-
1
-
-
0037841804
-
Evolution of the protein repertoire
-
C. Chothia, J. Gough, C. Vogel, and S.A. Teichmann Evolution of the protein repertoire Science 300 2003 1701 1703 10.1126/science.1085371
-
(2003)
Science
, vol.300
, pp. 1701-1703
-
-
Chothia, C.1
Gough, J.2
Vogel, C.3
Teichmann, S.A.4
-
2
-
-
0842268045
-
Supra-domains: Evolutionary units larger than single protein domains
-
C. Vogel, C. Berzuini, M. Bashton, J. Gough, and S.A. Teichmann Supra-domains: evolutionary units larger than single protein domains J. Mol. Biol. 336 2004 809 823 10.1016/j.jmb.2003.12.026
-
(2004)
J. Mol. Biol.
, vol.336
, pp. 809-823
-
-
Vogel, C.1
Berzuini, C.2
Bashton, M.3
Gough, J.4
Teichmann, S.A.5
-
3
-
-
16344391964
-
Rapid motif-based prediction of circular permutations in multi-domain proteins
-
J. Weiner, G. Thomas, and E. Bornberg-Bauer Rapid motif-based prediction of circular permutations in multi-domain proteins Bioinformatics 21 2005 932 937 10.1093/bioinformatics/bti085
-
(2005)
Bioinformatics
, vol.21
, pp. 932-937
-
-
Weiner, J.1
Thomas, G.2
Bornberg-Bauer, E.3
-
4
-
-
50849114838
-
Arrangements in the modular evolution of proteins
-
A.D. Moore, Å.K. Björklund, D. Ekman, E. Bornberg-Bauer, and A. Elofsson Arrangements in the modular evolution of proteins Trends Biochem. Sci. 33 2008 444 451 10.1016/j.tibs.2008.05.008
-
(2008)
Trends Biochem. Sci.
, vol.33
, pp. 444-451
-
-
Moore, A.D.1
Björklund, Å.K.2
Ekman, D.3
Bornberg-Bauer, E.4
Elofsson, A.5
-
5
-
-
78651412161
-
Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires
-
C.M. Zmasek, and A. Godzik Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires Genome Biol. 12 2011 R4 10.1186/gb-2011-12-1-r4
-
(2011)
Genome Biol.
, vol.12
, pp. R4
-
-
Zmasek, C.M.1
Godzik, A.2
-
6
-
-
84876281976
-
Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree
-
A.D. Moore, S. Grath, A. Schuler, A.K. Huylmans, and E. Bornberg-Bauer Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree Biochim. Biophys. Acta 1834 2013 898 907 10.1016/j.bbapap.2013.01.007
-
(2013)
Biochim. Biophys. Acta
, vol.1834
, pp. 898-907
-
-
Moore, A.D.1
Grath, S.2
Schuler, A.3
Huylmans, A.K.4
Bornberg-Bauer, E.5
-
7
-
-
75549086174
-
Eukaryotic protein domains as functional units of cellular evolution
-
J. Jin, X. Xie, C. Chen, J.G. Park, C. Stark, D.A. James, and et al. Eukaryotic protein domains as functional units of cellular evolution Sci. Signal 2 2009 ra76 10.1126/scisignal.2000546
-
(2009)
Sci. Signal
, vol.2
, pp. ra76
-
-
Jin, J.1
Xie, X.2
Chen, C.3
Park, J.G.4
Stark, C.5
James, D.A.6
-
8
-
-
84876528480
-
DcGO: Database of domain-centric ontologies on functions, phenotypes, diseases and more
-
H. Fang, and J. Gough dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more Nucleic Acids Res. 41 2013 D536 D544 10.1093/nar/gks1080
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D536-D544
-
-
Fang, H.1
Gough, J.2
-
9
-
-
62749097935
-
Genomic and structural aspects of protein evolution
-
C. Chothia, and J. Gough Genomic and structural aspects of protein evolution Biochem. J. 419 2009 15 28 10.1042/BJ20090122
-
(2009)
Biochem. J.
, vol.419
, pp. 15-28
-
-
Chothia, C.1
Gough, J.2
-
10
-
-
17544367678
-
Convergent evolution of domain architectures (is rare)
-
J. Gough Convergent evolution of domain architectures (is rare) Bioinformatics 21 2005 1464 1471 10.1093/bioinformatics/bti204
-
(2005)
Bioinformatics
, vol.21
, pp. 1464-1471
-
-
Gough, J.1
-
11
-
-
34548487255
-
Quantification of the elevated rate of domain rearrangements in metazoa
-
D. Ekman, A.K. Bjorklund, and A. Elofsson Quantification of the elevated rate of domain rearrangements in metazoa J. Mol. Biol. 372 2007 1337 1348 10.1016/j.jmb.2007.06.022
-
(2007)
J. Mol. Biol.
, vol.372
, pp. 1337-1348
-
-
Ekman, D.1
Bjorklund, A.K.2
Elofsson, A.3
-
13
-
-
58149203228
-
SUPERFAMILY-sophisticated comparative genomics, data mining, visualization and phylogeny
-
D. Wilson, R. Pethica, Y. Zhou, C. Talbot, C. Vogel, M. Madera, and et al. SUPERFAMILY-sophisticated comparative genomics, data mining, visualization and phylogeny Nucleic Acids Res. 37 2009 D380 D386 10.1093/nar/gkn762
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D380-D386
-
-
Wilson, D.1
Pethica, R.2
Zhou, Y.3
Talbot, C.4
Vogel, C.5
Madera, M.6
-
14
-
-
39549096663
-
Evolutionary history and functional implications of protein domains and their combinations in eukaryotes
-
M. Itoh, J.C. Nacher, K. Kuma, S. Goto, and M. Kanehisa Evolutionary history and functional implications of protein domains and their combinations in eukaryotes Genome Biol. 8 2007 R121 10.1186/gb-2007-8-6-r121
-
(2007)
Genome Biol.
, vol.8
, pp. R121
-
-
Itoh, M.1
Nacher, J.C.2
Kuma, K.3
Goto, S.4
Kanehisa, M.5
-
15
-
-
77951159012
-
Rapid diversification of cell signaling phenotypes by modular domain recombination
-
S.G. Peisajovich, J.E. Garbarino, P. Wei, and W.A. Lim Rapid diversification of cell signaling phenotypes by modular domain recombination Science 328 2010 368 372 10.1126/science.1182376
-
(2010)
Science
, vol.328
, pp. 368-372
-
-
Peisajovich, S.G.1
Garbarino, J.E.2
Wei, P.3
Lim, W.A.4
-
16
-
-
84901457312
-
The evolution of human cells in terms of protein innovation
-
A.J. Sardar, M.E. Oates, H. Fang, A.R.R. Forrest, H. Kawaji, J. Gough, and et al. The evolution of human cells in terms of protein innovation Mol. Biol. Evol. 31 2014 1364 1374 10.1093/molbev/mst139
-
(2014)
Mol. Biol. Evol.
, vol.31
, pp. 1364-1374
-
-
Sardar, A.J.1
Oates, M.E.2
Fang, H.3
Forrest, A.R.R.4
Kawaji, H.5
Gough, J.6
-
17
-
-
38549153238
-
Data growth and its impact on the SCOP database: New developments
-
A. Andreeva, D. Howorth, J.M. Chandonia, S.E. Brenner, T.J. Hubbard, C. Chothia, and et al. Data growth and its impact on the SCOP database: new developments Nucleic Acids Res. 36 2008 D419 D425 10.1093/nar/gkm993
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. D419-D425
-
-
Andreeva, A.1
Howorth, D.2
Chandonia, J.M.3
Brenner, S.E.4
Hubbard, T.J.5
Chothia, C.6
-
18
-
-
0035798406
-
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
-
J. Gough, K. Karplus, R. Hughey, and C. Chothia Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure J. Mol. Biol. 313 2001 903 919 10.1006/jmbi.2001.5080
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 903-919
-
-
Gough, J.1
Karplus, K.2
Hughey, R.3
Chothia, C.4
-
19
-
-
84941032473
-
The SUPERFAMILY 1.75 database in 2014: A doubling of data
-
M.E. Oates, J. Stahlhacke, D.V. Vavoulis, B. Smithers, O.J.L. Rackham, A.J. Sardar, and et al. The SUPERFAMILY 1.75 database in 2014: a doubling of data Nucleic Acids Res. 43 2015 D227 D233 10.1093/nar/gku1041
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D227-D233
-
-
Oates, M.E.1
Stahlhacke, J.2
Vavoulis, D.V.3
Smithers, B.4
Rackham, O.J.L.5
Sardar, A.J.6
-
20
-
-
84879668651
-
A daily-updated tree of (sequenced) life as a reference for genome research
-
H. Fang, M.E. Oates, R.B. Pethica, J.M. Greenwood, A.J. Sardar, O.J.L. Rackham, and et al. A daily-updated tree of (sequenced) life as a reference for genome research Sci. Rep. 3 2013 2015 10.1038/srep02015
-
(2013)
Sci. Rep.
, vol.3
, pp. 2015
-
-
Fang, H.1
Oates, M.E.2
Pethica, R.B.3
Greenwood, J.M.4
Sardar, A.J.5
Rackham, O.J.L.6
-
21
-
-
0035992053
-
The g-value paradox
-
M.W. Hahn, and G.A. Wray The g-value paradox Evol. Dev. 4 2002 73 75 10.1046/j.1525-142X.2002.01069.x
-
(2002)
Evol. Dev.
, vol.4
, pp. 73-75
-
-
Hahn, M.W.1
Wray, G.A.2
-
22
-
-
0035816218
-
Domain combinations in archaeal, eubacterial and eukaryotic proteomes
-
G. Apic, J. Gough, and S.A. Teichmann Domain combinations in archaeal, eubacterial and eukaryotic proteomes J. Mol. Biol. 310 2001 311 325 10.1006/jmbi.2001.4776
-
(2001)
J. Mol. Biol.
, vol.310
, pp. 311-325
-
-
Apic, G.1
Gough, J.2
Teichmann, S.A.3
-
23
-
-
84860138819
-
Evolution of protein domain architectures
-
K. Forslund, and E.L.L. Sonnhammer Evolution of protein domain architectures Methods Mol. Biol. 856 2012 187 216 10.1007/978-1-61779-585-5
-
(2012)
Methods Mol. Biol.
, vol.856
, pp. 187-216
-
-
Forslund, K.1
Sonnhammer, E.L.L.2
-
25
-
-
40449095056
-
Evolution of protein domain promiscuity in eukaryotes
-
M.K. Basu, L. Carmel, I.B. Rogozin, and E.V. Koonin Evolution of protein domain promiscuity in eukaryotes Genome Res. 18 2008 449 461 10.1101/gr.6943508
-
(2008)
Genome Res.
, vol.18
, pp. 449-461
-
-
Basu, M.K.1
Carmel, L.2
Rogozin, I.B.3
Koonin, E.V.4
-
26
-
-
65549111825
-
Domain mobility in proteins: Functional and evolutionary implications
-
M.K. Basu, E. Poliakov, and I.B. Rogozin Domain mobility in proteins: functional and evolutionary implications Br. Bioinform. 10 2009 205 216 10.1093/bib/bbn057
-
(2009)
Br. Bioinform.
, vol.10
, pp. 205-216
-
-
Basu, M.K.1
Poliakov, E.2
Rogozin, I.B.3
-
27
-
-
84908319821
-
DcGOR: An R package for analysing ontologies and protein domain annotations
-
H. Fang dcGOR: an R package for analysing ontologies and protein domain annotations PLoS Comput. Biol. 10 2014 e1003929 10.1371/journal.pcbi.1003929
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003929
-
-
Fang, H.1
-
28
-
-
33846044585
-
The SUPERFAMILY database in 2007: Families and functions
-
D. Wilson, M. Madera, C. Vogel, C. Chothia, and J. Gough The SUPERFAMILY database in 2007: families and functions Nucleic Acids Res. 35 2007 D308 D313 10.1093/nar/gkl910
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. D308-D313
-
-
Wilson, D.1
Madera, M.2
Vogel, C.3
Chothia, C.4
Gough, J.5
-
29
-
-
84874663959
-
A large-scale evaluation of computational protein function prediction
-
P. Radivojac, W.T. Clark, T.R. Oron, A.M. Schnoes, T. Wittkop, A. Sokolov, and et al. A large-scale evaluation of computational protein function prediction Nat. Methods 10 2013 221 227 10.1038/nmeth.2340
-
(2013)
Nat. Methods
, vol.10
, pp. 221-227
-
-
Radivojac, P.1
Clark, W.T.2
Oron, T.R.3
Schnoes, A.M.4
Wittkop, T.5
Sokolov, A.6
-
30
-
-
84887187427
-
A domain-centric solution to functional genomics via dcGO predictor
-
H. Fang, and J. Gough A domain-centric solution to functional genomics via dcGO predictor BMC Bioinforma. 14 Suppl. 3 2013 S9 10.1186/1471-2105-14-S3-S9
-
(2013)
BMC Bioinforma.
, vol.14
, pp. S9
-
-
Fang, H.1
Gough, J.2
-
31
-
-
84878740266
-
A disease-drug-phenotype matrix inferred by walking on a functional domain network
-
H. Fang, and J. Gough A disease-drug-phenotype matrix inferred by walking on a functional domain network Mol. Biosyst. 9 2013 1686 1696 10.1039/c3mb25495j
-
(2013)
Mol. Biosyst.
, vol.9
, pp. 1686-1696
-
-
Fang, H.1
Gough, J.2
-
32
-
-
78651274743
-
SUPERFAMILY 1.75 including a domain-centric gene ontology method
-
D.A. de Lima Morais, H. Fang, O.J. Rackham, D. Wilson, R. Pethica, C. Chothia, and et al. SUPERFAMILY 1.75 including a domain-centric gene ontology method Nucleic Acids Res. 39 2011 D427 D434 10.1093/nar/gkq1130
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D427-D434
-
-
De Lima Morais, D.A.1
Fang, H.2
Rackham, O.J.3
Wilson, D.4
Pethica, R.5
Chothia, C.6
-
33
-
-
84959795073
-
Phylogenetic analysis under Dollo's law
-
J.S. Farris Phylogenetic analysis under Dollo's law Syst. Zool. 26 1977 77 88 10.2307/2412867
-
(1977)
Syst. Zool.
, vol.26
, pp. 77-88
-
-
Farris, J.S.1
-
34
-
-
84908327053
-
The 'dnet' approach promotes emerging research on cancer patient survival
-
H. Fang, and J. Gough The 'dnet' approach promotes emerging research on cancer patient survival Genome Med. 6 2014 64 10.1186/s13073-014-0064-8
-
(2014)
Genome Med.
, vol.6
, pp. 64
-
-
Fang, H.1
Gough, J.2
-
35
-
-
79955490827
-
The multiple origins of complex multicellularity
-
A.H. Knoll The multiple origins of complex multicellularity Annu. Rev. Earth Planet. Sci. 39 2011 217 239 10.1146/annurev.earth.031208.100209
-
(2011)
Annu. Rev. Earth Planet. Sci.
, vol.39
, pp. 217-239
-
-
Knoll, A.H.1
-
36
-
-
0037223971
-
The evolution of signalling pathways in animal development
-
A. Pires-daSilva, and R.J. Sommer The evolution of signalling pathways in animal development Nat. Rev. Genet. 4 2003 39 49 10.1038/nrg977
-
(2003)
Nat. Rev. Genet.
, vol.4
, pp. 39-49
-
-
Pires-DaSilva, A.1
Sommer, R.J.2
-
37
-
-
84890282772
-
Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages
-
A. de Mendoza, A. Sebé-Pedrós, M.S. Šestak, M. Matejcic, G. Torruella, T. Domazet-Loso, and et al. Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages Proc. Natl. Acad. Sci. U. S. A. 110 2013 1 9 10.1073/pnas.1311818110
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. 1-9
-
-
De Mendoza, A.1
Sebé-Pedrós, A.2
Šestak, M.S.3
Matejcic, M.4
Torruella, G.5
Domazet-Loso, T.6
-
38
-
-
77953062527
-
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
-
D. Schmidt, M.D. Wilson, B. Ballester, P.C. Schwalie, G.D. Brown, A. Marshall, and et al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding Science 328 2010 1036 1040 10.1126/science.1186176
-
(2010)
Science
, vol.328
, pp. 1036-1040
-
-
Schmidt, D.1
Wilson, M.D.2
Ballester, B.3
Schwalie, P.C.4
Brown, G.D.5
Marshall, A.6
|