-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
-
(1990)
J Mol Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
2
-
-
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
-
3
-
-
0141519279
-
OrthoMCL: identification of ortholog groups for eukaryotic genomes
-
10.1101/gr.1224503, 403725, 12952885
-
Li L, Stoeckert JCJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome research 2003, 13(9):2178-2189. 10.1101/gr.1224503, 403725, 12952885.
-
(2003)
Genome research
, vol.13
, Issue.9
, pp. 2178-2189
-
-
Li, L.1
Stoeckert, J.C.J.2
Roos, D.S.3
-
4
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
10.1093/bioinformatics/bti125, 15531603
-
Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005, 21(7):951-960. 10.1093/bioinformatics/bti125, 15531603.
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 951-960
-
-
Soding, J.1
-
5
-
-
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, Schaffer 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(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
6
-
-
35648986069
-
Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties
-
10.1186/1471-2105-8-356, 2048517, 17888146
-
Boekhorst J, Snel B. Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties. BMC Bioinformatics 2007, 8:356. 10.1186/1471-2105-8-356, 2048517, 17888146.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 356
-
-
Boekhorst, J.1
Snel, B.2
-
7
-
-
56949097722
-
Evolution of genome architecture
-
10.1016/j.biocel.2008.09.015, 18929678
-
Koonin EV. Evolution of genome architecture. Int J Biochem Cell Biol 2009, 41(2):298-306. 10.1016/j.biocel.2008.09.015, 18929678.
-
(2009)
Int J Biochem Cell Biol
, vol.41
, Issue.2
, pp. 298-306
-
-
Koonin, E.V.1
-
8
-
-
25844471721
-
The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species
-
10.1101/gr.3672305, 1240090, 16169922
-
Byrne KP, Wolfe KH. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res 2005, 15(10):1456-1461. 10.1101/gr.3672305, 1240090, 16169922.
-
(2005)
Genome Res
, vol.15
, Issue.10
, pp. 1456-1461
-
-
Byrne, K.P.1
Wolfe, K.H.2
-
9
-
-
34548501747
-
Natural history and evolutionary principles of gene duplication in fungi
-
10.1038/nature06107, 17805289
-
Wapinski I, Pfeffer A, Friedman N, Regev A. Natural history and evolutionary principles of gene duplication in fungi. Nature 2007, 449(7158):54-61. 10.1038/nature06107, 17805289.
-
(2007)
Nature
, vol.449
, Issue.7158
, pp. 54-61
-
-
Wapinski, I.1
Pfeffer, A.2
Friedman, N.3
Regev, A.4
-
10
-
-
45749119940
-
Prediction of enzyme function by combining sequence similarity and protein interactions
-
10.1186/1471-2105-9-249, 2430716, 18505562
-
Espadaler J, Eswar N, Querol E, Aviles FX, Sali A, Marti-Renom MA, Oliva B. Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinformatics 2008, 9:249. 10.1186/1471-2105-9-249, 2430716, 18505562.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 249
-
-
Espadaler, J.1
Eswar, N.2
Querol, E.3
Aviles, F.X.4
Sali, A.5
Marti-Renom, M.A.6
Oliva, B.7
-
11
-
-
51349087811
-
Global alignment of multiple protein interaction networks with application to functional orthology detection
-
10.1073/pnas.0806627105, 2522262,2522262, 18725631
-
Singh R, Xu J, Berger B. Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc Natl Acad Sci USA 2008, 105(35):12763-12768. 10.1073/pnas.0806627105, 2522262,2522262, 18725631.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.35
, pp. 12763-12768
-
-
Singh, R.1
Xu, J.2
Berger, B.3
-
12
-
-
33644656793
-
Systematic identification of functional orthologs based on protein network comparison
-
10.1101/gr.4526006, 1415213, 16510899
-
Bandyopadhyay S, Sharan R, Ideker T. Systematic identification of functional orthologs based on protein network comparison. Genome Res 2006, 16(3):428-435. 10.1101/gr.4526006, 1415213, 16510899.
-
(2006)
Genome Res
, vol.16
, Issue.3
, pp. 428-435
-
-
Bandyopadhyay, S.1
Sharan, R.2
Ideker, T.3
-
13
-
-
58149177166
-
Reactome knowledgebase of human biological pathways and processes
-
Database, 10.1093/nar/gkn863, 2686536, 18981052
-
Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, et al. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 2009, (37 Database):D619-622. 10.1093/nar/gkn863, 2686536, 18981052.
-
(2009)
Nucleic Acids Res
, Issue.37
-
-
Matthews, L.1
Gopinath, G.2
Gillespie, M.3
Caudy, M.4
Croft, D.5
de Bono, B.6
Garapati, P.7
Hemish, J.8
Hermjakob, H.9
Jassal, B.10
-
14
-
-
38549170927
-
MIPS: analysis and annotation of genome information in 2007
-
Database, 2238900, 18158298
-
Mewes HW, Dietmann S, Frishman D, Gregory R, Mannhaupt G, Mayer KF, Munsterkotter M, Ruepp A, Spannagl M, Stumpflen V, et al. MIPS: analysis and annotation of genome information in 2007. Nucleic Acids Res 2008, (36 Database):D196-201. 2238900, 18158298.
-
(2008)
Nucleic Acids Res
, Issue.36
-
-
Mewes, H.W.1
Dietmann, S.2
Frishman, D.3
Gregory, R.4
Mannhaupt, G.5
Mayer, K.F.6
Munsterkotter, M.7
Ruepp, A.8
Spannagl, M.9
Stumpflen, V.10
-
15
-
-
38549163153
-
CORUM: the comprehensive resource of mammalian protein complexes
-
Database, 2238909, 17965090
-
Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, Waegele B, Schmidt T, Doudieu ON, Stumpflen V, et al. CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res 2008, (36 Database):D646-650. 2238909, 17965090.
-
(2008)
Nucleic Acids Res
, Issue.36
-
-
Ruepp, A.1
Brauner, B.2
Dunger-Kaltenbach, I.3
Frishman, G.4
Montrone, C.5
Stransky, M.6
Waegele, B.7
Schmidt, T.8
Doudieu, O.N.9
Stumpflen, V.10
-
16
-
-
33644644466
-
Identification and analysis of evolutionarily cohesive functional modules in protein networks
-
10.1101/gr.4336406, 1415216, 16449501
-
Campillos M, von Mering C, Jensen LJ, Bork P. Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Research 2006, 16(3):374-382. 10.1101/gr.4336406, 1415216, 16449501.
-
(2006)
Genome Research
, vol.16
, Issue.3
, pp. 374-382
-
-
Campillos, M.1
von Mering, C.2
Jensen, L.J.3
Bork, P.4
-
17
-
-
59149100474
-
Cohesive versus flexible evolution of functional modules in eukaryotes
-
10.1371/journal.pcbi.1000276, 2615111, 19180181
-
Fokkens L, Snel B. Cohesive versus flexible evolution of functional modules in eukaryotes. PLoS Comput Biol 2009, 5(1):e1000276. 10.1371/journal.pcbi.1000276, 2615111, 19180181.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.1
-
-
Fokkens, L.1
Snel, B.2
-
18
-
-
1542286745
-
Quantifying modularity in the evolution of biomolecular systems
-
10.1101/gr.1969504, 353226, 14993205
-
Snel B, Huynen MA. Quantifying modularity in the evolution of biomolecular systems. Genome Research 2004, 14(3):391-397. 10.1101/gr.1969504, 353226, 14993205.
-
(2004)
Genome Research
, vol.14
, Issue.3
, pp. 391-397
-
-
Snel, B.1
Huynen, M.A.2
-
19
-
-
17444385984
-
Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I)
-
10.1016/j.jmb.2005.02.067, 15843018
-
Gabaldon T, Rainey D, Huynen MA. Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I). Journal of molecular biology 2005, 348(4):857-870. 10.1016/j.jmb.2005.02.067, 15843018.
-
(2005)
Journal of molecular biology
, vol.348
, Issue.4
, pp. 857-870
-
-
Gabaldon, T.1
Rainey, D.2
Huynen, M.A.3
-
20
-
-
48249138077
-
Evolution of an RNP assembly system: a minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster
-
10.1073/pnas.0802287105, 2481332, 18621711
-
Kroiss M, Schultz J, Wiesner J, Chari A, Sickmann A, Fischer U. Evolution of an RNP assembly system: a minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster. Proc Natl Acad Sci USA 2008, 105(29):10045-10050. 10.1073/pnas.0802287105, 2481332, 18621711.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.29
, pp. 10045-10050
-
-
Kroiss, M.1
Schultz, J.2
Wiesner, J.3
Chari, A.4
Sickmann, A.5
Fischer, U.6
-
21
-
-
27744554510
-
Correlation between sequence conservation and the genomic context after gene duplication
-
10.1093/nar/gki913, 1275583, 16257980
-
Notebaart RA, Huynen MA, Teusink B, Siezen RJ, Snel B. Correlation between sequence conservation and the genomic context after gene duplication. Nucleic Acids Res 2005, 33(19):6164-6171. 10.1093/nar/gki913, 1275583, 16257980.
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.19
, pp. 6164-6171
-
-
Notebaart, R.A.1
Huynen, M.A.2
Teusink, B.3
Siezen, R.J.4
Snel, B.5
-
22
-
-
58549093939
-
Complex fate of paralogs
-
10.1186/1471-2148-8-337, 2628386, 19094234
-
Szklarczyk R, Huynen MA, Snel B. Complex fate of paralogs. BMC Evol Biol 2008, 8:337. 10.1186/1471-2148-8-337, 2628386, 19094234.
-
(2008)
BMC Evol Biol
, vol.8
, pp. 337
-
-
Szklarczyk, R.1
Huynen, M.A.2
Snel, B.3
-
23
-
-
33646347144
-
The origins and evolution of functional modules: lessons from protein complexes
-
10.1098/rstb.2005.1807, 1609335, 16524839
-
Pereira-Leal JB, Levy ED, Teichmann SA. The origins and evolution of functional modules: lessons from protein complexes. Philosophical transactions of the Royal Society of London Series B, Biological sciences 2006, 361(1467):507-517. 10.1098/rstb.2005.1807, 1609335, 16524839.
-
(2006)
Philosophical transactions of the Royal Society of London Series B, Biological sciences
, vol.361
, Issue.1467
, pp. 507-517
-
-
Pereira-Leal, J.B.1
Levy, E.D.2
Teichmann, S.A.3
-
24
-
-
33746255908
-
The coordinated evolution of yeast proteins is constrained by functional modularity
-
10.1016/j.tig.2006.06.008, 16797778
-
Chen Y, Dokholyan NV. The coordinated evolution of yeast proteins is constrained by functional modularity. Trends in genetics: TIG 2006, 22(8):416-419. 10.1016/j.tig.2006.06.008, 16797778.
-
(2006)
Trends in genetics: TIG
, vol.22
, Issue.8
, pp. 416-419
-
-
Chen, Y.1
Dokholyan, N.V.2
-
25
-
-
0037178788
-
Evidence for a mediator of RNA polymerase II transcriptional regulation conserved from yeast to man
-
10.1016/S0092-8674(02)00830-9, 12150923
-
Boube M, Joulia L, Cribbs DL, Bourbon HM. Evidence for a mediator of RNA polymerase II transcriptional regulation conserved from yeast to man. Cell 2002, 110(2):143-151. 10.1016/S0092-8674(02)00830-9, 12150923.
-
(2002)
Cell
, vol.110
, Issue.2
, pp. 143-151
-
-
Boube, M.1
Joulia, L.2
Cribbs, D.L.3
Bourbon, H.M.4
-
26
-
-
34547894695
-
Reconstructing the evolution of the mitochondrial ribosomal proteome
-
10.1093/nar/gkm441, 1950548, 17604309
-
Smits P, Smeitink JA, Heuvel LP, Huynen MA, Ettema TJ. Reconstructing the evolution of the mitochondrial ribosomal proteome. Nucleic Acids Res 2007, 35(14):4686-4703. 10.1093/nar/gkm441, 1950548, 17604309.
-
(2007)
Nucleic Acids Res
, vol.35
, Issue.14
, pp. 4686-4703
-
-
Smits, P.1
Smeitink, J.A.2
Heuvel, L.P.3
Huynen, M.A.4
Ettema, T.J.5
-
27
-
-
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
-
28
-
-
13444251422
-
Ensembl 2005
-
Database, 540092, 15608235
-
Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, et al. Ensembl 2005. Nucleic Acids Res 2005, (33 Database):D447-453. 540092, 15608235.
-
(2005)
Nucleic Acids Res
, Issue.33
-
-
Hubbard, T.1
Andrews, D.2
Caccamo, M.3
Cameron, G.4
Chen, Y.5
Clamp, M.6
Clarke, L.7
Coates, G.8
Cox, T.9
Cunningham, F.10
-
29
-
-
9144257886
-
The Pfam protein families database
-
Database, 10.1093/nar/gkh121, 308855, 14681378
-
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, et al. The Pfam protein families database. Nucleic Acids Res 2004, (32 Database):D138-141. 10.1093/nar/gkh121, 308855, 14681378.
-
(2004)
Nucleic Acids Res
, Issue.32
-
-
Bateman, A.1
Coin, L.2
Durbin, R.3
Finn, R.D.4
Hollich, V.5
Griffiths-Jones, S.6
Khanna, A.7
Marshall, M.8
Moxon, S.9
Sonnhammer, E.L.10
|