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Species Resource name Author Title Journal Year published Volume Pages Pubmed ID
DNA  Thermus the...  Tomikawa C, Yokogawa T, Kanai T, Hori H.  N7-Methylguanine at position 46 (m7G46) in tRNA from Thermus thermophilus is required for cell viability at high temperatures through a tRNA modification network.  Nucleic Acids Res.  2010  38(3)  942-57  19934251  
Silkworm  カイコ  Yamazaki Y, Akashi R, Banno Y, Endo T, Ezura H, Fukami-Kobayashi K, Inaba K, Isa T, Kamei K, Kasai F, Kobayashi M, Kurata N, Kusaba M, Matuzawa T, Mitani S, Nakamura T, Nakamura Y, Nakatsuji N, Naruse K, Niki H, Nitasaka E, Obata Y, Okamoto H, Okuma M, Sato K, Serikawa T, Shiroishi T, Sugawara H, Urushibara H, Yamamoto M, Yaoita Y, Yoshiki A, Kohara Y.  NBRP databases: databases of biological resources in Japan.  Nucleic Acids Res.  2010  38(Database issue)  D26-32  19934255  
Information  NBRP-DB  Yamazaki Y, Akashi R, Banno Y, Endo T, Ezura H, Fukami-Kobayashi K, Inaba K, Isa T, Kamei K, Kasai F, Kobayashi M, Kurata N, Kusaba M, Matuzawa T, Mitani S, Nakamura T, Nakamura Y, Nakatsuji N, Naruse K, Niki H, Nitasaka E, Obata Y, Okamoto H, Okuma M, Sato K, Serikawa T, Shiroishi T, Sugawara H, Urushibara H, Yamamoto M, Yaoita Y, Yoshiki A, Kohara Y.  NBRP databases: databases of biological resources in Japan.  Nucleic Acids Res.  2010  38(Database issue)  D26-32  19934255  
Medaka  ?  Herpin A, Nakamura S, Wagner TU, Tanaka M, Schartl M.  A highly conserved cis-regulatory motif directs differential gonadal synexpression of Dmrt1 transcripts during gonad development.  Nucleic Acids Res.  2009  37(5)  1510-20  19139075  
Drosophila    Ida H, Suzusho N, Suyari O, Yoshida H, Ohno K, Hirose F, Itoh M, Yamaguchi M.  Genetic screening for modifiers of the DREF pathway in Drosophila melanogaster: identification and characterization of HP6 as a novel target of DREF.  Nucleic Acids Res.  2009  37(5)  1423-37  19136464  
E.coli  ME7986(MG16...  Nakashima N, Tamura T.  Conditional gene silencing of multiple genes with antisense RNAs and generation of a mutator strain of Escherichia coli.  Nucleic Acids Res.  2009  37(15)  e103  19515932  
C.elegans    Reece-Hoyes JS, Deplancke B, Barrasa MI, Hatzold J, Smit RB, Arda HE, Pope PA, Gaudet J, Conradt B, Walhout AJ.  The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors.  Nucleic Acids Res.  2009  37(11)  3689-98  19372275  
Information  nigfly  Schulz JG, David G, Hassan BA.  A novel method for tissue-specific RNAi rescue in Drosophila.  Nucleic Acids Res.  2009  37(13)  e93  19483100  
Mouse    Weidenfeld-Baranboim K, Hasin T, Darlyuk I, Heinrich R, Elhanani O, Pan J, Yokoyama KK, Aronheim A.  The ubiquitously expressed bZIP inhibitor, JDP2, suppresses the transcription of its homologue immediate early gene counterpart, ATF3.  Nucleic Acids Res.  2009  37(7)  2194-203  19233874  
General Microbes  JCM9630  Yoshinari S, Shiba T, Inaoka DK, Itoh T, Kurisu G, Harada S, Kita K, Watanabe Y.  Functional importance of crenarchaea-specific extra-loop revealed by an X-ray structure of a heterotetrameric crenarchaeal splicing endonuclease.  Nucleic Acids Res.  2009  37(14)  4787-98  19515941  
Medaka  database  Ahsan B, Kobayashi D, Yamada T, Kasahara M, Sasaki S, Saito TL, Nagayasu Y, Doi K, Nakatani Y, Qu W, Jindo T, Shimada A, Naruse K, Toyoda A, Kuroki Y, Fujiyama A, Sasaki T, Shimizu A, Asakawa S, Shimizu N, Hashimoto S, Yang J, Lee Y, Matsushima K, Sugano S, Sakaizumi M, Narita T, Ohishi K, Haga S, Ohta F, Nomoto H, Nogata K, Morishita T, Endo T, Shin-I T, Takeda H, Kohara Y, Morishita S.  UTGB/medaka: genomic resource database for medaka biology.  Nucleic Acids Res.  2008  36(Database issue)  D747-52  17932069  
Information  Rice  Avraham S, Tung CW, Ilic K, Jaiswal P, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Stevens P, Vincent L, Zapata F, Ware D.  The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.  Nucleic Acids Res.  2008  36(Database issue)  D449-54  18194960  
Information  Oryzabase  Galperin MY  The Molecular Biology Database Collection: 2008 update.  Nucleic Acids Res.  2008  36(Database issue)  D2-4  18025043  
Information  Rice  Larmande P, Gay C, Lorieux M, Périn C, Bouniol M, Droc G, Sallaud C, Perez P, Barnola I, Biderre-Petit C, Martin J, Morel JB, Johnson AA, Bourgis F, Ghesquière A, Ruiz M, Courtois B, Guiderdoni E.  Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library.  Nucleic Acids Res.  2008  36(Database issue)  D1022-7  17947330  
Information  NBRP  Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata.  Nucleic Acids Res.  2008  36(Database issue)  D475-9  17981842  
Lotus / Glycine    Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata.  Nucleic Acids Res.  2008  36(Database issue)  D475-9  17981842  
Information  Rice  Mano S, Miwa T, Nishikawa S, Mimura T, Nishimura M.  The plant organelles database (PODB): a collection of visualized plant organelles and protocols for plant organelle research.  Nucleic Acids Res.  2008  36(Database issue)  D929-37  17932059  
Information  C.elegans  Duverger Y, Belougne J, Scaglione S, Brandli D, Beclin C, Ewbank JJ.  A semi-automated high-throughput approach to the generation of transposon insertion mutants in the nematode Caenorhabditis elegans.  Nucleic Acids Res.  2007  35(2)  e11  17164286  
Silkworm    Maita N, Aoyagi H, Osanai M, Shirakawa M, Fujiwara H.  Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies.  Nucleic Acids Res.  2007  35(12)  3918-27  17537809  
Information  E.coli  Miyauchi K, Ohara T, Suzuki T.  Automated parallel isolation of multiple species of non-coding RNAs by the reciprocal circulating chromatography method.  Nucleic Acids Res.  2007  35(4)  e24  17251194  
E.coli  ASKA  Sunita S, Purta E, Durawa M, Tkaczuk KL, Swaathi J, Bujnicki JM, Sivaraman J.  Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC.  Nucleic Acids Res.  2007  35(13)  4264-74  17576679  
Information  E.coli  Watt RM, Wang J, Leong M, Kung HF, Cheah KS, Liu D, Danchin A, Huang JD.  Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes.  Nucleic Acids Res.  2007  35(6)  e37  17272300  
Information  E.coli  Yamamoto Y, Mori M, Aiba Y, Tomita T, Chen W, Zhou JM, Uehara A, Ren Y, Kitamura Y, Komiyama M.  Chemical modification of Ce(IV)/EDTA-based artificial restriction DNA cutter for versatile manipulation of double-stranded DNA.  Nucleic Acids Res.  2007  35(7)  e53  17376805  
Yeast  BY5209(FY83...  Kim YH, Ishikawa D, Ha HP, Sugiyama M, Kaneko Y, Harashima S.  Chromosome XII context is important for rDNA function in yeast.  Nucleic Acids Res.  2006  34(10)  2914-24  16738130  
Arabidopsis  pda  Nour-Eldin HH, Hansen BG, Norholm MH, Jensen JK, Halkier BA.  Advancing uracil-excision based cloning towards an ideal technique for cloning PCR fragments.  Nucleic Acids Res.  2006  34(18)  e122  17000637  
Information  Rice  Pankaj Jaiswal et al.  Gramene: a bird's eye view of cereal genomes  Nucleic Acids Res.  2006  34  D717-D723  16381966  
Silkworm    Tsukioka H, Takahashi M, Mon H, Okano K, Mita K, Shimada T, Lee JM, Kawaguchi Y, Koga K, Kusakabe T.  Role of the silkworm argonaute2 homolog gene in double-strand break repair of extrachromosomal DNA.  Nucleic Acids Res.  2006  34(4)  1092-101  16478716  
Silkworm    Anzai T., Osanai, M., Hamada, M. and Fujiwara, H.  Functional roles of 3'-terminal structures of template RNA during in vivo retrotransposition of non-LTR retrotransposon, R1Bm.  Nucleic Acids Res.  2005  33  1993-2002  15814816  
Information  E.coli  Jun Yao, Jin Zhong and Alan M. Lambowitz  Gene targeting using randomly inserted group II introns (targetrons) recovered from an Escherichia coli gene disruption library.  Nucleic Acids Res.  2005  33  3351-3362  15947133  
Information  E.coli, Rice  Michael Y. Galperin  The Molecular Biology Database Collection: 2005 update.  Nucleic Acids Res.  2005  33  D5-D24  15608247  
Wheat  CS  Ogihara Y, Yamazaki Y, Murai K, Kanno A, Terachi T, Shiina T, Miyashita N, Nasuda S, Nakamura C, Mori N, Takumi S, Murata M, Futo S, Tsunewaki K.  Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome.  Nucleic Acids Res.  2005  33(19)  6235-6250  16260473  
Silkworm    Prasad, M. D., Muthulakshmi,M., Madhu, M., Arunkumar, K.P., Sreenu, V. B., Pavithra, V., Bose, B., Nagarajaram, H. A., Mita, K., Shimada, T., and Nagaraju, J.  SilkSatDb: A microsatellite database of the silkworm, Bombyx mori.  Nucleic Acids Res.  2005  33  D403-406  15608226  
Information  Arabidopsis  Sakurai, T., M. Satou, K. Akiyama, et al.  RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome.  Nucleic Acids Res.  2005  33  D647-D650  15608280  
E.coli  ME8568(HB10...  Singh NS, Das G, Seshadri A, Sangeetha R, Varshney U.  Evidence for a role of initiation factor 3 in recycling of ribosomal complexes stalled on mRNAs in Escherichia coli.  Nucleic Acids Res.  2005  33(17)  5591-601  16199751  
E.coli  ?CV-25(DH5a...  Fujikawa N, Kurumizaka H, Nureki O, Tanaka Y, Yamazoe M, Hiraga S, Yokoyama S.  Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein.  Nucleic Acids Res.  2004  32(1)  82-92  14704346  
Silkworm    Fujimoto,H., Hirukawa,Y., Tani,H., Matsuura,Y., Hashido,K., Tsuchida,K., Takada,N., Kobayashi,M. and Maekawa,H.  Integration of the 5' end of the retrotransposon, R2Bm, can be complemented by homologous recombination.  Nucleic Acids Res.  2004  32  1555-1565  14999096  
Information  Rice  J. Yazaki et al.  The Rice PIPELINE: a unification tool for plant functional genomics.  Nucleic Acids Res.  2004  32  D383-D387  14681439  
Information  Rice, E.coli  Michael Y. Galperin  The Molecular Biology Database Collection: 2004 update.  Nucleic Acids Res.  2004  32  D3-D22  14681349  
Yeast  CD16-1,FY99...  Saito T. T., Tougan T., Kasama T., Okuzaki D. and Nojima H.  Mcp7, a meiosis-specific coiled-coil protein of fission yeast, associates with Meu13 and is required for meiotic recombination.  Nucleic Acids Res.  2004  32(11)  3325-3339  15210864  
Cellular slime molds    Singh SR, Rekha N, Pillai B, Singh V, Naorem A, Sampath V, Srinivasan N, Sadhale PP.  Domainal organization of the lower eukaryotic homologs of the yeast RNA polymerase II core subunit Rpb7 reflects functional conservation.  Nucleic Acids Res.  2004  32(1)  201-10  14704357  
Information  Rice  Andreas D. Baxevanis  The Molecular Biology Database Collection: 2003 update.  Nucleic Acids Res.  2003  31(1)  1-12  12519937  
Information  E.coli  Eduardo P., C. Rocha and Antoine Danchin.  Gene essentiality determines chromosome organization in bacteria.  Nucleic Acids Res.  2003  31(22)  6570-6577  14602916  
Cellular slime molds    Gojkovic Z, Rislund L, Andersen B, Sandrini MP, Cook PF, Schnackerz KD, Piskur J.  Dihydropyrimidine amidohydrolases and dihydroorotases share the same origin and several enzymatic properties.  Nucleic Acids Res.  2003  31(6)  1683-92  12626710  
Cellular slime molds    Inagaki Y, Blouin C, Susko E, Roger AJ.  Assessing functional divergence in EF-1alpha and its paralogs in eukaryotes and archaebacteria.  Nucleic Acids Res.  2003  31(14)  4227-37  12853641  
Information  Mouse  Andreas D. Baxevanis  The Moldcular Biology Database Collections: 2002 update.  Nucleic Acids Res.  2002  30(1)  1-12  11752241  
Information    K. Higasa and K. Hayashi,  Ordered catenation of sequence-tagged sites and multiplexed SNP genotyping by sequencing.  Nucleic Acids Res.  2002  30(3)  e11  11809899  
Information  E.coli  Takeshi Kawabata et al.  GTOP: a database of protein structures predicted from genome sequences.  Nucleic Acids Res.  2002  30  294-298  11752318  
Cellular slime molds    Inagaki Y, Doolittle WF.  Class I release factors in ciliates with variant genetic codes.  Nucleic Acids Res.  2001  29(4)  921-7  11160924  
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