetic risk variants database for rheumatoid arthritis based on assessment of reproducibility between or within human populations.

The pancreatic expression database: recent extensions and updates.
Dayem Ullah AZ, Cutts RJ, Ghetia M, Gadaleta E, Hahn SA, Crnogorac-Jurcevic T, Lemoine NR, Chelala C

ppdb: plant promoter database version 3.0.
Hieno A, Naznin HA, Hyakumachi M, Sakurai T, Tokizawa M, Koyama H, Sato N, Nishiyama T, Hasebe M, Zimmer AD, Lang D, Reski R, Rensing SA, Obokata J, Yamamoto YY

DDBJ progress report: a new submission system for leading to a correct annotation.
Kosuge T, Mashima J, Kodama Y, Fujisawa T, Kaminuma E, Ogasawara O, Okubo K, Takagi T, Nakamura Y

WormBase 2014: new views of curated biology.
Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, Done J, Grove C, Howe K, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Ozersky P, Paulini M, Raciti D, Schindelman G, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wong JD, Yook K, Schedl T, Hodgkin J, Berriman M, Kersey P, Spieth J, Stein L, Sternberg PW

Data, information, knowledge and principle: back to metabolism in KEGG.
Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M

CPLM: a database of protein lysine modifications.
Liu Z, Wang Y, Gao T, Pan Z, Cheng H, Yang Q, Cheng Z, Guo A, Ren J, Xue Y

Pheno-Pub: a total support system for the publication of mouse phenotypic data on the web.
Suzuki T, Furuse T, Yamada I, Motegi H, Kozawa Y, Masuya H, Wakana S

ClinVar: public archive of relationships among sequence variation and human phenotype.
Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR

UniCarbKB: building a knowledge platform for glycoproteomics.
Campbell MP, Peterson R, Mariethoz J, Gasteiger E, Akune Y, Aoki-Kinoshita KF, Lisacek F, Packer NH

NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes.
Geisen S, Barturen G, Alganza ÁM, Hackenberg M, Oliver JL

RARGE II: an integrated phenotype database of Arabidopsis mutant traits using a controlled vocabulary.
Akiyama K, Kurotani A, Iida K, Kuromori T, Shinozaki K, Sakurai T

CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes.
Fujisawa T, Okamoto S, Katayama T, Nakao M, Yoshimura H, Kajiya-Kanegae H, Yamamoto S, Yano C, Yanaka Y, Maita H, Kaneko T, Tabata S, Nakamura Y

Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species.
Hirakawa H, Shirasawa K, Kosugi S, Tashiro K, Nakayama S, Yamada M, Kohara M, Watanabe A, Kishida Y, Fujishiro T, Tsuruoka H, Minami C, Sasamoto S, Kato M, Nanri K, Komaki A, Yanagi T, Guoxin Q, Maeda F, Ishikawa M, Kuhara S, Sato S, Tabata S, Isobe SN

Ribosomal Database Project: data and tools for high throughput rRNA analysis.
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM

SCOP2 prototype: a new approach to protein structure mining.
Andreeva A, Howorth D, Chothia C, Kulesha E, Murzin AG

iPfam: a database of protein family and domain interactions found in the Protein Data Bank.
Finn RD, Miller BL, Clements J, Bateman A

SABRE2: a database connecting plant EST/full-length cDNA clones with Arabidopsis information.
Fukami-Kobayashi K, Nakamura Y, Tamura T, Kobayashi M

Sequence analysis of the genome of carnation (Dianthus caryophyllus L.).
Yagi M, Kosugi S, Hirakawa H, Ohmiya A, Tanase K, Harada T, Kishimoto K, Nakayama M, Ichimura K, Onozaki T, Yamaguchi H, Sasaki N, Miyahara T, Nishizaki Y, Ozeki Y, Nakamura N, Suzuki T, Tanaka Y, Sato S, Shirasawa K, Isobe S, Miyamura Y, Watanabe A, Nakayama S, Kishida Y, Kohara M, Tabata S

Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases.
Asamizu E, Ichihara H, Nakaya A, Nakamura Y, Hirakawa H, Ishii T, Tamura T, Fukami-Kobayashi K, Nakajima Y, Tabata S

Temporal specification and bilaterality of human neocortical topographic gene expression.
Pletikos M, Sousa AM, Sedmak G, Meyer KA, Zhu Y, Cheng F, Li M, Kawasawa YI, Sestan N

bex-db: Bioinformatics workbench for comprehensive analysis of barley-expressed genes.
Tanaka T, Sakai H, Fujii N, Kobayashi F, Nakamura S, Itoh T, Matsumoto T, Wu J

An atlas of active enhancers across human cell types and tissues.
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest ARR, Carninci P, Rehli M, Sandelin A

A promoter-level mammalian expression atlas.

Expansion of coverage of Carbohydrate Structure Database (CSDB).

RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals.
Huang KY, Wu HY, Chen YJ, Lu CT, Su MG, Hsieh YC, Tsai CM, Lin KI, Huang HD, Lee TY, Chen YJ

Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis.
Fukushima A, Kusano M, Mejia RF, Iwasa M, Kobayashi M, Hayashi N, Watanabe-Takahashi A, Narisawa T, Tohge T, Hur M, Wurtele ES, Nikolau BJ, Saito K

Draft sequences of the radish (Raphanus sativus L.) genome.
Kitashiba H, Li F, Hirakawa H, Kawanabe T, Zou Z, Hasegawa Y, Tonosaki K, Shirasawa S, Fukushima A, Yokoi S, Takahata Y, Kakizaki T, Ishida M, Okamoto S, Sakamoto K, Shirasawa K, Tabata S, Nishio T

Tools and databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data.
Sakurai N, Ara T, Enomoto M, Motegi T, Morishita Y, Kurabayashi A, Iijima Y, Ogata Y, Nakajima D, Suzuki H, Shibata D

OMICtools: an informative directory for multi-omic data analysis.
Henry VJ, Bandrowski AE, Pepin AS, Gonzalez BJ, Desfeux A

RNAi screening of human glycogene orthologs in the nematode Caenorhabditis elegans and the construction of the C. elegans glycogene database.
Akiyoshi S, Nomura KH, Dejima K, Murata D, Matsuda A, Kanaki N, Takaki T, Mihara H, Nagaishi T, Furukawa S, Ando KG, Yoshina S, Mitani S, Togayachi A, Suzuki Y, Shikanai T, Narimatsu H, Nomura K

RiceVarMap: a comprehensive database of rice genomic variations.
Zhao H, Yao W, Ouyang Y, Yang W, Wang G, Lian X, Xing Y, Chen L, Xie W

DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.
Suzuki A, Wakaguri H, Yamashita R, Kawano S, Tsuchihara K, Sugano S, Suzuki Y, Nakai K

Rfam 12.0: updates to the RNA families database.
Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD

M-path: a compass for navigating potential metabolic pathways.
Araki M, Cox RS, Makiguchi H, Ogawa T, Taniguchi T, Miyaoku K, Nakatsui M, Hara KY, Kondo A

Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations.
González-Galarza FF, Takeshita LY, Santos EJ, Kempson F, Maia MH, da Silva AL, Teles e Silva AL, Ghattaoraya GS, Alfirevic A, Jones AR, Middleton D

Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan KN, Pettit JB, Rodriguez N, Schubert M, Wimalaratne SM, Zhao Y, Hermjakob H, Le Novère N, Laibe C

DB-AT: a 2015 update to the Full-parasites database brings a multitude of new transcriptomic data for apicomplexan parasites.
Jąkalski M, Wakaguri H, Kischka TG, Nishikawa Y, Kawazu S, Matsubayashi M, Kawahara F, Tsuji N, Cao S, Sunaga F, Xuan X, Okubo K, Igarashi I, Tuda J, Mongan AE, Eshita Y, Maeda R, Makałowski W, Suzuki Y, Yamagishi J

SNP-Seek database of SNPs derived from 3000 rice genomes.
Alexandrov N, Tai S, Wang W, Mansueto L, Palis K, Fuentes RR, Ulat VJ, Chebotarov D, Zhang G, Li Z, Mauleon R, Hamilton RS, McNally KL

MTGD: The Medicago truncatula genome database.
Krishnakumar V, Kim M, Rosen BD, Karamycheva S, Bidwell SL, Tang H, Town CD

Plant Omics Data Center: an integrated web repository for interspecies gene expression networks with NLP-based curation.
Ohyanagi H, Takano T, Terashima S, Kobayashi M, Kanno M, Morimoto K, Kanegae H, Sasaki Y, Saito M, Asano S, Ozaki S, Kudo T, Yokoyama K, Aya K, Suwabe K, Suzuki G, Aoki K, Kubo Y, Watanabe M, Matsuoka M, Yano K

Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles.
Blazie SM, Babb C, Wilky H, Rawls A, Park JG, Mangone M

Integrative analysis of 111 reference human epigenomes.

Comparative genome and transcriptome analyses of the social amoeba Acytostelium subglobosum that accomplishes multicellular development without germ-soma differentiation.
Urushihara H, Kuwayama H, Fukuhara K, Itoh T, Kagoshima H, Shin-I T, Toyoda A, Ohishi K, Taniguchi T, Noguchi H, Kuroki Y, Hata T, Uchi K, Mohri K, King JS, Insall RH, Kohara Y, Fujiyama A

Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data.

The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology.
Goodsell DS, Dutta S, Zardecki C, Voigt M, Berman HM, Burley SK

Improved Carbohydrate Structure Generalization Scheme for (1)H and (13)C NMR Simulations.

Determination of growth stages and metabolic profiles in Brachypodium distachyon for comparison of developmental context with Triticeae crops.
Onda Y, Hashimoto K, Yoshida T, Sakurai T, Sawada Y, Hirai MY, Toyooka K, Mochida K, Shinozaki K

The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome.
Berardini TZ, Reiser L, Li D, Mezheritsky Y, Muller R, Strait E, Huala E

BioModels: Content, Features, Functionality, and Use.
Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V

Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals.
['Nagasaki M', 'Yasuda J', 'Katsuoka F', 'Nariai N', 'Kojima K', 'Kawai Y', 'Yamaguchi-Kabata Y', 'Yokozawa J', 'Danjoh I', 'Saito S', 'Sato Y', 'Mimori T', 'Tsuda K', 'Saito R', 'Pan X', 'Nishikawa S', 'Ito S', 'Kuroki Y', 'Tanabe O', 'Fuse N', 'Kuriyama S', 'Kiyomoto H', 'Hozawa A', 'Minegishi N', 'Douglas Engel J', 'Kinoshita K', 'Kure S', 'Yaegashi N']

Carbohydrate Structure Database: tools for statistical analysis of bacterial, plant and fungal glycomes.

SubtiWiki 2.0--an integrated database for the model organism Bacillus subtilis.

GlyTouCan 1.0--The international glycan structure repository.
Aoki-Kinoshita K, Agravat S, Aoki NP, Arpinar S, Cummings RD, Fujita A, Fujita N, Hart GM, Haslam SM, Kawasaki T, Matsubara M, Moreman KW, Okuda S, Pierce M, Ranzinger R, Shikanai T, Shinmachi D, Solovieva E, Suzuki Y, Tsuchiya S, Yamada I, York WS, Zaia J, Narimatsu H

Bovine Genome Database: new tools for gleaning function from the Bos taurus genome.
Elsik CG, Unni DR, Diesh CM, Tayal A, Emery ML, Nguyen HN, Hagen DE

OpenTein: a database of digital whole-slide images of stem cell-derived teratomas.
Park SJ, Komiyama Y, Suemori H, Umezawa A, Nakai K

WormBase 2016: expanding to enable helminth genomic research.
Howe KL, Bolt BJ, Cain S, Chan J, Chen WJ, Davis P, Done J, Down T, Gao S, Grove C, Harris TW, Kishore R, Lee R, Lomax J, Li Y, Muller HM, Nakamura C, Nuin P, Paulini M, Raciti D, Schindelman G, Stanley E, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wright A, Yook K, Berriman M, Kersey P, Schedl T, Stein L, Sternberg PW

EMDataBank unified data resource for 3DEM.
Lawson CL, Patwardhan A, Baker ML, Hryc C, Garcia ES, Hudson BP, Lagerstedt I, Ludtke SJ, Pintilie G, Sala R, Westbrook JD, Berman HM, Kleywegt GJ, Chiu W

EffectiveDB--updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems.
Eichinger V, Nussbaumer T, Platzer A, Jehl MA, Arnold R, Rattei T

The Dfam database of repetitive DNA families.
Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, Smit AF, Wheeler TJ

ALCOdb: Gene Coexpression Database for Microalgae.
Aoki Y, Okamura Y, Ohta H, Kinoshita K, Obayashi T

The Pfam protein families database: towards a more sustainable future.
Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A

Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction.

ChemProt-3.0: a global chemical biology diseases mapping.
Kringelum J, Kjaerulff SK, Brunak S, Lund O, Oprea TI, Taboureau O

The ORFeome Collaboration: a genome-scale human ORF-clone resource.

Linking Virus Genomes with Host Taxonomy.
Mihara T, Nishimura Y, Shimizu Y, Nishiyama H, Yoshikawa G, Uehara H, Hingamp P, Goto S, Ogata H

CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state.
Monzon AM, Rohr CO, Fornasari MS, Parisi G

Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes.
Yasui Y, Hirakawa H, Ueno M, Matsui K, Katsube-Tanaka T, Yang SJ, Aii J, Sato S, Mori M

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets.

Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software.

The Tohoku Medical Megabank Project: Design and Mission.
Kuriyama S, Yaegashi N, Nagami F, Arai T, Kawaguchi Y, Osumi N, Sakaida M, Suzuki Y, Nakayama K, Hashizume H, Tamiya G, Kawame H, Suzuki K, Hozawa A, Nakaya N, Kikuya M, Metoki H, Tsuji I, Fuse N, Kiyomoto H, Sugawara J, Tsuboi A, Egawa S, Ito K, Chida K, Ishii T, Tomita H, Taki Y, Minegishi N, Ishii N, Yasuda J, Igarashi K, Shimizu R, Nagasaki M, Koshiba S, Kinoshita K, Ogishima S, Takai-Igarashi T, Tominaga T, Tanabe O, Ohuchi N, Shimosegawa T, Kure S, Tanaka H, Ito S, Hitomi J, Tanno K, Nakamura M, Ogasawara K, Kobayashi S, Sakata K, Satoh M, Shimizu A, Sasaki M, Endo R, Sobue K, Tohoku Medical Megabank Project Study Group T, Yamamoto M

LigandBox: A database for 3D structures of chemical compounds.
Kawabata T, Sugihara Y, Fukunishi Y, Nakamura H

PCDDB: new developments at the Protein Circular Dichroism Data Bank.
Whitmore L, Miles AJ, Mavridis L, Janes RW, Wallace BA

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.
Kinjo AR, Bekker GJ, Suzuki H, Tsuchiya Y, Kawabata T, Ikegawa Y, Nakamura H

Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements.
Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Verezemska O, Isbandi M, Thomas AD, Ali R, Sharma K, Kyrpides NC, Reddy TB

NGSmethDB 2017: enhanced methylomes and differential methylation.
Lebrón R, Gómez-Martín C, Carpena P, Bernaola-Galván P, Barturen G, Hackenberg M, Oliver JL

['Gramates LS', 'Marygold SJ', 'Santos GD', 'Urbano JM', 'Antonazzo G', 'Matthews BB', 'Rey AJ', 'Tabone CJ', 'Crosby MA', 'Emmert DB', 'Falls K', 'Goodman JL', 'Hu Y', 'Ponting L', 'Schroeder AJ', 'Strelets VB', 'Thurmond J', 'Zhou P']

A common language for physical mapping of the human genome.

The International Human Epigenome Consortium Data Portal.
Bujold D, Morais DAL, Gauthier C, Côté C, Caron M, Kwan T, Chen KC, Laperle J, Markovits AN, Pastinen T, Caron B, Veilleux A, Jacques PÉ, Bourque G

WormBase ParaSite - a comprehensive resource for helminth genomics.
Howe KL, Bolt BJ, Shafie M, Kersey P, Berriman M

ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.
Lee M, Lee K, Yu N, Jang I, Choi I, Kim P, Jang YE, Kim B, Kim S, Lee B, Kang J, Lee S

Rice SNP-seek database update: new SNPs, indels, and queries.
Mansueto L, Fuentes RR, Borja FN, Detras J, Abriol-Santos JM, Chebotarov D, Sanciangco M, Palis K, Copetti D, Poliakov A, Dubchak I, Solovyev V, Wing RA, Hamilton RS, Mauleon R, McNally KL, Alexandrov N

CyanoBase: a large-scale update on its 20th anniversary.
Fujisawa T, Narikawa R, Maeda SI, Watanabe S, Kanesaki Y, Kobayashi K, Nomata J, Hanaoka M, Watanabe M, Ehira S, Suzuki E, Awai K, Nakamura Y

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.

CSDB_GT: a new curated database on glycosyltransferases.

Development and application of an algorithm to compute weighted multiple glycan alignments.

PlantExpress: A Database Integrating OryzaExpress and ArthaExpress for Single-species and Cross-species Gene Expression Network Analyses with Microarray-Based Transcriptome Data.
Kudo T, Terashima S, Takaki Y, Tomita K, Saito M, Kanno M, Yokoyama K, Yano K

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.
Ruffier M, Kähäri A, Komorowska M, Keenan S, Laird M, Longden I, Proctor G, Searle S, Staines D, Taylor K, Vullo A, Yates A, Zerbino D, Flicek P

REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding.
Mizutani H, Sugawara H, Buckle AM, Sangawa T, Miyazono KI, Ohtsuka J, Nagata K, Shojima T, Nosaki S, Xu Y, Wang D, Hu X, Tanokura M, Yura K

Ortholog Identification and Comparative Analysis of Microbial Genomes Using MBGD and RECOG.

GlyTouCan: an accessible glycan structure repository.
Tiemeyer M, Aoki K, Paulson J, Cummings RD, York WS, Karlsson NG, Lisacek F, Packer NH, Campbell MP, Aoki NP, Fujita A, Matsubara M, Shinmachi D, Tsuchiya S, Yamada I, Pierce M, Ranzinger R, Narimatsu H, Aoki-Kinoshita KF

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.
Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, Yamaoka S, Nishihama R, Nakamura Y, Berger F, Adam C, Aki SS, Althoff F, Araki T, Arteaga-Vazquez MA, Balasubrmanian S, Barry K, Bauer D, Boehm CR, Briginshaw L, Caballero-Perez J, Catarino B, Chen F, Chiyoda S, Chovatia M, Davies KM, Delmans M, Demura T, Dierschke T, Dolan L, Dorantes-Acosta AE, Eklund DM, Florent SN, Flores-Sandoval E, Fujiyama A, Fukuzawa H, Galik B, Grimanelli D, Grimwood J, Grossniklaus U, Hamada T, Haseloff J, Hetherington AJ, Higo A, Hirakawa Y, Hundley HN, Ikeda Y, Inoue K, Inoue SI, Ishida S, Jia Q, Kakita M, Kanazawa T, Kawai Y, Kawashima T, Kennedy M, Kinose K, Kinoshita T, Kohara Y, Koide E, Komatsu K, Kopischke S, Kubo M, Kyozuka J, Lagercrantz U, Lin SS, Lindquist E, Lipzen AM, Lu CW, De Luna E, Martienssen RA, Minamino N, Mizutani M, Mizutani M, Mochizuki N, Monte I, Mosher R, Nagasaki H, Nakagami H, Naramoto S, Nishitani K, Ohtani M, Okamoto T, Okumura M, Phillips J, Pollak B, Reinders A, Rövekamp M, Sano R, Sawa S, Schmid MW, Shirakawa M, Solano R, Spunde A, Suetsugu N, Sugano S, Sugiyama A, Sun R, Suzuki Y, Takenaka M, Takezawa D, Tomogane H, Tsuzuki M, Ueda T, Umeda M, Ward JM, Watanabe Y, Yazaki K, Yokoyama R, Yoshitake Y, Yotsui I, Zachgo S, Schmutz J

The Pancreatic Expression Database: 2018 update.
Marzec J, Dayem Ullah AZ, Pirrò S, Gadaleta E, Crnogorac-Jurcevic T, Lemoine NR, Kocher HM, Chelala C

WormBase 2017: molting into a new stage.
Lee RYN, Howe KL, Harris TW, Arnaboldi V, Cain S, Chan J, Chen WJ, Davis P, Gao S, Grove C, Kishore R, Muller HM, Nakamura C, Nuin P, Paulini M, Raciti D, Rodgers F, Russell M, Schindelman G, Tuli MA, Van Auken K, Wang Q, Williams G, Wright A, Yook K, Berriman M, Kersey P, Schedl T, Stein L, Sternberg PW

GRASS: semi-automated NMR-based structure elucidation of saccharides.

TADB 2.0: an updated database of bacterial type II toxin-antitoxin loci.
Xie Y, Wei Y, Shen Y, Li X, Zhou H, Tai C, Deng Z, Ou HY

Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B, Milacic M, Roca CD, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Viteri G, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P

Melonet-DB, a Grand RNA-Seq Gene Expression Atlas in Melon (Cucumis melo L.).

MCAW-DB: A glycan profile database capturing the ambiguity of glycan recognition patterns.
Hosoda M, Takahashi Y, Shiota M, Shinmachi D, Inomoto R, Higashimoto S, Aoki-Kinoshita KF

Cluster analysis of amino acid indices for prediction of protein structure and function.

Wheat-embryo ribonucleates. III. Modified nucleotide constituents in each of the 5.8S, 18S and 26S ribonucleates.

Normal and abnormal development of human embryos: first report of the analysis of 1,213 intact embryos.
Nishimura H, Takano K, Tanimura T, Yasuda M

Holoprosencephaly in human embryos: epidemiologic studies of 150 cases.

Vibrio parahaemolyticus and related halophilic Vibrios.

Solvent-accessible surfaces of proteins and nucleic acids.

Neural tube defects and maternal hyperthermia in early pregnancy: epidemiology in a human embryo population.

Summary: the modified nucleosides of RNA.

Maidak BL, Larsen N, McCaughey MJ, Overbeek R, Olsen GJ, Fogel K, Blandy J, Woese CR

Flybrain, an on-line atlas and database of the Drosophila nervous system.
Armstrong JD, Kaiser K, Müller A, Fischbach KF, Merchant N, Strausfeld NJ

SubtiList: a relational database for the Bacillus subtilis genome.

SCOP: a structural classification of proteins database for the investigation of sequences and structures.
Murzin AG, Brenner SE, Hubbard T, Chothia C

FlyBase--the Drosophila genetic database.

FlyBase--the Drosophila database. The FlyBase Consortium.

Database of p53 gene somatic mutations in human tumors and cell lines.
Hollstein M, Rice K, Greenblatt MS, Soussi T, Fuchs R, Sørlie T, Hovig E, Smith-Sørensen B, Montesano R, Harris CC

PRINTS--a database of protein motif fingerprints.
Attwood TK, Beck ME, Bleasby AJ, Parry-Smith DJ

PRINTS--a protein motif fingerprint database.

HOVERGEN: a database of homologous vertebrate genes.

Quantitative analysis of affinity chromatography of trypsin. A new technique for investigation of protein-ligand interaction.

Nishikawa K, Ishino S, Takenaka H, Norioka N, Hirai T, Yao T, Seto Y

Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides.

A microsatellite linkage map of the porcine genome.
Rohrer GA, Alexander LJ, Keele JW, Smith TP, Beattie CW

A versatile system for detecting transposition in Arabidopsis.

Larsen N, Olsen GJ, Maidak BL, McCaughey MJ, Overbeek R, Macke TJ, Marsh TL, Woese CR

dbEST--database for "expressed sequence tags".

SRS--an indexing and retrieval tool for flat file data libraries.

Hazardous substances data bank (HSDB) as a source of environmental fate information on chemicals.

Somatic point mutations in the p53 gene of human tumors and cell lines: updated compilation.
Hollstein M, Shomer B, Greenblatt M, Soussi T, Hovig E, Montesano R, Harris CC

NRSub: a non-redundant database for Bacillus subtilis.

Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughey MJ, Woese CR

A World Wide Web (WWW) server database engine for an organelle database, MitoDat.
Lemkin PF, Chipperfield M, Merril C, Zullo S

SRS: information retrieval system for molecular biology data banks.

Retrotransposons of rice involved in mutations induced by tissue culture.
Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M

The organization of ribosomal RNA processing correlates with the distribution of nucleolar snRNAs.
Beven AF, Lee R, Razaz M, Leader DJ, Brown JW, Shaw PJ

Surprising similarities in structure comparison.

Schuler GD, Boguski MS, Stewart EA, Stein LD, Gyapay G, Rice K, White RE, Rodriguez-Tomé P, Aggarwal A, Bajorek E, Bentolila S, Birren BB, Butler A, Castle AB, Chiannilkulchai N, Chu A, Clee C, Cowles S, Day PJ, Dibling T, Drouot N, Dunham I, Duprat S, East C, Edwards C, Fan JB, Fang N, Fizames C, Garrett C, Green L, Hadley D, Harris M, Harrison P, Brady S, Hicks A, Holloway E, Hui L, Hussain S, Louis-Dit-Sully C, Ma J, MacGilvery A, Mader C, Maratukulam A, Matise TC, McKusick KB, Morissette J, Mungall A, Muselet D, Nusbaum HC, Page DC, Peck A, Perkins S, Piercy M, Qin F, Quackenbush J, Ranby S, Reif T, Rozen S, Sanders C, She X, Silva J, Slonim DK, Soderlund C, Sun WL, Tabar P, Thangarajah T, Vega-Czarny N, Vollrath D, Voyticky S, Wilmer T, Wu X, Adams MD, Auffray C, Walter NA, Brandon R, Dehejia A, Goodfellow PN, Houlgatte R, Hudson JR, Ide SE, Iorio KR, Lee WY, Seki N, Nagase T, Ishikawa K, Nomura N, Phillips C, Polymeropoulos MH, Sandusky M, Schmitt K, Berry R, Swanson K, Torres R, Venter JC, Sikela JM, Beckmann JS, Weissenbach J, Myers RM, Cox DR, James MR, Bentley D, Deloukas P, Lander ES, Hudson TJ

Image library of biological macromolecules.

Characterization and mapping of Ds-GUS-T-DNA lines for targeted insertional mutagenesis.
Smith D, Yanai Y, Liu YG, Ishiguro S, Okada K, Shibata D, Whittier RF, Fedoroff NV

Graphical interface for ProDom domain families.

Database of p53 gene somatic mutations in human tumors and cell lines: updated compilation and future prospects.
Hainaut P, Soussi T, Shomer B, Hollstein M, Greenblatt M, Hovig E, Harris CC, Montesano R

The human type I collagen mutation database.

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.

Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins.

GeneCards: integrating information about genes, proteins and diseases.
Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D

Retrotransposons of rice: their regulation and use for genome analysis.

Clusters of multiple different small nucleolar RNA genes in plants are expressed as and processed from polycistronic pre-snoRNAs.

PDB-REPRDB: a database of representative protein chains in PDB (Protein Data Bank).
Noguchi T, Onizuka K, Akiyama Y, Saito M

A streamlined mutation detection system: multicolor post-PCR fluorescence labeling and single-strand conformational polymorphism analysis by capillary electrophoresis.
Inazuka M, Wenz HM, Sakabe M, Tahira T, Hayashi K

Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library.
Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, Suyama A, Sugano S

A genomic perspective on protein families.

Genes and proteins of Escherichia coli K-12.

The non-redundant Bacillus subtilis (NRSub) database: update 1998.

CyanoBase, a www database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803.
Nakamura Y, Kaneko T, Hirosawa M, Miyajima N, Tabata S

Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D

Letovsky SI, Cottingham RW, Porter CJ, Li PW

IXDB, an X chromosome integrated database.
Leser U, Wagner R, Grigoriev A, Lehrach H, Roest Crollius H

Databases and software for the analysis of mutations in the human p53 gene, human hprt gene and both the lacI and lacZ gene in transgenic rodents.
Cariello NF, Douglas GR, Gorelick NJ, Hart DW, Wilson JD, Soussi T

IARC Database of p53 gene mutations in human tumors and cell lines: updated compilation, revised formats and new visualisation tools.
Hainaut P, Hernandez T, Robinson A, Rodriguez-Tome P, Flores T, Hollstein M, Harris CC, Montesano R

The Androgen Receptor Gene Mutations Database.
Gottlieb B, Lehvaslaiho H, Beitel LK, Lumbroso R, Pinsky L, Trifiro M

The Human Collagen Mutation Database 1998.

The ProDom database of protein domain families.

Current status of the SWISS-2DPAGE database.
Hoogland C, Sanchez JC, Tonella L, Bairoch A, Hochstrasser DF, Appel RD

The translational signal database, TransTerm, is now a relational database.
Dalphin ME, Brown CM, Stockwell PA, Tate WP

PDBsum: a Web-based database of summaries and analyses of all PDB structures.
Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM

FlyView, a Drosophila image database, and other Drosophila databases

An on-line database for zebrafish development and genetics research
Westerfield M, Doerry E, Kirkpatrick AE, Driever W, Douglas SA

Rapid access to biomedical knowledge with GeneCards and HotMolecBase: implications for the electrophoretic analysis of large sets of gene products.

3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules.

TMIG-2DPAGE: a new concept of two-dimensional gel protein database for research on aging.

Processing of vertebrate box C/D small nucleolar RNAs in plant cells.
Leader DJ, Clark GP, Boag J, Watters JA, Simpson CG, Watkins NJ, Maxwell ES, Brown JW

Small nucleolar RNAs and pre-rRNA processing in plants.

A transcription frame-based analysis of the genomic DNA sequence of a hyper-thermophilic archaeon for the identification of genes, pseudo-genes and operon structures.
Suckow JM, Amano N, Ohfuku Y, Kakinuma J, Koike H, Suzuki M

SMART, a simple modular architecture research tool: identification of signaling domains.
Schultz J, Milpetz F, Bork P, Ponting CP

Complete nucleotide sequences of 93-kb and 3.3-kb plasmids of an enterohemorrhagic Escherichia coli O157:H7 derived from Sakai outbreak.
Makino K, Ishii K, Yasunaga T, Hattori M, Yokoyama K, Yutsudo CH, Kubota Y, Yamaichi Y, Iida T, Yamamoto K, Honda T, Han CG, Ohtsubo E, Kasamatsu M, Hayashi T, Kuhara S, Shinagawa H

Localization and processing from a polycistronic precursor of novel snoRNAs in maize.

Repeats in genomic DNA: mining and meaning.

The complete genome of Bacillus subtilis: from sequence annotation to data management and analysis.

DBGET/LinkDB: an integrated database retrieval system.
Fujibuchi W, Goto S, Migimatsu H, Uchiyama I, Ogiwara A, Akiyama Y, Kanehisa M

High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper.
Seki M, Carninci P, Nishiyama Y, Hayashizaki Y, Shinozaki K

GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support.

Extension of CyanoBase. CyanoMutants: repository of mutant information on Synechocystis sp. strain PCC6803.
Nakamura Y, Kaneko T, Miyajima N, Tabata S

IXDB, an X chromosome integrated database (update).
Leser U, Roest Crollius H, Lehrach H, Sudbrak R

A new version of the RDP (Ribosomal Database Project).
Maidak BL, Cole JR, Parker CT, Garrity GM, Larsen N, Li B, Lilburn TG, McCaughey MJ, Olsen GJ, Overbeek R, Pramanik S, Schmidt TM, Tiedje JM, Woese CR

Hawkins V, Doll D, Bumgarner R, Smith T, Abajian C, Hood L, Nelson PS

Lefranc MP, Giudicelli V, Ginestoux C, Bodmer J, Müller W, Bontrop R, Lemaitre M, Malik A, Barbié V, Chaume D

Recent improvements of the ProDom database of protein domain families.

ProTherm: Thermodynamic Database for Proteins and Mutants.
Gromiha MM, An J, Kono H, Oobatake M, Uedaira H, Sarai A

The SWISS-2DPAGE database: what has changed during the last year.

Plant cis-acting regulatory DNA elements (PLACE) database: 1999.

The Eukaryotic Promoter Database (EPD): recent developments.
Périer RC, Junier T, Bonnard C, Bucher P

HUGE: a database for human large proteins identified by Kazusa cDNA sequencing project.

A database on cytogenetics in haematology and oncology.
Dorkeld F, Bernheim A, Dessen P, Huret JL

Keio Mutation Database for eye disease genes (KMeyeDB).

O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins.
Gupta R, Birch H, Rapacki K, Brunak S, Hansen JE

DOMO: a new database of aligned protein domains.

Zebrafish informatics and the ZFIN database.
Westerfield M, Doerry E, Kirkpatrick AE, Douglas SA

The gene search system. A method for efficient detection and rapid molecular identification of genes in Drosophila melanogaster.
Toba G, Ohsako T, Miyata N, Ohtsuka T, Seong KH, Aigaki T