-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul, S.F. et al. (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
-
2
-
-
79958082066
-
Detecting network communities: an application to phylogenetic analysis
-
Andrade, R.F. et al. (2011) Detecting network communities: an application to phylogenetic analysis. PLoS Comput. Biol., 7, e1001131.
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Andrade, R.F.1
-
3
-
-
79551607374
-
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution
-
Apeltsin, L. et al. (2011) Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinformatics, 27, 326-333.
-
(2011)
Bioinformatics
, vol.27
, pp. 326-333
-
-
Apeltsin, L.1
-
4
-
-
84864278347
-
Using sequence similarity networks for visualization of relationships across diverse protein superfamilies
-
Atkinson, H.J. et al. (2009) Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS ONE, 4, e4345.
-
(2009)
PLoS ONE
, vol.4
-
-
Atkinson, H.J.1
-
5
-
-
0034228914
-
Assessing a mixture model for clustering with the integrated completed likelihood
-
Biernacki, C. et al. (2000)Assessing a mixture model for clustering with the integrated completed likelihood. IEEE Trans. Pattern Anal. Mach. Intell., 22, 719-725.
-
(2000)
IEEE Trans. Pattern Anal. Mach. Intell.
, vol.22
, pp. 719-725
-
-
Biernacki, C.1
-
6
-
-
56349094785
-
Fast unfolding of communities in large networks
-
Blondel, V.D. et al. (2008) Fast unfolding of communities in large networks. J. Stat. Mech.-Theory E., 2008, P10008+.
-
(2008)
J. Stat. Mech. -Theory E.
, vol.2008
-
-
Blondel, V.D.1
-
7
-
-
33745027619
-
A gold standard set of mechanistically diverse enzyme superfamilies
-
Brown, S.D. et al. (2006) A gold standard set of mechanistically diverse enzyme superfamilies. Genome Biol., 7, R8.
-
(2006)
Genome Biol.
, vol.7
-
-
Brown, S.D.1
-
8
-
-
13444305296
-
The ProDom database of protein domain families: more emphasis on 3D
-
Bru, C. et al. (2005)The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res., 33, D212-D215.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Bru, C.1
-
10
-
-
77952988108
-
A new generation of homology search tools based on probabilistic inference
-
Eddy, S. (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform., 23, 205-211.
-
(2009)
Genome Inform.
, vol.23
, pp. 205-211
-
-
Eddy, S.1
-
11
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright, A.J. et al. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
-
12
-
-
75549090603
-
The Pfam protein families database
-
Finn, R.D. et al. (2010) The Pfam protein families database. Nucleic Acids Res., 38, D211-D222.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Finn, R.D.1
-
13
-
-
67749108209
-
INDELible: a flexible simulator of biological sequence evolution
-
Fletcher, W. and Yang, Z. (2009)INDELible: a flexible simulator of biological sequence evolution.Mol. Biol. Evol., 26, 1879-1888.
-
(2009)
Mol. Biol. Evol.
, vol.26
, pp. 1879-1888
-
-
Fletcher, W.1
Yang, Z.2
-
14
-
-
77949455880
-
Enrichment of homologs in insignificant BLAST hits by cocomplex network alignment
-
Fokkens, L. et al. (2010) Enrichment of homologs in insignificant BLAST hits by cocomplex network alignment. BMC Bioinformatics, 11, 86.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 86
-
-
Fokkens, L.1
-
15
-
-
74049087026
-
Community detection in graphs
-
Fortunato, S. (2010)Community detection in graphs. Phys. Rep., 486, 75-174.
-
(2010)
Phys. Rep.
, vol.486
, pp. 75-174
-
-
Fortunato, S.1
-
16
-
-
77949911836
-
Diversity of structure and function of response regulator output domains
-
Galperin, M.Y. (2010) Diversity of structure and function of response regulator output domains.Curr. Opin. Microbiol., 13, 150-159.
-
(2010)
Curr. Opin. Microbiol.
, vol.13
, pp. 150-159
-
-
Galperin, M.Y.1
-
17
-
-
0037062448
-
Community structure in social and biological networks
-
Girvan, M. and Newman, M.E. (2002) Community structure in social and biological networks.Proc. Natl Acad. Sci. USA, 99, 7821-7826.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 7821-7826
-
-
Girvan, M.1
Newman, M.E.2
-
18
-
-
77952296596
-
Homologous over-extension: a challenge for iterative similarity searches
-
Gonzalez, M.W. and Pearson, W.R. (2010)Homologous over-extension: a challenge for iterative similarity searches. Nucleic Acids Res., 38, 2177-2189.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 2177-2189
-
-
Gonzalez, M.W.1
Pearson, W.R.2
-
19
-
-
70350572462
-
Strategies to improve the robustness of agglomerative hierarchical clustering under data source variation for speaker diarization
-
Han, K.J. et al. (2008)Strategies to improve the robustness of agglomerative hierarchical clustering under data source variation for speaker diarization. IEEE T Audio Speech, 16, 1590-1601.
-
(2008)
IEEE T Audio Speech
, vol.16
, pp. 1590-1601
-
-
Han, K.J.1
-
20
-
-
68049142320
-
Multiple alignment of DNA sequences with MAFFT
-
Katoh, K. et al. (2009) Multiple alignment of DNA sequences with MAFFT. Methods Mol. Biol., 537, 39-64.
-
(2009)
Methods Mol. Biol.
, vol.537
, pp. 39-64
-
-
Katoh, K.1
-
21
-
-
33846025119
-
Protein homology network families reveal step-wise diversification of Type III and Type IV secretion systems
-
Medini, D. et al. (2006) Protein homology network families reveal step-wise diversification of Type III and Type IV secretion systems. PLoS Comput. Biol., 2, e173.
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
Medini, D.1
-
22
-
-
79955013072
-
Ultra-fast sequence clustering from similarity networks with SiLiX
-
Miele, V. et al. (2011) Ultra-fast sequence clustering from similarity networks with SiLiX. BMC Bioinformatics, 12, 116.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 116
-
-
Miele, V.1
-
23
-
-
0442296603
-
Estimation and prediction for stochastic blockstructures
-
Nowicki, K. and Snijders, T.A.B. (2001) Estimation and prediction for stochastic blockstructures.J. Am. Stat. Assoc., 96, 1077-1087.
-
(2001)
J. Am. Stat. Assoc.
, vol.96
, pp. 1077-1087
-
-
Nowicki, K.1
Snijders, T.A.B.2
-
24
-
-
33645523636
-
Spectral clustering of protein sequences
-
Paccanaro, A. et al. (2006)Spectral clustering of protein sequences. Nucleic Acids Res., 34, 1571-1580.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 1571-1580
-
-
Paccanaro, A.1
-
25
-
-
67649115335
-
Databases of homologous gene families for comparative genomics
-
Penel, S. et al. (2009)Databases of homologous gene families for comparative genomics. BMC Bioinformatics, 10 (Suppl. 6), S3.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 6
-
-
Penel, S.1
-
26
-
-
67649123146
-
Deciphering the connectivity structure of biological networks using MixNet
-
Picard, F. et al. (2009) Deciphering the connectivity structure of biological networks using MixNet. BMC Bioinformatics, 10 (Suppl. 6), S17.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 6
-
-
Picard, F.1
-
27
-
-
37549027613
-
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
-
Pruesse, E. et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res., 35, 7188-7196.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 7188-7196
-
-
Pruesse, E.1
-
28
-
-
38549163152
-
TreeFam: 2008 update
-
Ruan, J. et al. (2008)TreeFam: 2008 update. Nucleic Acids Res., 36, D735-D740.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Ruan, J.1
-
29
-
-
0242490780
-
Cytoscape: a software environment for integrated models of biomolecular interaction networks
-
Shannon, P. et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
-
(2003)
Genome Res.
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
-
30
-
-
44949207428
-
Sequence similarity network reveals common ancestry of multidomain proteins
-
Song, N. et al. (2008) Sequence similarity network reveals common ancestry of multidomain proteins. PLoS Comput. Biol., 4, e1000063.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Song, N.1
-
31
-
-
0035162592
-
The COG database: new developments in phylogenetic classification of proteins from complete genomes
-
Tatusov, R.L. et al. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res., 29, 22-28.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 22-28
-
-
Tatusov, R.L.1
-
32
-
-
59949096873
-
EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates
-
Vilella, A.J. et al. (2009) EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res., 19, 327-335.
-
(2009)
Genome Res.
, vol.19
, pp. 327-335
-
-
Vilella, A.J.1
-
33
-
-
77952983494
-
Partitioning biological data with transitivity clustering
-
Wittkop, T. et al. (2010) Partitioning biological data with transitivity clustering. Nat. Methods, 7, 419-420.
-
(2010)
Nat. Methods
, vol.7
, pp. 419-420
-
-
Wittkop, T.1
-
34
-
-
79957514991
-
Phylogeny inference based on spectral graph clustering
-
Zhang, S.B. et al. (2011) Phylogeny inference based on spectral graph clustering. J. Comput. Biol., 18, 627-637.
-
(2011)
J. Comput. Biol.
, vol.18
, pp. 627-637
-
-
Zhang, S.B.1
|