-
1
-
-
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, 96:4285-4288. 10.1073/pnas.96.8.4285, 16324, 10200254.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
2
-
-
0033832615
-
Predicting protein function by genomic context: quantitative evaluation and qualitative inferences
-
10.1101/gr.10.8.1204, 310926, 10958638
-
Huynen M, Snel B, Lathe W, Bork P. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res 10:1204-1210. 10.1101/gr.10.8.1204, 310926, 10958638.
-
Genome Res
, vol.10
, pp. 1204-1210
-
-
Huynen, M.1
Snel, B.2
Lathe, W.3
Bork, P.4
-
3
-
-
4644359828
-
Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns
-
10.1186/gb-2004-5-5-r32, 416468, 15128446
-
Glazko GV, Mushegian AR. Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns. Genome Biol 2004, 5:R32. 10.1186/gb-2004-5-5-r32, 416468, 15128446.
-
(2004)
Genome Biol
, vol.5
-
-
Glazko, G.V.1
Mushegian, A.R.2
-
4
-
-
0036259619
-
The use of phylogenetic profiles for gene predictions
-
Liberles D, Thoren A, von Heijne G, Elofsson A. The use of phylogenetic profiles for gene predictions. Current Genomics 2002, 3:131-137.
-
(2002)
Current Genomics
, vol.3
, pp. 131-137
-
-
Liberles, D.1
Thoren, A.2
von Heijne, G.3
Elofsson, A.4
-
5
-
-
55449127787
-
Predicting functional gene links from phylogenetic-statistical analyses of whole genomes
-
10.1371/journal.pcbi.0010003, 1183509, 16103904
-
Barker D, Pagel M. Predicting functional gene links from phylogenetic-statistical analyses of whole genomes. PLoS Comput Biol 2005, 1:e3. 10.1371/journal.pcbi.0010003, 1183509, 16103904.
-
(2005)
PLoS Comput Biol
, vol.1
-
-
Barker, D.1
Pagel, M.2
-
6
-
-
11244331236
-
A tree kernel to analyse phylogenetic profiles
-
Vert J. A tree kernel to analyse phylogenetic profiles. Bioinformatics 2002, 18(Suppl 1):S276-S284.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Vert, J.1
-
7
-
-
34447630272
-
An improved method for identifying functionally linked proteins using phylogenetic profiles
-
Cokus S, Mizutani S, Pellegrini M. An improved method for identifying functionally linked proteins using phylogenetic profiles. BMC Bioinformatics 2002, 8(Suppl 4):S7.
-
(2002)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 4
-
-
Cokus, S.1
Mizutani, S.2
Pellegrini, M.3
-
8
-
-
37249090179
-
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution
-
10.1098/rsif.2007.1047, 2405902, 17535793
-
Kensche PR, van Noort V, Dutilh BE, Huynen MA. Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J R Soc Interface 2008, 5:151-170. 10.1098/rsif.2007.1047, 2405902, 17535793.
-
(2008)
J R Soc Interface
, vol.5
, pp. 151-170
-
-
Kensche, P.R.1
van Noort, V.2
Dutilh, B.E.3
Huynen, M.A.4
-
9
-
-
33749608410
-
Comparative assessment of performance and genome dependence among phylogenetic profiling methods
-
10.1186/1471-2105-7-420, 1592128, 17005048
-
Snitkin ES, Gustafson AM, Mellor J, Wu J, DeLisi C. Comparative assessment of performance and genome dependence among phylogenetic profiling methods. BMC Bioinformatics 2006, 7:420. 10.1186/1471-2105-7-420, 1592128, 17005048.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 420
-
-
Snitkin, E.S.1
Gustafson, A.M.2
Mellor, J.3
Wu, J.4
DeLisi, C.5
-
10
-
-
34347374679
-
Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment
-
10.1186/1471-2105-8-173, 1904249, 17521444
-
Jothi R, Przytycka TM, Aravind L. Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics 2007, 8:173. 10.1186/1471-2105-8-173, 1904249, 17521444.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 173
-
-
Jothi, R.1
Przytycka, T.M.2
Aravind, L.3
-
11
-
-
48249103069
-
Testing the accuracy of eukaryotic phylogenetic profiles for prediction of biological function
-
Singh S, Wall DP. Testing the accuracy of eukaryotic phylogenetic profiles for prediction of biological function. Evol Bioinf 2008, 4:217-223.
-
(2008)
Evol Bioinf
, vol.4
, pp. 217-223
-
-
Singh, S.1
Wall, D.P.2
-
12
-
-
84984996500
-
The Gene Ontology project in 2008
-
10.1093/nar/gkm883, 2238979, 17984083
-
The Gene Ontology Consortium The Gene Ontology project in 2008. Nucleic Acids Res 2008, 36:D440-444. 10.1093/nar/gkm883, 2238979, 17984083.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
-
13
-
-
36949020644
-
Predicting protein function with hierarchical phylogenetic profiles: the Gene3D Phylo-Tuner method applied to eukaryotic genomes
-
Ranea JAG, Yeats C, Grant A, Orengo CA. Predicting protein function with hierarchical phylogenetic profiles: the Gene3D Phylo-Tuner method applied to eukaryotic genomes. PLoS Comput Biol 2008, 3:e237.
-
(2008)
PLoS Comput Biol
, vol.3
-
-
Ranea, J.A.G.1
Yeats, C.2
Grant, A.3
Orengo, C.A.4
-
14
-
-
40449110008
-
Coevolution of gene families in prokaryotes
-
10.1101/gr.6815508, 2259110, 18230804
-
Cordero OX, Snel B, Hogeweg P. Coevolution of gene families in prokaryotes. Genome Res 2008, 18:462-468. 10.1101/gr.6815508, 2259110, 18230804.
-
(2008)
Genome Res
, vol.18
, pp. 462-468
-
-
Cordero, O.X.1
Snel, B.2
Hogeweg, P.3
-
15
-
-
0042902833
-
The COG database: an updated version includes eukaryotes
-
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 2008, 4:41.
-
(2008)
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
-
16
-
-
65949096837
-
Co-evolutionary networks of genes and cellular processes across fungal species
-
10.1186/gb-2009-10-5-r48, 2687792, 19134172
-
Tuller T, Kupiec M, Ruppin E. Co-evolutionary networks of genes and cellular processes across fungal species. Genome Biol 2009, 10:R4. 10.1186/gb-2009-10-5-r48, 2687792, 19134172.
-
(2009)
Genome Biol
, vol.10
-
-
Tuller, T.1
Kupiec, M.2
Ruppin, E.3
-
17
-
-
0037250152
-
STRING: a database of predicted functional associations between proteins
-
10.1093/nar/gkg034, 165481, 12519996
-
von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res 2003, 31:258-261. 10.1093/nar/gkg034, 165481, 12519996.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 258-261
-
-
von Mering, C.1
Huynen, M.2
Jaeggi, D.3
Schmidt, S.4
Bork, P.5
Snel, B.6
-
18
-
-
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
-
19
-
-
59149102602
-
Phylogenetic and functional assessment of orthologs inference projects and methods
-
10.1371/journal.pcbi.1000262, 2612752, 19148271
-
Altenhoff AM, Dessimoz C. Phylogenetic and functional assessment of orthologs inference projects and methods. PloS Comput Biol 2009, 5:e1000262. 10.1371/journal.pcbi.1000262, 2612752, 19148271.
-
(2009)
PloS Comput Biol
, vol.5
-
-
Altenhoff, A.M.1
Dessimoz, C.2
-
20
-
-
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
-
21
-
-
58149203231
-
InterPro: the integrative protein signature database
-
10.1093/nar/gkn785, 2686546, 18940856
-
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJA, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res 2009, 37:D211-D215. 10.1093/nar/gkn785, 2686546, 18940856.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Hunter, S.1
Apweiler, R.2
Attwood, T.K.3
Bairoch, A.4
Bateman, A.5
Binns, D.6
Bork, P.7
Das, U.8
Daugherty, L.9
Duquenne, L.10
Finn, R.D.11
Gough, J.12
Haft, D.13
Hulo, N.14
Kahn, D.15
Kelly, E.16
Laugraud, A.17
Letunic, I.18
Lonsdale, D.19
Lopez, R.20
Madera, M.21
Maslen, J.22
McAnulla, C.23
McDowall, J.24
Mistry, J.25
Mitchell, A.26
Mulder, N.27
Natale, D.28
Orengo, C.29
Quinn, A.F.30
Selengut, J.D.31
Sigrist, C.J.A.32
Thimma, M.33
Thomas, P.D.34
Valentin, F.35
Wilson, D.36
Wu, C.H.37
Yeats, C.38
more..
-
22
-
-
36549015556
-
Inference of gene function based on gene fusion events: the rosetta-stone method
-
full_text, 18025684
-
Suhre K. Inference of gene function based on gene fusion events: the rosetta-stone method. Methods Mol Biol 2007, 396:31-41. full_text, 18025684.
-
(2007)
Methods Mol Biol
, vol.396
, pp. 31-41
-
-
Suhre, K.1
-
23
-
-
0034602344
-
A kingdom-level phylogeny of eukaryotes based on combined protein data
-
10.1126/science.290.5493.972, 11062127
-
Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 2000, 290:972-977. 10.1126/science.290.5493.972, 11062127.
-
(2000)
Science
, vol.290
, pp. 972-977
-
-
Baldauf, S.L.1
Roger, A.J.2
Wenk-Siefert, I.3
Doolittle, W.F.4
-
24
-
-
0037022379
-
The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba
-
10.1073/pnas.032662799, 122205, 11830664
-
Bapteste E, Brinkmann H, Lee JA, Moore DV, Sensen CW, Gordon P, Duruflé L, Gaasterland T, Lopez P, Müller M, Philippe H. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci USA 2002, 99:1414-1419. 10.1073/pnas.032662799, 122205, 11830664.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 1414-1419
-
-
Bapteste, E.1
Brinkmann, H.2
Lee, J.A.3
Moore, D.V.4
Sensen, C.W.5
Gordon, P.6
Duruflé, L.7
Gaasterland, T.8
Lopez, P.9
Müller, M.10
Philippe, H.11
-
25
-
-
17744386162
-
Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia
-
10.1093/molbev/msi111, 15703236
-
Philippe H, Lartillot N, Brinkmann H. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol 2005, 22:1246-1253. 10.1093/molbev/msi111, 15703236.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1246-1253
-
-
Philippe, H.1
Lartillot, N.2
Brinkmann, H.3
-
26
-
-
22744445156
-
Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes
-
10.1016/j.cub.2005.06.040, 16051178
-
Rodríguez-Ezpeleta N, Brinkmann H, Burey SC, Roure B, Burger G, Löffelhardt W, Bohnert HJ, Philippe H, Lang BF. Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Curr Biol 2005, 15:1325-1330. 10.1016/j.cub.2005.06.040, 16051178.
-
(2005)
Curr Biol
, vol.15
, pp. 1325-1330
-
-
Rodríguez-Ezpeleta, N.1
Brinkmann, H.2
Burey, S.C.3
Roure, B.4
Burger, G.5
Löffelhardt, W.6
Bohnert, H.J.7
Philippe, H.8
Lang, B.F.9
-
27
-
-
34249698083
-
Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata
-
10.1016/j.ympev.2006.11.001, 17174576
-
Moreira D, Heyden S, Bass D, López-García P, Chao E, Cavalier-Smith T. Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata. Mol Phylogenet Evol 2007, 44:255-266. 10.1016/j.ympev.2006.11.001, 17174576.
-
(2007)
Mol Phylogenet Evol
, vol.44
, pp. 255-266
-
-
Moreira, D.1
Heyden, S.2
Bass, D.3
López-García, P.4
Chao, E.5
Cavalier-Smith, T.6
-
28
-
-
0041919404
-
The root of the eukaryote tree pinpointed
-
10.1016/S0960-9822(03)00602-X, 12956967
-
Stechmann A, Cavalier-Smith T. The root of the eukaryote tree pinpointed. Curr Biol 2003, 13:R665-R666. 10.1016/S0960-9822(03)00602-X, 12956967.
-
(2003)
Curr Biol
, vol.13
-
-
Stechmann, A.1
Cavalier-Smith, T.2
-
29
-
-
84959795073
-
Phylogenetic analysis under Dollo's Law
-
Farris J. Phylogenetic analysis under Dollo's Law. Syst Zoology 1977, 26:77-88.
-
(1977)
Syst Zoology
, vol.26
, pp. 77-88
-
-
Farris, J.1
-
30
-
-
16444381885
-
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
-
10.1186/gb-2004-5-2-r7, 395751, 14759257
-
Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol 2004, 5:R7. 10.1186/gb-2004-5-2-r7, 395751, 14759257.
-
(2004)
Genome Biol
, vol.5
-
-
Koonin, E.V.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Krylov, D.M.5
Makarova, K.S.6
Mazumder, R.7
Mekhedov, S.L.8
Nikolskaya, A.N.9
Rao, B.S.10
Rogozin, I.B.11
Smirnov, S.12
Sorokin, A.V.13
Sverdlov, A.V.14
Vasudevan, S.15
Wolf, Y.I.16
Yin, J.J.17
Natale, D.A.18
-
31
-
-
33845898805
-
Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes
-
10.1093/bioinformatics/btl558, 17090580
-
Barker D, Meade A, Pagel M. Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics 2007, 23:14-20. 10.1093/bioinformatics/btl558, 17090580.
-
(2007)
Bioinformatics
, vol.23
, pp. 14-20
-
-
Barker, D.1
Meade, A.2
Pagel, M.3
-
32
-
-
42149175948
-
Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species
-
10.1073/pnas.0712248105, 2265158, 18299576
-
Martens C, Vandepoele K, de Peer YV. Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species. Proc Natl Acad Sci USA 2008, 105:3427-3432. 10.1073/pnas.0712248105, 2265158, 18299576.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 3427-3432
-
-
Martens, C.1
Vandepoele, K.2
de Peer, Y.V.3
-
33
-
-
13744252890
-
MAFFT version 5: improvement in accuracy of multiple sequence alignment
-
10.1093/nar/gki198, 548345, 15661851
-
Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 2005, 33:511-518. 10.1093/nar/gki198, 548345, 15661851.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
34
-
-
84888301229
-
TreeBest
-
Li H. TreeBest. , http://treesoft.sourceforge.net/treebest.shtml
-
-
-
Li, H.1
-
35
-
-
84888294921
-
Cliquer
-
Östergård PRJ. Cliquer. , http://users.tkk.fi/pat/cliquer.html
-
-
-
Östergård, P.R.J.1
-
36
-
-
84888296529
-
Nmclique
-
Nmclique. , http://www.cs.sunysb.edu/~algorith/implement/dimacs/distrib/color/graph
-
-
-
-
37
-
-
33846086800
-
STRING 7--recent developments in the integration and prediction of protein interactions
-
10.1093/nar/gkl825, 1669762, 17098935
-
von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P. STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 2007, 35:D358-D362. 10.1093/nar/gkl825, 1669762, 17098935.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
von Mering, C.1
Jensen, L.J.2
Kuhn, M.3
Chaffron, S.4
Doerks, T.5
Krüger, B.6
Snel, B.7
Bork, P.8
-
38
-
-
36549002108
-
Gene annotation and pathway mapping in KEGG
-
full_text, 18025687
-
Aoki-Kinoshita KF, Kanehisa M. Gene annotation and pathway mapping in KEGG. Methods Mol Biol 2007, 396:71-91. full_text, 18025687.
-
(2007)
Methods Mol Biol
, vol.396
, pp. 71-91
-
-
Aoki-Kinoshita, K.F.1
Kanehisa, M.2
-
39
-
-
0041358614
-
Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages
-
Date SV, Marcotte EM. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nature Biotechnol 2003, 21:1055-1062.
-
(2003)
Nature Biotechnol
, vol.21
, pp. 1055-1062
-
-
Date, S.V.1
Marcotte, E.M.2
|