-
1
-
-
0014800108
-
Distinguishing homologous from analogous proteins
-
10.2307/2412448, 5449325
-
Fitch WM. Distinguishing homologous from analogous proteins. Syst Zool 1970, 19(2):99-13. 10.2307/2412448, 5449325.
-
(1970)
Syst Zool
, vol.19
, Issue.2
, pp. 99-113
-
-
Fitch, W.M.1
-
2
-
-
0034178257
-
Homology a personal view on some of the problems
-
10.1016/S0168-9525(00)02005-9, 10782117
-
Fitch WM. Homology a personal view on some of the problems. Trends Genet 2000, 16(5):227-231. 10.1016/S0168-9525(00)02005-9, 10782117.
-
(2000)
Trends Genet
, vol.16
, Issue.5
, pp. 227-231
-
-
Fitch, W.M.1
-
3
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
10.1038/nrg1603, 15861208
-
Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 2005, 6(5):361-375. 10.1038/nrg1603, 15861208.
-
(2005)
Nat Rev Genet
, vol.6
, Issue.5
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
4
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: protein phylogenetic profiles
-
10.1073/pnas.96.8.4285, 16324, 10200254
-
Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 1999, 96(8):4285-4288. 10.1073/pnas.96.8.4285, 16324, 10200254.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, Issue.8
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
5
-
-
54849436208
-
The quest for orthologs: finding the corresponding gene across genomes
-
10.1016/j.tig.2008.08.009, 18819722
-
Kuzniar A, van Ham RC, Pongor S, Leunissen JA. The quest for orthologs: finding the corresponding gene across genomes. Trends Genet 2008, 24(11):539-551. 10.1016/j.tig.2008.08.009, 18819722.
-
(2008)
Trends Genet
, vol.24
, Issue.11
, pp. 539-551
-
-
Kuzniar, A.1
van Ham, R.C.2
Pongor, S.3
Leunissen, J.A.4
-
6
-
-
38549105500
-
OrthoDB: the hierarchical catalog of eukaryotic orthologs
-
2238902, 17947323, Database
-
Kriventseva EV, Rahman N, Espinosa O, Zdobnov EM. OrthoDB: the hierarchical catalog of eukaryotic orthologs. Nucleic Acids Res 2008, (36 Database):D271-275. 2238902, 17947323.
-
(2008)
Nucleic Acids Res
, Issue.36
-
-
Kriventseva, E.V.1
Rahman, N.2
Espinosa, O.3
Zdobnov, E.M.4
-
7
-
-
75549086594
-
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
-
10.1093/nar/gkp931, 2808972, 19892828, Database
-
Ostlund G, Schmitt T, Forslund K, Kostler T, Messina DN, Roopra S, Frings O, Sonnhammer EL. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res 2010, (38 Database):D196-203. 10.1093/nar/gkp931, 2808972, 19892828.
-
(2010)
Nucleic Acids Res
, Issue.38
-
-
Ostlund, G.1
Schmitt, T.2
Forslund, K.3
Kostler, T.4
Messina, D.N.5
Roopra, S.6
Frings, O.7
Sonnhammer, E.L.8
-
8
-
-
0033956060
-
The COG database: a tool for genome-scale analysis of protein functions and evolution
-
10.1093/nar/28.1.33, 102395, 10592175
-
Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000, 28(1):33-36. 10.1093/nar/28.1.33, 102395, 10592175.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 33-36
-
-
Tatusov, R.L.1
Galperin, M.Y.2
Natale, D.A.3
Koonin, E.V.4
-
9
-
-
33645320249
-
COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations
-
10.1093/bioinformatics/btl009, 1620014, 16434444
-
Jothi R, Zotenko E, Tasneem A, Przytycka TM. COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations. Bioinformatics 2006, 22(7):779-788. 10.1093/bioinformatics/btl009, 1620014, 16434444.
-
(2006)
Bioinformatics
, vol.22
, Issue.7
, pp. 779-788
-
-
Jothi, R.1
Zotenko, E.2
Tasneem, A.3
Przytycka, T.M.4
-
10
-
-
0142028973
-
Comprehensive analysis of orthologous protein domains using the HOPS database
-
10.1101/gr1305203, 403726, 14525933
-
Storm CE, Sonnhammer EL. Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res 2003, 13(10):2353-2362. 10.1101/gr1305203, 403726, 14525933.
-
(2003)
Genome Res
, vol.13
, Issue.10
, pp. 2353-2362
-
-
Storm, C.E.1
Sonnhammer, E.L.2
-
11
-
-
34347376565
-
Orthology prediction at scalable resolution by phylogenetic tree analysis
-
10.1186/1471-2105-8-83, 1838432, 17346331
-
van der Heijden RT, Snel B, van Noort V, Huynen MA. Orthology prediction at scalable resolution by phylogenetic tree analysis. BMC Bioinformatics 2007, 8:83. 10.1186/1471-2105-8-83, 1838432, 17346331.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 83
-
-
van der Heijden, R.T.1
Snel, B.2
van Noort, V.3
Huynen, M.A.4
-
12
-
-
33846039019
-
Ensembl 2007
-
10.1093/nar/gkl996, 1761443, 17148474, Database
-
Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, et al. Ensembl 2007. Nucleic Acids Res 2007, (35 Database):D610-617. 10.1093/nar/gkl996, 1761443, 17148474.
-
(2007)
Nucleic Acids Res
, Issue.35
-
-
Hubbard, T.J.1
Aken, B.L.2
Beal, K.3
Ballester, B.4
Caccamo, M.5
Chen, Y.6
Clarke, L.7
Coates, G.8
Cunningham, F.9
Cutts, T.10
-
13
-
-
58149200954
-
Database resources of the National Center for Biotechnology Information
-
10.1093/nar/gkn741, 2686545, 18940862, Database issue
-
Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2009, 37(Database issue):D5-15. 10.1093/nar/gkn741, 2686545, 18940862.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Sayers, E.W.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
-
14
-
-
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(9):1160-1175. 10.1089/cmb.2007.0048, 17990975.
-
(2007)
J Comput Biol
, vol.14
, Issue.9
, pp. 1160-1175
-
-
Fu, Z.1
Chen, X.2
Vacic, V.3
Nan, P.4
Zhong, Y.5
Jiang, T.6
-
15
-
-
46049121338
-
Clustering of main orthologs for multiple genomes
-
10.1142/S0219720008003540, 18574863
-
Fu Z, Jiang T. Clustering of main orthologs for multiple genomes. J Bioinform Comput Biol 2008, 6(3):573-584. 10.1142/S0219720008003540, 18574863.
-
(2008)
J Bioinform Comput Biol
, vol.6
, Issue.3
, pp. 573-584
-
-
Fu, Z.1
Jiang, T.2
-
16
-
-
33644876020
-
Pfam: clans, web tools and services
-
10.1093/nar/gkj149, 1347511, 16381856, Database
-
Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, et al. Pfam: clans, web tools and services. Nucleic Acids Res 2006, (34 Database):D247-251. 10.1093/nar/gkj149, 1347511, 16381856.
-
(2006)
Nucleic Acids Res
, Issue.34
-
-
Finn, R.D.1
Mistry, J.2
Schuster-Bockler, B.3
Griffiths-Jones, S.4
Hollich, V.5
Lassmann, T.6
Moxon, S.7
Marshall, M.8
Khanna, A.9
Durbin, R.10
-
17
-
-
1842861592
-
Structure, function and evolution of multidomain proteins
-
10.1016/j.sbi.2004.03.011, 15093836
-
Vogel C, Bashton M, Kerrison ND, Chothia C, Teichmann SA. Structure, function and evolution of multidomain proteins. Current opinion in structural biology 2004, 14(2):208-216. 10.1016/j.sbi.2004.03.011, 15093836.
-
(2004)
Current opinion in structural biology
, vol.14
, Issue.2
, pp. 208-216
-
-
Vogel, C.1
Bashton, M.2
Kerrison, N.D.3
Chothia, C.4
Teichmann, S.A.5
-
18
-
-
38549146894
-
The Pfam protein families database
-
2238907, 18039703, Database
-
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, et al. The Pfam protein families database. Nucleic Acids Res 2008, (36 Database):D281-288. 2238907, 18039703.
-
(2008)
Nucleic Acids Res
, Issue.36
-
-
Finn, R.D.1
Tate, J.2
Mistry, J.3
Coggill, P.C.4
Sammut, S.J.5
Hotz, H.R.6
Ceric, G.7
Forslund, K.8
Eddy, S.R.9
Sonnhammer, E.L.10
-
19
-
-
0036307754
-
The geometry of domain combination in proteins
-
10.1006/jmbi.2001.5288, 11812158
-
Bashton M, Chothia C. The geometry of domain combination in proteins. Journal of molecular biology 2002, 315(4):927-939. 10.1006/jmbi.2001.5288, 11812158.
-
(2002)
Journal of molecular biology
, vol.315
, Issue.4
, pp. 927-939
-
-
Bashton, M.1
Chothia, C.2
-
20
-
-
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. Journal of molecular biology 2001, 314(5):1041-1052. 10.1006/jmbi.2000.5197, 11743721.
-
(2001)
Journal of molecular biology
, vol.314
, Issue.5
, pp. 1041-1052
-
-
Remm, M.1
Storm, C.E.2
Sonnhammer, E.L.3
-
21
-
-
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, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29. 10.1038/75556, 10802651.
-
(2000)
Nat Genet
, vol.25
, Issue.1
, 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
-
22
-
-
67650497792
-
Nature of the protein universe
-
10.1073/pnas.0905029106, 2698892, 19541617
-
Levitt M. Nature of the protein universe. Proc Natl Acad Sci USA 2009, 106(27):11079-11084. 10.1073/pnas.0905029106, 2698892, 19541617.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.27
, pp. 11079-11084
-
-
Levitt, M.1
-
23
-
-
0036173130
-
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability
-
10.1093/bioinformatics/18.1.92, 11836216
-
Storm CE, Sonnhammer EL. Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 2002, 18(1):92-99. 10.1093/bioinformatics/18.1.92, 11836216.
-
(2002)
Bioinformatics
, vol.18
, Issue.1
, pp. 92-99
-
-
Storm, C.E.1
Sonnhammer, E.L.2
-
24
-
-
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
|