-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
0034649566
-
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
-
Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
-
(2000)
Nature
, vol.408
, pp. 796-815
-
-
-
3
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
4
-
-
2542542256
-
Ultraconserved elements in the human genome
-
Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D (2004) Ultraconserved elements in the human genome. Science 304: 1321-1325
-
(2004)
Science
, vol.304
, pp. 1321-1325
-
-
Bejerano, G.1
Pheasant, M.2
Makunin, I.3
Stephen, S.4
Kent, W.J.5
Mattick, J.S.6
Haussler, D.7
-
5
-
-
3843089328
-
Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes
-
USA
-
Bonnet E, Wuyts J, Rouze P, Van de Peer Y (2004) Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci USA 101: 11511-11516
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 11511-11516
-
-
Bonnet, E.1
Wuyts, J.2
Rouze, P.3
Van De Peer, Y.4
-
6
-
-
27244448022
-
Databases and information integration for the Medicago truncatula genome and transcriptome
-
Cannon SB, Crow JA, Heuer ML, Wang X, Cannon EKS, Dwan C, Lamblin AF, Vasdewani J, Mudge J, Cook A, et al (2005) Databases and information integration for the Medicago truncatula genome and transcriptome. Plant Physiol 138: 38-46
-
(2005)
Plant Physiol
, vol.138
, pp. 38-46
-
-
Cannon, S.B.1
Crow, J.A.2
Heuer, M.L.3
Wang, X.4
Cannon, E.K.S.5
Dwan, C.6
Lamblin, A.F.7
Vasdewani, J.8
Mudge, J.9
Cook, A.10
-
7
-
-
0035984048
-
Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants
-
Fulton TM, Van der Hoeven R, Eannetta NT, Tanksley SD (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14: 1457-1467
-
(2002)
Plant Cell
, vol.14
, pp. 1457-1467
-
-
Fulton, T.M.1
Van Der Hoeven, R.2
Eannetta, N.T.3
Tanksley, S.D.4
-
8
-
-
0037023349
-
A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)
-
Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100
-
(2002)
Science
, vol.296
, pp. 92-100
-
-
Goff, S.A.1
Ricke, D.2
Lan, T.H.3
Presting, G.4
Wang, R.5
Dunn, M.6
Glazebrook, J.7
Sessions, A.8
Oeller, P.9
Varma, H.10
-
9
-
-
13444306676
-
CYGD: The Comprehensive Yeast Genome Database
-
Güldener U, Münsterkötter M, Kastenmüller G, Strack N, van Helden J, Lemer C, Richelles J, Wodak SJ, Garcia-Martínez J, Pérez-Ortín JE, et al (2005) CYGD: the Comprehensive Yeast Genome Database. Nucleic Acids Res (Database issue) 33: D364-D368
-
(2005)
Nucleic Acids Res (Database Issue)
, vol.33
-
-
Güldener, U.1
Münsterkötter, M.2
Kastenmüller, G.3
Strack, N.4
Van Helden, J.5
Lemer, C.6
Richelles, J.7
Wodak, S.J.8
Garcia-Martínez, J.9
Pérez-Ortín, J.E.10
-
10
-
-
16544393690
-
Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis
-
Haberer G, Hindemitt T, Meyers BC, Mayer KF (2004) Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis. Plant Physiol 136: 3009-3022
-
(2004)
Plant Physiol
, vol.136
, pp. 3009-3022
-
-
Haberer, G.1
Hindemitt, T.2
Meyers, B.C.3
Mayer, K.F.4
-
11
-
-
10644283823
-
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
-
International Chicken Genome Sequencing Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716
-
(2004)
Nature
, vol.432
, pp. 695-716
-
-
-
12
-
-
0037250392
-
MOsDB: An integrated information resource for rice genomics
-
Karlowski WM, Schoof H, Janakiraman V, Stuempflen V, Mayer KFX (2003) MOsDB: an integrated information resource for rice genomics. Nucleic Acids Res 31: 190-192
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 190-192
-
-
Karlowski, W.M.1
Schoof, H.2
Janakiraman, V.3
Stuempflen, V.4
Mayer, K.F.X.5
-
13
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
14
-
-
0348062817
-
MaizeGDB, the community database for maize genetics and genomics
-
Lawrence CJ, Dong Q, Polacco ML, Seigfried TE, Brendel V (2004) MaizeGDB, the community database for maize genetics and genomics. Nucleic Acids Res 32: 393-397
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 393-397
-
-
Lawrence, C.J.1
Dong, Q.2
Polacco, M.L.3
Seigfried, T.E.4
Brendel, V.5
-
15
-
-
0012306021
-
Apollo: A sequence annotation editor
-
RESEARCH0082
-
Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Ricter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, et al (2002) Apollo: a sequence annotation editor. Genome Biology 3: RESEARCH0082
-
(2002)
Genome Biology
, vol.3
-
-
Lewis, S.E.1
Searle, S.M.J.2
Harris, N.3
Gibson, M.4
Iyer, V.5
Ricter, J.6
Wiel, C.7
Bayraktaroglu, L.8
Birney, E.9
Crosby, M.A.10
-
16
-
-
0343621499
-
Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana
-
Mayer K, Schuller C, Wambutt R, Murphy G, Volckaert G, Pohl T, Dusterhoft A, Stiekema W, Entian KD, Terryn N, et al (1999) Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 402: 769-777
-
(1999)
Nature
, vol.402
, pp. 769-777
-
-
Mayer, K.1
Schuller, C.2
Wambutt, R.3
Murphy, G.4
Volckaert, G.5
Pohl, T.6
Dusterhoft, A.7
Stiekema, W.8
Entian, K.D.9
Terryn, N.10
-
17
-
-
5144226813
-
Sequence composition and genome organization of maize
-
USA
-
Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, Yu Y, Wei F, Fuks G, Soderlund CA, Mayer KF, et al (2004) Sequence composition and genome organization of maize. Proc Natl Acad Sci USA 101: 14349-14354
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 14349-14354
-
-
Messing, J.1
Bharti, A.K.2
Karlowski, W.M.3
Gundlach, H.4
Kim, H.R.5
Yu, Y.6
Wei, F.7
Fuks, G.8
Soderlund, C.A.9
Mayer, K.F.10
-
18
-
-
9144242935
-
MIPS: Analysis and annotation of proteins from whole genomes
-
Mewes HW, Amid C, Arnold R, Frishman D, Güldener U, Mannhaupt G, Münsterkötter M, Pagel P, Strack N, Stümpflen V, et al (2004) MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res 32: 41-44
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 41-44
-
-
Mewes, H.W.1
Amid, C.2
Arnold, R.3
Frishman, D.4
Güldener, U.5
Mannhaupt, G.6
Münsterkötter, M.7
Pagel, P.8
Strack, N.9
Stümpflen, V.10
-
19
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
-
20
-
-
10244255212
-
Taverna: A tool for the composition and enactment of bioinformatics workflows
-
Oinn T, Addis M, Ferris J, Marvin D, Greenwood M, Carver T, Pocock MR, Wipat A, Li P (2004) Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 20: 3045-3054
-
(2004)
Bioinformatics
, vol.20
, pp. 3045-3054
-
-
Oinn, T.1
Addis, M.2
Ferris, J.3
Marvin, D.4
Greenwood, M.5
Carver, T.6
Pocock, M.R.7
Wipat, A.8
Li, P.9
-
21
-
-
0346362490
-
Maize genome sequencing by methylation filtration
-
Palmer LE, Rabinowicz PD, O'Shaughnessy AL, Balija VS, Nascimento LU, Dike S, de la Bastide M, Martienssen RA, McCombie WR (2003) Maize genome sequencing by methylation filtration. Science 302: 2115-2117
-
(2003)
Science
, vol.302
, pp. 2115-2117
-
-
Palmer, L.E.1
Rabinowicz, P.D.2
O'Shaughnessy, A.L.3
Balija, V.S.4
Nascimento, L.U.5
Dike, S.6
De La Bastide, M.7
Martienssen, R.A.8
McCombie, W.R.9
-
22
-
-
0037440690
-
ATIDB: Arabidopsis thaliana insertion database
-
Pan X, Liu H, Clarke J, Jones J, Bevan M, Stein L (2003) ATIDB: Arabidopsis thaliana insertion database. Nucleic Acids Res 31: 1245-1251
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 1245-1251
-
-
Pan, X.1
Liu, H.2
Clarke, J.3
Jones, J.4
Bevan, M.5
Stein, L.6
-
23
-
-
1842684068
-
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
-
Rat Genome Sequencing Project Consortium (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493-521
-
(2004)
Nature
, vol.428
, pp. 493-521
-
-
-
24
-
-
0036645146
-
MicroRNAs in plants
-
Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16: 1616-1626
-
(2002)
Genes Dev
, vol.16
, pp. 1616-1626
-
-
Reinhart, B.J.1
Weinstein, E.G.2
Rhoades, M.W.3
Bartel, B.4
Bartel, D.P.5
-
25
-
-
0037249498
-
The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
-
Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, et al (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31: 224-228
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 224-228
-
-
Rhee, S.Y.1
Beavis, W.2
Berardini, T.Z.3
Chen, G.4
Dixon, D.5
Doyle, A.6
Garcia-Hernandez, M.7
Huala, E.8
Lander, G.9
Montoya, M.10
-
26
-
-
13444283829
-
The PEDANT genome database in 2005
-
Riley ML, Schmidt T, Wagner C, Mewes HW, Frishman D (2005) The PEDANT genome database in 2005. Nucleic Acids Res 33: D308-D310
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Riley, M.L.1
Schmidt, T.2
Wagner, C.3
Mewes, H.W.4
Frishman, D.5
-
27
-
-
13444283777
-
PlantMarkers: A database of predicted molecular markers from plants
-
Rudd S, Schoof H, Mayet KFX (2005) PlantMarkers: a database of predicted molecular markers from plants. Nucleic Acids Res 33: D628-D632
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Rudd, S.1
Schoof, H.2
Mayet, K.F.X.3
-
28
-
-
84959057192
-
EuGène: An eukaryotic gene finder that combines several sources of evidences
-
O Gascuel, M-F Sagot, eds, LNCS 2066. Springer-Verlag, Heidelberg
-
Schiex T, Moisan A, Rouzé P (2001) EuGène: an eukaryotic gene finder that combines several sources of evidences. In O Gascuel, M-F Sagot, eds, Computational Biology. LNCS 2066. Springer-Verlag, Heidelberg, pp 111-125
-
(2001)
Computational Biology
, pp. 111-125
-
-
Schiex, T.1
Moisan, A.2
Rouzé, P.3
-
29
-
-
0037621711
-
Towards interoperability in genome databases: The MAtDB (MIPS Arabidopsis thaliana database) experience
-
Schoof H (2003) Towards interoperability in genome databases: the MAtDB (MIPS Arabidopsis thaliana database) experience. Comp Funct Genomics 4: 255-258
-
(2003)
Comp Funct Genomics
, vol.4
, pp. 255-258
-
-
Schoof, H.1
-
30
-
-
2942586988
-
The PlaNet consortium: A network of European plant databases connecting plant genome data in an integrated biological knowledge resource
-
Schoof H, Ernst R, Mayer KFX (2004) The PlaNet consortium: a network of European plant databases connecting plant genome data in an integrated biological knowledge resource. Comp Funct Genomics 5: 184-189
-
(2004)
Comp Funct Genomics
, vol.5
, pp. 184-189
-
-
Schoof, H.1
Ernst, R.2
Mayer, K.F.X.3
-
31
-
-
0036084355
-
MIPS Arabidopsis thaliana Database (MAtDB): An integrated biological knowledge resource based on the first complete plant genome
-
Schoof H, Zaccaria P, Gundlach H, Lemcke K, Rudd S, Kolesov G, Arnold R, Mewes HW, Mayer KFX (2002) MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res 30: 91-93
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 91-93
-
-
Schoof, H.1
Zaccaria, P.2
Gundlach, H.3
Lemcke, K.4
Rudd, S.5
Kolesov, G.6
Arnold, R.7
Mewes, H.W.8
Mayer, K.F.X.9
-
32
-
-
0000731748
-
Summaries of legume genomics projects from around the globe: Community resources for crops and models
-
VandenBosch KA, Stacey G (2003) Summaries of legume genomics projects from around the globe: community resources for crops and models. Plant Physiol 131: 840-865
-
(2003)
Plant Physiol
, vol.131
, pp. 840-865
-
-
VandenBosch, K.A.1
Stacey, G.2
-
33
-
-
0036086991
-
Gramene: A resource for comparative grass genomics
-
Ware D, Jaiswal P, Ni J, Pan X, Chang K, Clark K, Teytelman L, Schmidt S, Zhao W, Cartinhour S, et al (2002) Gramene: a resource for comparative grass genomics. Nucleic Acids Res 30: 103-105
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 103-105
-
-
Ware, D.1
Jaiswal, P.2
Ni, J.3
Pan, X.4
Chang, K.5
Clark, K.6
Teytelman, L.7
Schmidt, S.8
Zhao, W.9
Cartinhour, S.10
-
34
-
-
0345731466
-
Enrichment of gene-coding sequences in maize by genome filtration
-
Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, Lee Y, Zheng L, van Heeringen S, Karamycheva S, Bennetzen JL, et al (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302: 2118-2120
-
(2003)
Science
, vol.302
, pp. 2118-2120
-
-
Whitelaw, C.A.1
Barbazuk, W.B.2
Pertea, G.3
Chan, A.P.4
Cheung, F.5
Lee, Y.6
Zheng, L.7
Van Heeringen, S.8
Karamycheva, S.9
Bennetzen, J.L.10
-
35
-
-
27244434525
-
BioMOBY successfully integrates distributed heterogeneous bioinformatics web services. The PlaNet exemplar case
-
Wilkinson MD, Schoof H, Ernst R, Haase D (2005) BioMOBY successfully integrates distributed heterogeneous bioinformatics web services. The PlaNet exemplar case. Plant Physiol 138: 5-17
-
(2005)
Plant Physiol
, vol.138
, pp. 5-17
-
-
Wilkinson, M.D.1
Schoof, H.2
Ernst, R.3
Haase, D.4
-
36
-
-
0037935183
-
BioMOBY: An open source biological web services proposal
-
Wilkinson MD, Links M (2002) BioMOBY: an open source biological web services proposal. Brief Bioinform 3: 331-341
-
(2002)
Brief Bioinform
, vol.3
, pp. 331-341
-
-
Wilkinson, M.D.1
Links, M.2
-
37
-
-
0038797803
-
Annotation of the Arabidopsis genome
-
Wortman JR, Haas BJ, Hannick LI, Smith RK Jr, Maiti R, Ronning CM, Chan AP, Yu C, Ayele M, Whitelaw CA, et al (2003) Annotation of the Arabidopsis genome. Plant Physiol 132: 461-468
-
(2003)
Plant Physiol
, vol.132
, pp. 461-468
-
-
Wortman, J.R.1
Haas, B.J.2
Hannick, L.I.3
Smith Jr., R.K.4
Maiti, R.5
Ronning, C.M.6
Chan, A.P.7
Yu, C.8
Ayele, M.9
Whitelaw, C.A.10
-
38
-
-
0346494833
-
The Rice PIPELINE: A unification tool for plant functional genomics
-
Yazaki J, Kojima K, Suzuki K, Kishimoto N, Kikuchi S (2004) The Rice PIPELINE: a unification tool for plant functional genomics. Nucleic Acids Res 32: 383-387
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 383-387
-
-
Yazaki, J.1
Kojima, K.2
Suzuki, K.3
Kishimoto, N.4
Kikuchi, S.5
|