-
1
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
10.1038/35001009 10688190
-
Uetz P Giot L Cagney G Mansfield TA Judson RS Knight JR Lockshon D Narayan V Srinivasan M Pochart P A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 2000 403 6770 623-627 10.1038/35001009 10688190
-
(2000)
Nature
, vol.403
, Issue.6770
, pp. 623-627
-
-
Uetz, P.1
Giot, L.2
Cagney, G.3
Mansfield, T.A.4
Judson, R.S.5
Knight, J.R.6
Lockshon, D.7
Narayan, V.8
Srinivasan, M.9
Pochart, P.10
-
2
-
-
0035836765
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome
-
31875 11283351 10.1073/pnas.061034498
-
Ito T Chiba T Ozawa R Yoshida M Hattori M Sakaki Y A comprehensive two-hybrid analysis to explore the yeast protein interactome Proc Natl Acad Sci USA 2001 98 8 4569-4574 31875 11283351 10.1073/pnas.061034498
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, Issue.8
, pp. 4569-4574
-
-
Ito, T.1
Chiba, T.2
Ozawa, R.3
Yoshida, M.4
Hattori, M.5
Sakaki, Y.6
-
3
-
-
0035843145
-
The protein-protein interaction map of Helicobacter pylori
-
10.1038/35051615 11196647
-
Rain JC Selig L De Reuse H Battaglia V Reverdy C Simon S Lenzen G Petel F Wojcik J Schachter V The protein-protein interaction map of Helicobacter pylori Nature 2001 409 6817 211-215 10.1038/35051615 11196647
-
(2001)
Nature
, vol.409
, Issue.6817
, pp. 211-215
-
-
Rain, J.C.1
Selig, L.2
De Reuse, H.3
Battaglia, V.4
Reverdy, C.5
Simon, S.6
Lenzen, G.7
Petel, F.8
Wojcik, J.9
Schachter, V.10
-
4
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
10.1038/415141a 11805826
-
Gavin AC Bosche M Krause R Grandi P Marzioch M Bauer A Schultz J Rick JM Michon AM Cruciat CM Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 2002 415 6868 141-147 10.1038/415141a 11805826
-
(2002)
Nature
, vol.415
, Issue.6868
, pp. 141-147
-
-
Gavin, A.C.1
Bosche, M.2
Krause, R.3
Grandi, P.4
Marzioch, M.5
Bauer, A.6
Schultz, J.7
Rick, J.M.8
Michon, A.M.9
Cruciat, C.M.10
-
5
-
-
0345600247
-
A protein interaction map of Drosophila melanogaster
-
10.1126/science.1090289 14605208
-
Giot L Bader JS Brouwer C Chaudhuri A Kuang B Li Y Hao YL Ooi CE Godwin B Vitols E A protein interaction map of Drosophila melanogaster Science 2003 302 5651 1727-1736 10.1126/science.1090289 14605208
-
(2003)
Science
, vol.302
, Issue.5651
, pp. 1727-1736
-
-
Giot, L.1
Bader, J.S.2
Brouwer, C.3
Chaudhuri, A.4
Kuang, B.5
Li, Y.6
Hao, Y.L.7
Ooi, C.E.8
Godwin, B.9
Vitols, E.10
-
6
-
-
13444283630
-
Interaction network containing conserved and essential protein complexes in Escherichia coli
-
10.1038/nature03239 15690043
-
Butland G Peregrin-Alvarez JM Li J Yang W Yang X Canadien V Starostine A Richards D Beattie B Krogan N Interaction network containing conserved and essential protein complexes in Escherichia coli Nature 2005 433 7025 531-537 10.1038/nature03239 15690043
-
(2005)
Nature
, vol.433
, Issue.7025
, pp. 531-537
-
-
Butland, G.1
Peregrin-Alvarez, J.M.2
Li, J.3
Yang, W.4
Yang, X.5
Canadien, V.6
Starostine, A.7
Richards, D.8
Beattie, B.9
Krogan, N.10
-
7
-
-
27144530248
-
Towards a proteome-scale map of the human protein-protein interaction network
-
10.1038/nature04209 16189514
-
Rual JF Venkatesan K Hao T Hirozane-Kishikawa T Dricot A Li N Berriz GF Gibbons FD Dreze M Ayivi-Guedehoussou N Towards a proteome-scale map of the human protein-protein interaction network Nature 2005 437 7062 1173-1178 10.1038/nature04209 16189514
-
(2005)
Nature
, vol.437
, Issue.7062
, pp. 1173-1178
-
-
Rual, J.F.1
Venkatesan, K.2
Hao, T.3
Hirozane-Kishikawa, T.4
Dricot, A.5
Li, N.6
Berriz, G.F.7
Gibbons, F.D.8
Dreze, M.9
Ayivi-Guedehoussou, N.10
-
8
-
-
25144498379
-
A human protein-protein interaction network: A resource for annotating the proteome
-
10.1016/j.cell.2005.08.029 16169070
-
Stelzl U Worm U Lalowski M Haenig C Brembeck FH Goehler H Stroedicke M Zenkner M Schoenherr A Koeppen S A human protein-protein interaction network: A resource for annotating the proteome Cell 2005 122 6 957-968 10.1016/j.cell.2005.08.029 16169070
-
(2005)
Cell
, vol.122
, Issue.6
, pp. 957-968
-
-
Stelzl, U.1
Worm, U.2
Lalowski, M.3
Haenig, C.4
Brembeck, F.H.5
Goehler, H.6
Stroedicke, M.7
Zenkner, M.8
Schoenherr, A.9
Koeppen, S.10
-
9
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
10.1038/nature04670 16554755
-
Krogan NJ Cagney G Yu H Zhong G Guo X Ignatchenko A Li J Pu S Datta N Tikuisis AP Global landscape of protein complexes in the yeast Saccharomyces cerevisiae Nature 2006 440 7084 637-643 10.1038/ nature04670 16554755
-
(2006)
Nature
, vol.440
, Issue.7084
, pp. 637-643
-
-
Krogan, N.J.1
Cagney, G.2
Yu, H.3
Zhong, G.4
Guo, X.5
Ignatchenko, A.6
Li, J.7
Pu, S.8
Datta, N.9
Tikuisis, A.P.10
-
10
-
-
0033523989
-
Protein interaction maps for complete genomes based on gene fusion events
-
10.1038/47056 10573422
-
Enright AJ Iliopoulos I Kyrpides NC Ouzounis CA Protein interaction maps for complete genomes based on gene fusion events Nature 1999 402 6757 86-90 10.1038/47056 10573422
-
(1999)
Nature
, vol.402
, Issue.6757
, pp. 86-90
-
-
Enright, A.J.1
Iliopoulos, I.2
Kyrpides, N.C.3
Ouzounis, C.A.4
-
11
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
10.1126/science.285.5428.751 10427000
-
Marcotte EM Pellegrini M Ng HL Rice DW Yeates TO Eisenberg D Detecting protein function and protein-protein interactions from genome sequences Science 1999 285 5428 751-753 10.1126/science.285.5428.751 10427000
-
(1999)
Science
, vol.285
, Issue.5428
, pp. 751-753
-
-
Marcotte, E.M.1
Pellegrini, M.2
Ng, H.L.3
Rice, D.W.4
Yeates, T.O.5
Eisenberg, D.6
-
12
-
-
0031024670
-
Conserved clusters of functionally related genes in two bacterial genomes
-
10.1007/PL00006122 9010137
-
Tamames J Casari G Ouzounis C Valencia A Conserved clusters of functionally related genes in two bacterial genomes J Mol Evol 1997 44 1 66-73 10.1007/PL00006122 9010137
-
(1997)
J Mol Evol
, vol.44
, Issue.1
, pp. 66-73
-
-
Tamames, J.1
Casari, G.2
Ouzounis, C.3
Valencia, A.4
-
13
-
-
0032169271
-
Conservation of gene order: A fingerprint of proteins that physically interact
-
10.1016/S0968-0004(98)01274-2 9787636
-
Dandekar T Snel B Huynen M Bork P Conservation of gene order: A fingerprint of proteins that physically interact Trends Biochem Sci 1998 23 9 324-328 10.1016/S0968-0004(98)01274-2 9787636
-
(1998)
Trends Biochem Sci
, vol.23
, Issue.9
, pp. 324-328
-
-
Dandekar, T.1
Snel, B.2
Huynen, M.3
Bork, P.4
-
15
-
-
0030660581
-
A genomic perspective on protein families
-
10.1126/science.278.5338.631 9381173
-
Tatusov RL Koonin EV Lipman DJ A genomic perspective on protein families Science 1997 278 5338 631-637 10.1126/science.278.5338.631 9381173
-
(1997)
Science
, vol.278
, Issue.5338
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
16
-
-
0032568582
-
Measuring genome evolution
-
34486 9600883 10.1073/pnas.95.11.5849
-
Huynen MA Bork P Measuring genome evolution Proc Natl Acad Sci USA 1998 95 11 5849-5856 34486 9600883 10.1073/pnas.95.11.5849
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, Issue.11
, pp. 5849-5856
-
-
Huynen, M.A.1
Bork, P.2
-
17
-
-
0032242111
-
Microbial genescapes: Phyletic and functional patterns of ORF distribution among prokaryotes
-
10027190
-
Gaasterland T Ragan MA Microbial genescapes: Phyletic and functional patterns of ORF distribution among prokaryotes Microb Comp Genomics 1998 3 4 199-217 10027190
-
(1998)
Microb Comp Genomics
, vol.3
, Issue.4
, pp. 199-217
-
-
Gaasterland, T.1
Ragan, M.A.2
-
18
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
16324 10200254 10.1073/pnas.96.8.4285
-
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 16324 10200254 10.1073/pnas.96.8.4285
-
(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
-
19
-
-
0034595516
-
Co-evolution of proteins with their interaction partners
-
10.1006/jmbi.2000.3732 10860738
-
Goh CS Bogan AA Joachimiak M Walther D Cohen FE Co-evolution of proteins with their interaction partners J Mol Biol 2000 299 2 283-293 10.1006/ jmbi.2000.3732 10860738
-
(2000)
J Mol Biol
, vol.299
, Issue.2
, pp. 283-293
-
-
Goh, C.S.1
Bogan, A.A.2
Joachimiak, M.3
Walther, D.4
Cohen, F.E.5
-
20
-
-
0035177259
-
Similarity of phylogenetic trees as indicator of protein-protein interaction
-
10.1093/protein/14.9.609 11707606
-
Pazos F Valencia A Similarity of phylogenetic trees as indicator of protein-protein interaction Protein Eng 2001 14 9 609-614 10.1093/ protein/14.9.609 11707606
-
(2001)
Protein Eng
, vol.14
, Issue.9
, pp. 609-614
-
-
Pazos, F.1
Valencia, A.2
-
21
-
-
0036435908
-
Co-evolutionary analysis reveals insights into protein-protein interactions
-
10.1016/S0022-2836(02)01038-0 12421567
-
Goh CS Cohen FE Co-evolutionary analysis reveals insights into protein-protein interactions J Mol Biol 2002 324 1 177-192 10.1016/ S0022-2836(02)01038-0 12421567
-
(2002)
J Mol Biol
, vol.324
, Issue.1
, pp. 177-192
-
-
Goh, C.S.1
Cohen, F.E.2
-
22
-
-
0037436412
-
Exploiting the co-evolution of interacting proteins to discover interaction specificity
-
10.1016/S0022-2836(03)00114-1 12614624
-
Ramani AK Marcotte EM Exploiting the co-evolution of interacting proteins to discover interaction specificity J Mol Biol 2003 327 1 273-284 10.1016/S0022-2836(03)00114-1 12614624
-
(2003)
J Mol Biol
, vol.327
, Issue.1
, pp. 273-284
-
-
Ramani, A.K.1
Marcotte, E.M.2
-
23
-
-
0242559070
-
Inferring protein interactions from phylogenetic distance matrices
-
10.1093/bioinformatics/btg278 14594708
-
Gertz J Elfond G Shustrova A Weisinger M Pellegrini M Cokus S Rothschild B Inferring protein interactions from phylogenetic distance matrices Bioinformatics 2003 19 16 2039-2045 10.1093/bioinformatics/btg278 14594708
-
(2003)
Bioinformatics
, vol.19
, Issue.16
, pp. 2039-2045
-
-
Gertz, J.1
Elfond, G.2
Shustrova, A.3
Weisinger, M.4
Pellegrini, M.5
Cokus, S.6
Rothschild, B.7
-
24
-
-
29144461552
-
Predicting protein-protein interaction by searching evolutionary tree automorphism space
-
1618802 15961463 10.1093/bioinformatics/bti1009
-
Jothi R Kann MG Przytycka TM Predicting protein-protein interaction by searching evolutionary tree automorphism space Bioinformatics 2005 21 Suppl 1 i241-i250 1618802 15961463 10.1093/bioinformatics/bti1009
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Jothi, R.1
Kann, M.G.2
Przytycka, T.M.3
-
25
-
-
24644502565
-
Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome
-
10.1016/j.jmb.2005.07.005 16139301
-
Pazos F Ranea JA Juan D Sternberg MJ Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome J Mol Biol 2005 352 4 1002-1015 10.1016/j.jmb.2005.07.005 16139301
-
(2005)
J Mol Biol
, vol.352
, Issue.4
, pp. 1002-1015
-
-
Pazos, F.1
Ranea, J.A.2
Juan, D.3
Sternberg, M.J.4
-
26
-
-
24144476642
-
The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships
-
10.1093/bioinformatics/bti564 15994190
-
Sato T Yamanishi Y Kanehisa M Toh H The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships Bioinformatics 2005 21 17 3482-3489 10.1093/bioinformatics/bti564 15994190
-
(2005)
Bioinformatics
, vol.21
, Issue.17
, pp. 3482-3489
-
-
Sato, T.1
Yamanishi, Y.2
Kanehisa, M.3
Toh, H.4
-
27
-
-
33748333117
-
Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein protein interactions
-
1618801 16949097
-
Jothi R Cherukuri PF Tasneem A Przytycka TM Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein protein interactions J Mol Biol 2006 1618801 16949097
-
(2006)
J Mol Biol
-
-
Jothi, R.1
Cherukuri, P.F.2
Tasneem, A.3
Przytycka, T.M.4
-
28
-
-
34248513211
-
Predicting protein domain interactions from coevolution of conserved regions
-
10.1002/prot.21347 17357158
-
Kann MG Jothi R Cherukuri PF Przytycka TM Predicting protein domain interactions from coevolution of conserved regions Proteins 2007 67 4 811-820 10.1002/prot.21347 17357158
-
(2007)
Proteins
, vol.67
, Issue.4
, pp. 811-820
-
-
Kann, M.G.1
Jothi, R.2
Cherukuri, P.F.3
Przytycka, T.M.4
-
29
-
-
2942695714
-
Coevolution of gene expression among interacting proteins
-
439012 15175431 10.1073/pnas.0402591101
-
Fraser HB Hirsh AE Wall DP Eisen MB Coevolution of gene expression among interacting proteins Proc Natl Acad Sci USA 2004 101 24 9033-9038 439012 15175431 10.1073/pnas.0402591101
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.24
, pp. 9033-9038
-
-
Fraser, H.B.1
Hirsh, A.E.2
Wall, D.P.3
Eisen, M.B.4
-
30
-
-
25444531429
-
Computational verification of protein-protein interactions by orthologous co-expression
-
555590 15740634 10.1186/1471-2105-6-40
-
Tirosh I Barkai N Computational verification of protein-protein interactions by orthologous co-expression BMC Bioinformatics 2005 6 40 555590 15740634 10.1186/1471-2105-6-40
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 40
-
-
Tirosh, I.1
Barkai, N.2
-
31
-
-
55449127787
-
Predicting functional gene links from phylogenetic-statistical analyses of whole genomes
-
1183509 16103904 10.1371/journal.pcbi.0010003
-
Barker D Pagel M Predicting functional gene links from phylogenetic-statistical analyses of whole genomes PLoS Comput Biol 2005 1 1 e3 1183509 16103904 10.1371/journal.pcbi.0010003
-
(2005)
PLoS Comput Biol
, vol.1
-
-
Barker, D.1
Pagel, M.2
-
32
-
-
33744829032
-
Inferring functional linkages between proteins from evolutionary scenarios
-
10.1016/j.jmb.2006.04.011 16674974
-
Zhou Y Wang R Li L Xia X Sun Z Inferring functional linkages between proteins from evolutionary scenarios J Mol Biol 2006 359 4 1150-1159 10.1016/j.jmb.2006.04.011 16674974
-
(2006)
J Mol Biol
, vol.359
, Issue.4
, pp. 1150-1159
-
-
Zhou, Y.1
Wang, R.2
Li, L.3
Xia, X.4
Sun, Z.5
-
33
-
-
0036225307
-
Comparative analysis of chloroplast genomes: Functional annotation, genome-based phylogeny, and deduced evolutionary patterns
-
187516 11932241 10.1101/gr.209402
-
De Las Rivas J Lozano JJ Ortiz AR Comparative analysis of chloroplast genomes: Functional annotation, genome-based phylogeny, and deduced evolutionary patterns Genome Res 2002 12 4 567-583 187516 11932241 10.1101/gr.209402
-
(2002)
Genome Res
, vol.12
, Issue.4
, pp. 567-583
-
-
De Las Rivas, J.1
Lozano, J.J.2
Ortiz, A.R.3
-
34
-
-
0036081482
-
Predictome: A database of putativefunctional links between proteins
-
99135 11752322 10.1093/nar/30.1.306
-
Mellor JC Yanai I Clodfelter KH Mintseris J DeLisi C Predictome: A database of putativefunctional links between proteins Nucleic Acids Res 2002 30 1 306-309 99135 11752322 10.1093/nar/30.1.306
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.1
, pp. 306-309
-
-
Mellor, J.C.1
Yanai, I.2
Clodfelter, K.H.3
Mintseris, J.4
DeLisi, C.5
-
35
-
-
0037125989
-
Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae
-
129455 12200547 10.1073/pnas.182380799
-
Tettelin H Masignani V Cieslewicz MJ Eisen JA Peterson S Wessels MR Paulsen IT Nelson KE Margarit I Read TD Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae Proc Natl Acad Sci USA 2002 99 19 12391-12396 129455 12200547 10.1073/pnas.182380799
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, Issue.19
, pp. 12391-12396
-
-
Tettelin, H.1
Masignani, V.2
Cieslewicz, M.J.3
Eisen, J.A.4
Peterson, S.5
Wessels, M.R.6
Paulsen, I.T.7
Nelson, K.E.8
Margarit, I.9
Read, T.D.10
-
36
-
-
0038486918
-
The balance of driving forces during genome evolution in prokaryotes
-
403731 12840037 10.1101/gr.1092603
-
Kunin V Ouzounis CA The balance of driving forces during genome evolution in prokaryotes Genome Res 2003 13 7 1589-1594 403731 12840037 10.1101/gr.1092603
-
(2003)
Genome Res
, vol.13
, Issue.7
, pp. 1589-1594
-
-
Kunin, V.1
Ouzounis, C.A.2
-
37
-
-
0037458108
-
Trait-to-gene: A computational method for predicting the function of uncharacterized genes
-
10.1016/S0960-9822(03)00009-5 12546786
-
Levesque M Shasha D Kim W Surette MG Benfey PN Trait-to-gene: A computational method for predicting the function of uncharacterized genes Curr Biol 2003 13 2 129-133 10.1016/S0960-9822(03)00009-5 12546786
-
(2003)
Curr Biol
, vol.13
, Issue.2
, pp. 129-133
-
-
Levesque, M.1
Shasha, D.2
Kim, W.3
Surette, M.G.4
Benfey, P.N.5
-
38
-
-
0038104835
-
Comparing bacterial genomes through conservation profiles
-
430882 12695324 10.1101/gr.678303
-
Martin MJ Herrero J Mateos A Dopazo J Comparing bacterial genomes through conservation profiles Genome Res 2003 13 5 991-998 430882 12695324 10.1101/gr.678303
-
(2003)
Genome Res
, vol.13
, Issue.5
, pp. 991-998
-
-
Martin, M.J.1
Herrero, J.2
Mateos, A.3
Dopazo, J.4
-
39
-
-
0037350415
-
The phylogenetic extent of metabolic enzymes and pathways
-
430287 12618373 10.1101/gr.246903
-
Peregrin-Alvarez JM Tsoka S Ouzounis CA The phylogenetic extent of metabolic enzymes and pathways Genome Res 2003 13 3 422-427 430287 12618373 10.1101/gr.246903
-
(2003)
Genome Res
, vol.13
, pp. 422-427
-
-
Peregrin-Alvarez, J.M.1
Tsoka, S.2
Ouzounis, C.A.3
-
40
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
403769 14597658 10.1101/gr.1239303
-
Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N Schwikowski B Ideker T Cytoscape: A software environment for integrated models of biomolecular interaction networks Genome Res 2003 13 11 2498-2504 403769 14597658 10.1101/gr.1239303
-
(2003)
Genome Res
, vol.13
, Issue.11
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
41
-
-
0037249403
-
MBGD: Microbial genome database for comparative analysis
-
165556 12519947 10.1093/nar/gkg109
-
Uchiyama I MBGD: Microbial genome database for comparative analysis Nucleic Acids Res 2003 31 1 58-62 165556 12519947 10.1093/nar/gkg109
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.1
, pp. 58-62
-
-
Uchiyama, I.1
-
42
-
-
0037250152
-
STRING: A database of predicted functional associations between proteins
-
165481 12519996 10.1093/nar/gkg034
-
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 165481 12519996 10.1093/nar/gkg034
-
(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
-
43
-
-
0042889111
-
Identification of functional links between genes using phylogenetic profiles
-
10.1093/bioinformatics/btg187 12912833
-
Wu J Kasif S DeLisi C Identification of functional links between genes using phylogenetic profiles Bioinformatics 2003 19 12 1524-1530 10.1093/ bioinformatics/btg187 12912833
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1524-1530
-
-
Wu, J.1
Kasif, S.2
DeLisi, C.3
-
44
-
-
3042615963
-
Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1
-
419780 15140832 10.1101/gr.1993504
-
Baliga NS Bjork SJ Bonneau R Pan M Iloanusi C Kottemann MC Hood L DiRuggiero J Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1 Genome Res 2004 14 6 1025-1035 419780 15140832 10.1101/gr.1993504
-
(2004)
Genome Res
, vol.14
, Issue.6
, pp. 1025-1035
-
-
Baliga, N.S.1
Bjork, S.J.2
Bonneau, R.3
Pan, M.4
Iloanusi, C.5
Kottemann, M.C.6
Hood, L.7
DiRuggiero, J.8
-
45
-
-
8744235102
-
Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea
-
525680 15520287 10.1101/gr.2700304
-
Baliga NS Bonneau R Facciotti MT Pan M Glusman G Deutsch EW Shannon P Chiu Y Weng RS Gan RR Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea Genome Res 2004 14 11 2221-2234 525680 15520287 10.1101/gr.2700304
-
(2004)
Genome Res
, vol.14
, Issue.11
, pp. 2221-2234
-
-
Baliga, N.S.1
Bonneau, R.2
Facciotti, M.T.3
Pan, M.4
Glusman, G.5
Deutsch, E.W.6
Shannon, P.7
Chiu, Y.8
Weng, R.S.9
Gan, R.R.10
-
46
-
-
10044281116
-
Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1
-
507877 15287974 10.1186/gb-2004-5-8-r52
-
Bonneau R Baliga NS Deutsch EW Shannon P Hood L Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1 Genome Biol 2004 5 8 R52 507877 15287974 10.1186/ gb-2004-5-8-r52
-
(2004)
Genome Biol
, vol.5
, Issue.8
-
-
Bonneau, R.1
Baliga, N.S.2
Deutsch, E.W.3
Shannon, P.4
Hood, L.5
-
47
-
-
6044244615
-
'Conserved hypothetical' proteins: Prioritization of targets for experimental study
-
524295 15479782 10.1093/nar/gkh885
-
Galperin MY Koonin EV 'Conserved hypothetical' proteins: Prioritization of targets for experimental study Nucleic Acids Res 2004 32 18 5452-5463 524295 15479782 10.1093/nar/gkh885
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.18
, pp. 5452-5463
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
48
-
-
4444301196
-
Phylogenetic profiling of the Arabidopsis thaliana proteome: What proteins distinguish plants from other organisms?
-
507878 15287975 10.1186/gb-2004-5-8-r53
-
Gutierrez RA Green PJ Keegstra K Ohlrogge JB Phylogenetic profiling of the Arabidopsis thaliana proteome: What proteins distinguish plants from other organisms? Genome Biol 2004 5 8 R53 507878 15287975 10.1186/ gb-2004-5-8-r53
-
(2004)
Genome Biol
, vol.5
, Issue.8
-
-
Gutierrez, R.A.1
Green, P.J.2
Keegstra, K.3
Ohlrogge, J.B.4
-
49
-
-
4444351940
-
The plant-specific database. Classification of Arabidopsis proteins based on their phylogenetic profile
-
520760 15326280 10.1104/pp.104.043687
-
Gutierrez RA Larson MD Wilkerson C The plant-specific database. Classification of Arabidopsis proteins based on their phylogenetic profile Plant Physiol 2004 135 4 1888-1892 520760 15326280 10.1104/ pp.104.043687
-
(2004)
Plant Physiol
, vol.135
, Issue.4
, pp. 1888-1892
-
-
Gutierrez, R.A.1
Larson, M.D.2
Wilkerson, C.3
-
50
-
-
0346505465
-
A cross-genomic approach for systematic mapping of phenotypic traits to genes
-
314287 14707173 10.1101/gr.1586704
-
Jim K Parmar K Singh M Tavazoie S A cross-genomic approach for systematic mapping of phenotypic traits to genes Genome Res 2004 14 1 109-115 314287 14707173 10.1101/gr.1586704
-
(2004)
Genome Res
, vol.14
, Issue.1
, pp. 109-115
-
-
Jim, K.1
Parmar, K.2
Singh, M.3
Tavazoie, S.4
-
51
-
-
8744308029
-
Properties of overlapping genes are conserved across microbial genomes
-
525685 15520290 10.1101/gr.2433104
-
Johnson ZI Chisholm SW Properties of overlapping genes are conserved across microbial genomes Genome Res 2004 14 11 2268-2272 525685 15520290 10.1101/gr.2433104
-
(2004)
Genome Res
, vol.14
, Issue.11
, pp. 2268-2272
-
-
Johnson, Z.I.1
Chisholm, S.W.2
-
52
-
-
3543106033
-
Genome-wide identification of genes likely to be involved in human genetic disease
-
434425 15181176 10.1093/nar/gkh605
-
Lopez-Bigas N Ouzounis CA Genome-wide identification of genes likely to be involved in human genetic disease Nucleic Acids Res 2004 32 10 3108-3114 434425 15181176 10.1093/nar/gkh605
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.10
, pp. 3108-3114
-
-
Lopez-Bigas, N.1
Ouzounis, C.A.2
-
53
-
-
1542286754
-
Comparative analysis of protein domain organization
-
535408 14993202 10.1101/gr.1610504
-
Ye Y Godzik A Comparative analysis of protein domain organization Genome Res 2004 14 3 343-353 535408 14993202 10.1101/gr.1610504
-
(2004)
Genome Res
, vol.14
, Issue.3
, pp. 343-353
-
-
Ye, Y.1
Godzik, A.2
-
55
-
-
14644418424
-
Improving genome annotations using phylogenetic profile anomaly detection
-
10.1093/bioinformatics/bti027 15374867
-
Mikkelsen TS Galagan JE Mesirov JP Improving genome annotations using phylogenetic profile anomaly detection Bioinformatics 2005 21 4 464-470 10.1093/bioinformatics/bti027 15374867
-
(2005)
Bioinformatics
, vol.21
, Issue.4
, pp. 464-470
-
-
Mikkelsen, T.S.1
Galagan, J.E.2
Mesirov, J.P.3
-
56
-
-
14544283040
-
An exponential core in the heart of the yeast protein interaction network
-
10.1093/molbev/msi024 15496552
-
Pereira-Leal JB Audit B Peregrin-Alvarez JM Ouzounis CA An exponential core in the heart of the yeast protein interaction network Mol Biol Evol 2005 22 3 421-425 10.1093/molbev/msi024 15496552
-
(2005)
Mol Biol Evol
, vol.22
, Issue.3
, pp. 421-425
-
-
Pereira-Leal, J.B.1
Audit, B.2
Peregrin-Alvarez, J.M.3
Ouzounis, C.A.4
-
57
-
-
14644388890
-
Making connections between novel transcription factors and their DNA motifs
-
546533 15653829 10.1101/gr.3069205
-
Tan K McCue LA Stormo GD Making connections between novel transcription factors and their DNA motifs Genome Res 2005 15 2 312-320 546533 15653829 10.1101/gr.3069205
-
(2005)
Genome Res
, vol.15
, Issue.2
, pp. 312-320
-
-
Tan, K.1
McCue, L.A.2
Stormo, G.D.3
-
58
-
-
28444484981
-
Identifying the conserved network of cis-regulatory sites of a eukaryotic genome
-
1297658 16301543 10.1073/pnas.0505147102
-
Wang T Stormo GD Identifying the conserved network of cis-regulatory sites of a eukaryotic genome Proc Natl Acad Sci USA 2005 102 48 17400-17405 1297658 16301543 10.1073/pnas.0505147102
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.48
, pp. 17400-17405
-
-
Wang, T.1
Stormo, G.D.2
-
59
-
-
33748542591
-
Prediction of functional modules based on gene distributions in microbial genomes
-
16901107
-
Wu H Mao F Su Z Olman V Xu Y Prediction of functional modules based on gene distributions in microbial genomes Genome Inform 2005 16 2 247-259 16901107
-
(2005)
Genome Inform
, vol.16
, Issue.2
, pp. 247-259
-
-
Wu, H.1
Mao, F.2
Su, Z.3
Olman, V.4
Xu, Y.5
-
60
-
-
19144367138
-
Prediction of functional modules based on comparative genome analysis and Gene Ontology application
-
1130488 15901854 10.1093/nar/gki573
-
Wu H Su Z Mao F Olman V Xu Y Prediction of functional modules based on comparative genome analysis and Gene Ontology application Nucleic Acids Res 2005 33 9 2822-2837 1130488 15901854 10.1093/nar/gki573
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.9
, pp. 2822-2837
-
-
Wu, H.1
Su, Z.2
Mao, F.3
Olman, V.4
Xu, Y.5
-
61
-
-
34548216842
-
Life in hot carbon monoxide: The complete genome sequence of Carboxydothermus hydrogenoformans Z-2901
-
1287953 16311624 10.1371/journal.pgen.0010065
-
Wu M Ren Q Durkin AS Daugherty SC Brinkac LM Dodson RJ Madupu R Sullivan SA Kolonay JF Haft DH Life in hot carbon monoxide: The complete genome sequence of Carboxydothermus hydrogenoformans Z-2901 PLoS Genet 2005 1 5 e65 1287953 16311624 10.1371/journal.pgen.0010065
-
(2005)
PLoS Genet
, vol.1
, Issue.5
-
-
Wu, M.1
Ren, Q.2
Durkin, A.S.3
Daugherty, S.C.4
Brinkac, L.M.5
Dodson, R.J.6
Madupu, R.7
Sullivan, S.A.8
Kolonay, J.F.9
Haft, D.H.10
-
62
-
-
33747817416
-
Roundup: A multi-genome repository of orthologs and evolutionary distances
-
10.1093/bioinformatics/btl286 16777906
-
Deluca TF Wu IH Pu J Monaghan T Peshkin L Singh S Wall DP Roundup: A multi-genome repository of orthologs and evolutionary distances Bioinformatics 2006 22 16 2044-2046 10.1093/bioinformatics/btl286 16777906
-
(2006)
Bioinformatics
, vol.22
, Issue.16
, pp. 2044-2046
-
-
Deluca, T.F.1
Wu, I.H.2
Pu, J.3
Monaghan, T.4
Peshkin, L.5
Singh, S.6
Wall, D.P.7
-
63
-
-
33747139057
-
The outcomes of pathway database computations depend on pathway ontology
-
1540720 16893953 10.1093/nar/gkl438
-
Green ML Karp PD The outcomes of pathway database computations depend on pathway ontology Nucleic Acids Res 2006 34 13 3687-3697 1540720 16893953 10.1093/nar/gkl438
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.13
, pp. 3687-3697
-
-
Green, M.L.1
Karp, P.D.2
-
64
-
-
30344442462
-
Inferring functional information from domain co-evolution
-
10.1093/bioinformatics/bti723 16301205
-
Kim Y Koyuturk M Topkara U Grama A Subramaniam S Inferring functional information from domain co-evolution Bioinformatics 2006 22 1 40-49 10.1093/bioinformatics/bti723 16301205
-
(2006)
Bioinformatics
, vol.22
, Issue.1
, pp. 40-49
-
-
Kim, Y.1
Koyuturk, M.2
Topkara, U.3
Grama, A.4
Subramaniam, S.5
-
65
-
-
33644845048
-
Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships
-
10.1002/prot.20830 16385560
-
Kim Y Subramaniam S Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships Proteins 2006 62 4 1115-1124 10.1002/prot.20830 16385560
-
(2006)
Proteins
, vol.62
, Issue.4
, pp. 1115-1124
-
-
Kim, Y.1
Subramaniam, S.2
-
66
-
-
31844441997
-
Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis
-
1360294 16428773 10.1128/IAI.74.2.1233-1242.2006
-
Rachman H Strong M Ulrichs T Grode L Schuchhardt J Mollenkopf H Kosmiadi GA Eisenberg D Kaufmann SH Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis Infect Immun 2006 74 2 1233-1242 1360294 16428773 10.1128/IAI.74.2.1233-1242.2006
-
(2006)
Infect Immun
, vol.74
, Issue.2
, pp. 1233-1242
-
-
Rachman, H.1
Strong, M.2
Ulrichs, T.3
Grode, L.4
Schuchhardt, J.5
Mollenkopf, H.6
Kosmiadi, G.A.7
Eisenberg, D.8
Kaufmann, S.H.9
-
67
-
-
33644870184
-
Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102
-
1363776 16473855 10.1093/nar/gkj496
-
Su Z Mao F Dam P Wu H Olman V Paulsen IT Palenik B Xu Y Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102 Nucleic Acids Res 2006 34 3 1050-1065 1363776 16473855 10.1093/nar/gkj496
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.3
, pp. 1050-1065
-
-
Su, Z.1
Mao, F.2
Dam, P.3
Wu, H.4
Olman, V.5
Paulsen, I.T.6
Palenik, B.7
Xu, Y.8
-
68
-
-
33646823661
-
Identification of fungal sphingolipid C9-methyltransferases by phylogenetic profiling
-
10.1074/jbc.M512864200 16339149
-
Ternes P Sperling P Albrecht S Franke S Cregg JM Warnecke D Heinz E Identification of fungal sphingolipid C9-methyltransferases by phylogenetic profiling J Biol Chem 2006 281 9 5582-5592 10.1074/ jbc.M512864200 16339149
-
(2006)
J Biol Chem
, vol.281
, Issue.9
, pp. 5582-5592
-
-
Ternes, P.1
Sperling, P.2
Albrecht, S.3
Franke, S.4
Cregg, J.M.5
Warnecke, D.6
Heinz, E.7
-
69
-
-
31644444476
-
MaGe: A microbial genome annotation system supported by synteny results
-
1326237 16407324 10.1093/nar/gkj406
-
Vallenet D Labarre L Rouy Z Barbe V Bocs S Cruveiller S Lajus A Pascal G Scarpelli C Medigue C MaGe: A microbial genome annotation system supported by synteny results Nucleic Acids Res 2006 34 1 53-65 1326237 16407324 10.1093/nar/gkj406
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.1
, pp. 53-65
-
-
Vallenet, D.1
Labarre, L.2
Rouy, Z.3
Barbe, V.4
Bocs, S.5
Cruveiller, S.6
Lajus, A.7
Pascal, G.8
Scarpelli, C.9
Medigue, C.10
-
70
-
-
33644780644
-
Gene annotation and network inference by phylogenetic profiling
-
1388238 16503966 10.1186/1471-2105-7-80
-
Wu J Hu Z DeLisi C Gene annotation and network inference by phylogenetic profiling BMC Bioinformatics 2006 7 80 1388238 16503966 10.1186/ 1471-2105-7-80
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 80
-
-
Wu, J.1
Hu, Z.2
DeLisi, C.3
-
71
-
-
0037057376
-
Genomic functional annotation using co-evolution profiles of gene clusters
-
RESEARCH0060 133444 12429059 10.1186/gb-2002-3-11-research0060
-
Zheng Y Roberts RJ Kasif S Genomic functional annotation using co-evolution profiles of gene clusters Genome Biol 2002 3 11 RESEARCH0060 133444 12429059 10.1186/gb-2002-3-11-research0060
-
(2002)
Genome Biol
, vol.3
, Issue.11
-
-
Zheng, Y.1
Roberts, R.J.2
Kasif, S.3
-
72
-
-
0041358614
-
Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages
-
10.1038/nbt861 12923548
-
Date SV Marcotte EM Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages Nat Biotechnol 2003 21 9 1055-1062 10.1038/nbt861 12923548
-
(2003)
Nat Biotechnol
, vol.21
, Issue.9
, pp. 1055-1062
-
-
Date, S.V.1
Marcotte, E.M.2
-
73
-
-
0347364646
-
Genome evolution reveals biochemical networks and functional modules
-
307584 14673105 10.1073/pnas.2136809100
-
von Mering C Zdobnov EM Tsoka S Ciccarelli FD Pereira-Leal JB Ouzounis CA Bork P Genome evolution reveals biochemical networks and functional modules Proc Natl Acad Sci USA 2003 100 26 15428-15433 307584 14673105 10.1073/pnas.2136809100
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.26
, pp. 15428-15433
-
-
von Mering, C.1
Zdobnov, E.M.2
Tsoka, S.3
Ciccarelli, F.D.4
Pereira-Leal, J.B.5
Ouzounis, C.A.6
Bork, P.7
-
74
-
-
4644359828
-
Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns
-
416468 15128446 10.1186/gb-2004-5-5-r32
-
Glazko GV Mushegian AR Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns Genome Biol 2004 5 5 R32 416468 15128446 10.1186/gb-2004-5-5-r32
-
(2004)
Genome Biol
, vol.5
, Issue.5
-
-
Glazko, G.V.1
Mushegian, A.R.2
-
75
-
-
11144319853
-
Use of logic relationships to decipher protein network organization
-
10.1126/science.1103330 15618515
-
Bowers PM Cokus SJ Eisenberg D Yeates TO Use of logic relationships to decipher protein network organization Science 2004 306 5705 2246-2249 10.1126/science.1103330 15618515
-
(2004)
Science
, vol.306
, Issue.5705
, pp. 2246-2249
-
-
Bowers, P.M.1
Cokus, S.J.2
Eisenberg, D.3
Yeates, T.O.4
-
76
-
-
9444239213
-
A probabilistic functional network of yeast genes
-
10.1126/science.1099511 15567862
-
Lee I Date SV Adai AT Marcotte EM A probabilistic functional network of yeast genes Science 2004 306 5701 1555-1558 10.1126/science.1099511 15567862
-
(2004)
Science
, vol.306
, Issue.5701
, pp. 1555-1558
-
-
Lee, I.1
Date, S.V.2
Adai, A.T.3
Marcotte, E.M.4
-
77
-
-
27144556456
-
Utilizing logical relationships in genomic data to decipher cellular processes
-
10.1111/j.1742-4658.2005.04946.x 16218945
-
Bowers PM O'Connor BD Cokus SJ Sprinzak E Yeates TO Eisenberg D Utilizing logical relationships in genomic data to decipher cellular processes Febs J 2005 272 20 5110-5118 10.1111/j.1742-4658.2005.04946.x 16218945
-
(2005)
Febs J
, vol.272
, Issue.20
, pp. 5110-5118
-
-
Bowers, P.M.1
O'Connor, B.D.2
Cokus, S.J.3
Sprinzak, E.4
Yeates, T.O.5
Eisenberg, D.6
-
78
-
-
33745942567
-
Extraction of phylogenetic network modules from the metabolic network
-
1501048 16533389 10.1186/1471-2105-7-130
-
Yamada T Kanehisa M Goto S Extraction of phylogenetic network modules from the metabolic network BMC Bioinformatics 2006 7 130 1501048 16533389 10.1186/1471-2105-7-130
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 130
-
-
Yamada, T.1
Kanehisa, M.2
Goto, S.3
-
79
-
-
33644644466
-
Identification and analysis of evolutionarily cohesive functional modules in protein networks
-
1415216 16449501 10.1101/gr.4336406
-
Campillos M von Mering C Jensen LJ Bork P Identification and analysis of evolutionarily cohesive functional modules in protein networks Genome Res 2006 16 374-382 1415216 16449501 10.1101/gr.4336406
-
(2006)
Genome Res
, vol.16
, pp. 374-382
-
-
Campillos, M.1
von Mering, C.2
Jensen, L.J.3
Bork, P.4
-
80
-
-
1542286745
-
Quantifying modularity in the evolution of biomolecular systems
-
353226 14993205 10.1101/gr.1969504
-
Snel B Huynen MA Quantifying modularity in the evolution of biomolecular systems Genome Res 2004 14 3 391-397 353226 14993205 10.1101/gr.1969504
-
(2004)
Genome Res
, vol.14
, Issue.3
, pp. 391-397
-
-
Snel, B.1
Huynen, M.A.2
-
81
-
-
0034710981
-
Localizing proteins in the cell from their phylogenetic profiles
-
17303 11035803 10.1073/pnas.220399497
-
Marcotte EM Xenarios I van Der Bliek AM Eisenberg D Localizing proteins in the cell from their phylogenetic profiles Proc Natl Acad Sci USA 2000 97 22 12115-12120 17303 11035803 10.1073/pnas.220399497
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, Issue.22
, pp. 12115-12120
-
-
Marcotte, E.M.1
Xenarios, I.2
van Der Bliek, A.M.3
Eisenberg, D.4
-
82
-
-
24044546509
-
Refined phylogenetic profiles method for predicting protein-protein interactions
-
10.1093/bioinformatics/bti532 15947018
-
Sun J Xu J Liu Z Liu Q Zhao A Shi T Li Y Refined phylogenetic profiles method for predicting protein-protein interactions Bioinformatics 2005 21 16 3409-3415 10.1093/bioinformatics/bti532 15947018
-
(2005)
Bioinformatics
, vol.21
, Issue.16
, pp. 3409-3415
-
-
Sun, J.1
Xu, J.2
Liu, Z.3
Liu, Q.4
Zhao, A.5
Shi, T.6
Li, Y.7
-
84
-
-
0346252661
-
Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps
-
291866 14654685 10.1093/nar/gkg924
-
Strong M Graeber TG Beeby M Pellegrini M Thompson MJ Yeates TO Eisenberg D Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps Nucleic Acids Res 2003 31 24 7099-7109 291866 14654685 10.1093/nar/gkg924
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.24
, pp. 7099-7109
-
-
Strong, M.1
Graeber, T.G.2
Beeby, M.3
Pellegrini, M.4
Thompson, M.J.5
Yeates, T.O.6
Eisenberg, D.7
-
85
-
-
0347824672
-
Inference of protein functionand protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: A combined computational approach
-
193659 12952538 10.1186/gb-2003-4-9-r59
-
Strong M Mallick P Pellegrini M Thompson MJ Eisenberg D Inference of protein functionand protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: A combined computational approach Genome Biol 2003 4 9 R59 193659 12952538 10.1186/gb-2003-4-9-r59
-
(2003)
Genome Biol
, vol.4
, Issue.9
-
-
Strong, M.1
Mallick, P.2
Pellegrini, M.3
Thompson, M.J.4
Eisenberg, D.5
-
86
-
-
4644231028
-
Prolinks: A database of protein functional linkages derived from coevolution
-
416471 15128449 10.1186/gb-2004-5-5-r35
-
Bowers PM Pellegrini M Thompson MJ Fierro J Yeates TO Eisenberg D Prolinks: A database of protein functional linkages derived from coevolution Genome Biol 2004 5 5 R35 416471 15128449 10.1186/ gb-2004-5-5-r35
-
(2004)
Genome Biol
, vol.5
, Issue.5
-
-
Bowers, P.M.1
Pellegrini, M.2
Thompson, M.J.3
Fierro, J.4
Yeates, T.O.5
Eisenberg, D.6
-
87
-
-
9244239761
-
A domain interaction map based on phylogenetic profiling
-
10.1016/j.jmb.2004.10.019 15561146
-
Pagel P Wong P Frishman D A domain interaction map based on phylogenetic profiling J Mol Biol 2004 344 5 1331-1346 10.1016/j.jmb.2004.10.019 15561146
-
(2004)
J Mol Biol
, vol.344
, Issue.5
, pp. 1331-1346
-
-
Pagel, P.1
Wong, P.2
Frishman, D.3
-
89
-
-
33749608410
-
Comparative assessment of performance and genome dependence among phylogenetic profiling methods
-
17005048 10.1186/1471-2105-7-420
-
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 1592128 17005048 10.1186/1471-2105-7-420
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.420
, pp. 420
-
-
Snitkin, E.S.1
Gustafson, A.M.2
Mellor, J.3
Wu, J.4
DeLisi, C.5
-
90
-
-
19544393944
-
Protein function prediction using the Protein Link EXplorer (PLEX)
-
10.1093/bioinformatics/bti313 15701682
-
Date SV Marcotte EM Protein function prediction using the Protein Link EXplorer (PLEX) Bioinformatics 2005 21 10 2558-2559 10.1093/ bioinformatics/bti313 15701682
-
(2005)
Bioinformatics
, vol.21
, Issue.10
, pp. 2558-2559
-
-
Date, S.V.1
Marcotte, E.M.2
-
91
-
-
84886763400
-
KEGG Orthology
-
KEGG Orthology http://www.genome.jp/dbget-bin/get_htext?KO+-s+F+-f+F+B
-
-
-
-
92
-
-
13844271592
-
Detection of parallel functional modules by comparative analysis of genome sequences
-
10.1038/nbt1065 15696156
-
Li H Pellegrini M Eisenberg D Detection of parallel functional modules by comparative analysis of genome sequences Nat Biotechnol 2005 23 2 253-260 10.1038/nbt1065 15696156
-
(2005)
Nat Biotechnol
, vol.23
, Issue.2
, pp. 253-260
-
-
Li, H.1
Pellegrini, M.2
Eisenberg, D.3
-
93
-
-
2342526611
-
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
-
419445 15121896 10.1093/nar/gkh555
-
Kolker E Makarova KS Shabalina S Picone AF Purvine S Holzman T Cherny T Armbruster D Munson RS Jr Kolesov G Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae Nucleic Acids Res 2004 32 8 2353-2361 419445 15121896 10.1093/nar/gkh555
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.8
, pp. 2353-2361
-
-
Kolker, E.1
Makarova, K.S.2
Shabalina, S.3
Picone, A.F.4
Purvine, S.5
Holzman, T.6
Cherny, T.7
Armbruster, D.8
Munson Jr., R.S.9
Kolesov, G.10
-
94
-
-
2942622384
-
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes
-
149225 12515582 10.1186/1471-2148-3-2
-
Mirkin BG Fenner TI Galperin MY Koonin EV Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes BMC Evol Biol 2003 3 2 149225 12515582 10.1186/1471-2148-3-2
-
(2003)
BMC Evol Biol
, vol.3
, pp. 2
-
-
Mirkin, B.G.1
Fenner, T.I.2
Galperin, M.Y.3
Koonin, E.V.4
-
95
-
-
0036846746
-
The origin and evolution of model organisms
-
10.1038/nrg929 12415314
-
Hedges SB The origin and evolution of model organisms Nat Rev Genet 2002 3 11 838-849 10.1038/nrg929 12415314
-
(2002)
Nat Rev Genet
, vol.3
, Issue.11
, pp. 838-849
-
-
Hedges, S.B.1
|