Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae.
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Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana.
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Sources of bias in the detection and reporting of p53 mutations in human cancer: analysis of the IARC p53 mutation database.
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Finding a mouse: the International Mouse Strain Resource (IMSR).
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IRIS: Integrated Risk Information System database.
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Combining sensitive database searches with multiple intermediates to detect distant homologues.
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Genome analysis: Assigning protein coding regions to three-dimensional structures.
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TOXLINE: evolution of an online interactive bibliographic database.
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The Kidney Development Database.
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date: 1999

Zebrafish in the Net.
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Splicing-independent processing of plant box C/D and box H/ACA small nucleolar RNAs.
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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.
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publication name: Hum. Mutat.
creator: Hernandez-Boussard T, Rodriguez-Tome P, Montesano R, Hainaut P
date: 1999

The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes.
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publication name: Genetics
creator: Spradling AC, Stern D, Beaton A, Rhem EJ, Laverty T, Mozden N, Misra S, Rubin GM
date: 1999

A handful of intron-containing genes produces the lion's share of yeast mRNA.
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publication name: RNA
creator: Ares M, Grate L, Pauling MH
date: 1999

SWEET - WWW-based rapid 3D construction of oligo- and polysaccharides.
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publication name: Bioinformatics
creator: Bohne A, Lang E, von der Lieth CW
date: 1999

The protein information resource (PIR).
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publication name: Nucleic Acids Res.
creator: 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
date: 2000

The EcoCyc and MetaCyc databases.
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publication name: Nucleic Acids Res.
creator: Karp PD, Riley M, Saier M, Paulsen IT, Paley SM, Pellegrini-Toole A
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EMGLib: the enhanced microbial genomes library (update 2000).
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publication name: Nucleic Acids Res.
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CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000.
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publication name: Nucleic Acids Res.
creator: Nakamura Y, Kaneko T, Tabata S
date: 2000

INE: a rice genome database with an integrated map view.
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publication name: Nucleic Acids Res.
creator: Sakata K, Antonio BA, Mukai Y, Nagasaki H, Sakai Y, Makino K, Sasaki T
date: 2000

The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse. The Mouse Genome Database Group.
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publication name: Nucleic Acids Res.
creator: Blake JA, Eppig JT, Richardson JE, Davisson MT
date: 2000

NCBI's LocusLink and RefSeq.
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publication name: Nucleic Acids Res.
creator: Maglott DR, Katz KS, Sicotte H, Pruitt KD
date: 2000

MAGEST: MAboya gene expression patterns and sequence tags.
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publication name: Nucleic Acids Res.
creator: Kawashima T, Kawashima S, Kanehisa M, Nishida H, Makabe KW
date: 2000

BodyMap: a human and mouse gene expression database.
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publication name: Nucleic Acids Res.
creator: Hishiki T, Kawamoto S, Morishita S, Okubo K
date: 2000

The TIGR gene indices: reconstruction and representation of expressed gene sequences.
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publication name: Nucleic Acids Res.
creator: Quackenbush J, Liang F, Holt I, Pertea G, Upton J
date: 2000

5S ribosomal RNA database Y2K.
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publication name: Nucleic Acids Res.
creator: Szymanski M, Barciszewska MZ, Barciszewski J, Erdmann VA
date: 2000

The tmRNA website.
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publication name: Nucleic Acids Res.
creator: Williams KP
date: 2000

The RDP (Ribosomal Database Project) continues.
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publication name: Nucleic Acids Res.
creator: Maidak BL, Cole JR, Lilburn TG, Parker CT, Saxman PR, Stredwick JM, Garrity GM, Li B, Olsen GJ, Pramanik S, Schmidt TM, Tiedje JM
date: 2000

UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs.
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publication name: Nucleic Acids Res.
creator: Pesole G, Liuni S, Grillo G, Licciulli F, Larizza A, Makalowski W, Saccone C
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The prostate expression database (PEDB): status and enhancements in 2000.
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publication name: Nucleic Acids Res.
creator: Nelson PS, Clegg N, Eroglu B, Hawkins V, Bumgarner R, Smith T, Hood L
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IMGT, the international ImMunoGeneTics database.
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publication name: Nucleic Acids Res.
creator: Ruiz M, Giudicelli V, Ginestoux C, Stoehr P, Robinson J, Bodmer J, Marsh SG, Bontrop R, Lemaitre M, Lefranc G, Chaume D, Lefranc MP
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The Protein Data Bank.
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publication name: Nucleic Acids Res.
creator: Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE
date: 2000

The IMB Jena Image Library of biological macromolecules.
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publication name: Nucleic Acids Res.
creator: Reichert J, Jabs A, Slickers P, Sühnel J
date: 2000

ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons.
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publication name: Nucleic Acids Res.
creator: Corpet F, Servant F, Gouzy J, Kahn D
date: 2000

ProTherm, version 2.0: thermodynamic database for proteins and mutants.
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publication name: Nucleic Acids Res.
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The 1999 SWISS-2DPAGE database update.
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publication name: Nucleic Acids Res.
creator: Hoogland C, Sanchez JC, Tonella L, Binz PA, Bairoch A, Hochstrasser DF, Appel RD
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DIP: the database of interacting proteins.
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publication name: Nucleic Acids Res.
creator: Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D
date: 2000

Codon usage tabulated from international DNA sequence databases: status for the year 2000.
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publication name: Nucleic Acids Res.
creator: Nakamura Y, Gojobori T, Ikemura T
date: 2000

The eukaryotic promoter database (EPD).
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publication name: Nucleic Acids Res.
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date: 2000

HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project.
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publication name: Nucleic Acids Res.
creator: Kikuno R, Nagase T, Suyama M, Waki M, Hirosawa M, Ohara O
date: 2000

Atlas of genetics and cytogenetics in oncology and haematology, an interactive database.
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publication name: Nucleic Acids Res.
creator: Huret JL, Minor SL, Dorkeld F, Dessen P, Bernheim A
date: 2000

dbSNP: a database of single nucleotide polymorphisms.
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publication name: Nucleic Acids Res.
creator: Smigielski EM, Sirotkin K, Ward M, Sherry ST
date: 2000

HGBASE: a database of SNPs and other variations in and around human genes.
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publication name: Nucleic Acids Res.
creator: Brookes AJ, Lehväslaiho H, Siegfried M, Boehm JG, Yuan YP, Sarkar CM, Bork P, Ortigao F
date: 2000

Keio Mutation Database (KMDB) for human disease gene mutations.
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publication name: Nucleic Acids Res.
creator: Minoshima S, Mitsuyama S, Ohno S, Kawamura T, Shimizu N
date: 2000

AAindex: amino acid index database.
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publication name: Nucleic Acids Res.
creator: Kawashima S, Kanehisa M
date: 2000

A linkage map of 243 DNA markers in an intercross of Göttingen miniature and Meishan pigs.
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publication name: Anim. Genet.
creator: 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
date: 1999

Eye disorder database "KMeyeDB".
type: Article
publication name: Hum. Mutat.
creator: Minoshima S, Mitsuyama S, Ohno S, Kawamura T, Shimizu N
date: 2000

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.
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publication name: Proc. Natl. Acad. Sci. U.S.A.
creator: Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, Sakaki Y
date: 2000

Construction and evaluation of a porcine bacterial artificial chromosome library.
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publication name: Anim. Genet.
creator: Suzuki K, Asakawa S, Iida M, Shimanuki S, Fujishima N, Hiraiwa H, Murakami Y, Shimizu N, Yasue H
date: 2000

Chromosome of the enterohemorrhagic Escherichia coli O157:H7; comparative analysis with K-12 MG1655 revealed the acquisition of a large amount of foreign DNAs.
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publication name: DNA Res.
creator: 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
date: 1999

A large scale structural analysis of cDNAs in a unicellular green alga, Chlamydomonas reinhardtii. I. Generation of 3433 non-redundant expressed sequence tags.
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publication name: DNA Res.
creator: Asamizu E, Nakamura Y, Sato S, Fukuzawa H, Tabata S
date: 1999

Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development.
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publication name: Development
creator: 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
date: 2000

Androgen insensitivity.
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publication name: Am. J. Med. Genet.
creator: Gottlieb B, Pinsky L, Beitel LK, Trifiro M
date: 1999

Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast.
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publication name: Nucleic Acids Res.
creator: Davis CA, Grate L, Spingola M, Ares M
date: 2000

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.
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publication name: Genes Genet. Syst.
creator: 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
date: 1999

Statistical analysis of the 5' untranslated region of human mRNA using "Oligo-Capped" cDNA libraries.
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publication name: Genomics
creator: Suzuki Y, Ishihara D, Sasaki M, Nakagawa H, Hata H, Tsunoda T, Watanabe M, Komatsu T, Ota T, Isogai T, Suyama A, Sugano S
date: 2000

Large-scale screening of intracellular protein localization in living fission yeast cells by the use of a GFP-fusion genomic DNA library.
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publication name: Genes Cells
creator: Ding DQ, Tomita Y, Yamamoto A, Chikashige Y, Haraguchi T, Hiraoka Y
date: 2000

Generation of 7137 non-redundant expressed sequence tags from a legume, Lotus japonicus.
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publication name: DNA Res.
creator: Asamizu E, Nakamura Y, Sato S, Tabata S
date: 2000

Fibrillarin genes encode both a conserved nucleolar protein and a novel small nucleolar RNA involved in ribosomal RNA methylation in Arabidopsis thaliana.
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publication name: J. Biol. Chem.
creator: Barneche F, Steinmetz F, Echeverría M
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A filamentous phage associated with recent pandemic Vibrio parahaemolyticus O3:K6 strains.
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publication name: J. Clin. Microbiol.
creator: Nasu H, Iida T, Sugahara T, Yamaichi Y, Park KS, Yokoyama K, Makino K, Shinagawa H, Honda T
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Cn3D: sequence and structure views for Entrez.
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publication name: Trends Biochem. Sci.
creator: Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH
date: 2000

PIR: a new resource for bioinformatics.
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publication name: Bioinformatics
creator: McGarvey PB, Huang H, Barker WC, Orcutt BC, Garavelli JS, Srinivasarao GY, Yeh LS, Xiao C, Wu CH
date: 2000

Genome-wide analysis of oral cancer--early results from the Cancer Genome Anatomy Project.
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publication name: Oral Oncol.
creator: Shillitoe EJ, May M, Patel V, Lethanakul C, Ensley JF, Strausberg RL, Gutkind JS
date: 2000

SAGEmap: a public gene expression resource.
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publication name: Genome Res.
creator: Lash AE, Tolstoshev CM, Wagner L, Schuler GD, Strausberg RL, Riggins GJ, Altschul SF
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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.
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publication name: DNA Res.
creator: Asamizu E, Nakamura Y, Sato S, Tabata S
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Analysis of expressed sequence tags of flower buds in Lotus japonicus.
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publication name: DNA Res.
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Generation of 10,154 expressed sequence tags from a leafy gametophyte of a marine red alga, Porphyra yezoensis.
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publication name: DNA Res.
creator: Nikaido I, Asamizu E, Nakajima M, Nakamura Y, Saga N, Tabata S
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The Cancer Genome Anatomy Project: EST sequencing and the genetics of cancer progression.
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publication name: Neoplasia
creator: Krizman DB, Wagner L, Lash A, Strausberg RL, Emmert-Buck MR
date: 1999

The "Atlas of genetics and cytogenetics in oncology and haematology" on the internet and a review on infant leukemias.
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publication name: Cancer Genet. Cytogenet.
creator: Huret JL, Dessen P, Le Minor S, Bernheim A
date: 2000

Pig cloning by microinjection of fetal fibroblast nuclei.
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publication name: Science
creator: Onishi A, Iwamoto M, Akita T, Mikawa S, Takeda K, Awata T, Hanada H, Perry AC
date: 2000

Repbase update: a database and an electronic journal of repetitive elements.
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publication name: Trends Genet.
creator: Jurka J
date: 2000

STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.
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publication name: Nucleic Acids Res.
creator: Snel B, Lehmann G, Bork P, Huynen MA
date: 2000

An automatic homology modeling method consisting of database searches and simulated annealing.
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publication name: J. Mol. Graph. Model.
creator: Ogata K, Umeyama H
date: 2000

Better access to information about clinical trials.
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publication name: Ann. Intern. Med.
creator: McCray AT
date: 2000

BodyMap: a collection of 3' ESTs for analysis of human gene expression information.
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publication name: Genome Res.
creator: 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
date: 2000

Precise estimation of allele frequencies of single-nucleotide polymorphisms by a quantitative SSCP analysis of pooled DNA.
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publication name: Am. J. Hum. Genet.
creator: Sasaki T, Tahira T, Suzuki A, Higasa K, Kukita Y, Baba S, Hayashi K
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Generation of expressed sequence tags from low-CO2 and high-CO2 adapted cells of Chlamydomonas reinhardtii.
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publication name: DNA Res.
creator: Asamizu E, Miura K, Kucho K, Inoue Y, Fukuzawa H, Ohyama K, Nakamura Y, Tabata S
date: 2000

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.
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publication name: Syst. Appl. Microbiol.
creator: Ohnishi M, Murata T, Nakayama K, Kuhara S, Hattori M, Kurokawa K, Yasunaga T, Yokoyama K, Makino K, Shinagawa H, Hayashi T
date: 2000

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.
type: Article
publication name: Gene
creator: 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
date: 2000

Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
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publication name: Science
creator: 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
date: 2000

Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium.
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publication name: Proc. Natl. Acad. Sci. U.S.A.
creator: 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
date: 2000

Protein Information Resource: a community resource for expert annotation of protein data.
type: Article
publication name: Nucleic Acids Res.
creator: 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
date: 2001

CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins.
type: Article
publication name: Nucleic Acids Res.
creator: Kriventseva EV, Fleischmann W, Zdobnov EM, Apweiler R
date: 2001

TIGRFAMs: a protein family resource for the functional identification of proteins.
type: Article
publication name: Nucleic Acids Res.
creator: Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, White O
date: 2001

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.
type: Article
publication name: Nucleic Acids Res.
creator: Apweiler R, Biswas M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Phan I, Zdobnov E
date: 2001

iProClass: an integrated, comprehensive and annotated protein classification database.
type: Article
publication name: Nucleic Acids Res.
creator: Wu CH, Xiao C, Hou Z, Huang H, Barker WC
date: 2001

FULL-malaria: a database for a full-length enriched cDNA library from human malaria parasite, Plasmodium falciparum.
type: Article
publication name: Nucleic Acids Res.
creator: Watanabe J, Sasaki M, Suzuki Y, Sugano S
date: 2001

WormBase: network access to the genome and biology of Caenorhabditis elegans.
type: Article
publication name: Nucleic Acids Res.
creator: Stein L, Sternberg P, Durbin R, Thierry-Mieg J, Spieth J
date: 2001

The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research.
type: Article
publication name: Nucleic Acids Res.
creator: Sprague J, Doerry E, Douglas S, Westerfield M
date: 2001

The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant.
type: Article
publication name: Nucleic Acids Res.
creator: 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
date: 2001

The ARKdb: genome databases for farmed and other animals.
type: Article
publication name: Nucleic Acids Res.
creator: Hu J, Mungall C, Law A, Papworth R, Nelson JP, Brown A, Simpson I, Leckie S, Burt DW, Hillyard AL, Archibald AL
date: 2001

GenMapDB: a database of mapped human BAC clones.
type: Article
publication name: Nucleic Acids Res.
creator: Morley M, Arcaro M, Burdick J, Yonescu R, Reid T, Kirsch IR, Cheung VG
date: 2001

The Stanford Microarray Database.
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publication name: Nucleic Acids Res.
creator: 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
date: 2001

The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species.
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publication name: Nucleic Acids Res.
creator: Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J
date: 2001

The RDP-II (Ribosomal Database Project).
type: Article
publication name: Nucleic Acids Res.
creator: Maidak BL, Cole JR, Lilburn TG, Parker CT, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM
date: 2001

IMGT, the international ImMunoGeneTics database.
type: Article
publication name: Nucleic Acids Res.
creator: Lefranc MP
date: 2001

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB).
type: Article
publication name: Nucleic Acids Res.
creator: Noguchi T, Matsuda H, Akiyama Y
date: 2001

PDBsum: summaries and analyses of PDB structures.
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publication name: Nucleic Acids Res.
creator: Laskowski RA
date: 2001

DIP: The Database of Interacting Proteins: 2001 update.
type: Article
publication name: Nucleic Acids Res.
creator: Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D
date: 2001

Aminoacyl-tRNA synthetases database.
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publication name: Nucleic Acids Res.
creator: Szymanski M, Deniziak MA, Barciszewski J
date: 2001

Atlas of Genetics and Cytogenetics in Oncology and Haematology, updated.
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publication name: Nucleic Acids Res.
creator: Huret JL, Dessen P, Bernheim A
date: 2001

dbSNP: the NCBI database of genetic variation.
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publication name: Nucleic Acids Res.
creator: Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K
date: 2001

STRBase: a short tandem repeat DNA database for the human identity testing community.
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publication name: Nucleic Acids Res.
creator: Ruitberg CM, Reeder DJ, Butler JM
date: 2001

The KMDB/MutationView: a mutation database for human disease genes.
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publication name: Nucleic Acids Res.
creator: Minoshima S, Mitsuyama S, Ohtsubo M, Kawamura T, Ito S, Shibamoto S, Ito F, Shimizu N
date: 2001

ICB database: the gyrB database for identification and classification of bacteria.
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publication name: Nucleic Acids Res.
creator: Watanabe K, Nelson J, Harayama S, Kasai H
date: 2001

Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems.
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publication name: Nucleic Acids Res.
creator: Horn F, Vriend G, Cohen FE
date: 2001

Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database searches.
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publication name: Gene
creator: Kawabata T, Arisaka F, Nishikawa K
date: 2000

TOXNET: an evolving web resource for toxicology and environmental health information.
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publication name: Toxicology
creator: Wexler P
date: 2001

Quantitative trait loci (QTL) analysis in a Meishan x Göttingen cross population.
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publication name: Anim. Genet.
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Functional and structural genomics using PEDANT.
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Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays.
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Contribution of the Tos17 retrotransposon to rice functional genomics.
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Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi.
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Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana.
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A new cancer genome anatomy project web resource for the community.
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A comprehensive two-hybrid analysis to explore the yeast protein interactome.
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A systematic analysis of human disease-associated gene sequences in Drosophila melanogaster.
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yMGV: a database for visualization and data mining of published genome-wide yeast expression data.
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Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive gene duplications generated multiple isoforms predicting new ribosomal RNA 2'-O-methylation sites.
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MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products.
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GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles.
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Cell-free translation reconstituted with purified components.
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PicSNP: a browsable catalog of nonsynonymous single nucleotide polymorphisms in the human genome.
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The Cancer Genome Anatomy Project: new resources for reading the molecular signatures of cancer.
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Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites.
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A functional update of the Escherichia coli K-12 genome.
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Knowledge representation of signal transduction pathways.
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Structural and functional features of eukaryotic mRNA untranslated regions.
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Diversification of Escherichia coli genomes: are bacteriophages the major contributors?
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LINUCS: linear notation for unique description of carbohydrate sequences.
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A comparative genomics approach for studying ancestral proteins and evolution.
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In silico analysis of cancer through the Cancer Genome Anatomy Project.
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An integrated analysis and database system for full-length cDNA.
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Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs.
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Thermodynamic database for protein-nucleic acid interactions (ProNIT).
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DNA Data Bank of Japan (DDBJ) for genome scale research in life science.
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The Protein Information Resource: an integrated public resource of functional annotation of proteins.
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The Ensembl genome database project.
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BRENDA, enzyme data and metabolic information.
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The MetaCyc Database.
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Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more.
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yMGV: helping biologists with yeast microarray data mining.
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Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags.
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Homophila: human disease gene cognates in Drosophila.
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HOWDY: an integrated database system for human genome research.
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JSNP: a database of common gene variations in the Japanese population.
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PharmGKB: the Pharmacogenetics Knowledge Base.
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HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project.
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The tmRNA Website: invasion by an intron.
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HERVd: database of human endogenous retroviruses.
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Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.
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READ: RIKEN Expression Array Database.
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The human (PEDB) and mouse (mPEDB) Prostate Expression Databases.
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The IMB Jena Image Library of Biological Macromolecules: 2002 update.
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SCOP database in 2002: refinements accommodate structural genomics.
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GTOP: a database of protein structures predicted from genome sequences.
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ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0.
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The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data.
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DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs.
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UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002.
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S/MARt DB: a database on scaffold/matrix attached regions.
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MDB: the Metalloprotein Database and Browser at The Scripps Research Institute.
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InBase: the Intein Database.
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HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources.
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SWEET-DB: an attempt to create annotated data collections for carbohydrates.
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Multiple snoRNA gene clusters from Arabidopsis.
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BRENDA: a resource for enzyme data and metabolic information.
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Database and analysis system for cDNA clones obtained from full-length enriched cDNA libraries.
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The EBI SRS server--recent developments.
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Comparison of sequences of cDNA clones obtained from oligo-capping cDNA libraries with those from unigene.
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Genome-wide transcriptional orchestration of circadian rhythms in Drosophila.
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The Mouse Tumor Biology Database: a public resource for cancer genetics and pathology of the mouse.
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Untranslated regions of mRNAs.
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Functional annotation of a full-length Arabidopsis cDNA collection.
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Functional genomics of the social amoebae, Dictyostelium discoideum.
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Physiological genomics of Escherichia coli protein families.
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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.
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Thermodynamic databases for proteins and protein-nucleic acid interactions.
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Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays.
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The IARC TP53 database: new online mutation analysis and recommendations to users.
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[LIPIDBANK for Web, the newly developed lipid database].
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Searching yeast intron data at Ares lab Web site.
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An international database and integrated analysis tools for the study of cancer gene expression.
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An anatomy of normal and malignant gene expression.
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A novel gene organization: intronic snoRNA gene clusters from Oryza sativa.
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Comparison of genome structures of vibrios, bacteria possessing two chromosomes.
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Intercellular coupling mechanism for synchronized and noise-resistant circadian oscillators.
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A transcription factor response element for gene expression during circadian night.
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Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray.
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Filamentous bacteriophages of vibrios are integrated into the dif-like site of the host chromosome.
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The EBI SRS server-new features.
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A new resource of locally transposed Dissociation elements for screening gene-knockout lines in silico on the Arabidopsis genome.
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Oligosaccharide specificity of galectins: a search by frontal affinity chromatography.
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ProDom: automated clustering of homologous domains.
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PROSITE: a documented database using patterns and profiles as motif descriptors.
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A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome.
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GETDB, a database compiling expression patterns and molecular locations of a collection of Gal4 enhancer traps.
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Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12.
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CDART: protein homology by domain architecture.
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Annotating regulatory DNA based on man-mouse genomic comparison.
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GeneCards 2002: towards a complete, object-oriented, human gene compendium.
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Functional SNPs in the lymphotoxin-alpha gene that are associated with susceptibility to myocardial infarction.
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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.
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Visualization by comprehensive microarray analysis of gene expression programs during transdifferentiation of mesophyll cells into xylem cells.
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TAIR: a resource for integrated Arabidopsis data.
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Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray.
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Hemi-stranded SSCP analysis of SNPs in short sequence-tagged sites.
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publication name: BioTechniques
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date: 2002

The cancer genome anatomy project: online resources to reveal the molecular signatures of cancer.
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creator: Strausberg RL, Buetow KH, Greenhut SF, Grouse LH, Schaefer CF
date: 2002

http://rdf.ncbi.nlm.nih.gov/pubmed/12465718
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title: 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.
publication name: DNA Res.
creator: Okazaki N, Kikuno R, Ohara R, Inamoto S, Hara Y, Nagase T, Ohara O, Koga H
date: 2002

The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans.
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The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants.
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publication name: Mol. Genet. Genomics
creator: Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, Nakazono M, Hirai A, Kadowaki K
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Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.
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publication name: Proc. Natl. Acad. Sci. U.S.A.
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Genomic diversity of enterohemorrhagic Escherichia coli O157 revealed by whole genome PCR scanning.
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publication name: Proc. Natl. Acad. Sci. U.S.A.
creator: Ohnishi M, Terajima J, Kurokawa K, Nakayama K, Murata T, Tamura K, Ogura Y, Watanabe H, Hayashi T
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Multiple promoter inversions generate surface antigenic variation in Mycoplasma penetrans.
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publication name: J. Bacteriol.
creator: Horino A, Sasaki Y, Sasaki T, Kenri T
date: 2003

Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae.
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publication name: Yeast
creator: Warringer J, Blomberg A
date: 2003

SNP detection and allele frequency determination by SSCP.
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publication name: Methods Mol. Biol.
creator: Tahira T, Suzuki A, Kukita Y, Hayashi K
date: 2003

CORG: a database for COmparative Regulatory Genomics.
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publication name: Nucleic Acids Res.
creator: Dieterich C, Wang H, Rateitschak K, Luz H, Vingron M
date: 2003

MBGD: microbial genome database for comparative analysis.
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publication name: Nucleic Acids Res.
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date: 2003

ArrayExpress--a public repository for microarray gene expression data at the EBI.
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publication name: Nucleic Acids Res.
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date: 2003

MEPD: a Medaka gene expression pattern database.
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publication name: Nucleic Acids Res.
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The Stanford Microarray Database: data access and quality assessment tools.
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publication name: Nucleic Acids Res.
creator: 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
date: 2003

ASAP: the Alternative Splicing Annotation Project.
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publication name: Nucleic Acids Res.
creator: Lee C, Atanelov L, Modrek B, Xing Y
date: 2003

WormBase: a cross-species database for comparative genomics.
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publication name: Nucleic Acids Res.
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date: 2003

GrainGenes, the genome database for small-grain crops.
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publication name: Nucleic Acids Res.
creator: Matthews DE, Carollo VL, Lazo GR, Anderson OD
date: 2003

The PEDANT genome database.
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publication name: Nucleic Acids Res.
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date: 2003

The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.
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publication name: Nucleic Acids Res.
creator: 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
date: 2003

WorfDB: the Caenorhabditis elegans ORFeome Database.
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publication name: Nucleic Acids Res.
creator: Vaglio P, Lamesch P, Reboul J, Rual JF, Martinez M, Hill D, Vidal M
date: 2003

STRING: a database of predicted functional associations between proteins.
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creator: von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B
date: 2003

Studies on energy-linked reactions: isolation, characterisation and genetic analysis of trialkyl-tin-resistant mutants of Saccharomyces cerevisiae.
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Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003.
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Online Mendelian Inheritance in Animals (OMIA): a comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals.
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creator: Nicholas FW
date: 2003

IMGT, the international ImMunoGeneTics database.
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publication name: Nucleic Acids Res.
creator: Lefranc MP
date: 2003

The Protein Information Resource.
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publication name: Nucleic Acids Res.
creator: 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
date: 2003

The TIGRFAMs database of protein families.
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publication name: Nucleic Acids Res.
creator: Haft DH, Selengut JD, White O
date: 2003

Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters.
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publication name: Nucleic Acids Res.
creator: Kriventseva EV, Servant F, Apweiler R
date: 2003

iProClass: an integrated database of protein family, function and structure information.
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publication name: Nucleic Acids Res.
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date: 2003

TMPDB: a database of experimentally-characterized transmembrane topologies.
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publication name: Nucleic Acids Res.
creator: Ikeda M, Arai M, Okuno T, Shimizu T
date: 2003

Plant snoRNA database.
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publication name: Nucleic Acids Res.
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date: 2003

Rfam: an RNA family database.
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publication name: Nucleic Acids Res.
creator: Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR
date: 2003

The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy.
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publication name: Nucleic Acids Res.
creator: ['Cole JR', 'Chai B', 'Marsh TL', 'Farris RJ', 'Wang Q', 'Kulam SA', 'Chandra S', 'McGarrell DM', 'Schmidt TM', 'Garrity GM', 'Tiedje JM']
date: 2003

tmRDB (tmRNA database).
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publication name: Nucleic Acids Res.
creator: Zwieb C, Gorodkin J, Knudsen B, Burks J, Wower J
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Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species.
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PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003.
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RNABase: an annotated database of RNA structures.
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Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins.
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date: 2003

Gene discovery in oral squamous cell carcinoma through the Head and Neck Cancer Genome Anatomy Project: confirmation by microarray analysis.
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publication name: Oral Oncol.
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date: 2003

Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae.
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publication name: Lancet
creator: 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
date: 2003

Unique amino acid composition of proteins in halophilic bacteria.
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creator: Fukuchi S, Yoshimune K, Wakayama M, Moriguchi M, Nishikawa K
date: 2003

Development of 50 gene-associated microsatellite markers using BAC clones and the construction of a linkage map of swine chromosome 4.
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publication name: Anim. Genet.
creator: Fujishima-Kanaya N, Toki D, Suzuki K, Sawazaki T, Hiraiwa H, Iida M, Hayashi T, Uenishi H, Wada Y, Ito Y, Awata T
date: 2003

[Orphanet, an information site on rare diseases].
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publication name: Soins
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C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression.
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Essential Bacillus subtilis genes.
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publication name: Proc. Natl. Acad. Sci. U.S.A.
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Human chromosome 7: DNA sequence and biology.
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publication name: Science
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Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis.
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http://rdf.ncbi.nlm.nih.gov/pubmed/12693553
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creator: Okazaki N, Kikuno R, Ohara R, Inamoto S, Aizawa H, Yuasa S, Nakajima D, Nagase T, Ohara O, Koga H
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Construction of a full-length enriched and a 5'-end enriched cDNA library using the oligo-capping method.
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Analysis of 5'-end sequences of chimpanzee cDNAs.
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Novel gene encoding a Ca2+-binding protein and under hexokinase-dependent sugar regulation.
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publication name: Biosci. Biotechnol. Biochem.
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The Cancer Genome Anatomy Project: power tools for cancer biologists.
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New allele frequency database: http://www.allelefrequencies.net.
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Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins.
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creator: Kaji H, Saito H, Yamauchi Y, Shinkawa T, Taoka M, Hirabayashi J, Kasai K, Takahashi N, Isobe T
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Construction of a new porcine whole-genome framework map using a radiation hybrid panel.
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creator: Hamasima N, Suzuki H, Mikawa A, Morozumi T, Plastow G, Mitsuhashi T
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Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures.
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[The integrated database for mutations in disease-causing genes: Mutation View/KMDB].
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RAS oncogenes: the first 30 years.
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Changing patterns of gene expression in dictyostelium prestalk cell subtypes recognized by in situ hybridization with genes from microarray analyses.
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publication name: Eukaryotic Cell
creator: Maeda M, Sakamoto H, Iranfar N, Fuller D, Maruo T, Ogihara S, Morio T, Urushihara H, Tanaka Y, Loomis WF
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Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution.
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publication name: Genome Res.
creator: 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
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Kinase pathway database: an integrated protein-kinase and NLP-based protein-interaction resource.
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publication name: Genome Res.
creator: Koike A, Kobayashi Y, Takagi T
date: 2003

Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution.
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IMGT/PhyloGene: an on-line tool for comparative analysis of immunoglobulin and T cell receptor genes.
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Inferring higher functional information for RIKEN mouse full-length cDNA clones with FACTS.
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AHMII: Agent to Help Microbial Information Integration.
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ExPASy: The proteomics server for in-depth protein knowledge and analysis.
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Microarray analysis of embryonic retinoic acid target genes in the ascidian Ciona intestinalis.
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Protein informatics towards function identification.
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Identification of protein functions from a molecular surface database, eF-site.
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Review of the BRENDA Database.
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GeneLoc: exon-based integration of human genome maps.
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Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
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Genomic structure around joining segments and constant regions of swine T-cell receptor alpha/delta (TRA/TRD) locus.
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publication name: Immunology
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Conservation of the syntenies between porcine chromosome 7 and human chromosomes 6, 14 and 15 demonstrated by radiation hybrid mapping and linkage analysis.
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Identification of protein biochemical functions by similarity search using the molecular surface database eF-site.
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Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8.
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Cytochrome p450 complement (CYPome) of the avermectin-producer Streptomyces avermitilis and comparison to that of Streptomyces coelicolor A3(2).
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Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome.
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publication name: Plant Cell
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Dynamic molecules: molecular dynamics for everyone. An internet-based access to molecular dynamic simulations: basic concepts.
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Rice gene expression in response to N-acetylchitooligosaccharide elicitor: comprehensive analysis by DNA microarray with randomly selected ESTs.
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Frontal affinity chromatography as a tool for elucidation of sugar recognition properties of lectins.
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The COG database: an updated version includes eukaryotes.
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First RFLP linkage map of red clover ( Trifolium pratense L.) based on cDNA probes and its transferability to other red clover germplasm.
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The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids.
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Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways.
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An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.
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The novel MYB protein EARLY-PHYTOCHROME-RESPONSIVE1 is a component of a slave circadian oscillator in Arabidopsis.
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Comparative analysis of the genomes of cyanobacteria and plants.
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Quantitative metabolome analysis using capillary electrophoresis mass spectrometry.
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A gene expression atlas of the central nervous system based on bacterial artificial chromosomes.
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The yeast mitochondrial proteome, a study of fermentative and respiratory growth.
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The construction of an EST database for Bombyx mori and its application.
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Announcing the worldwide Protein Data Bank.
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High-resolution yeast phenomics resolves different physiological features in the saline response.
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ACLAME: a CLAssification of Mobile genetic Elements.
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HERVd: the Human Endogenous RetroViruses Database: update.
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Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities.
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Xpro: database of eukaryotic protein-encoding genes.
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DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics.
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The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.
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HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development.
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The European ribosomal RNA database.
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The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts.
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ProTherm, version 4.0: thermodynamic database for proteins and mutants.
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The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.
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ESTHER, the database of the alpha/beta-hydrolase fold superfamily of proteins.
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RPG: the Ribosomal Protein Gene database.
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SCOP database in 2004: refinements integrate structure and sequence family data.
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The KEGG resource for deciphering the genome.
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GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins.
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SCMD: Saccharomyces cerevisiae Morphological Database.
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dictyBase: a new Dictyostelium discoideum genome database.
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Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species.
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The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants.
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date: 2004

The Rice PIPELINE: a unification tool for plant functional genomics.
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Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003.
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MaizeGDB, the community database for maize genetics and genomics.
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WormBase: a multi-species resource for nematode biology and genomics.
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BRENDA, the enzyme database: updates and major new developments.
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IntEnz, the integrated relational enzyme database.
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MetaCyc: a multiorganism database of metabolic pathways and enzymes.
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The Database of Interacting Proteins: 2004 update.
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FREP: a database of functional repeats in mouse cDNAs.
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The Mouse SAGE Site: database of public mouse SAGE libraries.
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publication name: Nucleic Acids Res.
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date: 2004

PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries.
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HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE.
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publication name: Nucleic Acids Res.
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RTCGD: retroviral tagged cancer gene database.
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CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature.
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EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes.
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GermOnline, a cross-species community knowledgebase on germ cell differentiation.
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Complete sequencing and characterization of 21,243 full-length human cDNAs.
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date: 2004

GeneAnnot: interfacing GeneCards with high-throughput gene expression compendia.
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publication name: Brief. Bioinformatics
creator: Chalifa-Caspi V, Shmueli O, Benjamin-Rodrig H, Rosen N, Shmoish M, Yanai I, Ophir R, Kats P, Safran M, Lancet D
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Automated indexing of the Hazardous Substances Data Bank (HSDB).
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ArrayExpress: a public database of gene expression data at EBI.
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CIBEX: center for information biology gene expression database.
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Gene Unscrambler for detangling scrambled genes in ciliates.
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publication name: Bioinformatics
creator: Cavalcanti AR, Landweber LF
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GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures.
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publication name: Bioinformatics
creator: Yabuki Y, Mukai Y, Swindells MB, Suwa M
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A reference ontology for biomedical informatics: the Foundational Model of Anatomy.
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OQAFMA Querying agent for the Foundational Model of Anatomy: a prototype for providing flexible and efficient access to large semantic networks.
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eF-site and PDBjViewer: database and viewer for protein functional sites.
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publication name: Bioinformatics
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date: 2004

GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes.
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publication name: Bioinformatics
creator: Chalifa-Caspi V, Yanai I, Ophir R, Rosen N, Shmoish M, Benjamin-Rodrig H, Shklar M, Stein TI, Shmueli O, Safran M, Lancet D
date: 2004

Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis.
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publication name: Physiol. Genomics
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Toxoplasma gondii genomics: shedding light on pathogenesis and chemotherapy.
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A collection of 11 800 single-copy Ds transposon insertion lines in Arabidopsis.
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Het-PDB Navi.: a database for protein-small molecule interactions.
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Data mining the protein data bank: automatic detection and assignment of carbohydrate structures.
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Expression profiling with arrays of randomly disrupted genes in mouse embryonic stem cells leads to in vivo functional analysis.
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Investigation of differentially expressed genes during the development of mouse cerebellum.
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publication name: Brain Res. Gene Expr. Patterns
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The iProClass integrated database for protein functional analysis.
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Genomics approach to abscisic acid- and gibberellin-responsive genes in rice.
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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.
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Development of Ciona intestinalis juveniles (through 2nd ascidian stage).
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ProMode: a database of normal mode analyses on protein molecules with a full-atom model.
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ONCOMINE: a cancer microarray database and integrated data-mining platform.
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publication name: Neoplasia
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Development and evaluation of an Arabidopsis whole genome Affymetrix probe array.
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Large-scale RT-PCR recovery of full-length cDNA clones.
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FREX: a query interface for biological processes with hierarchical and recursive structures.
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publication name: In Silico Biol. (Gedrukt)
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Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
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Colourful history of Japan's rat resources.
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The androgen receptor gene mutations database (ARDB): 2004 update.
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Update of mouse microsatellite database of Japan (MMDBJ).
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pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files.
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publication name: BMC Bioinformatics
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A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins: generation and evaluation of anti-mKIAA antibodies.
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Large-scale isolation of ESTs from medaka embryos and its application to medaka developmental genetics.
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publication name: Mech. Dev.
creator: 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
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Public web-based services from the European Bioinformatics Institute.
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GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates.
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KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains.
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CD-Search: protein domain annotations on the fly.
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The International Protein Index: an integrated database for proteomics experiments.
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Nuclear receptors and disease: androgen receptor.
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Comparative genomic hybridization (CGH)-arrays pave the way for identification of novel cancer-related genes.
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CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data.
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Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project.
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Bioinformatics for glycomics: status, methods, requirements and perspectives.
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TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks.
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SWISS-2DPAGE, ten years later.
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Rice mutant resources for gene discovery.
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Characteristics of the Lotus japonicus gene repertoire deduced from large-scale expressed sequence tag (EST) analysis.
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Detection of large-scale variation in the human genome.
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5'-end SAGE for the analysis of transcriptional start sites.
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A genome-wide and nonredundant mouse transcription factor database.
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Developments of geriatric autopsy database and Internet-based database of Japanese single nucleotide polymorphisms for geriatric research (JG-SNP).
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publication name: Mech. Ageing Dev.
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Stable isotope labeling of Arabidopsis thaliana for an NMR-based metabolomics approach.
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The MeSH translation maintenance system: structure, interface design, and implementation.
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Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism.
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Mitochondrial genome variation in eastern Asia and the peopling of Japan.
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The complete genomic sequence of Nocardia farcinica IFM 10152.
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Construction of a human glycogene library and comprehensive functional analysis.
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Control of cell type proportioning in Dictyostelium discoideum by differentiation-inducing factor as determined by in situ hybridization.
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C. elegans ORFeome version 3.1: increasing the coverage of ORFeome resources with improved gene predictions.
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Systematic recovery and analysis of full-ORF human cDNA clones.
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The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
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WormBase as an integrated platform for the C. elegans ORFeome.
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A comprehensive gene expression analysis toward the understanding of growth and differentiation of tobacco BY-2 cells.
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Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1.
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A simple statistical method for discriminating outer membrane proteins with better accuracy.
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Sequence features of Oxytricha trifallax (class Spirotrichea) macronuclear telomeric and subtelomeric sequences.
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publication name: Protist
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Contribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC-end sequence-SNP analysis.
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Transporter database, TP-Search: a web-accessible comprehensive database for research in pharmacokinetics of drugs.
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Rat Phenome Project: the untapped potential of existing rat strains.
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Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions.
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Current status of medaka genetics and genomics. The Medaka Genome Initiative (MGI).
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NONCODE: an integrated knowledge database of non-coding RNAs.
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Rfam: annotating non-coding RNAs in complete genomes.
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UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.
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The ProDom database of protein domain families: more emphasis on 3D.
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Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB.
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PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids.
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The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis.
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The PEDANT genome database in 2005.
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Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation.
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The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information.
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WormBase: a comprehensive data resource for Caenorhabditis biology and genomics.
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EzCatDB: the Enzyme Catalytic-mechanism Database.
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Reactome: a knowledgebase of biological pathways.
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STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
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DED: Database of Evolutionary Distances.
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L1Base: from functional annotation to prediction of active LINE-1 elements.
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Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues.
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5'SAGE: 5'-end Serial Analysis of Gene Expression database.
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ArrayExpress--a public repository for microarray gene expression data at the EBI.
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NCBI GEO: mining millions of expression profiles--database and tools.
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The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms.
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The Stanford Microarray Database accommodates additional microarray platforms and data formats.
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HOPPSIGEN: a database of human and mouse processed pseudogenes.
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IMGT, the international ImMunoGeneTics information system.
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RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome.
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Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.
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The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.
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Visualizing the laboratory mouse: capturing phenotype information.
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http://rdf.ncbi.nlm.nih.gov/pubmed/15644576
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Characterization of full-length enriched expressed sequence tags of stress-treated poplar leaves.
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System-level identification of transcriptional circuits underlying mammalian circadian clocks.
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[International public gene expression database (CIBEX) and data submission].
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Inferring the mode of speciation from genomic data: a study of the great apes.
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Identification of the ligand binding sites on the molecular surface of proteins.
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Identification of ciliated sensory neuron-expressed genes in Caenorhabditis elegans using targeted pull-down of poly(A) tails.
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Molecular pathology of the androgen receptor in male (in)fertility.
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Efficient tree-matching methods for accurate carbohydrate database queries.
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Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.
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Comparative promoter region analysis powered by CORG.
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Effects of dioxin on gene expression in female reproductive system in the rat.
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Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues.
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Genomic structure of eight porcine chemokine receptors and intergene sharing of an exon between CCR1 and XCR1.
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Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas.
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A gene expression map of Arabidopsis thaliana development.
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Filtering high-throughput protein-protein interaction data using a combination of genomic features.
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Application of residue distribution along the sequence for discriminating outer membrane proteins.
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A resource of 5,814 dissociation transposon-tagged and sequence-indexed lines of Arabidopsis transposed from start loci on chromosome 5.
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Application of InChI to curate, index, and query 3-D structures.
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Comparison of the transcript profiles from the root and the nodulating root of the model legume Lotus japonicus by serial analysis of gene expression.
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Analysis of expressed sequence tags in prothallia of Adiantum capillus-veneris.
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Comparative analysis of carbohydrate-binding properties of two tandem repeat-type Jacalin-related lectins, Castanea crenata agglutinin and Cycas revoluta leaf lectin.
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The predictive power of the CluSTr database.
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IMGT-Choreography for immunogenetics and immunoinformatics.
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dbQSNP: a database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods.
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InterProScan: protein domains identifier.
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A human protein atlas for normal and cancer tissues based on antibody proteomics.
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Heavy-atom Database System: a tool for the preparation of heavy-atom derivatives of protein crystals based on amino-acid sequence and crystallization conditions.
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An integrated database of the ascidian, Ciona intestinalis: towards functional genomics.
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A web tool for comparative genomics: G-compass.
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Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB).
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GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research.
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Terminology model discovery using natural language processing and visualization techniques.
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miRBase: microRNA sequences, targets and gene nomenclature.
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snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs.
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PINT: Protein-protein Interactions Thermodynamic Database.
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ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions.
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ChimerDB--a knowledgebase for fusion sequences.
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LOCATE: a mouse protein subcellular localization database.
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Pfam: clans, web tools and services.
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HUMHOT: a database of human meiotic recombination hot spots.
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SMART 5: domains in the context of genomes and networks.
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The EROP-Moscow oligopeptide database.
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ISfinder: the reference centre for bacterial insertion sequences.
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PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees.
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From genomics to chemical genomics: new developments in KEGG.
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ODB: a database of operons accumulating known operons across multiple genomes.
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dictyBase, the model organism database for Dictyostelium discoideum.
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WormBase: better software, richer content.
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Pathguide: a pathway resource list.
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MetaCyc: a multiorganism database of metabolic pathways and enzymes.
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AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB.
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DBTGR: a database of tunicate promoters and their regulatory elements.
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TreeFam: a curated database of phylogenetic trees of animal gene families.
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BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression.
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The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.
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DrugBank: a comprehensive resource for in silico drug discovery and exploration.
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GLIDA: GPCR-ligand database for chemical genomic drug discovery.
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BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.
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The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information.
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IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences.
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Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns.
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Chemical compound navigator: a web-based chem-BLAST, chemical taxonomy-based search engine for browsing compounds.
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2DDB - a bioinformatics solution for analysis of quantitative proteomics data.
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Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumption.
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The genomic structure and a novel alternatively spliced form of porcine pTalpha chain.
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Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.
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Kazusa mammalian cDNA resources: towards functional characterization of KIAA gene products.
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RARTF: database and tools for complete sets of Arabidopsis transcription factors.
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Comprehensive structural analysis of the genome of red clover (Trifolium pratense L.).
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InCeP: intracellular pathway based on mKIAA protein-protein interactions.
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Systematic analysis of the visual projection neurons of Drosophila melanogaster. I. Lobula-specific pathways.
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ET viewer: an application for predicting and visualizing functional sites in protein structures.
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A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis.
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Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance.
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TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB.
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ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins.
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ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.
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GlyNest and CASPER: two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interface.
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Alternative splicing in human transcriptome: functional and structural influence on proteins.
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The Candida Genome Database: facilitating research on Candida albicans molecular biology.
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Comparative promoter analysis in vertebrate genomes with the CORG workbench.
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Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*.
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Mass identification of chloroplast proteins of endosymbiont origin by phylogenetic profiling based on organism-optimized homologous protein groups.
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Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii.
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Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.
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Gene expression omnibus: microarray data storage, submission, retrieval, and analysis.
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Data storage and analysis in ArrayExpress.
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Functional genomic analysis of commercial baker's yeast during initial stages of model dough-fermentation.
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dictyBase and the Dicty Stock Center.
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The semantics of procedures and diseases in SNOMED CT.
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WormBase: methods for data mining and comparative genomics.
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Identification and classification of genes required for tolerance to freeze-thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains.
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Biomedical knowledge navigation by literature clustering.
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The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse.
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Rate and polarity of gene fusion and fission in Oryza sativa and Arabidopsis thaliana.
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Practical aspects of uniform stable isotope labeling of higher plants for heteronuclear NMR-based metabolomics.
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Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the EzCatDB database.
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A first global analysis of plasmid encoded proteins in the ACLAME database.
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OriDB: a DNA replication origin database.
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OmicBrowse: a browser of multidimensional omics annotations.
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InSatDb: a microsatellite database of fully sequenced insect genomes.
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TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences.
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The TIGR Plant Transcript Assemblies database.
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CancerGenes: a gene selection resource for cancer genome projects.
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ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes.
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Sequence resources at the Candida Genome Database.
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The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data.
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PigGIS: Pig Genomic Informatics System.
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Event ontology: a pathway-centric ontology for biological processes.
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STRING 7--recent developments in the integration and prediction of protein interactions.
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NCBI GEO: mining tens of millions of expression profiles--database and tools update.
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Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.
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fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences.
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WormBase: new content and better access.
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PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits.
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A large-scale full-length cDNA analysis to explore the budding yeast transcriptome.
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The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.
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Analysis of the genomic structure of the porcine CD1 gene cluster.
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Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome.
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H-DBAS: alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational.
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VISTA Enhancer Browser--a database of tissue-specific human enhancers.
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ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis.
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ArrayExpress--a public database of microarray experiments and gene expression profiles.
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MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups.
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Developments in CORG: a gene-centric comparative genomics resource.
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MMDB: annotating protein sequences with Entrez's 3D-structure database.
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CDD: a conserved domain database for interactive domain family analysis.
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Computational design and experimental evaluation of glycosyltransferase mutants: engineering of a blood type B galactosyltransferase with enhanced glucosyltransferase activity.
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RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes.
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TassDB: a database of alternative tandem splice sites.
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The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction.
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PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences.
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RNAdb 2.0--an expanded database of mammalian non-coding RNAs.
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PROPHECY--a yeast phenome database, update 2006.
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PEDANT genome database: 10 years online.
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The Rat Genome Database, update 2007--easing the path from disease to data and back again.
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Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs.
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NCBI GEO standards and services for microarray data.
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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).
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D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples.
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TRDB--the Tandem Repeats Database.
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A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes.
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The Stanford Microarray Database: implementation of new analysis tools and open source release of software.
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Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de.
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BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.
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SNPSTR: a database of compound microsatellite-SNP markers.
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MaizeGDB's new data types, resources and activities.
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GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages.
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Birth and death of genes promoted by transposable elements in Oryza sativa.
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LactMed-new NLM database on drugs and lactation.
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Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.
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MutationView/KMcancerDB: a database for cancer gene mutations.
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AphidBase: a database for aphid genomic resources.
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New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA.
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Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature.
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Functional genomics of commercial baker's yeasts that have different abilities for sugar utilization and high-sucrose tolerance under different sugar conditions.
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CellMontage: similar expression profile search server.
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LOCATE: a mammalian protein subcellular localization database.
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The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes.
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Novel definition files for human GeneChips based on GeneAnnot.
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Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets.
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TreeFam: 2008 Update.
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The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.
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The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.
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Analysis of expressed sequence tags (ESTs) from Lentinula edodes.
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publication name: Appl. Microbiol. Biotechnol.
creator: Suizu T, Zhou GL, Oowatari Y, Kawamukai M
date: 2008

Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350.
type: Article
publication name: J. Bacteriol.
creator: Ohnishi Y, Ishikawa J, Hara H, Suzuki H, Ikenoya M, Ikeda H, Yamashita A, Hattori M, Horinouchi S
date: 2008

ASPicDB: a database resource for alternative splicing analysis.
type: Article
publication name: Bioinformatics
creator: 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
date: 2008

Profiling of Escherichia coli Chromosome database.
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publication name: Methods Mol. Biol.
creator: Yamazaki Y, Niki H, Kato J
date: 2008

The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access.
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publication name: Plant J.
creator: 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
date: 2008

FAMS and FAMSBASE for protein structure.
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publication name: Curr Protoc Bioinformatics
creator: Umeyama H, Iwadate M
date: 2004

BioCompass: a novel functional inference tool that utilizes MeSH hierarchy to analyze groups of genes.
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publication name: In Silico Biol. (Gedrukt)
creator: Nakazato T, Takinaka T, Mizuguchi H, Matsuda H, Bono H, Asogawa M
date: 2008

TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles.
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publication name: Comput Biol Chem
creator: Ou YY, Gromiha MM, Chen SA, Suwa M
date: 2008

Software.ncrna.org: web servers for analyses of RNA sequences.
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publication name: Nucleic Acids Res.
creator: Asai K, Kiryu H, Hamada M, Tabei Y, Sato K, Matsui H, Sakakibara Y, Terai G, Mituyama T
date: 2008

Aspergillus oryzae atfB encodes a transcription factor required for stress tolerance in conidia.
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publication name: Fungal Genet. Biol.
creator: Sakamoto K, Arima TH, Iwashita K, Yamada O, Gomi K, Akita O
date: 2008

The RAS/MAPK syndromes: novel roles of the RAS pathway in human genetic disorders.
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publication name: Hum. Mutat.
creator: Aoki Y, Niihori T, Narumi Y, Kure S, Matsubara Y
date: 2008

Structural classification of CDR-H3 revisited: a lesson in antibody modeling.
type: Article
publication name: Proteins
creator: Kuroda D, Shirai H, Kobori M, Nakamura H
date: 2008

Efficient production of monoclonal antibodies recognizing specific structures in Caenorhabditis elegans embryos using an antigen subtraction method.
type: Article
publication name: Genes Cells
creator: Takeda K, Watanabe C, Qadota H, Hanazawa M, Sugimoto A
date: 2008

Genome structure of the legume, Lotus japonicus.
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publication name: DNA Res.
creator: 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
date: 2008

Soybean seed extracts preferentially express genomic loci of Bradyrhizobium japonicum in the initial interaction with soybean, Glycine max (L.) Merr.
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publication name: DNA Res.
creator: 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
date: 2008

An improved scoring scheme for predicting glycan structures from gene expression data.
type: Article
publication name: Genome Inform
creator: Suga A, Yamanishi Y, Hashimoto K, Goto S, Kanehisa M
date: 2007

TriMEDB: a database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae.
type: Article
publication name: BMC Plant Biol.
creator: Mochida K, Saisho D, Yoshida T, Sakurai T, Shinozaki K
date: 2008

Cerebellar development transcriptome database (CDT-DB): profiling of spatio-temporal gene expression during the postnatal development of mouse cerebellum.
type: Article
publication name: Neural Netw
creator: Sato A, Sekine Y, Saruta C, Nishibe H, Morita N, Sato Y, Sadakata T, Shinoda Y, Kojima T, Furuichi T
date: 2008

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.
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publication name: Southeast Asian J. Trop. Med. Public Health
creator: Sakaguchi H, Usami M, Ando H, Ohata A
date: 2007

A gene wiki for community annotation of gene function.
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publication name: PLoS Biol.
creator: Huss JW, Orozco C, Goodale J, Wu C, Batalov S, Vickers TJ, Valafar F, Su AI
date: 2008

The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server.
type: Article
publication name: J Proteomics
creator: Hoogland C, Mostaguir K, Appel RD, Lisacek F
date: 2008

The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature.
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publication name: Comp. Funct. Genomics
creator: Yamamoto S, Asanuma T, Takagi T, Fukuda KI
date: 2004

Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles.
type: Article
publication name: BMC Plant Biol.
creator: Yura K, Go M
date: 2008

Resources for global risk assessment: the International Toxicity Estimates for Risk (ITER) and Risk Information Exchange (RiskIE) databases.
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publication name: Toxicol. Appl. Pharmacol.
creator: Wullenweber A, Kroner O, Kohrman M, Maier A, Dourson M, Rak A, Wexler P, Tomljanovic C
date: 2008

Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules.
type: Article
publication name: Genome Biol.
creator: Hodis E, Prilusky J, Martz E, Silman I, Moult J, Sussman JL
date: 2008

Trends in large-scale mouse mutagenesis: from genetics to functional genomics.
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publication name: Nat. Rev. Genet.
creator: Gondo Y
date: 2008

bold: The Barcode of Life Data System (http://www.barcodinglife.org).
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publication name: Mol. Ecol. Notes
creator: Ratnasingham S, Hebert PD
date: 2007

Systematic classification of CDR-L3 in antibodies: implications of the light chain subtypes and the VL-VH interface.
type: Article
publication name: Proteins
creator: Kuroda D, Shirai H, Kobori M, Nakamura H
date: 2009

GlycomeDB - integration of open-access carbohydrate structure databases.
type: Article
publication name: BMC Bioinformatics
creator: Ranzinger R, Herget S, Wetter T, von der Lieth CW
date: 2008

DiProDB: a database for dinucleotide properties.
type: Article
publication name: Nucleic Acids Res.
creator: Friedel M, Nikolajewa S, Sühnel J, Wilhelm T
date: 2009

Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock.
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publication name: Proc. Natl. Acad. Sci. U.S.A.
creator: Kumaki Y, Ukai-Tadenuma M, Uno KD, Nishio J, Masumoto KH, Nagano M, Komori T, Shigeyoshi Y, Hogenesch JB, Ueda HR
date: 2008

Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database.
type: Article
publication name: BioData Min
creator: Arita M, Suwa K
date: 2008

PID: the Pathway Interaction Database.
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publication name: Nucleic Acids Res.
creator: Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH
date: 2009

BodyParts3D: 3D structure database for anatomical concepts.
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publication name: Nucleic Acids Res.
creator: Mitsuhashi N, Fujieda K, Tamura T, Kawamoto S, Takagi T, Okubo K
date: 2009

The Universal Protein Resource (UniProt) 2009.
type: Article
publication name: Nucleic Acids Res.
creator: []
date: 2009

PiSite: a database of protein interaction sites using multiple binding states in the PDB.
type: Article
publication name: Nucleic Acids Res.
creator: Higurashi M, Ishida T, Kinoshita K
date: 2009

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.
type: Article
publication name: Nucleic Acids Res.
creator: Takeda J, Suzuki Y, Sakate R, Sato Y, Seki M, Irie T, Takeuchi N, Ueda T, Nakao M, Sugano S, Gojobori T, Imanishi T
date: 2008

MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database.
type: Article
publication name: Nucleic Acids Res.
creator: Ahsan B, Saito TL, Hashimoto S, Muramatsu K, Tsuda M, Sasaki A, Matsushima K, Aigaki T, Morishita S
date: 2009

McKusick's Online Mendelian Inheritance in Man (OMIM).
type: Article
publication name: Nucleic Acids Res.
creator: Amberger J, Bocchini CA, Scott AF, Hamosh A
date: 2009

tRNADB-CE: tRNA gene database curated manually by experts.
type: Article
publication name: Nucleic Acids Res.
creator: Abe T, Ikemura T, Ohara Y, Uehara H, Kinouchi M, Kanaya S, Yamada Y, Muto A, Inokuchi H
date: 2009

RAPID: Resource of Asian Primary Immunodeficiency Diseases.
type: Article
publication name: Nucleic Acids Res.
creator: 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
date: 2009

TMFunction: database for functional residues in membrane proteins.
type: Article
publication name: Nucleic Acids Res.
creator: Gromiha MM, Yabuki Y, Suresh MX, Thangakani AM, Suwa M, Fukui K
date: 2009

Distribution and effects of nonsense polymorphisms in human genes.
type: Article
publication name: PLoS ONE
creator: Yamaguchi-Kabata Y, Shimada MK, Hayakawa Y, Minoshima S, Chakraborty R, Gojobori T, Imanishi T
date: 2008

The Human Protein Atlas--a tool for pathology.
type: Article
publication name: J. Pathol.
creator: Pontén F, Jirström K, Uhlen M
date: 2008

BioCaster: detecting public health rumors with a Web-based text mining system.
type: Article
publication name: Bioinformatics
creator: Collier N, Doan S, Kawazoe A, Goodwin RM, Conway M, Tateno Y, Ngo QH, Dien D, Kawtrakul A, Takeuchi K, Shigematsu M, Taniguchi K
date: 2008

PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes.
type: Article
publication name: Nucleic Acids Res.
creator: Everett L, Vo A, Hannenhalli S
date: 2009

Human immunodeficiency virus type 1, human protein interaction database at NCBI.
type: Article
publication name: Nucleic Acids Res.
creator: Fu W, Sanders-Beer BE, Katz KS, Maglott DR, Pruitt KD, Ptak RG
date: 2009

DDBJ dealing with mass data produced by the second generation sequencer.
type: Article
publication name: Nucleic Acids Res.
creator: Sugawara H, Ikeo K, Fukuchi S, Gojobori T, Tateno Y
date: 2009

NCBI Reference Sequences: current status, policy and new initiatives.
type: Article
publication name: Nucleic Acids Res.
creator: Pruitt KD, Tatusova T, Klimke W, Maglott DR
date: 2009

Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library.
type: Article
publication name: DNA Res.
creator: 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
date: 2008

ProSeg: a database of local structures of protein segments.
type: Article
publication name: J. Comput. Aided Mol. Des.
creator: Sawada Y, Honda S
date: 2009

NCBI GEO: archive for high-throughput functional genomic data.
type: Article
publication name: Nucleic Acids Res.
creator: 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
date: 2009

STRING 8--a global view on proteins and their functional interactions in 630 organisms.
type: Article
publication name: Nucleic Acids Res.
creator: 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
date: 2009

PEDANT covers all complete RefSeq genomes.
type: Article
publication name: Nucleic Acids Res.
creator: 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
date: 2009

Database resources of the National Center for Biotechnology Information.
type: Article
publication name: Nucleic Acids Res.
creator: 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
date: 2009

The National Center for Biotechnology Information's Protein Clusters Database.
type: Article
publication name: Nucleic Acids Res.
creator: 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
date: 2009

The RNA WikiProject: community annotation of RNA families.
type: Article
publication name: RNA
creator: Daub J, Gardner PP, Tate J, Ramsköld D, Manske M, Scott WG, Weinberg Z, Griffiths-Jones S, Bateman A
date: 2008

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.
type: Article
publication name: Nucleic Acids Res.
creator: Mituyama T, Yamada K, Hattori E, Okida H, Ono Y, Terai G, Yoshizawa A, Komori T, Asai K
date: 2009

HGVbaseG2P: a central genetic association database.
type: Article
publication name: Nucleic Acids Res.
creator: Thorisson GA, Lancaster O, Free RC, Hastings RK, Sarmah P, Dash D, Brahmachari SK, Brookes AJ
date: 2009

PharmGKB: understanding the effects of individual genetic variants.
type: Article
publication name: Drug Metab. Rev.
creator: Sangkuhl K, Berlin DS, Altman RB, Klein TE
date: 2008

HMDB: a knowledgebase for the human metabolome.
type: Article
publication name: Nucleic Acids Res.
creator: 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
date: 2009

ATTED-II provides coexpressed gene networks for Arabidopsis.
type: Article
publication name: Nucleic Acids Res.
creator: Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K
date: 2009

Rfam: updates to the RNA families database.
type: Article
publication name: Nucleic Acids Res.
creator: Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A
date: 2009

Implementation of GenePattern within the Stanford Microarray Database.
type: Article
publication name: Nucleic Acids Res.
creator: Hubble J, Demeter J, Jin H, Mao M, Nitzberg M, Reddy TB, Wymore F, Zachariah ZK, Sherlock G, Ball CA
date: 2009

VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts.
type: Article
publication name: Nucleic Acids Res.
creator: Shimada MK, Matsumoto R, Hayakawa Y, Sanbonmatsu R, Gough C, Yamaguchi-Kabata Y, Yamasaki C, Imanishi T, Gojobori T
date: 2009

tRNAdb 2009: compilation of tRNA sequences and tRNA genes.
type: Article
publication name: Nucleic Acids Res.
creator: Jühling F, Mörl M, Hartmann RK, Sprinzl M, Stadler PF, Pütz J
date: 2009

The GOA database in 2009--an integrated Gene Ontology Annotation resource.
type: Article
publication name: Nucleic Acids Res.
creator: Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R
date: 2009

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences.
type: Article
publication name: Nucleic Acids Res.
creator: Portales-Casamar E, Arenillas D, Lim J, Swanson MI, Jiang S, McCallum A, Kirov S, Wasserman WW
date: 2009

dictyBase--a Dictyostelium bioinformatics resource update.
type: Article
publication name: Nucleic Acids Res.
creator: Fey P, Gaudet P, Curk T, Zupan B, Just EM, Basu S, Merchant SN, Bushmanova YA, Shaulsky G, Kibbe WA, Chisholm RL
date: 2009

Petabyte-scale innovations at the European Nucleotide Archive.
type: Article
publication name: Nucleic Acids Res.
creator: 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
date: 2009

SMART 6: recent updates and new developments.
type: Article
publication name: Nucleic Acids Res.
creator: Letunic I, Doerks T, Bork P
date: 2009

IMGT, the international ImMunoGeneTics information system.
type: Article
publication name: Nucleic Acids Res.
creator: 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
date: 2009

Minimotif miner 2nd release: a database and web system for motif search.
type: Article
publication name: Nucleic Acids Res.
creator: Rajasekaran S, Balla S, Gradie P, Gryk MR, Kadaveru K, Kundeti V, Maciejewski MW, Mi T, Rubino N, Vyas J, Schiller MR
date: 2009

Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes.
type: Article
publication name: Nucleic Acids Res.
creator: Winsor GL, Van Rossum T, Lo R, Khaira B, Whiteside MD, Hancock RE, Brinkman FS
date: 2009

VIPERdb2: an enhanced and web API enabled relational database for structural virology.
type: Article
publication name: Nucleic Acids Res.
creator: Carrillo-Tripp M, Shepherd CM, Borelli IA, Venkataraman S, Lander G, Natarajan P, Johnson JE, Brooks CL, Reddy VS
date: 2009

GtRNAdb: a database of transfer RNA genes detected in genomic sequence.
type: Article
publication name: Nucleic Acids Res.
creator: Chan PP, Lowe TM
date: 2009

BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009.
type: Article
publication name: Nucleic Acids Res.
creator: Chang A, Scheer M, Grote A, Schomburg I, Schomburg D
date: 2009

CDD: specific functional annotation with the Conserved Domain Database.
type: Article
publication name: Nucleic Acids Res.
creator: 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
date: 2009

Transterm: a database to aid the analysis of regulatory sequences in mRNAs.
type: Article
publication name: Nucleic Acids Res.
creator: Jacobs GH, Chen A, Stevens SG, Stockwell PA, Black MA, Tate WP, Brown CM
date: 2009

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

The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions.
type: Article
publication name: Nucleic Acids Res.
creator: Fukuchi S, Homma K, Sakamoto S, Sugawara H, Tateno Y, Gojobori T, Nishikawa K
date: 2009

Human Protein Reference Database--2009 update.
type: Article
publication name: Nucleic Acids Res.
creator: 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
date: 2009

PDBsum new things.
type: Article
publication name: Nucleic Acids Res.
creator: Laskowski RA
date: 2009

Changes in gene expression of commercial baker's yeast during an air-drying process that simulates dried yeast production.
type: Article
publication name: J. Biosci. Bioeng.
creator: Nakamura T, Mizukami-Murata S, Ando A, Murata Y, Takagi H, Shima J
date: 2008

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.
type: Article
publication name: Nucleic Acids Res.
creator: Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM
date: 2009

SpBase: the sea urchin genome database and web site.
type: Article
publication name: Nucleic Acids Res.
creator: Cameron RA, Samanta M, Yuan A, He D, Davidson E
date: 2009

AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse.
type: Article
publication name: Nucleic Acids Res.
creator: Shionyu M, Yamaguchi A, Shinoda K, Takahashi K, Go M
date: 2009

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.
type: Article
publication name: Nucleic Acids Res.
creator: 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
date: 2009

Cataloguing the HIV type 1 human protein interaction network.
type: Article
publication name: AIDS Res. Hum. Retroviruses
creator: Ptak RG, Fu W, Sanders-Beer BE, Dickerson JE, Pinney JW, Robertson DL, Rozanov MN, Katz KS, Maglott DR, Pruitt KD, Dieffenbach CW
date: 2008

Systematic NMR analysis of stable isotope labeled metabolite mixtures in plant and animal systems: coarse grained views of metabolic pathways.
type: Article
publication name: PLoS ONE
creator: Chikayama E, Suto M, Nishihara T, Shinozaki K, Hirayama T, Kikuchi J
date: 2008

PRIMe: a Web site that assembles tools for metabolomics and transcriptomics.
type: Article
publication name: In Silico Biol. (Gedrukt)
creator: Akiyama K, Chikayama E, Yuasa H, Shimada Y, Tohge T, Shinozaki K, Hirai MY, Sakurai T, Kikuchi J, Saito K
date: 2008

Human protein factory for converting the transcriptome into an in vitro-expressed proteome,.
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publication name: Nat. Methods
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Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics.
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DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins.
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publication name: Bioinformatics
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date: 2009

MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions.
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publication name: Bioinformatics
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date: 2009

Gclust: trans-kingdom classification of proteins using automatic individual threshold setting.
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publication name: Bioinformatics
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date: 2009

Analysis and validation of carbohydrate three-dimensional structures.
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Genome-wide validation of Magnaporthe grisea gene structures based on transcription evidence.
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International Gene Trap Project: towards gene-driven saturation mutagenesis in mice.
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Massive transcriptional start site analysis of human genes in hypoxia cells.
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Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins.
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HIV-host interactions: a map of viral perturbation of the host system.
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Searching the Mouse Genome Informatics (MGI) resources for information on mouse biology from genotype to phenotype.
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date: 2009

Data mining the PDB for glyco-related data.
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Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans.
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Newly discovered breast cancer susceptibility loci on 3p24 and 17q23.2.
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A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1).
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The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.
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The regulated retrotransposon transcriptome of mammalian cells.
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Tiny RNAs associated with transcription start sites in animals.
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PrognoScan: a new database for meta-analysis of the prognostic value of genes.
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Fast linear feature detection using multiple directional non-maximum suppression.
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Web API for biology with a workflow navigation system.
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Evaluation of haplotype inference using definitive haplotype data obtained from complete hydatidiform moles, and its significance for the analyses of positively selected regions.
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TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics.
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Unique inbred strain MSM/Ms established from the Japanese wild mouse.
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MIMAS 3.0 is a Multiomics Information Management and Annotation System.
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publication name: BMC Bioinformatics
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Evolution of pathogenicity and sexual reproduction in eight Candida genomes.
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PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning.
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Functional and evolutionary insights into human brain development through global transcriptome analysis.
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publication name: Neuron
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E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs.
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publication name: Bioinformatics
creator: Yamanishi Y, Hattori M, Kotera M, Goto S, Kanehisa M
date: 2009

From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations.
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Soybean proteome database: a data resource for plant differential omics.
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ChEBI: an open bioinformatics and cheminformatics resource.
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publication name: Curr Protoc Bioinformatics
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Gendoo: functional profiling of gene and disease features using MeSH vocabulary.
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The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.
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[Genome-wide association study of gastric cancer and GeMDBJ database].
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Agouti C57BL/6N embryonic stem cells for mouse genetic resources.
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Unlocking the secrets of the genome.
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date: 2009

Next-generation gene targeting in the mouse for functional genomics.
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Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans.
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date: 2009

The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.
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Annotating the human genome with Disease Ontology.
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date: 2009

Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis.
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Genome-wide association database developed in the Japanese Integrated Database Project.
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National BioResource Project-Rat and related activities.
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ArachnoServer: a database of protein toxins from spiders.
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publication name: BMC Genomics
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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.
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An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow.
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publication name: BMC Bioinformatics
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Computational overview of GPCR gene universe to support reverse chemical genomics study.
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QuickGO: a web-based tool for Gene Ontology searching.
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The Gene Wiki: community intelligence applied to human gene annotation.
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Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences.
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The completion of the Mammalian Gene Collection (MGC).
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Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression.
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The University of Minnesota Biocatalysis/Biodegradation Database: improving public access.
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Recode-2: new design, new search tools, and many more genes.
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Collection of Macaca fascicularis cDNAs derived from bone marrow, kidney, liver, pancreas, spleen, and thymus.
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publication name: BMC Res Notes
creator: Osada N, Hirata M, Tanuma R, Suzuki Y, Sugano S, Terao K, Kusuda J, Kameoka Y, Hashimoto K, Takahashi I
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SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.
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RESOPS: a database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures.
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New tools at the Candida Genome Database: biochemical pathways and full-text literature search.
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Non-susceptibility genes to Bombyx densovirus type 1, Nid-1 and nsd-1, affect distinct steps of the viral infection pathway.
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KAIKObase: an integrated silkworm genome database and data mining tool.
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date: 2009

G-compass: a web-based comparative genome browser between human and other vertebrate genomes.
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publication name: Bioinformatics
creator: Kawahara Y, Sakate R, Matsuya A, Murakami K, Sato Y, Zhang H, Gojobori T, Itoh T, Imanishi T
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REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.
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The IntAct molecular interaction database in 2010.
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DDBJ launches a new archive database with analytical tools for next-generation sequence data.
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SALAD database: a motif-based database of protein annotations for plant comparative genomics.
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The NCBI BioSystems database.
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Chemical Entities of Biological Interest: an update.
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PROSITE, a protein domain database for functional characterization and annotation.
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UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.
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PepX: a structural database of non-redundant protein-peptide complexes.
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CyanoBase: the cyanobacteria genome database update 2010.
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Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing.
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Genome-wide analysis of host gene expression in the silkworm cells infected with Bombyx mori nucleopolyhedrovirus.
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Ensembl Genomes: extending Ensembl across the taxonomic space.
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In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean.
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The immune epitope database 2.0.
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ChimerDB 2.0--a knowledgebase for fusion genes updated.
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The Proteomics Identifications database: 2010 update.
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MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.
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WormBase: a comprehensive resource for nematode research.
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DBTSS provides a tissue specific dynamic view of Transcription Start Sites.
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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.
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EuPathDB: a portal to eukaryotic pathogen databases.
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BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.
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LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors.
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publication name: Bioinformatics
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H-InvDB in 2009: extended database and data mining resources for human genes and transcripts.
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ACLAME: a CLAssification of Mobile genetic Elements, update 2010.
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The European Bioinformatics Institute's data resources.
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NCBI Peptidome: a new repository for mass spectrometry proteomics data.
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Monooxygenation of rifampicin catalyzed by the rox gene product of Nocardia farcinica: structure elucidation, gene identification and role in drug resistance.
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publication name: J. Antibiot.
creator: Hoshino Y, Fujii S, Shinonaga H, Arai K, Saito F, Fukai T, Satoh H, Miyazaki Y, Ishikawa J
date: 2010

SMPDB: The Small Molecule Pathway Database.
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publication name: Nucleic Acids Res.
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date: 2010

Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis.
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publication name: Microbiology (Reading, Engl.)
creator: Lammers CR, Flórez LA, Schmeisky AG, Roppel SF, Mäder U, Hamoen L, Stülke J
date: 2010

Archiving next generation sequencing data.
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publication name: Nucleic Acids Res.
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date: 2010

Planarians maintain a constant ratio of different cell types during changes in body size by using the stem cell system.
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publication name: Zool. Sci.
creator: Takeda H, Nishimura K, Agata K
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H-DBAS: human-transcriptome database for alternative splicing: update 2010.
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publication name: Nucleic Acids Res.
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date: 2010

Yellow-e determines the color pattern of larval head and tail spots of the silkworm Bombyx mori.
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publication name: J. Biol. Chem.
creator: Ito K, Katsuma S, Yamamoto K, Kadono-Okuda K, Mita K, Shimada T
date: 2010

AtMetExpress development: a phytochemical atlas of Arabidopsis development.
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publication name: Plant Physiol.
creator: Matsuda F, Hirai MY, Sasaki E, Akiyama K, Yonekura-Sakakibara K, Provart NJ, Sakurai T, Shimada Y, Saito K
date: 2010

A CD36-related transmembrane protein is coordinated with an intracellular lipid-binding protein in selective carotenoid transport for cocoon coloration.
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publication name: J. Biol. Chem.
creator: 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
date: 2010

Howdy, partner! How your practice can team up with hospitals to recruit physicians.
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publication name: MGMA Connex
creator: Miller P, Mosley K

A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58.
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publication name: Dev. Cell
creator: 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
date: 2009

Molecular characterization and functional analysis of novel carboxyl/cholinesterases with GQSAG motif in the silkworm Bombyx mori.
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publication name: Insect Biochem. Mol. Biol.
creator: Tsubota T, Shimomura M, Ogura T, Seino A, Nakakura T, Mita K, Shinoda T, Shiotsuki T
date: 2010

Expression profiling of novel bacteria-induced genes from the silkworm, Bombyx mori.
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publication name: Arch. Insect Biochem. Physiol.
creator: Tanaka H, Suzuki N, Nakajima Y, Sato M, Sagisaka A, Fujita K, Ishibashi J, Imanishi S, Mita K, Yamakawa M
date: 2010

Single-cell gene profiling of planarian stem cells using fluorescent activated cell sorting and its "index sorting" function for stem cell research.
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publication name: Dev. Growth Differ.
creator: Hayashi T, Shibata N, Okumura R, Kudome T, Nishimura O, Tarui H, Agata K
date: 2010

Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information.
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publication name: BMC Med Genomics
creator: Zhang Y, De S, Garner JR, Smith K, Wang SA, Becker KG
date: 2010

Profiling polar and semipolar plant metabolites throughout extraction processes using a combined solution-state and high-resolution magic angle spinning NMR approach.
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publication name: Anal. Chem.
creator: Sekiyama Y, Chikayama E, Kikuchi J
date: 2010

Cancer proteome-expression database: Genome Medicine Database of Japan Proteomics.
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publication name: Expert Rev Proteomics
creator: Kondo T
date: 2010

Identification and molecular characterization of a sex chromosome rearrangement causing a soft and pliable (spli) larval body phenotype in the silkworm, Bombyx mori.
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publication name: Genome
creator: Fujii T, Kuwazaki S, Yamamoto K, Abe H, Ohnuma A, Katsuma S, Mita K, Shimada T
date: 2010

Analysis of CASP8 targets, predictions and assessment methods.
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publication name: Database (Oxford)
creator: Shi S, Pei J, Sadreyev RI, Kinch LN, Majumdar I, Tong J, Cheng H, Kim BH, Grishin NV
date: 2009

The Homeodomain Resource: a comprehensive collection of sequence, structure, interaction, genomic and functional information on the homeodomain protein family.
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publication name: Database (Oxford)
creator: Moreland RT, Ryan JF, Pan C, Baxevanis AD
date: 2009

miRò: a miRNA knowledge base.
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publication name: Database (Oxford)
creator: Laganà A, Forte S, Giudice A, Arena MR, Puglisi PL, Giugno R, Pulvirenti A, Shasha D, Ferro A
date: 2009

Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs.
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publication name: Database (Oxford)
creator: Wissler L, Dattolo E, Moore AD, Reusch TB, Olsen JL, Migliaccio M, Bornberg-Bauer E, Procaccini G
date: 2009

The Prion Disease Database: a comprehensive transcriptome resource for systems biology research in prion diseases.
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publication name: Database (Oxford)
creator: Gehlenborg N, Hwang D, Lee IY, Yoo H, Baxter D, Petritis B, Pitstick R, Marzolf B, Dearmond SJ, Carlson GA, Hood L
date: 2009

A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki.
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publication name: Database (Oxford)
creator: Flórez LA, Roppel SF, Schmeisky AG, Lammers CR, Stülke J
date: 2009

SDOP-DB: a comparative standardized-protocol database for mouse phenotypic analyses.
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publication name: Bioinformatics
creator: 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
date: 2010

An atlas of combinatorial transcriptional regulation in mouse and man.
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publication name: Cell
creator: 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
date: 2010

Interaction networks as a tool to investigate the mechanisms of aging.
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publication name: Biogerontology
creator: Chautard E, Thierry-Mieg N, Ricard-Blum S
date: 2010

KMeyeDB: a graphical database of mutations in genes that cause eye diseases.
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publication name: Hum. Mutat.
creator: Kawamura T, Ohtsubo M, Mitsuyama S, Ohno-Nakamura S, Shimizu N, Minoshima S
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Performance of common genetic variants in breast-cancer risk models.
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publication name: N. Engl. J. Med.
creator: 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
date: 2010

CaMPDB: a resource for calpain and modulatory proteolysis.
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publication name: Genome Inform
creator: duVerle D, Takigawa I, Ono Y, Sorimachi H, Mamitsuka H
date: 2010

Cell migration that orients the dorsoventral axis is coordinated with anteroposterior patterning mediated by Hedgehog signaling in the early spider embryo.
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publication name: Development
creator: Akiyama-Oda Y, Oda H
date: 2010

Analysis of motor function modulated by cholinergic neurons in planarian Dugesia japonica.
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publication name: Neuroscience
creator: Nishimura K, Kitamura Y, Taniguchi T, Agata K
date: 2010

Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics.
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publication name: BMC Genomics
creator: 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
date: 2010

Myosin-dependent endoplasmic reticulum motility and F-actin organization in plant cells.
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publication name: Proc. Natl. Acad. Sci. U.S.A.
creator: Ueda H, Yokota E, Kutsuna N, Shimada T, Tamura K, Shimmen T, Hasezawa S, Dolja VV, Hara-Nishimura I
date: 2010

A full-length enriched cDNA library and expressed sequence tag analysis of the parasitic weed, Striga hermonthica.
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publication name: BMC Plant Biol.
creator: Yoshida S, Ishida JK, Kamal NM, Ali AM, Namba S, Shirasu K
date: 2010

Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases.
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publication name: DNA Res.
creator: Hijikata A, Raju R, Keerthikumar S, Ramabadran S, Balakrishnan L, Ramadoss SK, Pandey A, Mohan S, Ohara O
date: 2010

Bioinformatics and molecular modeling in glycobiology.
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publication name: Cell. Mol. Life Sci.
creator: Frank M, Schloissnig S
date: 2010

Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways.
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publication name: J. Plant Res.
creator: Obayashi T, Kinoshita K
date: 2010

Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.
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publication name: Proc. Natl. Acad. Sci. U.S.A.
creator: 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
date: 2010

Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms.
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publication name: BMC Genomics
creator: Yamamoto T, Nagasaki H, Yonemaru J, Ebana K, Nakajima M, Shibaya T, Yano M
date: 2010

CyanoClust: comparative genome resources of cyanobacteria and plastids.
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publication name: Database (Oxford)
creator: Sasaki NV, Sato N
date: 2010

TassDB2 - A comprehensive database of subtle alternative splicing events.
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publication name: BMC Bioinformatics
creator: 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
date: 2010

An interspecific linkage map of SSR and intronic polymorphism markers in tomato.
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publication name: Theor. Appl. Genet.
creator: 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
date: 2010

A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing.
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publication name: BMC Evol. Biol.
creator: Shimada MK, Hayakawa Y, Takeda J, Gojobori T, Imanishi T
date: 2010

PathPred: an enzyme-catalyzed metabolic pathway prediction server.
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publication name: Nucleic Acids Res.
creator: Moriya Y, Shigemizu D, Hattori M, Tokimatsu T, Kotera M, Goto S, Kanehisa M
date: 2010

Molecular evolution of lepidopteran silk proteins: insights from the ghost moth, Hepialus californicus.
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publication name: J. Mol. Evol.
creator: Collin MA, Mita K, Sehnal F, Hayashi CY
date: 2010

SIMCOMP/SUBCOMP: chemical structure search servers for network analyses.
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publication name: Nucleic Acids Res.
creator: Hattori M, Tanaka N, Kanehisa M, Goto S
date: 2010

AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome.
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publication name: Insect Mol. Biol.
creator: Legeai F, Shigenobu S, Gauthier JP, Colbourne J, Rispe C, Collin O, Richards S, Wilson AC, Murphy T, Tagu D
date: 2010

Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice.
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publication name: Plant J.
creator: Yan H, Kikuchi S, Neumann P, Zhang W, Wu Y, Chen F, Jiang J
date: 2010

Developmental atlas of the early first trimester human embryo.
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publication name: Dev. Dyn.
creator: Yamada S, Samtani RR, Lee ES, Lockett E, Uwabe C, Shiota K, Anderson SA, Lo CW
date: 2010

Genome-wide germline analyses on cancer susceptibility and GeMDBJ database: Gastric cancer as an example.
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publication name: Cancer Sci.
creator: Yoshida T, Ono H, Kuchiba A, Saeki N, Sakamoto H
date: 2010

Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants.
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publication name: Plant Physiol.
creator: 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
date: 2010

The landscape of C. elegans 3'UTRs.
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publication name: Science
creator: 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
date: 2010

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.
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publication name: Bioinformatics
creator: Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM
date: 2010

A definitive haplotype map as determined by genotyping duplicated haploid genomes finds a predominant haplotype preference at copy-number variation events.
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publication name: Am. J. Hum. Genet.
creator: Kukita Y, Yahara K, Tahira T, Higasa K, Sonoda M, Yamamoto K, Kato K, Wake N, Hayashi K
date: 2010

A mutation database for amyotrophic lateral sclerosis.
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publication name: Hum. Mutat.
creator: Yoshida M, Takahashi Y, Koike A, Fukuda Y, Goto J, Tsuji S
date: 2010

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.
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publication name: BMC Syst Biol
creator: 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
date: 2010

Extended morphological processing: a practical method for automatic spot detection of biological markers from microscopic images.
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publication name: BMC Bioinformatics
creator: Kimori Y, Baba N, Morone N
date: 2010

Orthopaedic literature and MeSH.
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publication name: Clin. Orthop. Relat. Res.
creator: Nelson SJ, Schulman JL
date: 2010

MassBank: a public repository for sharing mass spectral data for life sciences.
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publication name: J Mass Spectrom
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The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program.
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publication name: Genome Res.
creator: 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
date: 2010

Efficient plant gene identification based on interspecies mapping of full-length cDNAs.
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publication name: DNA Res.
creator: Amano N, Tanaka T, Numa H, Sakai H, Itoh T
date: 2010

GeneCards Version 3: the human gene integrator.
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publication name: Database (Oxford)
creator: 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
date: 2010

PmiRKB: a plant microRNA knowledge base.
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publication name: Nucleic Acids Res.
creator: Meng Y, Gou L, Chen D, Mao C, Jin Y, Wu P, Chen M
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The RINGS resource for glycome informatics analysis and data mining on the Web.
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publication name: OMICS
creator: Akune Y, Hosoda M, Kaiya S, Shinmachi D, Aoki-Kinoshita KF
date: 2010

Alternative splicing of genes during neuronal differentiation of NT2 pluripotential human embryonal carcinoma cells.
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publication name: FEBS Lett.
creator: Wakamatsu A, Imai J, Watanabe S, Isogai T
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MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis.
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publication name: Nucleic Acids Res.
creator: Gelly JC, Orgeur M, Jacq C, Lelandais G
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TRIP Database: a manually curated database of protein-protein interactions for mammalian TRP channels.
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publication name: Nucleic Acids Res.
creator: Shin YC, Shin SY, So I, Kwon D, Jeon JH
date: 2011

MatrixDB, the extracellular matrix interaction database.
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publication name: Nucleic Acids Res.
creator: Chautard E, Fatoux-Ardore M, Ballut L, Thierry-Mieg N, Ricard-Blum S
date: 2011

Biological databases at DNA Data Bank of Japan in the era of next-generation sequencing technologies.
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publication name: Adv. Exp. Med. Biol.
creator: Kodama Y, Kaminuma E, Saruhashi S, Ikeo K, Sugawara H, Tateno Y, Nakamura Y
date: 2010

DAnCER: disease-annotated chromatin epigenetics resource.
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publication name: Nucleic Acids Res.
creator: 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
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DDPC: Dragon Database of Genes associated with Prostate Cancer.
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publication name: Nucleic Acids Res.
creator: Maqungo M, Kaur M, Kwofie SK, Radovanovic A, Schaefer U, Schmeier S, Oppon E, Christoffels A, Bajic VB
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DBASS3 and DBASS5: databases of aberrant 3'- and 5'-splice sites.
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publication name: Nucleic Acids Res.
creator: Buratti E, Chivers M, Hwang G, Vorechovsky I
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TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea.
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publication name: Nucleic Acids Res.
creator: Shao Y, Harrison EM, Bi D, Tai C, He X, Ou HY, Rajakumar K, Deng Z
date: 2011

BSDB: the biomolecule stretching database.
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publication name: Nucleic Acids Res.
creator: Sikora M, Sulkowska JI, Witkowski BS, Cieplak M
date: 2011

Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes.
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publication name: Nucleic Acids Res.
creator: Winsor GL, Lam DK, Fleming L, Lo R, Whiteside MD, Yu NY, Hancock RE, Brinkman FS
date: 2011

ChemProt: a disease chemical biology database.
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publication name: Nucleic Acids Res.
creator: Taboureau O, Nielsen SK, Audouze K, Weinhold N, Edsgärd D, Roque FS, Kouskoumvekaki I, Bora A, Curpan R, Jensen TS, Brunak S, Oprea TI
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The Protein Ontology: a structured representation of protein forms and complexes.
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creator: 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
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The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish.
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publication name: Nucleic Acids Res.
creator: Lu J, Peatman E, Yang Q, Wang S, Hu Z, Reecy J, Kucuktas H, Liu Z
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EMDataBank.org: unified data resource for CryoEM.
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publication name: Nucleic Acids Res.
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The NIH Roadmap Epigenomics Mapping Consortium.
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publication name: Nat. Biotechnol.
creator: 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
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HitPredict: a database of quality assessed protein-protein interactions in nine species.
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publication name: Nucleic Acids Res.
creator: Patil A, Nakai K, Nakamura H
date: 2011

CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge.
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publication name: Nucleic Acids Res.
creator: Ahmed J, Meinel T, Dunkel M, Murgueitio MS, Adams R, Blasse C, Eckert A, Preissner S, Preissner R
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SuperSweet--a resource on natural and artificial sweetening agents.
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publication name: Nucleic Acids Res.
creator: Ahmed J, Preissner S, Dunkel M, Worth CL, Eckert A, Preissner R
date: 2011

The Pancreatic Expression database: 2011 update.
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publication name: Nucleic Acids Res.
creator: Cutts RJ, Gadaleta E, Hahn SA, Crnogorac-Jurcevic T, Lemoine NR, Chelala C
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FragmentStore--a comprehensive database of fragments linking metabolites, toxic molecules and drugs.
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publication name: Nucleic Acids Res.
creator: Ahmed J, Worth CL, Thaben P, Matzig C, Blasse C, Dunkel M, Preissner R
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NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data.
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publication name: Nucleic Acids Res.
creator: Hackenberg M, Barturen G, Oliver JL
date: 2011

Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics.
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publication name: Nucleic Acids Res.
creator: Fei Z, Joung JG, Tang X, Zheng Y, Huang M, Lee JM, McQuinn R, Tieman DM, Alba R, Klee HJ, Giovannoni JJ
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BriX: a database of protein building blocks for structural analysis, modeling and design.
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publication name: Nucleic Acids Res.
creator: Vanhee P, Verschueren E, Baeten L, Stricher F, Serrano L, Rousseau F, Schymkowitz J
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WebGeSTer DB--a transcription terminator database.
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publication name: Nucleic Acids Res.
creator: Mitra A, Kesarwani AK, Pal D, Nagaraja V
date: 2011

The Autophagy Database: an all-inclusive information resource on autophagy that provides nourishment for research.
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publication name: Nucleic Acids Res.
creator: Homma K, Suzuki K, Sugawara H
date: 2011

The European Nucleotide Archive.
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publication name: Nucleic Acids Res.
creator: 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
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AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species.
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publication name: Nucleic Acids Res.
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date: 2011

The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources.
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publication name: Nucleic Acids Res.
creator: Gremse M, Chang A, Schomburg I, Grote A, Scheer M, Ebeling C, Schomburg D
date: 2011

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0.
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publication name: Nucleic Acids Res.
creator: 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
date: 2011

ZFIN: enhancements and updates to the Zebrafish Model Organism Database.
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publication name: Nucleic Acids Res.
creator: 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
date: 2011

RBPDB: a database of RNA-binding specificities.
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publication name: Nucleic Acids Res.
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date: 2011

RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans.
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creator: Lee TY, Bo-Kai Hsu J, Chang WC, Huang HD
date: 2011

SNP discovery and linkage map construction in cultivated tomato.
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GPCRDB: information system for G protein-coupled receptors.
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publication name: Nucleic Acids Res.
creator: Vroling B, Sanders M, Baakman C, Borrmann A, Verhoeven S, Klomp J, Oliveira L, de Vlieg J, Vriend G
date: 2011

YPA: an integrated repository of promoter features in Saccharomyces cerevisiae.
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publication name: Nucleic Acids Res.
creator: Chang DT, Huang CY, Wu CY, Wu WS
date: 2011

GlycomeDB--a unified database for carbohydrate structures.
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publication name: Nucleic Acids Res.
creator: Ranzinger R, Herget S, von der Lieth CW, Frank M
date: 2011

ThYme: a database for thioester-active enzymes.
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publication name: Nucleic Acids Res.
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date: 2011

RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions.
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publication name: Nucleic Acids Res.
creator: Sato Y, Antonio BA, Namiki N, Takehisa H, Minami H, Kamatsuki K, Sugimoto K, Shimizu Y, Hirochika H, Nagamura Y
date: 2011

CADgene: a comprehensive database for coronary artery disease genes.
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publication name: Nucleic Acids Res.
creator: Liu H, Liu W, Liao Y, Cheng L, Liu Q, Ren X, Shi L, Tu X, Wang QK, Guo AY
date: 2011

CCDB: a curated database of genes involved in cervix cancer.
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publication name: Nucleic Acids Res.
creator: Agarwal SM, Raghav D, Singh H, Raghava GP
date: 2011

TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology.
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publication name: Nucleic Acids Res.
creator: Hong D, Park SS, Ju YS, Kim S, Shin JY, Kim S, Yu SB, Lee WC, Lee S, Park H, Kim JI, Seo JS
date: 2011

ODB: a database for operon organizations, 2011 update.
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publication name: Nucleic Acids Res.
creator: Okuda S, Yoshizawa AC
date: 2011

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.
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publication name: Nucleic Acids Res.
creator: 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
date: 2011

ASD: a comprehensive database of allosteric proteins and modulators.
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publication name: Nucleic Acids Res.
creator: 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
date: 2011

VnD: a structure-centric database of disease-related SNPs and drugs.
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publication name: Nucleic Acids Res.
creator: Yang JO, Oh S, Ko G, Park SJ, Kim WY, Lee B, Lee S
date: 2011

REPAIRtoire--a database of DNA repair pathways.
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publication name: Nucleic Acids Res.
creator: Milanowska K, Krwawicz J, Papaj G, Kosinski J, Poleszak K, Lesiak J, Osinska E, Rother K, Bujnicki JM
date: 2011

SAHG, a comprehensive database of predicted structures of all human proteins.
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publication name: Nucleic Acids Res.
creator: 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
date: 2011

The UCSC Cancer Genomics Browser: update 2011.
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publication name: Nucleic Acids Res.
creator: 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
date: 2011

Rfam: Wikipedia, clans and the "decimal" release.
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publication name: Nucleic Acids Res.
creator: Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A
date: 2011

The mouse Gene Expression Database (GXD): 2011 update.
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publication name: Nucleic Acids Res.
creator: Finger JH, Smith CM, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA, Richardson JE, Ringwald M
date: 2011

DDBJ progress report.
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creator: Kaminuma E, Kosuge T, Kodama Y, Aono H, Mashima J, Gojobori T, Sugawara H, Ogasawara O, Takagi T, Okubo K, Nakamura Y
date: 2011

The sequence read archive.
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publication name: Nucleic Acids Res.
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date: 2011

BRENDA, the enzyme information system in 2011.
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creator: Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Söhngen C, Stelzer M, Thiele J, Schomburg D
date: 2011

Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations.
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publication name: Nucleic Acids Res.
creator: Gonzalez-Galarza FF, Christmas S, Middleton D, Jones AR
date: 2011

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.
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publication name: Nucleic Acids Res.
creator: 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
date: 2011

Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera.
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publication name: Nucleic Acids Res.
creator: Munoz-Torres MC, Reese JT, Childers CP, Bennett AK, Sundaram JP, Childs KL, Anzola JM, Milshina N, Elsik CG
date: 2011

GenBank.
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publication name: Nucleic Acids Res.
creator: Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW
date: 2011

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments.
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publication name: Nucleic Acids Res.
creator: 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
date: 2011

miRTarBase: a database curates experimentally validated microRNA-target interactions.
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publication name: Nucleic Acids Res.
creator: 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
date: 2011

tRNADB-CE 2011: tRNA gene database curated manually by experts.
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publication name: Nucleic Acids Res.
creator: Abe T, Ikemura T, Sugahara J, Kanai A, Ohara Y, Uehara H, Kinouchi M, Kanaya S, Yamada Y, Muto A, Inokuchi H
date: 2011

Effective--a database of predicted secreted bacterial proteins.
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publication name: Nucleic Acids Res.
creator: Jehl MA, Arnold R, Rattei T
date: 2011

PCDDB: the Protein Circular Dichroism Data Bank, a repository for circular dichroism spectral and metadata.
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publication name: Nucleic Acids Res.
creator: Whitmore L, Woollett B, Miles AJ, Klose DP, Janes RW, Wallace BA
date: 2011

LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana.
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publication name: Nucleic Acids Res.
creator: Rastogi S, Rost B
date: 2011

AREsite: a database for the comprehensive investigation of AU-rich elements.
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date: 2011

NCBI Epigenomics: a new public resource for exploring epigenomic data sets.
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date: 2011

The RIKEN integrated database of mammals.
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date: 2011

Gramene database in 2010: updates and extensions.
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date: 2011

BISC: binary subcomplexes in proteins database.
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publication name: Nucleic Acids Res.
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date: 2011

dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa.
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creator: Gaudet P, Fey P, Basu S, Bushmanova YA, Dodson R, Sheppard KA, Just EM, Kibbe WA, Chisholm RL
date: 2011

Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome.
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publication name: BMC Genomics
creator: Reese JT, Childers CP, Sundaram JP, Dickens CM, Childs KL, Vile DC, Elsik CG
date: 2010

LSD: a leaf senescence database.
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publication name: Nucleic Acids Res.
creator: Liu X, Li Z, Jiang Z, Zhao Y, Peng J, Jin J, Guo H, Luo J
date: 2011

Identification of nocobactin NA biosynthetic gene clusters in Nocardia farcinica.
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creator: Hoshino Y, Chiba K, Ishino K, Fukai T, Igarashi Y, Yazawa K, Mikami Y, Ishikawa J
date: 2011

SPIKE: a database of highly curated human signaling pathways.
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creator: Paz A, Brownstein Z, Ber Y, Bialik S, David E, Sagir D, Ulitsky I, Elkon R, Kimchi A, Avraham KB, Shiloh Y, Shamir R
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FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system.
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creator: 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
date: 2011

KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data.
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publication name: Nucleic Acids Res.
creator: 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
date: 2011

EcoCyc: a comprehensive database of Escherichia coli biology.
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publication name: Nucleic Acids Res.
creator: 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
date: 2011

dbDNV: a resource of duplicated gene nucleotide variants in human genome.
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publication name: Nucleic Acids Res.
creator: Ho MR, Tsai KW, Chen CH, Lin WC
date: 2011

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.
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date: 2011

NCBI GEO: archive for functional genomics data sets--10 years on.
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date: 2011

CDD: a Conserved Domain Database for the functional annotation of proteins.
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publication name: Nucleic Acids Res.
creator: 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
date: 2011

lncRNAdb: a reference database for long noncoding RNAs.
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creator: Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS
date: 2011

PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes.
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date: 2011

Entrez Gene: gene-centered information at NCBI.
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The Plant Organelles Database 2 (PODB2): an updated resource containing movie data of plant organelle dynamics.
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date: 2011

Bovine Genome Database: integrated tools for genome annotation and discovery.
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date: 2011

iCOD: an integrated clinical omics database based on the systems-pathology view of disease.
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publication name: BMC Genomics
creator: Shimokawa K, Mogushi K, Shoji S, Hiraishi A, Ido K, Mizushima H, Tanaka H
date: 2010

GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle.
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publication name: Database (Oxford)
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Bacterial carbohydrate structure database 3: principles and realization.
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IsoBase: a database of functionally related proteins across PPI networks.
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TMPad: an integrated structural database for helix-packing folds in transmembrane proteins.
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OryzaExpress: an integrated database of gene expression networks and omics annotations in rice.
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publication name: Plant Cell Physiol.
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ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants.
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publication name: Plant Cell Physiol.
creator: Obayashi T, Nishida K, Kasahara K, Kinoshita K
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Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life.
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publication name: BMC Evol. Biol.
creator: Wissler L, Codoñer FM, Gu J, Reusch TB, Olsen JL, Procaccini G, Bornberg-Bauer E
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Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice.
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publication name: BMC Plant Biol.
creator: Sato Y, Antonio B, Namiki N, Motoyama R, Sugimoto K, Takehisa H, Minami H, Kamatsuki K, Kusaba M, Hirochika H, Nagamura Y
date: 2011

ARTADE2DB: improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses.
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publication name: Plant Cell Physiol.
creator: 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
date: 2011

Systematizing and cloning of genes involved in the cerebellar cortex circuit development.
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TOMATOMA: a novel tomato mutant database distributing Micro-Tom mutant collections.
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publication name: Plant Cell Physiol.
creator: Saito T, Ariizumi T, Okabe Y, Asamizu E, Hiwasa-Tanase K, Fukuda N, Mizoguchi T, Yamazaki Y, Aoki K, Ezura H
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Flybrain neuron database: a comprehensive database system of the Drosophila brain neurons.
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publication name: J. Comp. Neurol.
creator: Shinomiya K, Matsuda K, Oishi T, Otsuna H, Ito K
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The Mouse Tumor Biology Database (MTB): a central electronic resource for locating and integrating mouse tumor pathology data.
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publication name: Vet. Pathol.
creator: Begley DA, Krupke DM, Neuhauser SB, Richardson JE, Bult CJ, Eppig JT, Sundberg JP
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Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis.
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Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis.
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Classification and annotation of the relationship between protein structural change and ligand binding.
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Gene orders in the upstream of 16S rRNA genes divide genera of the family Halobacteriaceae into two groups.
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GRIPDB - G protein coupled Receptor Interaction Partners DataBase.
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publication name: J. Recept. Signal Transduct. Res.
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Fabry-database.org: database of the clinical phenotypes, genotypes and mutant α-galactosidase A structures in Fabry disease.
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The Rat Genome Database pathway portal.
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publication name: Database (Oxford)
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OryzaPG-DB: rice proteome database based on shotgun proteogenomics.
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Allie: a database and a search service of abbreviations and long forms.
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publication name: Database (Oxford)
creator: Yamamoto Y, Yamaguchi A, Bono H, Takagi T
date: 2011

Methods and strategies for gene structure curation in WormBase.
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publication name: Database (Oxford)
creator: Williams GW, Davis PA, Rogers AS, Bieri T, Ozersky P, Spieth J
date: 2011

The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video.
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publication name: Database (Oxford)
creator: Harper LC, Schaeffer ML, Thistle J, Gardiner JM, Andorf CM, Campbell DA, Cannon EK, Braun BL, Birkett SM, Lawrence CJ, Sen TZ
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Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases.
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On determining firing delay time of transitions for petri net based signaling pathways by introducing stochastic decision rules.
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Bacteroides stercorirosoris sp. nov. and Bacteroides faecichinchillae sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces.
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Lactobacillus nasuensis sp. nov., a lactic acid bacterium isolated from silage, and emended description of the genus Lactobacillus.
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Bacteroides sartorii is an earlier heterotypic synonym of Bacteroides chinchillae and has priority.
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The InterPro BioMart: federated query and web service access to the InterPro Resource.
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publication name: Database (Oxford)
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Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV.
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creator: Kawano S, Ono H, Takagi T, Bono H
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Development of a classification scheme for disease-related enzyme information.
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Enzymatic activity and protein interactions in alpha/beta hydrolase fold proteins: moonlighting versus promiscuity.
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Network-based analysis and characterization of adverse drug-drug interactions.
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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.
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The Sequence Read Archive: explosive growth of sequencing data.
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A potent inhibitor of SIK2, 3, 3', 7-trihydroxy-4'-methoxyflavon (4'-O-methylfisetin), promotes melanogenesis in B16F10 melanoma cells.
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The Histone Database: an integrated resource for histones and histone fold-containing proteins.
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Spatio-temporal transcriptome of the human brain.
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PomBase: a comprehensive online resource for fission yeast.
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Crystal structure of the predicted phospholipase LYPLAL1 reveals unexpected functional plasticity despite close relationship to acyl protein thioesterases.
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SMART 7: recent updates to the protein domain annotation resource.
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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.
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IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature.
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WormBase 2012: more genomes, more data, new website.
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The Gene Wiki in 2011: community intelligence applied to human gene annotation.
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PSCDB: a database for protein structural change upon ligand binding.
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PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits.
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MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.
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SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis.
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InterPro in 2011: new developments in the family and domain prediction database.
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The Gene Ontology: enhancements for 2011.
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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
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IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins.
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From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource.
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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.
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The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments.
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Saccharomyces Genome Database: the genomics resource of budding yeast.
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GeneSigDB: a manually curated database and resource for analysis of gene expression signatures.
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GeneDB--an annotation database for pathogens.
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INOH: ontology-based highly structured database of signal transduction pathways.
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NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy.
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OriDB, the DNA replication origin database updated and extended.
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The IntAct molecular interaction database in 2012.
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The UniProt-GO Annotation database in 2011.
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KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research.
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The Pfam protein families database.
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MMDB: 3D structures and macromolecular interactions.
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PoSSuM: a database of similar protein-ligand binding and putative pockets.
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NONCODE v3.0: integrative annotation of long noncoding RNAs.
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BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.
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RecountDB: a database of mapped and count corrected transcribed sequences.
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HGPD: Human Gene and Protein Database, 2012 update.
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Database resources of the National Center for Biotechnology Information.
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SNPedia: a wiki supporting personal genome annotation, interpretation and analysis.
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The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools.
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PubChem's BioAssay Database.
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GenBank.
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Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences.
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Mining the Gene Wiki for functional genomic knowledge.
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Database for crude drugs and Kampo medicine.
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Towards understanding how molecular networks evolve in plants.
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Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation.
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The androgen receptor gene mutations database: 2012 update.
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Genotypic and phenotypic characterization of lactic acid bacteria isolated from Italian ryegrass silage.
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Therapeutic chaperone effect of N-octyl 4-epi-β-valienamine on murine G(M1)-gangliosidosis.
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Ovarian Kaleidoscope database: ten years and beyond.
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The structure of the nervous system of the nematode Caenorhabditis elegans.
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Statistical organelle dissection of Arabidopsis guard cells using image database LIPS.
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IRView: a database and viewer for protein interacting regions.
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Protuboxepin A, a marine fungal metabolite, inducing metaphase arrest and chromosomal misalignment in tumor cells.
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The Rice Proteogenomics Database OryzaPG-DB: Development, Expansion, and New Features.
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GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
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TP Atlas: integration and dissemination of advances in Targeted Proteins Research Program (TPRP)-structural biology project phase II in Japan.
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CancerProView: a graphical image database of cancer-related genes and proteins.
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Soybean Proteome Database 2012: update on the comprehensive data repository for soybean proteomics.
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Infectious endogenous retroviruses in cats and emergence of recombinant viruses.
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Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome.
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The genome of melon (Cucumis melo L.).
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RIKEN tandem mass spectral database (ReSpect) for phytochemicals: a plant-specific MS/MS-based data resource and database.
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Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of Theileria-induced leukocyte transformation.
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Transcriptome tomography for brain analysis in the web-accessible anatomical space.
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TRIP database 2.0: a manually curated information hub for accessing TRP channel interaction network.
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The UCSC Cancer Genomics Browser: update 2013.
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Sagace: a web-based search engine for biomedical databases in Japan.
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MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.
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DaizuBase, an integrated soybean genome database including BAC-based physical maps.
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Virtual metagenome reconstruction from 16S rRNA gene sequences.
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Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR.
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An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values.
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WDDD: Worm Developmental Dynamics Database.
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creator: Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D
date: 1998

GDB: the Human Genome Database.
type: Article
publication name: Nucleic Acids Res.
creator: Letovsky SI, Cottingham RW, Porter CJ, Li PW
date: 1998

IXDB, an X chromosome integrated database.
type: Article
publication name: Nucleic Acids Res.
creator: Leser U, Wagner R, Grigoriev A, Lehrach H, Roest Crollius H
date: 1998

The tmRNA Website.
type: Article
publication name: Nucleic Acids Res.
creator: Williams KP, Bartel DP
date: 1998

The RNA modification database--1998.
type: Article
publication name: Nucleic Acids Res.
creator: McCloskey JA, Crain PF
date: 1998

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.
type: Article
publication name: Nucleic Acids Res.
creator: Cariello NF, Douglas GR, Gorelick NJ, Hart DW, Wilson JD, Soussi T
date: 1998

IARC Database of p53 gene mutations in human tumors and cell lines: updated compilation, revised formats and new visualisation tools.
type: Article
publication name: Nucleic Acids Res.
creator: Hainaut P, Hernandez T, Robinson A, Rodriguez-Tome P, Flores T, Hollstein M, Harris CC, Montesano R
date: 1998

The Androgen Receptor Gene Mutations Database.
type: Article
publication name: Nucleic Acids Res.
creator: Gottlieb B, Lehvaslaiho H, Beitel LK, Lumbroso R, Pinsky L, Trifiro M
date: 1998

The Human Collagen Mutation Database 1998.
type: Article
publication name: Nucleic Acids Res.
creator: Dalgleish R
date: 1998

The ProDom database of protein domain families.
type: Article
publication name: Nucleic Acids Res.
creator: Corpet F, Gouzy J, Kahn D
date: 1998

Current status of the SWISS-2DPAGE database.
type: Article
publication name: Nucleic Acids Res.
creator: Hoogland C, Sanchez JC, Tonella L, Bairoch A, Hochstrasser DF, Appel RD
date: 1998

The translational signal database, TransTerm, is now a relational database.
type: Article
publication name: Nucleic Acids Res.
creator: Dalphin ME, Brown CM, Stockwell PA, Tate WP
date: 1998

The Eukaryotic Promoter Database EPD.
type: Article
publication name: Nucleic Acids Res.
creator: Cavin Périer R, Junier T, Bucher P
date: 1998

PDBsum: a Web-based database of summaries and analyses of all PDB structures.
type: Article
publication name: Trends Biochem. Sci.
creator: Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM
date: 1997

FlyView, a Drosophila image database, and other Drosophila databases
type: Article
publication name: Semin. Cell Dev. Biol.
creator: Janning W
date: 1997

An on-line database for zebrafish development and genetics research
type: Article
publication name: Semin. Cell Dev. Biol.
creator: Westerfield M, Doerry E, Kirkpatrick AE, Driever W, Douglas SA
date: 1997

Rapid access to biomedical knowledge with GeneCards and HotMolecBase: implications for the electrophoretic analysis of large sets of gene products.
type: Article
publication name: Electrophoresis
creator: Rebhan M, Prilusky J
date: 1997

3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules.
type: Article
publication name: Bioinformatics
creator: An J, Nakama T, Kubota Y, Sarai A
date: 1998

TMIG-2DPAGE: a new concept of two-dimensional gel protein database for research on aging.
type: Article
publication name: Electrophoresis
creator: Toda T, Kaji K, Kimura N
date: 1998

Processing of vertebrate box C/D small nucleolar RNAs in plant cells.
type: Article
publication name: Eur. J. Biochem.
creator: Leader DJ, Clark GP, Boag J, Watters JA, Simpson CG, Watkins NJ, Maxwell ES, Brown JW
date: 1998

Small nucleolar RNAs and pre-rRNA processing in plants.
type: Article
publication name: Plant Cell
creator: Brown JW, Shaw PJ
date: 1998

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.
type: Article
publication name: FEBS Lett.
creator: Suckow JM, Amano N, Ohfuku Y, Kakinuma J, Koike H, Suzuki M
date: 1998

SMART, a simple modular architecture research tool: identification of signaling domains.
type: Article
publication name: Proc. Natl. Acad. Sci. U.S.A.
creator: Schultz J, Milpetz F, Bork P, Ponting CP
date: 1998

Complete nucleotide sequences of 93-kb and 3.3-kb plasmids of an enterohemorrhagic Escherichia coli O157:H7 derived from Sakai outbreak.
type: Article
publication name: DNA Res.
creator: 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
date: 1998

Localization and processing from a polycistronic precursor of novel snoRNAs in maize.
type: Article
publication name: J. Cell. Sci.
creator: Shaw PJ, Beven AF, Leader DJ, Brown JW
date: 1998

Repeats in genomic DNA: mining and meaning.
type: Article
publication name: Curr. Opin. Struct. Biol.
creator: Jurka J
date: 1998

The complete genome of Bacillus subtilis: from sequence annotation to data management and analysis.
type: Article
publication name: FEBS Lett.
creator: Moszer I
date: 1998

DBGET/LinkDB: an integrated database retrieval system.
type: Article
publication name: Pac Symp Biocomput
creator: Fujibuchi W, Goto S, Migimatsu H, Uchiyama I, Ogiwara A, Akiyama Y, Kanehisa M
date: 1998

A database of macromolecular motions.
type: Article
publication name: Nucleic Acids Res.
creator: Gerstein M, Krebs W
date: 1998

High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper.
type: Article
publication name: Plant J.
creator: Seki M, Carninci P, Nishiyama Y, Hayashizaki Y, Shinozaki K
date: 1998

GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support.
type: Article
publication name: Bioinformatics
creator: Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D
date: 1998

Extension of CyanoBase. CyanoMutants: repository of mutant information on Synechocystis sp. strain PCC6803.
type: Article
publication name: Nucleic Acids Res.
creator: Nakamura Y, Kaneko T, Miyajima N, Tabata S
date: 1999

IXDB, an X chromosome integrated database (update).
type: Article
publication name: Nucleic Acids Res.
creator: Leser U, Roest Crollius H, Lehrach H, Sudbrak R
date: 1999

The tmRNA website.
type: Article
publication name: Nucleic Acids Res.
creator: Williams KP
date: 1999

A new version of the RDP (Ribosomal Database Project).
type: Article
publication name: Nucleic Acids Res.
creator: 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
date: 1999

PEDB: the Prostate Expression Database.
type: Article
publication name: Nucleic Acids Res.
creator: Hawkins V, Doll D, Bumgarner R, Smith T, Abajian C, Hood L, Nelson PS
date: 1999

IMGT, the international ImMunoGeneTics database.
type: Article
publication name: Nucleic Acids Res.
creator: Lefranc MP, Giudicelli V, Ginestoux C, Bodmer J, Müller W, Bontrop R, Lemaitre M, Malik A, Barbié V, Chaume D
date: 1999

Recent improvements of the ProDom database of protein domain families.
type: Article
publication name: Nucleic Acids Res.
creator: Corpet F, Gouzy J, Kahn D
date: 1999

ProTherm: Thermodynamic Database for Proteins and Mutants.
type: Article
publication name: Nucleic Acids Res.
creator: Gromiha MM, An J, Kono H, Oobatake M, Uedaira H, Sarai A
date: 1999

The SWISS-2DPAGE database: what has changed during the last year.
type: Article
publication name: Nucleic Acids Res.
creator: Hoogland C, Sanchez JC, Tonella L, Bairoch A, Hochstrasser DF, Appel RD
date: 1999

Plant cis-acting regulatory DNA elements (PLACE) database: 1999.
type: Article
publication name: Nucleic Acids Res.
creator: Higo K, Ugawa Y, Iwamoto M, Korenaga T
date: 1999

The Eukaryotic Promoter Database (EPD): recent developments.
type: Article
publication name: Nucleic Acids Res.
creator: Périer RC, Junier T, Bonnard C, Bucher P
date: 1999

HUGE: a database for human large proteins identified by Kazusa cDNA sequencing project.
type: Article
publication name: Nucleic Acids Res.
creator: Suyama M, Nagase T, Ohara O
date: 1999

A database on cytogenetics in haematology and oncology.
type: Article
publication name: Nucleic Acids Res.
creator: Dorkeld F, Bernheim A, Dessen P, Huret JL
date: 1999

The Protein Mutant Database.
type: Article
publication name: Nucleic Acids Res.
creator: Kawabata T, Ota M, Nishikawa K
date: 1999

Keio Mutation Database for eye disease genes (KMeyeDB).
type: Article
publication name: Nucleic Acids Res.
creator: Minoshima S, Mitsuyama S, Ohno S, Kawamura T, Shimizu N
date: 1999

AAindex: Amino Acid Index Database.
type: Article
publication name: Nucleic Acids Res.
creator: Kawashima S, Ogata H, Kanehisa M
date: 1999

O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins.
type: Article
publication name: Nucleic Acids Res.
creator: Gupta R, Birch H, Rapacki K, Brunak S, Hansen JE
date: 1999

DOMO: a new database of aligned protein domains.
type: Article
publication name: Trends Biochem. Sci.
creator: Gracy J, Argos P
date: 1998

Zebrafish informatics and the ZFIN database.
type: Article
publication name: Methods Cell Biol.
creator: Westerfield M, Doerry E, Kirkpatrick AE, Douglas SA
date: 1999

The gene search system. A method for efficient detection and rapid molecular identification of genes in Drosophila melanogaster.
type: Article
publication name: Genetics
creator: Toba G, Ohsako T, Miyata N, Ohtsuka T, Seong KH, Aigaki T
date: 1999