-
1
-
-
27644472372
-
Orthologs, paralogs, and evolutionary genomics
-
10.1146/annurev.genet.39.073003.114725, 16285863
-
Koonin EV. Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 2005, 39:309-338. 10.1146/annurev.genet.39.073003.114725, 16285863.
-
(2005)
Annu Rev Genet
, vol.39
, pp. 309-338
-
-
Koonin, E.V.1
-
2
-
-
65449142156
-
How confident can we be that orthologs are similar, but paralogs differ?
-
10.1016/j.tig.2009.03.004, 19368988
-
Studer RA, Robinson-Rechavi M. How confident can we be that orthologs are similar, but paralogs differ?. Trends Genet 2009, 25:210-216. 10.1016/j.tig.2009.03.004, 19368988.
-
(2009)
Trends Genet
, vol.25
, pp. 210-216
-
-
Studer, R.A.1
Robinson-Rechavi, M.2
-
3
-
-
0013017592
-
RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs
-
10.1186/1471-2105-3-14, 116988, 12028595
-
Zmasek CM, Eddy SR. RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics 2002, 3:14. 10.1186/1471-2105-3-14, 116988, 12028595.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 14
-
-
Zmasek, C.M.1
Eddy, S.R.2
-
4
-
-
0142028973
-
Comprehensive analysis of orthologous protein domains using the HOPS database
-
10.1101/gr1305203, 403726, 14525933
-
Storm CEV, Sonnhammer ELL. Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res 2003, 13:2353-2362. 10.1101/gr1305203, 403726, 14525933.
-
(2003)
Genome Res
, vol.13
, pp. 2353-2362
-
-
Storm, C.E.V.1
Sonnhammer, E.L.L.2
-
5
-
-
0036173130
-
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability
-
10.1093/bioinformatics/18.1.92, 11836216
-
Storm CEV, Sonnhammer ELL. Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 2002, 18:92-99. 10.1093/bioinformatics/18.1.92, 11836216.
-
(2002)
Bioinformatics
, vol.18
, pp. 92-99
-
-
Storm, C.E.V.1
Sonnhammer, E.L.L.2
-
6
-
-
33746582319
-
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database
-
10.1186/1471-2105-7-201, 1523372, 16608522
-
Dehal PS, Boore JL. A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database. BMC Bioinformatics 2006, 7:201. 10.1186/1471-2105-7-201, 1523372, 16608522.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 201
-
-
Dehal, P.S.1
Boore, J.L.2
-
7
-
-
33749342164
-
Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human
-
10.1371/journal.pcbi.0020133, 1584324, 17009864
-
Goodstadt L, Ponting CP. Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PLoS Comput Biol 2006, 2:e133. 10.1371/journal.pcbi.0020133, 1584324, 17009864.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Goodstadt, L.1
Ponting, C.P.2
-
8
-
-
33644876458
-
TreeFam: a curated database of phylogenetic trees of animal gene families
-
10.1093/nar/gkj118, 1347480, 16381935
-
Li H, Coghlan A, Ruan J, Coin LJ, Hériché J, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res 2006, 34:D572-D580. 10.1093/nar/gkj118, 1347480, 16381935.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Li, H.1
Coghlan, A.2
Ruan, J.3
Coin, L.J.4
Hériché, J.5
Osmotherly, L.6
Li, R.7
Liu, T.8
Zhang, Z.9
Bolund, L.10
Wong, G.K.11
Zheng, W.12
Dehal, P.13
Wang, J.14
Durbin, R.15
-
9
-
-
0141626909
-
Detecting putative orthologs
-
10.1093/bioinformatics/btg213, 15593400
-
Wall DP, Fraser HB, Hirsh AE. Detecting putative orthologs. Bioinformatics 2003, 19:1710-1711. 10.1093/bioinformatics/btg213, 15593400.
-
(2003)
Bioinformatics
, vol.19
, pp. 1710-1711
-
-
Wall, D.P.1
Fraser, H.B.2
Hirsh, A.E.3
-
10
-
-
33747817416
-
Roundup: a multi-genome repository of orthologs and evolutionary distances
-
10.1093/bioinformatics/btl286, 16777906
-
Deluca TF, Wu I, Pu J, Monaghan T, Peshkin L, Singh S, Wall DP. Roundup: a multi-genome repository of orthologs and evolutionary distances. Bioinformatics 2006, 22:2044-2046. 10.1093/bioinformatics/btl286, 16777906.
-
(2006)
Bioinformatics
, vol.22
, pp. 2044-2046
-
-
Deluca, T.F.1
Wu, I.2
Pu, J.3
Monaghan, T.4
Peshkin, L.5
Singh, S.6
Wall, D.P.7
-
11
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
10.1093/nar/25.17.3389, 146917, 9254694
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
12
-
-
0042902833
-
The COG database: an updated version includes eukaryotes
-
10.1186/1471-2105-4-41, 222959, 12969510
-
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, 4:41. 10.1186/1471-2105-4-41, 222959, 12969510.
-
(2003)
BMC Bioinformatics
, vol.4
, 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
-
13
-
-
0035162592
-
The COG database: new developments in phylogenetic classification of proteins from complete genomes
-
10.1093/nar/29.1.22, 29819, 11125040
-
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 2001, 29:22-28. 10.1093/nar/29.1.22, 29819, 11125040.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 22-28
-
-
Tatusov, R.L.1
Natale, D.A.2
Garkavtsev, I.V.3
Tatusova, T.A.4
Shankavaram, U.T.5
Rao, B.S.6
Kiryutin, B.7
Galperin, M.Y.8
Fedorova, N.D.9
Koonin, E.V.10
-
14
-
-
0036125446
-
Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA)
-
10.1101/gr.212002, 155294, 11875039
-
Lee Y, Sultana R, Pertea G, Cho J, Karamycheva S, Tsai J, Parvizi B, Cheung F, Antonescu V, White J, Holt I, Liang F, Quackenbush J. Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Res 2002, 12:493-502. 10.1101/gr.212002, 155294, 11875039.
-
(2002)
Genome Res
, vol.12
, pp. 493-502
-
-
Lee, Y.1
Sultana, R.2
Pertea, G.3
Cho, J.4
Karamycheva, S.5
Tsai, J.6
Parvizi, B.7
Cheung, F.8
Antonescu, V.9
White, J.10
Holt, I.11
Liang, F.12
Quackenbush, J.13
-
15
-
-
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, 314:1041-1052. 10.1006/jmbi.2000.5197, 11743721.
-
(2001)
J Mol Biol
, vol.314
, pp. 1041-1052
-
-
Remm, M.1
Storm, C.E.2
Sonnhammer, E.L.3
-
16
-
-
13444256478
-
Inparanoid: a comprehensive database of eukaryotic orthologs
-
10.1093/nar/gki107, 540061, 15608241
-
O'Brien KP, Remm M, Sonnhammer ELL. Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res 2005, 33:D476-D480. 10.1093/nar/gki107, 540061, 15608241.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
O'Brien, K.P.1
Remm, M.2
Sonnhammer, E.L.L.3
-
17
-
-
33747892409
-
Automatic clustering of orthologs and inparalogs shared by multiple proteomes
-
10.1093/bioinformatics/btl213, 16873526
-
Alexeyenko A, Tamas I, Liu G, Sonnhammer ELL. Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 2006, 22:e9-15. 10.1093/bioinformatics/btl213, 16873526.
-
(2006)
Bioinformatics
, vol.22
-
-
Alexeyenko, A.1
Tamas, I.2
Liu, G.3
Sonnhammer, E.L.L.4
-
18
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
10.1093/nar/30.7.1575, 101833, 11917018
-
Enright AJ, Dongen SV, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002, 30:1575-1584. 10.1093/nar/30.7.1575, 101833, 11917018.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Dongen, S.V.2
Ouzounis, C.A.3
-
19
-
-
0141519279
-
OrthoMCL: identification of ortholog groups for eukaryotic genomes
-
10.1101/gr.1224503, 403725, 12952885
-
Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13:2178-2189. 10.1101/gr.1224503, 403725, 12952885.
-
(2003)
Genome Res
, vol.13
, pp. 2178-2189
-
-
Li, L.1
Stoeckert, C.J.2
Roos, D.S.3
-
20
-
-
33644787447
-
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
-
10.1093/nar/gkj123, 1347485, 16381887
-
Chen F, Mackey AJ, Stoeckert CJ, Roos DS. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 2006, 34:D363-D368. 10.1093/nar/gkj123, 1347485, 16381887.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Chen, F.1
Mackey, A.J.2
Stoeckert, C.J.3
Roos, D.S.4
-
21
-
-
0345863935
-
The KEGG resource for deciphering the genome
-
10.1093/nar/gkh063, 308797, 14681412
-
Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004, 32:D277-D280. 10.1093/nar/gkh063, 308797, 14681412.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Okuno, Y.4
Hattori, M.5
-
22
-
-
36048967894
-
MSOAR: a high-throughput ortholog assignment system based on genome rearrangement
-
10.1089/cmb.2007.0048, 17990975
-
Fu Z, Chen X, Vacic V, Nan P, Zhong Y, Jiang T. MSOAR: a high-throughput ortholog assignment system based on genome rearrangement. J Comput Biol 2007, 14:1160-1175. 10.1089/cmb.2007.0048, 17990975.
-
(2007)
J Comput Biol
, vol.14
, pp. 1160-1175
-
-
Fu, Z.1
Chen, X.2
Vacic, V.3
Nan, P.4
Zhong, Y.5
Jiang, T.6
-
23
-
-
34548555911
-
OMA Browser--exploring orthologous relations across 352 complete genomes
-
10.1093/bioinformatics/btm295, 17545180
-
Schneider A, Dessimoz C, Gonnet GH. OMA Browser--exploring orthologous relations across 352 complete genomes. Bioinformatics 2007, 23:2180-2182. 10.1093/bioinformatics/btm295, 17545180.
-
(2007)
Bioinformatics
, vol.23
, pp. 2180-2182
-
-
Schneider, A.1
Dessimoz, C.2
Gonnet, G.H.3
-
24
-
-
38549092091
-
Database resources of the National Center for Biotechnology Information
-
10.1093/nar/gkm1000, 2238880, 18045790
-
Wheeler DL, 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, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2008, 36:D13-D21. 10.1093/nar/gkm1000, 2238880, 18045790.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Wheeler, D.L.1
Barrett, T.2
Benson, D.A.3
Bryant, S.H.4
Canese, K.5
Chetvernin, V.6
Church, D.M.7
Dicuccio, M.8
Edgar, R.9
Federhen, S.10
Feolo, M.11
Geer, L.Y.12
Helmberg, W.13
Kapustin, Y.14
Khovayko, O.15
Landsman, D.16
Lipman, D.J.17
Madden, T.L.18
Maglott, D.R.19
Miller, V.20
Ostell, J.21
Pruitt, K.D.22
Schuler, G.D.23
Shumway, M.24
Sequeira, E.25
Sherry, S.T.26
Sirotkin, K.27
Souvorov, A.28
Starchenko, G.29
Tatusov, R.L.30
Tatusova, T.A.31
Wagner, L.32
Yaschenko, E.33
more..
-
25
-
-
37849023306
-
Assessing performance of orthology detection strategies applied to eukaryotic genomes
-
10.1371/journal.pone.0000383, 1849888, 17440619
-
Chen F, Mackey AJ, Vermunt JK, Roos DS. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS ONE 2007, 2:e383. 10.1371/journal.pone.0000383, 1849888, 17440619.
-
(2007)
PLoS ONE
, vol.2
-
-
Chen, F.1
Mackey, A.J.2
Vermunt, J.K.3
Roos, D.S.4
-
26
-
-
0034992826
-
The closest BLAST hit is often not the nearest neighbor
-
Koski LB, Golding GB. The closest BLAST hit is often not the nearest neighbor. J Mol Evol 2001, 52:540-542.
-
(2001)
J Mol Evol
, vol.52
, pp. 540-542
-
-
Koski, L.B.1
Golding, G.B.2
-
27
-
-
2442707676
-
The Ensembl automatic gene annotation system
-
10.1101/gr.1858004, 479124, 15123590
-
Curwen V, Eyras E, Andrews TD, Clarke L, Mongin E, Searle SMJ, Clamp M. The Ensembl automatic gene annotation system. Genome Res 2004, 14:942-950. 10.1101/gr.1858004, 479124, 15123590.
-
(2004)
Genome Res
, vol.14
, pp. 942-950
-
-
Curwen, V.1
Eyras, E.2
Andrews, T.D.3
Clarke, L.4
Mongin, E.5
Searle, S.M.J.6
Clamp, M.7
-
28
-
-
59949096873
-
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
-
10.1101/gr.073585.107, 2652215, 19029536
-
Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 2009, 19:327-335. 10.1101/gr.073585.107, 2652215, 19029536.
-
(2009)
Genome Res
, vol.19
, pp. 327-335
-
-
Vilella, A.J.1
Severin, J.2
Ureta-Vidal, A.3
Heng, L.4
Durbin, R.5
Birney, E.6
-
29
-
-
25444516195
-
Gene finding in the chicken genome
-
10.1186/1471-2105-6-131, 1174864, 15924626
-
Eyras E, Reymond A, Castelo R, Bye JM, Camara F, Flicek P, Huckle EJ, Parra G, Shteynberg DD, Wyss C, Rogers J, Antonarakis SE, Birney E, Guigo R, Brent MR. Gene finding in the chicken genome. BMC Bioinformatics 2005, 6:131. 10.1186/1471-2105-6-131, 1174864, 15924626.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 131
-
-
Eyras, E.1
Reymond, A.2
Castelo, R.3
Bye, J.M.4
Camara, F.5
Flicek, P.6
Huckle, E.J.7
Parra, G.8
Shteynberg, D.D.9
Wyss, C.10
Rogers, J.11
Antonarakis, S.E.12
Birney, E.13
Guigo, R.14
Brent, M.R.15
-
30
-
-
0037417884
-
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes
-
10.1073/pnas.0337561100, 298740, 12552088
-
Guigo R, Dermitzakis ET, Agarwal P, Ponting CP, Parra G, Reymond A, Abril JF, Keibler E, Lyle R, Ucla C, Antonarakis SE, Brent MR. Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc Natl Acad Sci USA 2003, 100:1140-1145. 10.1073/pnas.0337561100, 298740, 12552088.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 1140-1145
-
-
Guigo, R.1
Dermitzakis, E.T.2
Agarwal, P.3
Ponting, C.P.4
Parra, G.5
Reymond, A.6
Abril, J.F.7
Keibler, E.8
Lyle, R.9
Ucla, C.10
Antonarakis, S.E.11
Brent, M.R.12
-
31
-
-
77951621301
-
The genome sequence of taurine cattle: a window to ruminant biology and evolution
-
10.1126/science.1169588, 19390049, The Bovine Genome Sequencing and Analysis Consortium
-
Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen H, Chrast J, Câmara F, Ermolaeva O, Henrichsen CN, et al. The Bovine Genome Sequencing and Analysis Consortium The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 2009, 324:522-528. 10.1126/science.1169588, 19390049, The Bovine Genome Sequencing and Analysis Consortium.
-
(2009)
Science
, vol.324
, pp. 522-528
-
-
Elsik, C.G.1
Tellam, R.L.2
Worley, K.C.3
Gibbs, R.A.4
Muzny, D.M.5
Weinstock, G.M.6
Adelson, D.L.7
Eichler, E.E.8
Elnitski, L.9
Guigó, R.10
Hamernik, D.L.11
Kappes, S.M.12
Lewin, H.A.13
Lynn, D.J.14
Nicholas, F.W.15
Reymond, A.16
Rijnkels, M.17
Skow, L.C.18
Zdobnov, E.M.19
Schook, L.20
Womack, J.21
Alioto, T.22
Antonarakis, S.E.23
Astashyn, A.24
Chapple, C.E.25
Chen, H.26
Chrast, J.27
Câmara, F.28
Ermolaeva, O.29
Henrichsen, C.N.30
more..
-
32
-
-
0032871834
-
Finding families for genomic ORFans
-
10.1093/bioinformatics/15.9.759, 10498776
-
Fisher D, Eisenberg D. Finding families for genomic ORFans. Bioinformatics 1999, 15(9):759-762. 10.1093/bioinformatics/15.9.759, 10498776.
-
(1999)
Bioinformatics
, vol.15
, Issue.9
, pp. 759-762
-
-
Fisher, D.1
Eisenberg, D.2
-
33
-
-
0142028990
-
An Evolutionary Analysis of Orphan Genes in
-
Domazet-Loso T, Tautz D. An Evolutionary Analysis of Orphan Genes in. Drosophila Genome Res 2009, 13:2213-2219.
-
(2009)
Drosophila Genome Res
, vol.13
, pp. 2213-2219
-
-
Domazet-Loso, T.1
Tautz, D.2
-
34
-
-
60149097110
-
Origin of primate orphan genes: a comparative genomics approach
-
10.1093/molbev/msn281, 19064677
-
Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, Estivill X, Albà MM. Origin of primate orphan genes: a comparative genomics approach. Mol Biol Evol 2009, 26:603-612. 10.1093/molbev/msn281, 19064677.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 603-612
-
-
Toll-Riera, M.1
Bosch, N.2
Bellora, N.3
Castelo, R.4
Armengol, L.5
Estivill, X.6
Albà, M.M.7
-
35
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
10.1038/nature01262, 12466850, Mouse Genome Sequencing Consortium
-
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, et al. Mouse Genome Sequencing Consortium Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562. 10.1038/nature01262, 12466850, Mouse Genome Sequencing Consortium.
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Waterston, R.H.1
Lindblad-Toh, K.2
Birney, E.3
Rogers, J.4
Abril, J.F.5
Agarwal, P.6
Agarwala, R.7
Ainscough, R.8
Alexandersson, M.9
An, P.10
Antonarakis, S.E.11
Attwood, J.12
Baertsch, R.13
Bailey, J.14
Barlow, K.15
Beck, S.16
Berry, E.17
Birren, B.18
Bloom, T.19
Bork, P.20
Botcherby, M.21
Bray, N.22
Brent, M.R.23
Brown, D.G.24
Brown, S.D.25
Bult, C.26
Burton, J.27
Butler, J.28
Campbell, R.D.29
more..
-
36
-
-
28644447707
-
Genome sequence, comparative analysis and haplotype structure of the domestic dog
-
10.1038/nature04338, 16341006
-
Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin C, Cook A, Cuff J, Daly MJ, DeCaprio D, Gnerre S, et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 2005, 438:803-819. 10.1038/nature04338, 16341006.
-
(2005)
Nature
, vol.438
, pp. 803-819
-
-
Lindblad-Toh, K.1
Wade, C.M.2
Mikkelsen, T.S.3
Karlsson, E.K.4
Jaffe, D.B.5
Kamal, M.6
Clamp, M.7
Chang, J.L.8
Kulbokas, E.J.9
Zody, M.C.10
Mauceli, E.11
Xie, X.12
Breen, M.13
Wayne, R.K.14
Ostrander, E.A.15
Ponting, C.P.16
Galibert, F.17
Smith, D.R.18
DeJong, P.J.19
Kirkness, E.20
Alvarez, P.21
Biagi, T.22
Brockman, W.23
Butler, J.24
Chin, C.25
Cook, A.26
Cuff, J.27
Daly, M.J.28
DeCaprio, D.29
Gnerre, S.30
more..
-
37
-
-
74549149059
-
Gene Ontology website for the present paper
-
Gene Ontology website for the present paper. , http://www.itb.cnr.it/ptp/annotation
-
-
-
-
38
-
-
74549212054
-
Non orthologous gene analysis website for the current paper
-
Non orthologous gene analysis website for the current paper. , http://www.itb.cnr.it/idralab/non_orthologs
-
-
-
-
39
-
-
37648999313
-
Distinguishing protein-coding and noncoding genes in the human genome
-
10.1073/pnas.0709013104, 2148306, 18040051
-
Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, Lander ES. Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci USA 2007, 104:19428-19433. 10.1073/pnas.0709013104, 2148306, 18040051.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 19428-19433
-
-
Clamp, M.1
Fry, B.2
Kamal, M.3
Xie, X.4
Cuff, J.5
Lin, M.F.6
Kellis, M.7
Lindblad-Toh, K.8
Lander, E.S.9
-
40
-
-
0141815541
-
Analysis of singleton ORFans in fully sequenced microbial genomes
-
10.1002/prot.10423, 14517975
-
Siew N, Fischer D. Analysis of singleton ORFans in fully sequenced microbial genomes. Proteins 2003, 53:241-251. 10.1002/prot.10423, 14517975.
-
(2003)
Proteins
, vol.53
, pp. 241-251
-
-
Siew, N.1
Fischer, D.2
-
41
-
-
34247253767
-
Identification and characterization of insect-specific proteins by genome data analysis
-
10.1186/1471-2164-8-93, 1852559, 17407609
-
Zhang G, Wang H, Shi J, Wang X, Zheng H, Wong GK, Clark T, Wang W, Wang J, Kang L. Identification and characterization of insect-specific proteins by genome data analysis. BMC Genomics 2007, 8:93. 10.1186/1471-2164-8-93, 1852559, 17407609.
-
(2007)
BMC Genomics
, vol.8
, pp. 93
-
-
Zhang, G.1
Wang, H.2
Shi, J.3
Wang, X.4
Zheng, H.5
Wong, G.K.6
Clark, T.7
Wang, W.8
Wang, J.9
Kang, L.10
-
42
-
-
0034708444
-
Comparative genomics of the eukaryotes
-
10.1126/science.287.5461.2204, 2754258, 10731134
-
Rubin GM, Yandell MD, Wortman JR, Miklos GLG, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LS, Gong F, Guan P, Harris NL, Hay BA, Hoskins RA, Li J, Li Z, Hynes RO, Jones SJ, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O'Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Lewis S. Comparative genomics of the eukaryotes. Science 2000, 287:2204-2215. 10.1126/science.287.5461.2204, 2754258, 10731134.
-
(2000)
Science
, vol.287
, pp. 2204-2215
-
-
Rubin, G.M.1
Yandell, M.D.2
Wortman, J.R.3
Miklos, G.L.G.4
Nelson, C.R.5
Hariharan, I.K.6
Fortini, M.E.7
Li, P.W.8
Apweiler, R.9
Fleischmann, W.10
Cherry, J.M.11
Henikoff, S.12
Skupski, M.P.13
Misra, S.14
Ashburner, M.15
Birney, E.16
Boguski, M.S.17
Brody, T.18
Brokstein, P.19
Celniker, S.E.20
Chervitz, S.A.21
Coates, D.22
Cravchik, A.23
Gabrielian, A.24
Galle, R.F.25
Gelbart, W.M.26
George, R.A.27
Goldstein, L.S.28
Gong, F.29
Guan, P.30
Harris, N.L.31
Hay, B.A.32
Hoskins, R.A.33
Li, J.34
Li, Z.35
Hynes, R.O.36
Jones, S.J.37
Kuehl, P.M.38
Lemaitre, B.39
Littleton, J.T.40
Morrison, D.K.41
Mungall, C.42
O'Farrell, P.H.43
Pickeral, O.K.44
Shue, C.45
Vosshall, L.B.46
Zhang, J.47
Zhao, Q.48
Zheng, X.H.49
Lewis, S.50
more..
-
43
-
-
67749145754
-
Global discovery of primate-specific genes in the human genome
-
10.1073/pnas.0904569106, 19581580
-
Tay S, Blythe J, Lipovich L. Global discovery of primate-specific genes in the human genome. Proc Natl Acad Sci USA 2009, 106:12019-12024. 10.1073/pnas.0904569106, 19581580.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 12019-12024
-
-
Tay, S.1
Blythe, J.2
Lipovich, L.3
-
44
-
-
58549117346
-
Annotation of 390 bovine miRNA genes by sequence similarity with other species
-
10.1111/j.1365-2052.2008.01780.x, 18945293
-
Strozzi F, Mazza R, Malinverni R, Williams JL. Annotation of 390 bovine miRNA genes by sequence similarity with other species. Anim Genet 2009, 40:125. 10.1111/j.1365-2052.2008.01780.x, 18945293.
-
(2009)
Anim Genet
, vol.40
, pp. 125
-
-
Strozzi, F.1
Mazza, R.2
Malinverni, R.3
Williams, J.L.4
-
45
-
-
33746755926
-
Improving the specificity of high-throughput ortholog prediction
-
10.1186/1471-2105-7-270, 1524997, 16729895
-
Fulton DL, Li YY, Laird MR, Horsman BGS, Roche FM, Brinkman FSL. Improving the specificity of high-throughput ortholog prediction. BMC Bioinformatics 2006, 7:270. 10.1186/1471-2105-7-270, 1524997, 16729895.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 270
-
-
Fulton, D.L.1
Li, Y.Y.2
Laird, M.R.3
Horsman, B.G.S.4
Roche, F.M.5
Brinkman, F.S.L.6
-
46
-
-
58149185123
-
Ensembl 2009
-
10.1093/nar/gkn828, 2686571, 19033362
-
Hubbard TJP, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek P. Ensembl 2009. Nucleic Acids Res 2009, 37:D690-D697. 10.1093/nar/gkn828, 2686571, 19033362.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Hubbard, T.J.P.1
Aken, B.L.2
Ayling, S.3
Ballester, B.4
Beal, K.5
Bragin, E.6
Brent, S.7
Chen, Y.8
Clapham, P.9
Clarke, L.10
Coates, G.11
Fairley, S.12
Fitzgerald, S.13
Fernandez-Banet, J.14
Gordon, L.15
Graf, S.16
Haider, S.17
Hammond, M.18
Holland, R.19
Howe, K.20
Jenkinson, A.21
Johnson, N.22
Kahari, A.23
Keefe, D.24
Keenan, S.25
Kinsella, R.26
Kokocinski, F.27
Kulesha, E.28
Lawson, D.29
Longden, I.30
Megy, K.31
Meidl, P.32
Overduin, B.33
Parker, A.34
Pritchard, B.35
Rios, D.36
Schuster, M.37
Slater, G.38
Smedley, D.39
Spooner, W.40
Spudich, G.41
Trevanion, S.42
Vilella, A.43
Vogel, J.44
White, S.45
Wilder, S.46
Zadissa, A.47
Birney, E.48
Cunningham, F.49
Curwen, V.50
Durbin, R.51
Fernandez-Suarez, X.M.52
Herrero, J.53
Kasprzyk, A.54
Proctor, G.55
Smith, J.56
Searle, S.57
Flicek, P.58
more..
-
47
-
-
9144269670
-
EnsMart: a generic system for fast and flexible access to biological data
-
10.1101/gr.1645104, 314293, 14707178
-
Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, Birney E. EnsMart: a generic system for fast and flexible access to biological data. Genome Res 2004, 14:160-169. 10.1101/gr.1645104, 314293, 14707178.
-
(2004)
Genome Res
, vol.14
, pp. 160-169
-
-
Kasprzyk, A.1
Keefe, D.2
Smedley, D.3
London, D.4
Spooner, W.5
Melsopp, C.6
Hammond, M.7
Rocca-Serra, P.8
Cox, T.9
Birney, E.10
-
48
-
-
74549208161
-
NCBI data repository for BLAST formatted database
-
NCBI data repository for BLAST formatted database. , ftp://ftp.ncbi.nih.gov/blast/
-
-
-
-
49
-
-
1842607847
-
R: A language and environment for statistical computing
-
R Foundation for Statistical Computing. Vienna, Austria, ISBN 3-900051-07-0, URL, R Development Core Team
-
R Development Core Team R: A language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria, ISBN 3-900051-07-0, URL, R Development Core Team., http://www.R-project.org
-
-
-
-
50
-
-
0043122927
-
WU-Blast2 server at the European Bioinformatics Institute
-
10.1093/nar/gkg573, 168979, 12824421
-
Lopez R, Silventoinen V, Robinson S, Kibria A, Gish W. WU-Blast2 server at the European Bioinformatics Institute. Nucleic Acids Res 2003, 31:3795-3798. 10.1093/nar/gkg573, 168979, 12824421.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3795-3798
-
-
Lopez, R.1
Silventoinen, V.2
Robinson, S.3
Kibria, A.4
Gish, W.5
-
51
-
-
18644368714
-
The Bioperl toolkit: Perl modules for the life sciences
-
10.1101/gr.361602, 187536, 12368254
-
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JGR, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002, 12:1611-1618. 10.1101/gr.361602, 187536, 12368254.
-
(2002)
Genome Res
, vol.12
, pp. 1611-1618
-
-
Stajich, J.E.1
Block, D.2
Boulez, K.3
Brenner, S.E.4
Chervitz, S.A.5
Dagdigian, C.6
Fuellen, G.7
Gilbert, J.G.R.8
Korf, I.9
Lapp, H.10
Lehväslaiho, H.11
Matsalla, C.12
Mungall, C.J.13
Osborne, B.I.14
Pocock, M.R.15
Schattner, P.16
Senger, M.17
Stein, L.D.18
Stupka, E.19
Wilkinson, M.D.20
Birney, E.21
more..
-
52
-
-
39049158092
-
MySQL website
-
MySQL website. , http://dev.mysql.com/
-
-
-
-
53
-
-
2442666425
-
The Ensembl core software libraries
-
10.1101/gr.1857204, 479122, 15123588
-
Stabenau A, McVicker G, Melsopp C, Proctor G, Clamp M, Birney E. The Ensembl core software libraries. Genome Res 2004, 14:929-933. 10.1101/gr.1857204, 479122, 15123588.
-
(2004)
Genome Res
, vol.14
, pp. 929-933
-
-
Stabenau, A.1
McVicker, G.2
Melsopp, C.3
Proctor, G.4
Clamp, M.5
Birney, E.6
-
54
-
-
0031586003
-
Prediction of complete gene structures in human genomic DNA
-
10.1006/jmbi.1997.0951, 9149143
-
Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268:78-94. 10.1006/jmbi.1997.0951, 9149143.
-
(1997)
J Mol Biol
, vol.268
, pp. 78-94
-
-
Burge, C.1
Karlin, S.2
-
55
-
-
57349175113
-
Ruby on Rails website
-
Ruby on Rails website. , http://rubyonrails.org/
-
-
-
-
56
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
10.1038/75556, 10802651
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29. 10.1038/75556, 10802651.
-
(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
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
57
-
-
84871130356
-
The Gene Ontology Database
-
The Gene Ontology Database. , http://archive.geneontology.org/full/2009-01-01/go_200901-termdb.rdf-xml .gz
-
-
-
-
58
-
-
58149187893
-
The GOA database in 2009--an integrated Gene Ontology Annotation resource
-
10.1093/nar/gkn803, 2686469, 18957448
-
Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res 2009, 37:D396-D403. 10.1093/nar/gkn803, 2686469, 18957448.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Barrell, D.1
Dimmer, E.2
Huntley, R.P.3
Binns, D.4
O'Donovan, C.5
Apweiler, R.6
-
59
-
-
74549194624
-
The EBI Gene Ontology Annotation (GOA) database
-
The EBI Gene Ontology Annotation (GOA) database. , ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_un iprot.gz
-
-
-
-
60
-
-
58149191270
-
The Universal Protein Resource (UniProt) 2009
-
10.1093/nar/gkn664, 2686606, 18836194
-
Consortium U. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 2009, 37:D169-D174. 10.1093/nar/gkn664, 2686606, 18836194.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Consortium, U.1
-
61
-
-
84870451705
-
The UniprotKB database
-
The UniprotKB database. , ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebas e/complete/uniprot_trembl.fasta.gz
-
-
-
|