-
1
-
-
0034649566
-
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
-
AGI 10.1038/35048692 11130711
-
AGI Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 2000, 408(6814):796-815. 10.1038/35048692 11130711
-
(2000)
Nature
, vol.408
, Issue.6814
, pp. 796-815
-
-
-
2
-
-
33748760611
-
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
-
16973872
-
Tuskan GA Difazio S Jansson S Bohlmann J Grigoriev I Hellsten U Putnam N Ralph S Rombauts S Salamov A Schein J Sterck L Aerts A Bhalerao RR Bhalerao RP Blaudez D Boerjan W Brun A Brunner A Busov V Campbell M Carlson J Chalot M Chapman J Chen GL Cooper D Coutinho PM Couturier J Covert S Cronk Q Cunningham R Davis J Degroeve S Dejardin A Depamphilis C Detter J Dirks B Dubchak I Duplessis S Ehlting J Ellis B Gendler K Goodstein D Gribskov M Grimwood J Groover A Gunter L Hamberger B Heinze B Helariutta Y Henrissat B Holligan D Holt R Huang W Islam-Faridi N Jones S Jones-Rhoades M Jorgensen R Joshi C Kangasjarvi J Karlsson J Kelleher C Kirkpatrick R Kirst M Kohler A Kalluri U Larimer F Leebens-Mack J Leple JC Locascio P Lou Y Lucas S Martin F Montanini B Napoli C Nelson DR Nelson C Nieminen K Nilsson O Pereda V Peter G Philippe R Pilate G Poliakov A Razumovskaya J Richardson P Rinaldi C Ritland K Rouze P Ryaboy D Schmutz J Schrader J Segerman B Shin H Siddiqui A Sterky F Terry A et al The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) Science (New York, NY) 2006, 313(5793): 1596-1604. 16973872
-
(2006)
Science (New York, NY)
, vol.313
, Issue.5793
, pp. 1596-1604
-
-
Tuskan, G.A.1
Difazio, S.2
Jansson, S.3
Bohlmann, J.4
Grigoriev, I.5
Hellsten, U.6
Putnam, N.7
Ralph, S.8
Rombauts, S.9
Salamov, A.10
Schein, J.11
Sterck, L.12
Aerts, A.13
Bhalerao, R.R.14
Bhalerao, R.P.15
Blaudez, D.16
Boerjan, W.17
Brun, A.18
Brunner, A.19
Busov, V.20
Campbell, M.21
Carlson, J.22
Chalot, M.23
Chapman, J.24
Chen, G.L.25
Cooper, D.26
Coutinho, P.M.27
Couturier, J.28
Covert, S.29
Cronk, Q.30
Cunningham, R.31
Davis, J.32
Degroeve, S.33
Dejardin, A.34
Depamphilis, C.35
Detter, J.36
Dirks, B.37
Dubchak, I.38
Duplessis, S.39
Ehlting, J.40
Ellis, B.41
Gendler, K.42
Goodstein, D.43
Gribskov, M.44
Grimwood, J.45
Groover, A.46
Gunter, L.47
Hamberger, B.48
Heinze, B.49
Helariutta, Y.50
Henrissat, B.51
Holligan, D.52
Holt, R.53
Huang, W.54
Islam-Faridi, N.55
Jones, S.56
Jones-Rhoades, M.57
Jorgensen, R.58
Joshi, C.59
Kangasjarvi, J.60
Karlsson, J.61
Kelleher, C.62
Kirkpatrick, R.63
Kirst, M.64
Kohler, A.65
Kalluri, U.66
Larimer, F.67
Leebens-Mack, J.68
Leple, J.C.69
Locascio, P.70
Lou, Y.71
Lucas, S.72
Martin, F.73
Montanini, B.74
Napoli, C.75
Nelson, D.R.76
Nelson, C.77
Nieminen, K.78
Nilsson, O.79
Pereda, V.80
Peter, G.81
Philippe, R.82
Pilate, G.83
Poliakov, A.84
Razumovskaya, J.85
Richardson, P.86
Rinaldi, C.87
Ritland, K.88
Rouze, P.89
Ryaboy, D.90
Schmutz, J.91
Schrader, J.92
Segerman, B.93
Shin, H.94
Siddiqui, A.95
Sterky, F.96
Terry, A.97
more..
-
3
-
-
34848886909
-
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
-
10.1038/nature06148 17721507
-
Jaillon O Aury JM Noel B Policriti A Clepet C Casagrande A Choisne N Aubourg S Vitulo N Jubin C Vezzi A Legeai F Hugueney P Dasilva C Horner D Mica E Jublot D Poulain J Bruyere C Billault A Segurens B Gouyvenoux M Ugarte E Cattonaro F Anthouard V Vico V Del Fabbro C Alaux M Di Gaspero G Dumas V Felice N Paillard S Juman I Moroldo M Scalabrin S Canaguier A Le Clainche I Malacrida G Durand E Pesole G Laucou V Chatelet P Merdinoglu D Delledonne M Pezzotti M Lecharny A Scarpelli C Artiguenave F Pe ME Valle G Morgante M Caboche M Adam-Blondon AF Weissenbach J Quetier F Wincker P The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Nature 2007, 449(7161):463-467. 10.1038/nature06148 17721507
-
(2007)
Nature
, vol.449
, Issue.7161
, pp. 463-467
-
-
Jaillon, O.1
Aury, J.M.2
Noel, B.3
Policriti, A.4
Clepet, C.5
Casagrande, A.6
Choisne, N.7
Aubourg, S.8
Vitulo, N.9
Jubin, C.10
Vezzi, A.11
Legeai, F.12
Hugueney, P.13
Dasilva, C.14
Horner, D.15
Mica, E.16
Jublot, D.17
Poulain, J.18
Bruyere, C.19
Billault, A.20
Segurens, B.21
Gouyvenoux, M.22
Ugarte, E.23
Cattonaro, F.24
Anthouard, V.25
Vico, V.26
Del Fabbro, C.27
Alaux, M.28
Di Gaspero, G.29
Dumas, V.30
Felice, N.31
Paillard, S.32
Juman, I.33
Moroldo, M.34
Scalabrin, S.35
Canaguier, A.36
Le Clainche, I.37
Malacrida, G.38
Durand, E.39
Pesole, G.40
Laucou, V.41
Chatelet, P.42
Merdinoglu, D.43
Delledonne, M.44
Pezzotti, M.45
Lecharny, A.46
Scarpelli, C.47
Artiguenave, F.48
Pe, M.E.49
Valle, G.50
Morgante, M.51
Caboche, M.52
Adam-Blondon, A.F.53
Weissenbach, J.54
Quetier, F.55
Wincker, P.56
more..
-
4
-
-
84907150192
-
The map-based sequence of the rice genome
-
IRGSP 10.1038/nature03895 16100779
-
IRGSP The map-based sequence of the rice genome Nature 2005, 436(7052):793-800. 10.1038/nature03895 16100779
-
(2005)
Nature
, vol.436
, Issue.7052
, pp. 793-800
-
-
-
6
-
-
3042692995
-
Beyond Arabidopsis. Translational biology meets evolutionary developmental biology
-
514096 15208409 10.1104/pp.104.041632
-
Irish VF Benfey PN Beyond Arabidopsis. Translational biology meets evolutionary developmental biology Plant physiology 2004, 135(2):611-614. 514096 15208409 10.1104/pp.104.041632
-
(2004)
Plant Physiology
, vol.135
, Issue.2
, pp. 611-614
-
-
Irish, V.F.1
Benfey, P.N.2
-
7
-
-
27644472372
-
Orthologs, paralogs, and evolutionary genomics
-
10.1146/annurev.genet.39.073003.114725 16285863
-
Koonin EV Orthologs, paralogs, and evolutionary genomics Annual review of genetics 2005, 39:309-338. 10.1146/annurev.genet.39.073003.114725 16285863
-
(2005)
Annual Review of Genetics
, vol.39
, pp. 309-338
-
-
Koonin, E.V.1
-
9
-
-
33646884846
-
DRTF: A database of rice transcription factors
-
10.1093/bioinformatics/btl107 16551659
-
Gao G Zhong Y Guo A Zhu Q Tang W Zheng W Gu X Wei L Luo J DRTF: A database of rice transcription factors Bioinformatics (Oxford, England) 2006, 22(10):1286-1287. 10.1093/bioinformatics/btl107 16551659
-
(2006)
Bioinformatics (Oxford, England)
, vol.22
, Issue.10
, pp. 1286-1287
-
-
Gao, G.1
Zhong, Y.2
Guo, A.3
Zhu, Q.4
Tang, W.5
Zheng, W.6
Gu, X.7
Wei, L.8
Luo, J.9
-
10
-
-
19544382556
-
DATF: A database of Arabidopsis transcription factors
-
10.1093/bioinformatics/bti334 15731212
-
Guo A He K Liu D Bai S Gu X Wei L Luo J DATF: A database of Arabidopsis transcription factors Bioinformatics (Oxford, England) 2005, 21(10):2568-2569. 10.1093/bioinformatics/bti334 15731212
-
(2005)
Bioinformatics (Oxford, England)
, vol.21
, Issue.10
, pp. 2568-2569
-
-
Guo, A.1
He, K.2
Liu, D.3
Bai, S.4
Gu, X.5
Wei, L.6
Luo, J.7
-
11
-
-
34247234601
-
The rice kinase database. A phylogenomic database for the rice kinome
-
1803753 17172291 10.1104/pp.106.087270
-
Dardick C Chen J Richter T Ouyang S Ronald P The rice kinase database. A phylogenomic database for the rice kinome Plant physiology 2007, 143(2):579-586. 1803753 17172291 10.1104/pp.106.087270
-
(2007)
Plant Physiology
, vol.143
, Issue.2
, pp. 579-586
-
-
Dardick, C.1
Chen, J.2
Richter, T.3
Ouyang, S.4
Ronald, P.5
-
14
-
-
13444256478
-
Inparanoid: A comprehensive database of eukaryotic orthologs
-
Database 540061 15608241
-
O'Brien KP Remm M Sonnhammer EL Inparanoid: A comprehensive database of eukaryotic orthologs Nucleic acids research 2005, 33(Database):D476-480. 540061 15608241
-
(2005)
Nucleic Acids Research
, vol.33
-
-
O'Brien, K.P.1
Remm, M.2
Sonnhammer, E.L.3
-
15
-
-
0141626909
-
Detecting putative orthologs
-
10.1093/bioinformatics/btg213 15593400
-
Wall DP Fraser HB Hirsh AE Detecting putative orthologs Bioinformatics (Oxford, England) 2003, 19(13):1710-1711. 10.1093/bioinformatics/btg213 15593400
-
(2003)
Bioinformatics (Oxford, England)
, vol.19
, Issue.13
, pp. 1710-1711
-
-
Wall, D.P.1
Fraser, H.B.2
Hirsh, A.E.3
-
16
-
-
0031976258
-
Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis
-
9521918
-
Eisen JA Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis Genome Res 1998, 8(3):163-167. 9521918
-
(1998)
Genome Res
, vol.8
, Issue.3
, pp. 163-167
-
-
Eisen, J.A.1
-
17
-
-
0038518196
-
Phylogenomics: Intersection of evolution and genomics
-
12805538
-
Eisen JA Fraser CM Phylogenomics: Intersection of evolution and genomics Science (New York, NY) 2003, 300(5626):1706-1707. 12805538
-
(2003)
Science (New York, NY)
, vol.300
, Issue.5626
, pp. 1706-1707
-
-
Eisen, J.A.1
Fraser, C.M.2
-
18
-
-
0013017592
-
RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
-
116988 12028595 10.1186/1471-2105-3-14
-
Zmasek CM Eddy SR RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs BMC Bioinformatics 2002, 3(1):14. 116988 12028595 10.1186/1471-2105-3-14
-
(2002)
BMC Bioinformatics
, vol.3
, Issue.1
, pp. 14
-
-
Zmasek, C.M.1
Eddy, S.R.2
-
19
-
-
37849023306
-
Assessing performance of orthology detection strategies applied to eukaryotic genomes
-
1849888 17440619 10.1371/journal.pone.0000383
-
Chen F Mackey AJ Vermunt JK Roos DS Assessing performance of orthology detection strategies applied to eukaryotic genomes PLoS ONE 2007, 2(4):e383. 1849888 17440619 10.1371/journal.pone.0000383
-
(2007)
PLoS ONE
, vol.2
, Issue.4
-
-
Chen, F.1
Mackey, A.J.2
Vermunt, J.K.3
Roos, D.S.4
-
20
-
-
33745022802
-
Benchmarking ortholog identification methods using functional genomics data
-
1557999 16613613 10.1186/gb-2006-7-4-r31
-
Hulsen T Huynen MA de Vlieg J Groenen PM Benchmarking ortholog identification methods using functional genomics data Genome biology 2006, 7(4):R31. 1557999 16613613 10.1186/gb-2006-7-4-r31
-
(2006)
Genome Biology
, vol.7
, Issue.4
-
-
Hulsen, T.1
Huynen, M.A.2
de Vlieg, J.3
Groenen, P.M.4
-
21
-
-
27244445968
-
Genome cluster database. A sequence family analysis platform for Arabidopsis and rice
-
1104159 15888677 10.1104/pp.104.059048
-
Horan K Lauricha J Bailey-Serres J Raikhel N Girke T Genome cluster database. A sequence family analysis platform for Arabidopsis and rice Plant physiology 2005, 138(1):47-54. 1104159 15888677 10.1104/ pp.104.059048
-
(2005)
Plant Physiology
, vol.138
, Issue.1
, pp. 47-54
-
-
Horan, K.1
Lauricha, J.2
Bailey-Serres, J.3
Raikhel, N.4
Girke, T.5
-
22
-
-
18844427708
-
Floral gene resources from basal angiosperms for comparative genomics research
-
1083416 15799777 10.1186/1471-2229-5-5
-
Albert VA Soltis DE Carlson JE Farmerie WG Wall PK Ilut DC Solow TM Mueller LA Landherr LL Hu Y Buzgo M Kim S Yoo MJ Frohlich MW Perl-Treves R Schlarbaum SE Bliss BJ Zhang X Tanksley SD Oppenheimer DG Soltis PS Ma H DePamphilis CW Leebens-Mack JH Floral gene resources from basal angiosperms for comparative genomics research BMC plant biology 2005, 5:5. 1083416 15799777 10.1186/1471-2229-5-5
-
(2005)
BMC Plant Biology
, vol.5
, pp. 5
-
-
Albert, V.A.1
Soltis, D.E.2
Carlson, J.E.3
Farmerie, W.G.4
Wall, P.K.5
Ilut, D.C.6
Solow, T.M.7
Mueller, L.A.8
Landherr, L.L.9
Hu, Y.10
Buzgo, M.11
Kim, S.12
Yoo, M.J.13
Frohlich, M.W.14
Perl-Treves, R.15
Schlarbaum, S.E.16
Bliss, B.J.17
Zhang, X.18
Tanksley, S.D.19
Oppenheimer, D.G.20
Soltis, P.S.21
Ma, H.22
DePamphilis, C.W.23
Leebens-Mack, J.H.24
more..
-
23
-
-
0011542799
-
The Pfam protein families database
-
99071 11752314 10.1093/nar/30.1.276
-
Bateman A Birney E Cerruti L Durbin R Etwiller L Eddy SR Griffiths-Jones S Howe KL Marshall M Sonnhammer EL The Pfam protein families database Nucleic acids research 2002, 30(1):276-280. 99071 11752314 10.1093/nar/ 30.1.276
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.1
, pp. 276-280
-
-
Bateman, A.1
Birney, E.2
Cerruti, L.3
Durbin, R.4
Etwiller, L.5
Eddy, S.R.6
Griffiths-Jones, S.7
Howe, K.L.8
Marshall, M.9
Sonnhammer, E.L.10
-
24
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
101833 11917018 10.1093/nar/30.7.1575
-
Enright AJ Van Dongen S Ouzounis CA An efficient algorithm for large-scale detection of protein families Nucleic acids research 2002, 30(7):1575-1584. 101833 11917018 10.1093/nar/30.7.1575
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.7
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
25
-
-
0043163718
-
Protein families and TRIBES in genome sequence space
-
169885 12888524 10.1093/nar/gkg495
-
Enright AJ Kunin V Ouzounis CA Protein families and TRIBES in genome sequence space Nucleic acids research 2003, 31(15):4632-4638. 169885 12888524 10.1093/nar/gkg495
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.15
, pp. 4632-4638
-
-
Enright, A.J.1
Kunin, V.2
Ouzounis, C.A.3
-
27
-
-
0037249498
-
The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
-
165523 12519987 10.1093/nar/gkg076
-
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 The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community Nucleic acids research 2003, 31(1):224-228. 165523 12519987 10.1093/nar/gkg076
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, 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
Miller, N.11
Mueller, L.A.12
Mundodi, S.13
Reiser, L.14
Tacklind, J.15
Weems, D.C.16
Wu, Y.17
Xu, I.18
Yoo, D.19
Yoon, J.20
Zhang, P.21
more..
-
28
-
-
13444282474
-
InterPro, progress and status in 2005
-
Database 540060 15608177
-
Mulder NJ Apweiler R Attwood TK Bairoch A Bateman A Binns D Bradley P Bork P Bucher P Cerutti L Copley R Courcelle E Das U Durbin R Fleischmann W Gough J Haft D Harte N Hulo N Kahn D Kanapin A Krestyaninova M Lonsdale D Lopez R Letunic I Madera M Maslen J McDowall J Mitchell A Nikolskaya AN Orchard S Pagni M Ponting CP Quevillon E Selengut J Sigrist CJ Silventoinen V Studholme DJ Vaughan R Wu CH InterPro, progress and status in 2005 Nucleic acids research 2005, 33(Database):D201-205. 540060 15608177
-
(2005)
Nucleic Acids Research
, vol.33
-
-
Mulder, N.J.1
Apweiler, R.2
Attwood, T.K.3
Bairoch, A.4
Bateman, A.5
Binns, D.6
Bradley, P.7
Bork, P.8
Bucher, P.9
Cerutti, L.10
Copley, R.11
Courcelle, E.12
Das, U.13
Durbin, R.14
Fleischmann, W.15
Gough, J.16
Haft, D.17
Harte, N.18
Hulo, N.19
Kahn, D.20
Kanapin, A.21
Krestyaninova, M.22
Lonsdale, D.23
Lopez, R.24
Letunic, I.25
Madera, M.26
Maslen, J.27
McDowall, J.28
Mitchell, A.29
Nikolskaya, A.N.30
Orchard, S.31
Pagni, M.32
Ponting, C.P.33
Quevillon, E.34
Selengut, J.35
Sigrist, C.J.36
Silventoinen, V.37
Studholme, D.J.38
Vaughan, R.39
Wu, C.H.40
more..
-
30
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
390337 15034147 10.1093/nar/gkh340
-
Edgar RC MUSCLE: Multiple sequence alignment with high accuracy and high throughput Nucleic acids research 2004, 32(5):1792-1797. 390337 15034147 10.1093/nar/gkh340
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
-
31
-
-
2542558960
-
LEON: Multiple aLignment Evaluation Of Neighbours
-
390283 14982955 10.1093/nar/gkh294
-
Thompson JD Prigent V Poch O LEON: Multiple aLignment Evaluation Of Neighbours Nucleic acids research 2004, 32(4):1298-1307. 390283 14982955 10.1093/nar/gkh294
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.4
, pp. 1298-1307
-
-
Thompson, J.D.1
Prigent, V.2
Poch, O.3
-
32
-
-
33644792802
-
Improvement in the accuracy of multiple sequence alignment program MAFFT
-
16362903
-
Katoh K Kuma K Miyata T Toh H Improvement in the accuracy of multiple sequence alignment program MAFFT Genome informatics 2005, 16(1):22-33. 16362903
-
(2005)
Genome Informatics
, vol.16
, Issue.1
, pp. 22-33
-
-
Katoh, K.1
Kuma, K.2
Miyata, T.3
Toh, H.4
-
33
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
548345 15661851 10.1093/nar/gki198
-
Katoh K Kuma K Toh H Miyata T MAFFT version 5: Improvement in accuracy of multiple sequence alignment Nucleic acids research 2005, 33(2):511-518. 548345 15661851 10.1093/nar/gki198
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.2
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
34
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
-
135756 12136088 10.1093/nar/gkf436
-
Katoh K Misawa K Kuma K Miyata T MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform Nucleic acids research 2002, 30(14):3059-3066. 135756 12136088 10.1093/nar/gkf436
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.14
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.3
Miyata, T.4
-
35
-
-
33750736013
-
The accuracy of several multiple sequence alignment programs for proteins
-
1633746 17062146 10.1186/1471-2105-7-471
-
Nuin PA Wang Z Tillier ER The accuracy of several multiple sequence alignment programs for proteins BMC Bioinformatics 2006, 7(1):471. 1633746 17062146 10.1186/1471-2105-7-471
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.1
, pp. 471
-
-
Nuin, P.A.1
Wang, Z.2
Tillier, E.R.3
-
36
-
-
0032988850
-
BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
-
10.1093/bioinformatics/15.1.87 10068696
-
Thompson JD Plewniak F Poch O BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs Bioinformatics (Oxford, England) 1999, 15(1):87-88. 10.1093/bioinformatics/15.1.87 10068696
-
(1999)
Bioinformatics (Oxford, England)
, vol.15
, Issue.1
, pp. 87-88
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
37
-
-
0038391401
-
RASCAL: Rapid scanning and correction of multiple sequence alignments
-
10.1093/bioinformatics/btg133 12801878
-
Thompson JD Thierry JC Poch O RASCAL: Rapid scanning and correction of multiple sequence alignments Bioinformatics (Oxford, England) 2003, 19(9):1155-1161. 10.1093/bioinformatics/btg133 12801878
-
(2003)
Bioinformatics (Oxford, England)
, vol.19
, Issue.9
, pp. 1155-1161
-
-
Thompson, J.D.1
Thierry, J.C.2
Poch, O.3
-
38
-
-
0034843597
-
AL2CO: Calculation of positional conservation in a protein sequence alignment
-
10.1093/bioinformatics/17.8.700 11524371
-
Pei J Grishin NV AL2CO: Calculation of positional conservation in a protein sequence alignment Bioinformatics (Oxford, England) 2001, 17(8):700-712. 10.1093/bioinformatics/17.8.700 11524371
-
(2001)
Bioinformatics (Oxford, England)
, vol.17
, Issue.8
, pp. 700-712
-
-
Pei, J.1
Grishin, N.V.2
-
39
-
-
0031743421
-
Profile hidden Markov models
-
10.1093/bioinformatics/14.9.755 9918945
-
Eddy SR Profile hidden Markov models Bioinformatics (Oxford, England) 1998, 14(9):755-763. 10.1093/bioinformatics/14.9.755 9918945
-
(1998)
Bioinformatics (Oxford, England)
, vol.14
, Issue.9
, pp. 755-763
-
-
Eddy, S.R.1
-
40
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
10.1080/10635150390235520 14530136
-
Guindon S Gascuel O A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 2003, 52(5):696-704. 10.1080/10635150390235520 14530136
-
(2003)
Syst Biol
, vol.52
, Issue.5
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
41
-
-
0034791426
-
A simple algorithm to infer gene duplication and speciation events on a gene tree
-
10.1093/bioinformatics/17.9.821 11590098
-
Zmasek CM Eddy SR A simple algorithm to infer gene duplication and speciation events on a gene tree Bioinformatics (Oxford, England) 2001, 17(9):821-828. 10.1093/bioinformatics/17.9.821 11590098
-
(2001)
Bioinformatics (Oxford, England)
, vol.17
, Issue.9
, pp. 821-828
-
-
Zmasek, C.M.1
Eddy, S.R.2
-
42
-
-
0035861990
-
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
-
10.1006/jmbi.2000.5197 11743721
-
Remm M Storm CE Sonnhammer EL Automatic clustering of orthologs and in-paralogs from pairwise species comparisons J Mol Biol 2001, 314(5):1041-1052. 10.1006/jmbi.2000.5197 11743721
-
(2001)
J Mol Biol
, vol.314
, Issue.5
, pp. 1041-1052
-
-
Remm, M.1
Storm, C.E.2
Sonnhammer, E.L.3
-
43
-
-
0034974688
-
Identification of a MADS-box gene, FLOWERING LOCUS M, that represses flowering
-
10.1046/j.1365-313x.2001.01024.x 11389763
-
Scortecci KC Michaels SD Amasino RM Identification of a MADS-box gene, FLOWERING LOCUS M, that represses flowering Plant J 2001, 26(2):229-236. 10.1046/j.1365-313x.2001.01024.x 11389763
-
(2001)
Plant J
, vol.26
, Issue.2
, pp. 229-236
-
-
Scortecci, K.C.1
Michaels, S.D.2
Amasino, R.M.3
-
44
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
222959 12969510 10.1186/1471-2105-4-41
-
Tatusov RL Fedorova ND Jackson JD Jacobs AR Kiryutin B Koonin EV Krylov DM Mazumder R Mekhedov SL Nikolskaya AN Rao BS Smirnov S Sverdlov AV Vasudevan S Wolf YI Yin JJ Natale DA The COG database: An updated version includes eukaryotes BMC Bioinformatics 2003, 4(1):41. 222959 12969510 10.1186/1471-2105-4-41
-
(2003)
BMC Bioinformatics
, vol.4
, Issue.1
, pp. 41
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Kiryutin, B.5
Koonin, E.V.6
Krylov, D.M.7
Mazumder, R.8
Mekhedov, S.L.9
Nikolskaya, A.N.10
Rao, B.S.11
Smirnov, S.12
Sverdlov, A.V.13
Vasudevan, S.14
Wolf, Y.I.15
Yin, J.J.16
Natale, D.A.17
-
45
-
-
2442659778
-
Incorrectly predicted genes in rice?
-
10.1016/j.gene.2004.02.039 15177695
-
Cruveiller S Jabbari K Clay O Bernardi G Incorrectly predicted genes in rice? Gene 2004, 333:187-188. 10.1016/j.gene.2004.02.039 15177695
-
(2004)
Gene
, vol.333
, pp. 187-188
-
-
Cruveiller, S.1
Jabbari, K.2
Clay, O.3
Bernardi, G.4
-
47
-
-
0033635895
-
Effects of sequence alignment and structural domains of ribosomal DNA on phylogeny reconstruction for the protozoan family sarcocystidae
-
11110900
-
Mugridge NB Morrison DA Jakel T Heckeroth AR Tenter AM Johnson AM Effects of sequence alignment and structural domains of ribosomal DNA on phylogeny reconstruction for the protozoan family sarcocystidae Molecular biology and evolution 2000, 17(12):1842-1853. 11110900
-
(2000)
Molecular Biology and Evolution
, vol.17
, Issue.12
, pp. 1842-1853
-
-
Mugridge, N.B.1
Morrison, D.A.2
Jakel, T.3
Heckeroth, A.R.4
Tenter, A.M.5
Johnson, A.M.6
-
50
-
-
0034791551
-
Evolutionary HMMs: A Bayesian approach to multiple alignment
-
10.1093/bioinformatics/17.9.803 11590097
-
Holmes I Bruno WJ Evolutionary HMMs: A Bayesian approach to multiple alignment Bioinformatics (Oxford, England) 2001, 17(9):803-820. 10.1093/ bioinformatics/17.9.803 11590097
-
(2001)
Bioinformatics (Oxford, England)
, vol.17
, Issue.9
, pp. 803-820
-
-
Holmes, I.1
Bruno, W.J.2
-
51
-
-
33645310990
-
Protein molecular function prediction by Bayesian phylogenomics
-
1246806 16217548 10.1371/journal.pcbi.0010045
-
Engelhardt BE Jordan MI Muratore KE Brenner SE Protein molecular function prediction by Bayesian phylogenomics PLoS computational biology 2005, 1(5):e45. 1246806 16217548 10.1371/journal.pcbi.0010045
-
(2005)
PLoS Computational Biology
, vol.1
, Issue.5
-
-
Engelhardt, B.E.1
Jordan, M.I.2
Muratore, K.E.3
Brenner, S.E.4
-
53
-
-
0037023384
-
A draft sequence of the rice genome (Oryza sativa L. ssp. indica)
-
11935017
-
Yu J Hu S Wang J Wong GK Li S Liu B Deng Y Dai L Zhou Y Zhang X Cao M Liu J Sun J Tang J Chen Y Huang X Lin W Ye C Tong W Cong L Geng J Han Y Li L Li W Hu G Huang X Li W Li J Liu Z Li L Liu J Qi Q Liu J Li L Li T Wang X Lu H Wu T Zhu M Ni P Han H Dong W Ren X Feng X Cui P Li X Wang H Xu X Zhai W Xu Z Zhang J He S Zhang J Xu J Zhang K Zheng X Dong J Zeng W Tao L Ye J Tan J Ren X Chen X He J Liu D Tian W Tian C Xia H Bao Q Li G Gao H Cao T Wang J Zhao W Li P Chen W Wang X Zhang Y Hu J Wang J Liu S Yang J Zhang G Xiong Y Li Z Mao L Zhou C Zhu Z Chen R Hao B Zheng W Chen S Guo W Li G Liu S Tao M Wang J Zhu L Yuan L Yang H A draft sequence of the rice genome (Oryza sativa L. ssp. indica) Science (New York, NY) 2002, 296(5565):79-92. 11935017
-
(2002)
Science (New York, NY)
, vol.296
, Issue.5565
, pp. 79-92
-
-
Yu, J.1
Hu, S.2
Wang, J.3
Wong, G.K.4
Li, S.5
Liu, B.6
Deng, Y.7
Dai, L.8
Zhou, Y.9
Zhang, X.10
Cao, M.11
Liu, J.12
Sun, J.13
Tang, J.14
Chen, Y.15
Huang, X.16
Lin, W.17
Ye, C.18
Tong, W.19
Cong, L.20
Geng, J.21
Han, Y.22
Li, L.23
Li, W.24
Hu, G.25
Huang, X.26
Li, W.27
Li, J.28
Liu, Z.29
Li, L.30
Liu, J.31
Qi, Q.32
Liu, J.33
Li, L.34
Li, T.35
Wang, X.36
Lu, H.37
Wu, T.38
Zhu, M.39
Ni, P.40
Han, H.41
Dong, W.42
Ren, X.43
Feng, X.44
Cui, P.45
Li, X.46
Wang, H.47
Xu, X.48
Zhai, W.49
Xu, Z.50
Zhang, J.51
He, S.52
Zhang, J.53
Xu, J.54
Zhang, K.55
Zheng, X.56
Dong, J.57
Zeng, W.58
Tao, L.59
Ye, J.60
Tan, J.61
Ren, X.62
Chen, X.63
He, J.64
Liu, D.65
Tian, W.66
Tian, C.67
Xia, H.68
Bao, Q.69
Li, G.70
Gao, H.71
Cao, T.72
Wang, J.73
Zhao, W.74
Li, P.75
Chen, W.76
Wang, X.77
Zhang, Y.78
Hu, J.79
Wang, J.80
Liu, S.81
Yang, J.82
Zhang, G.83
Xiong, Y.84
Li, Z.85
Mao, L.86
Zhou, C.87
Zhu, Z.88
Chen, R.89
Hao, B.90
Zheng, W.91
Chen, S.92
Guo, W.93
Li, G.94
Liu, S.95
Tao, M.96
Wang, J.97
Zhu, L.98
Yuan, L.99
Yang, H.100
more..
-
54
-
-
20144366003
-
The Genomes of Oryza sativa: A history of duplications
-
546038 15685292 10.1371/journal.pbio.0030038
-
Yu J Wang J Lin W Li S Li H Zhou J Ni P Dong W Hu S Zeng C Zhang J Zhang Y Li R Xu Z Li S Li X Zheng H Cong L Lin L Yin J Geng J Li G Shi J Liu J Lv H Li J Wang J Deng Y Ran L Shi X Wang X Wu Q Li C Ren X Wang J Wang X Li D Liu D Zhang X Ji Z Zhao W Sun Y Zhang Z Bao J Han Y Dong L Ji J Chen P Wu S Liu J Xiao Y Bu D Tan J Yang L Ye C Zhang J Xu J Zhou Y Yu Y Zhang B Zhuang S Wei H Liu B Lei M Yu H Li Y Xu H Wei S He X Fang L Zhang Z Zhang Y Huang X Su Z Tong W Li J Tong Z Li S Ye J Wang L Fang L Lei T Chen C Chen H Xu Z Li H Huang H Zhang F Xu H Li N Zhao C Li S Dong L Huang Y Li L Xi Y Qi Q Li W Zhang B Hu W Zhang Y Tian X Jiao Y Liang X Jin J Gao L Zheng W Hao B Liu S Wang W Yuan L Cao M McDermott J Samudrala R Wang J Wong GK Yang H The Genomes of Oryza sativa: A history of duplications PLoS biology 2005, 3(2):e38. 546038 15685292 10.1371/ journal.pbio.0030038
-
(2005)
PLoS Biology
, vol.3
, Issue.2
-
-
Yu, J.1
Wang, J.2
Lin, W.3
Li, S.4
Li, H.5
Zhou, J.6
Ni, P.7
Dong, W.8
Hu, S.9
Zeng, C.10
Zhang, J.11
Zhang, Y.12
Li, R.13
Xu, Z.14
Li, S.15
Li, X.16
Zheng, H.17
Cong, L.18
Lin, L.19
Yin, J.20
Geng, J.21
Li, G.22
Shi, J.23
Liu, J.24
Lv, H.25
Li, J.26
Wang, J.27
Deng, Y.28
Ran, L.29
Shi, X.30
Wang, X.31
Wu, Q.32
Li, C.33
Ren, X.34
Wang, J.35
Wang, X.36
Li, D.37
Liu, D.38
Zhang, X.39
Ji, Z.40
Zhao, W.41
Sun, Y.42
Zhang, Z.43
Bao, J.44
Han, Y.45
Dong, L.46
Ji, J.47
Chen, P.48
Wu, S.49
Liu, J.50
Xiao, Y.51
Bu, D.52
Tan, J.53
Yang, L.54
Ye, C.55
Zhang, J.56
Xu, J.57
Zhou, Y.58
Yu, Y.59
Zhang, B.60
Zhuang, S.61
Wei, H.62
Liu, B.63
Lei, M.64
Yu, H.65
Li, Y.66
Xu, H.67
Wei, S.68
He, X.69
Fang, L.70
Zhang, Z.71
Zhang, Y.72
Huang, X.73
Su, Z.74
Tong, W.75
Li, J.76
Tong, Z.77
Li, S.78
Ye, J.79
Wang, L.80
Fang, L.81
Lei, T.82
Chen, C.83
Chen, H.84
Xu, Z.85
Li, H.86
Huang, H.87
Zhang, F.88
Xu, H.89
Li, N.90
Zhao, C.91
Li, S.92
Dong, L.93
Huang, Y.94
Li, L.95
Xi, Y.96
Qi, Q.97
Li, W.98
Zhang, B.99
Hu, W.100
Zhang, Y.101
Tian, X.102
Jiao, Y.103
Liang, X.104
Jin, J.105
Gao, L.106
Zheng, W.107
Hao, B.108
Liu, S.109
Wang, W.110
Yuan, L.111
Cao, M.112
McDermott, J.113
Samudrala, R.114
Wang, J.115
Wong, G.K.116
Yang, H.117
more..
-
55
-
-
43549097999
-
-
Ftp site for TAIR Arabidopsis thaliana genome annotations ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/
-
Ftp site for TAIR Arabidopsis thaliana genome annotations ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/
-
-
-
-
56
-
-
43549120203
-
-
Ftp site for TIGR Oryza sativa genome annotations ftp://ftp.tigr.org/pub/ data/EukaryoticΡojects/o_sativa/annotation_las/pseudomolecules/ version_4.0
-
Ftp site for TIGR Oryza sativa genome annotations ftp://ftp.tigr.org/pub/ data/EukaryoticΡojects/o_sativa/annotation_las/pseudomolecules/ version_4.0
-
-
-
-
60
-
-
0033638015
-
CAST: An iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts
-
10.1093/bioinformatics/16.10.915 11120681
-
Promponas VJ Enright AJ Tsoka S Kreil DP Leroy C Hamodrakas S Sander C Ouzounis CA CAST: An iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts Bioinformatics (Oxford, England) 2000, 16(10):915-922. 10.1093/bioinformatics/16.10.915 11120681
-
(2000)
Bioinformatics (Oxford, England)
, vol.16
, Issue.10
, pp. 915-922
-
-
Promponas, V.J.1
Enright, A.J.2
Tsoka, S.3
Kreil, D.P.4
Leroy, C.5
Hamodrakas, S.6
Sander, C.7
Ouzounis, C.A.8
-
61
-
-
0035025126
-
ATV: Display and manipulation of annotated phylogenetic trees
-
10.1093/bioinformatics/17.4.383 11301314
-
Zmasek CM Eddy SR ATV: Display and manipulation of annotated phylogenetic trees Bioinformatics (Oxford, England) 2001, 17(4):383-384. 10.1093/bioinformatics/17.4.383 11301314
-
(2001)
Bioinformatics (Oxford, England)
, vol.17
, Issue.4
, pp. 383-384
-
-
Zmasek, C.M.1
Eddy, S.R.2
-
62
-
-
33644877416
-
OryGenesDB: A database for rice reverse genetics
-
Database 1347375 16381969 10.1093/nar/gkj012
-
Droc G Ruiz M Larmande P Pereira A Piffanelli P Morel JB Dievart A Courtois B Guiderdoni E Perin C OryGenesDB: A database for rice reverse genetics Nucleic acids research 2006, 34(Database):D736-740. 1347375 16381969 10.1093/nar/gkj012
-
(2006)
Nucleic Acids Research
, vol.34
-
-
Droc, G.1
Ruiz, M.2
Larmande, P.3
Pereira, A.4
Piffanelli, P.5
Morel, J.B.6
Dievart, A.7
Courtois, B.8
Guiderdoni, E.9
Perin, C.10
-
64
-
-
43549119730
-
-
CINES web site http://www.cines.fr/anglais0.html
-
CINES Web Site
-
-
|