-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., andLipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
2
-
-
2342651581
-
Bayesian gene/species tree reconciliation and orthology analysis using MCMC
-
Arvestad, L., Berglund, A. C., Lagergren, J., andSennblad, B. (2003). Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics 19(Suppl. 1), 7-15.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
, pp. 7-15
-
-
Arvestad, L.1
Berglund, A.C.2
Lagergren, J.3
Sennblad, B.4
-
3
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The gene ontology consortium
-
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., et al. (2000). Gene ontology: Tool for the unification of biology. The gene ontology consortium. Nat. Genet. 25, 25-29.
-
(2000)
Nat. Genet.
, vol.25
, 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
Harris, M.A.11
Hill, D.P.12
-
4
-
-
33745067419
-
The gain and loss of genes during 600 million years of vertebrate evolution
-
Blomme, T., Vandepoele, K., De Bodt, S., Simillion, C., Maere, S., andVan de Peer, Y. (2006). The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol. 7, R43.
-
(2006)
Genome Biol.
, vol.7
-
-
Blomme, T.1
Vandepoele, K.2
De Bodt, S.3
Simillion, C.4
Maere, S.5
Van De Peer, Y.6
-
5
-
-
25844471721
-
The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species
-
Byrne, K. P., andWolfe, K. H. (2005). The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15, 1456-1461.
-
(2005)
Genome Res.
, vol.15
, pp. 1456-1461
-
-
Byrne, K.P.1
Wolfe, K.H.2
-
6
-
-
46149104377
-
Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution
-
Carroll, S. B. (2008). Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution. Cell 134, 25-36.
-
(2008)
Cell
, vol.134
, pp. 25-36
-
-
Carroll, S.B.1
-
7
-
-
0038724989
-
Finding functional features in Saccharomyces genomes by phylogenetic footprinting
-
DOI 10.1126/science.1084337
-
Cliften, P., Sudarsanam, P., Desikan, A., Fulton, L., Fulton, B., Majors, J., Waterston, R., Cohen, B. A., andJohnston, M. (2003). Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301, 71-76. (Pubitemid 36801562)
-
(2003)
Science
, vol.301
, Issue.5629
, pp. 71-76
-
-
Cliften, P.1
Sudarsanam, P.2
Desikan, A.3
Fulton, L.4
Fulton, B.5
Majors, J.6
Waterston, R.7
Cohen, B.A.8
Johnston, M.9
-
8
-
-
33646230540
-
Functional partitioning of yeast co-expression networks after genome duplication
-
Conant, G. C., andWolfe, K. H. (2006). Functional partitioning of yeast co-expression networks after genome duplication. PLoS Biol. 4, e109.
-
(2006)
PLoS Biol.
, vol.4
-
-
Conant, G.C.1
Wolfe, K.H.2
-
9
-
-
18844407538
-
Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast
-
DOI 10.1534/genetics.104.036871
-
Deutschbauer, A. M., Jaramillo, D. F., Proctor, M., Kumm, J., Hillenmeyer, M. E., Davis, R. W., Nislow, C., andGiaever, G. (2005). Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics 169, 1915-1925. (Pubitemid 40695608)
-
(2005)
Genetics
, vol.169
, Issue.4
, pp. 1915-1925
-
-
Deutschbauer, A.M.1
Jaramillo, D.F.2
Proctor, M.3
Kumm, J.4
Hillenmeyer, M.E.5
Davis, R.W.6
Nislow, C.7
Giaever, G.8
-
10
-
-
11144355642
-
The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome
-
Dietrich, F. S., Voegeli, S., Brachat, S., Lerch, A., Gates, K., Steiner, S., Mohr, C., Phlmann, R., Luedi, P., Choi, S., Wing, R. A., Flavier, A., et al. (2004). The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304, 304-307.
-
(2004)
Science
, vol.304
, pp. 304-307
-
-
Dietrich, F.S.1
Voegeli, S.2
Brachat, S.3
Lerch, A.4
Gates, K.5
Steiner, S.6
Mohr, C.7
Phlmann, R.8
Luedi, P.9
Choi, S.10
Wing, R.A.11
Flavier, A.12
-
11
-
-
20744436518
-
Tree pattern matching in phylogenetic trees: Automatic search for orthologs or paralogs in homologous gene sequence databases
-
DOI 10.1093/bioinformatics/bti325
-
Dufayard, J. F., Duret, L., Penel, S., Gouy, M., Rechenmann, F., andPerrire, G. (2005). Tree pattern matching in phylogenetic trees: Automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics 21, 2596-2603. (Pubitemid 40852303)
-
(2005)
Bioinformatics
, vol.21
, Issue.11
, pp. 2596-2603
-
-
Dufayard, J.-F.1
Duret, L.2
Penel, S.3
Gouy, M.4
Rechenmann, F.5
Perriere, G.6
-
12
-
-
33645981936
-
A hybrid micro-macroevolutionary approach to gene tree reconstruction
-
Durand, D., Halldrsson, B. V., andVernot, B. (2006). A hybrid micro-macroevolutionary approach to gene tree reconstruction. J. Comput. Biol. 13, 320-335.
-
(2006)
J. Comput. Biol.
, vol.13
, pp. 320-335
-
-
Durand, D.1
Halldrsson, B.V.2
Vernot, B.3
-
13
-
-
0003516147
-
-
Cambridge University Press, Cambridge
-
Durbin, R., Eddy, S., Krogh, A., andMitchison, G. (1998). Biological sequence analysis. Cambridge University Press, Cambridge.
-
(1998)
Biological Sequence Analysis
-
-
Durbin, R.1
Eddy, S.2
Krogh, A.3
Mitchison, G.4
-
14
-
-
0031976258
-
Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis
-
Eisen, J. A. (1998). Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 8, 163-167.
-
(1998)
Genome Res.
, vol.8
, pp. 163-167
-
-
Eisen, J.A.1
-
15
-
-
0038518196
-
Phylogenomics: Intersection of evolution and genomics
-
Eisen, J. A., andFraser, C. M. (2003). Phylogenomics: Intersection of evolution and genomics. Science 300, 1706-1707.
-
(2003)
Science
, vol.300
, pp. 1706-1707
-
-
Eisen, J.A.1
Fraser, C.M.2
-
16
-
-
0036595632
-
Phylogenetic analysis and gene functional predictions: Phylogenomics in action
-
Eisen, J. A., andWu, M. (2002). Phylogenetic analysis and gene functional predictions: Phylogenomics in action. Theor. Popul. Biol. 61, 481-487.
-
(2002)
Theor. Popul. Biol.
, vol.61
, pp. 481-487
-
-
Eisen, J.A.1
Wu, M.2
-
17
-
-
33645310990
-
Protein molecular function prediction by Bayesian phylogenomics
-
Engelhardt, B. E., Jordan, M. I., Muratore, K. E., andBrenner, S. E. (2005). Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput. Biol. 1, e45.
-
(2005)
PLoS Comput. Biol.
, vol.1
-
-
Engelhardt, B.E.1
Jordan, M.I.2
Muratore, K.E.3
Brenner, S.E.4
-
18
-
-
43249118838
-
Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus
-
Fedorova, N. D., Khaldi, N., Joardar, V. S., Maiti, R., Amedeo, P., Anderson, M. J., Crabtree, J., Silva, J. C., Badger, J. H., Albarraq, A., Angiuoli, S., Bussey, H., et al. (2008). Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet. 4, e1000046.
-
(2008)
PLoS Genet.
, vol.4
-
-
Fedorova, N.D.1
Khaldi, N.2
Joardar, V.S.3
Maiti, R.4
Amedeo, P.5
Anderson, M.J.6
Crabtree, J.7
Silva, J.C.8
Badger, J.H.9
Albarraq, A.10
Angiuoli, S.11
Bussey, H.12
-
19
-
-
0003991673
-
-
Sinauer Associates, Inc., Sunderland, MA
-
Felsenstein, J. (2004). Inferring Phylogenies. Sinauer Associates, Inc., Sunderland, MA.
-
(2004)
Inferring Phylogenies
-
-
Felsenstein, J.1
-
20
-
-
0014800108
-
Distinguishing homologous from analogous proteins
-
Fitch, W. M. (1970). Distinguishing homologous from analogous proteins. Syst. Zool. 19(2), 99-113.
-
(1970)
Syst. Zool.
, vol.19
, Issue.2
, pp. 99-113
-
-
Fitch, W.M.1
-
21
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin, A. C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dmpelfeld, B., Edelmann, A., Heurtier, M. A., et al. (2006). Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636.
-
(2006)
Nature
, vol.440
, pp. 631-636
-
-
Gavin, A.C.1
Aloy, P.2
Grandi, P.3
Krause, R.4
Boesche, M.5
Marzioch, M.6
Rau, C.7
Jensen, L.J.8
Bastuck, S.9
Dmpelfeld, B.10
Edelmann, A.11
Heurtier, M.A.12
-
22
-
-
19344365947
-
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
-
Gerber, A. P., Herschlag, D., andBrown, P. O. (2004). Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol. 2, E79.
-
(2004)
PLoS Biol.
, vol.2
-
-
Gerber, A.P.1
Herschlag, D.2
Brown, P.O.3
-
23
-
-
0000365320
-
Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by Cladorams constructed from globin sequences
-
Goodman, M., Czelusniak, J., William Moore, G., Romero-Herrera, A. E., andMatsuda, G. (1979). Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by Cladorams constructed from globin sequences. Syst. Zool. 28(2), 132-163.
-
(1979)
Syst. Zool.
, vol.28
, Issue.2
, pp. 132-163
-
-
Goodman, M.1
Czelusniak, J.2
William Moore, G.3
Romero-Herrera, A.E.4
Matsuda, G.5
-
24
-
-
33749342164
-
Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human
-
Goodstadt, L., andPonting, C. (2006). Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PLoS Comput. Biol. 2(9), e133.
-
(2006)
PLoS Comput. Biol.
, vol.2
, Issue.9
-
-
Goodstadt, L.1
Ponting, C.2
-
25
-
-
2642580659
-
Duplicate genes increase gene expression diversity within and between species
-
Gu, Z., Rifkin, S. A., White, K. P., andLi, W. H. (2004). Duplicate genes increase gene expression diversity within and between species. Nat. Genet. 36, 577-579.
-
(2004)
Nat. Genet.
, vol.36
, pp. 577-579
-
-
Gu, Z.1
Rifkin, S.A.2
White, K.P.3
Li, W.H.4
-
26
-
-
36048950933
-
Gene family evolution across 12 Drosophila genomes
-
Hahn, M. W., Han, M. V., andHan, S. G. (2007). Gene family evolution across 12 Drosophila genomes. PLoS Genet. 3, e197.
-
(2007)
PLoS Genet.
, vol.3
-
-
Hahn, M.W.1
Han, M.V.2
Han, S.G.3
-
27
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., Macisaac, K. D., Danford, T. W., Hannett, N. M., Tagne, J. B., Reynolds, D. B., Yoo, J., Jennings, E. G., Zeitlinger, J., et al. (2004). Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104.
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
Macisaac, K.D.5
Danford, T.W.6
Hannett, N.M.7
Tagne, J.B.8
Reynolds, D.B.9
Yoo, J.10
Jennings, E.G.11
Zeitlinger, J.12
-
28
-
-
15544389841
-
Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution
-
DOI 10.1534/genetics.104.037051
-
He, X., andZhang, J. (2005). Rapid subfunctionalization accompanied by prolonged and substantial neo-functionalization in duplicate gene evolution. Genetics 169, 1157-1164. (Pubitemid 40404340)
-
(2005)
Genetics
, vol.169
, Issue.2
, pp. 1157-1164
-
-
He, X.1
Zhang, J.2
-
29
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton, R., Armour, C. D., Bennett, H. A., Coffey, E., Dai, H., He, Y. D., Kidd, M. J., King, A. M., et al. (2000). Functional discovery via a compendium of expression profiles. Cell 102, 109-126.
-
(2000)
Cell
, vol.102
, pp. 109-126
-
-
Hughes, T.R.1
Marton, M.J.2
Jones, A.R.3
Roberts, C.J.4
Stoughton, R.5
Armour, C.D.6
Bennett, H.A.7
Coffey, E.8
Dai, H.9
He, Y.D.10
Kidd, M.J.11
King, A.M.12
-
30
-
-
1542285166
-
A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae
-
Huisinga, K. L., andPugh, B. F. (2004). A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol. Cell 13, 573-585.
-
(2004)
Mol. Cell
, vol.13
, pp. 573-585
-
-
Huisinga, K.L.1
Pugh, B.F.2
-
31
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones, D. T., Taylor, W. R., andThornton, J. M. (1992). The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8, 275-282.
-
(1992)
Comput. Appl. Biosci.
, Issue.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
32
-
-
33645320249
-
COCO-CL: Hierarchical clustering of homology relations based on evolutionary correlations
-
Jothi, R., Zotenko, E., Tasneem, A., andPrzytycka, T. M. (2006). COCO-CL: Hierarchical clustering of homology relations based on evolutionary correlations. Bioinformatics 22, 779-788.
-
(2006)
Bioinformatics
, vol.22
, pp. 779-788
-
-
Jothi, R.1
Zotenko, E.2
Tasneem, A.3
Przytycka, T.M.4
-
33
-
-
15044353444
-
Transcription control reprogramming in genetic backup circuits
-
Kafri, R., Bar-Even, A., andPilpel, Y. (2005). Transcription control reprogramming in genetic backup circuits. Nat. Genet. 37, 295-299.
-
(2005)
Nat. Genet.
, vol.37
, pp. 295-299
-
-
Kafri, R.1
Bar-Even, A.2
Pilpel, Y.3
-
34
-
-
27244436714
-
Expansion of the Biocyc collection of pathway/genome databases to 160 genomes
-
DOI 10.1093/nar/gki892
-
Karp, P. D., Ouzounis, C. A., Moore-Kochlacs, C., Goldovsky, L., Kaipa, P., Ahrn, D., Tsoka, S., Darzentas, N., Kunin, V., andLpez-Bigas, N. (2005). Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 33, 6083-6089. (Pubitemid 41742547)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.19
, pp. 6083-6089
-
-
Karp, P.D.1
Ouzounis, C.A.2
Moore-Kochlacs, C.3
Goldovsky, L.4
Kaipa, P.5
Ahren, D.6
Tsoka, S.7
Darzentas, N.8
Kunin, V.9
Lopez-Bigas, N.10
-
35
-
-
65349186490
-
Relationship between phylogenetic distribution and genomic features in Neurospora crassa
-
Kasuga, T., Mannhaupt, G., andGlass, N. L. (2009). Relationship between phylogenetic distribution and genomic features in Neurospora crassa. PLoS One 4, e5286.
-
(2009)
PLoS One
, vol.4
-
-
Kasuga, T.1
Mannhaupt, G.2
Glass, N.L.3
-
36
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
DOI 10.1038/nature01644
-
Kellis, M., Patterson, N., Endrizzi, M., Birren, B., andLander, E. S. (2003). Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241-254. (Pubitemid 40852689)
-
(2003)
Nature
, vol.423
, Issue.6937
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
37
-
-
1942452749
-
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
-
Kellis, M., Birren, B. W., andLander, E. S. (2004a). Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428, 617-624.
-
(2004)
Nature
, vol.428
, pp. 617-624
-
-
Kellis, M.1
Birren, B.W.2
Lander, E.S.3
-
38
-
-
3142592324
-
Methods in comparative genomics: Genome correspondence, gene identification and regulatory motif discovery
-
Kellis, M., Patterson, N., Birren, B., Berger, B., and Lander, E. S. (2004b). Methods in comparative genomics: Genome correspondence, gene identification and regulatory motif discovery. J. Comput. Biol. 11, 319-355.
-
(2004)
J. Comput. Biol.
, vol.11
, pp. 319-355
-
-
Kellis, M.1
Patterson, N.2
Birren, B.3
Berger, B.4
Lander, E.S.5
-
39
-
-
52449116204
-
Elusive origins of the extra genes in Aspergillus oryzae
-
Khaldi, N., andWolfe, K. H. (2008). Elusive origins of the extra genes in Aspergillus oryzae. PLoS One 3, e3036.
-
(2008)
PLoS One
, vol.3
-
-
Khaldi, N.1
Wolfe, K.H.2
-
40
-
-
0034992826
-
The closest BLAST hit is often not the nearest neighbor
-
Koski, L. B., andGolding, G. B. (2001). The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52, 540-542.
-
(2001)
J. Mol. Evol.
, vol.52
, pp. 540-542
-
-
Koski, L.B.1
Golding, G.B.2
-
41
-
-
0141519279
-
OrthoMCL: Identification of ortholog groups for eukaryotic genomes
-
DOI 10.1101/gr.1224503
-
Li, L., Stoeckert, C. J., andRoos, D. S. (2003). OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189. (Pubitemid 37161775)
-
(2003)
Genome Research
, vol.13
, Issue.9
, pp. 2178-2189
-
-
Li, L.1
Stoeckert Jr., C.J.2
Roos, D.S.3
-
42
-
-
33644876458
-
TreeFam: A curated database of phylogenetic trees of animal gene families
-
Li, H., Coghlan, A., Ruan, J., Coin, L. J., Hrich, J. K., Osmotherly, L., Li, R., Liu, T., Zhang, Z., Bolund, L., Wong, G. K., Zheng, W., et al. (2006). TreeFam: A curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34, D572-D580.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Li, H.1
Coghlan, A.2
Ruan, J.3
Coin, L.J.4
Hrich, J.K.5
Osmotherly, L.6
Li, R.7
Liu, T.8
Zhang, Z.9
Bolund, L.10
Wong, G.K.11
Zheng, W.12
-
43
-
-
48949087976
-
Revisiting the Saccharomyces cerevisiae predicted ORFeome
-
Li, Q. R., Carvunis, A. R., Yu, H., Han, J. D., Zhong, Q., Simonis, N., Tam, S., Hao, T., Klitgord, N. J., Dupuy, D., Mou, D., Wapinski, I., et al. (2008). Revisiting the Saccharomyces cerevisiae predicted ORFeome. Genome Res. 18, 1294-1303.
-
(2008)
Genome Res.
, vol.18
, pp. 1294-1303
-
-
Li, Q.R.1
Carvunis, A.R.2
Yu, H.3
Han, J.D.4
Zhong, Q.5
Simonis, N.6
Tam, S.7
Hao, T.8
Klitgord, N.J.9
Dupuy, D.10
Mou, D.11
Wapinski, I.12
-
44
-
-
4744343021
-
The altered evolutionary trajectories of gene duplicates
-
DOI 10.1016/j.tig.2004.09.001, PII S0168952504002501
-
Lynch, M., andKatju, V. (2004). The altered evolutionary trajectories of gene duplicates. Trends Genet. 20, 544-549. (Pubitemid 39314561)
-
(2004)
Trends in Genetics
, vol.20
, Issue.11
, pp. 544-549
-
-
Lynch, M.1
Katju, V.2
-
45
-
-
0038486898
-
Divergence in the spatial pattern of gene expression between human duplicate genes
-
Makova, K. D., andLi, W. H. (2003). Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res. 13, 1638-1645.
-
(2003)
Genome Res.
, vol.13
, pp. 1638-1645
-
-
Makova, K.D.1
Li, W.H.2
-
46
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
Marcotte, E. M., Pellegrini, M., Ng, H. L., Rice, D. W., Yeates, T. O., andEisenberg, D. (1999). Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751-753.
-
(1999)
Science
, vol.285
, 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
-
47
-
-
0036081347
-
MIPS: A database for genomes and protein sequences
-
Mewes, H. W., Frishman, D., Gldener, U., Mannhaupt, G., Mayer, K., Mokrejs, M., Morgenstern, B., Mnsterktter, M., Rudd, S., andWeil, B. (2002). MIPS: A database for genomes and protein sequences. Nucleic Acids Res. 30, 31-34. (Pubitemid 34679496)
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.1
, pp. 31-34
-
-
Mewes, H.W.1
Frishman, D.2
Guldener, U.3
Mannhaupt, G.4
Mayer, K.5
Mokrejs, M.6
Morgenstern, B.7
Munsterkotter, M.8
Rudd, S.9
Weil, B.10
-
48
-
-
34248683235
-
Retention of protein complex membership by ancient duplicated gene products in budding yeast
-
DOI 10.1016/j.tig.2007.03.012, PII S016895250700114X
-
Musso, G., Zhang, Z., andEmili, A. (2007). Retention of protein complex membership by ancient duplicated gene products in budding yeast. Trends Genet. 23, 266-269. (Pubitemid 46770897)
-
(2007)
Trends in Genetics
, vol.23
, Issue.6
, pp. 266-269
-
-
Musso, G.1
Zhang, Z.2
Emili, A.3
-
49
-
-
33745220278
-
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
-
Newman, J. R., Ghaemmaghami, S., Ihmels, J., Breslow, D. K., Noble, M., DeRisi, J. L., andWeissman, J. S. (2006). Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441, 840-846.
-
(2006)
Nature
, vol.441
, pp. 840-846
-
-
Newman, J.R.1
Ghaemmaghami, S.2
Ihmels, J.3
Breslow, D.K.4
Noble, M.5
DeRisi, J.L.6
Weissman, J.S.7
-
50
-
-
0032919364
-
KEGG: Kyoto encyclopedia of genes and genomes
-
DOI 10.1093/nar/27.1.29
-
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., andKanehisa, M. (1999). KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 27, 29-34. (Pubitemid 29209394)
-
(1999)
Nucleic Acids Research
, vol.27
, Issue.1
, pp. 29-34
-
-
Ogata, H.1
Goto, S.2
Sato, K.3
Fujibuchi, W.4
Bono, H.5
Kanehisa, M.6
-
52
-
-
0038157152
-
Dosage sensitivity and the evolution of gene families in yeast
-
Papp, B., Pl, C., andHurst, L. D. (2003). Dosage sensitivity and the evolution of gene families in yeast. Nature 424, 194-197.
-
(2003)
Nature
, vol.424
, pp. 194-197
-
-
Papp, B.1
Pl, C.2
Hurst, L.D.3
-
53
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson, W. R., and Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85(8), 2444-2448.
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, Issue.8
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
54
-
-
0030928378
-
Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut, A., andGrassly, N. C. (1997). Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13(3), 235-238.
-
(1997)
Comput. Appl. Biosci.
, vol.13
, Issue.3
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.2
-
55
-
-
33847064282
-
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
-
Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B. J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., Stark, C., Ho, Y., et al. (2006). Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J. Biol. 5, 11.
-
(2006)
J. Biol.
, vol.5
, pp. 11
-
-
Reguly, T.1
Breitkreutz, A.2
Boucher, L.3
Breitkreutz, B.J.4
Hon, G.C.5
Myers, C.L.6
Parsons, A.7
Friesen, H.8
Oughtred, R.9
Tong, A.10
Stark, C.11
Ho, Y.12
-
56
-
-
0035861990
-
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
-
Remm, M., Storm, C. E., andSonnhammer, E. L. (2001). Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 314, 1041-1052.
-
(2001)
J. Mol. Biol.
, Issue.314
, pp. 1041-1052
-
-
Remm, M.1
Storm, C.E.2
Sonnhammer, E.L.3
-
57
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou, N., andNei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
-
(1987)
Mol. Biol. Evol.
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
58
-
-
33645023614
-
Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts
-
Scannell, D. R., Byrne, K. P., Gordon, J. L., Wong, S., andWolfe, K. H. (2006). Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440, 341-345.
-
(2006)
Nature
, vol.440
, pp. 1090-1098
-
-
Scannell, D.R.1
Byrne, K.P.2
Gordon, J.L.3
Wong, S.4
Wolfe, K.H.5
-
59
-
-
6944244084
-
A module map showing conditional activity of expression modules in cancer
-
Segal, E., Friedman, N., Koller, D., and Regev, A. (2004). A module map showing conditional activity of expression modules in cancer. Nat. Genet. 36, 1090-1098.
-
(2004)
Nat. Genet.
, vol.36
, pp. 1090-1098
-
-
Segal, E.1
Friedman, N.2
Koller, D.3
Regev, A.4
-
60
-
-
31544482407
-
Mapping pathways and phenotypes by systematic gene overexpression
-
DOI 10.1016/j.molcel.2005.12.011, PII S1097276505018538
-
Sopko, R., Huang, D., Preston, N., Chua, G., Papp, B., Kafadar, K., Snyder, M., Oliver, S. G., Cyert, M., Hughes, T. R., Boone, C., andAndrews, B. (2006). Mapping pathways and phenotypes by systematic gene overexpression. Mol. Cell 21, 319-330. (Pubitemid 43163527)
-
(2006)
Molecular Cell
, vol.21
, Issue.3
, pp. 319-330
-
-
Sopko, R.1
Huang, D.2
Preston, N.3
Chua, G.4
Papp, B.5
Kafadar, K.6
Snyder, M.7
Oliver, S.G.8
Cyert, M.9
Hughes, T.R.10
Boone, C.11
Andrews, B.12
-
61
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov, R. L., Koonin, E. V., andLipman, D. J. (1997). A genomic perspective on protein families. Science 278, 631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
62
-
-
33745583768
-
A genetic signature of interspecies variations in gene expression
-
Tirosh, I., Weinberger, A., Carmi, M., andBarkai, N. (2006). A genetic signature of interspecies variations in gene expression. Nat. Genet. 38, 830-834.
-
(2006)
Nat. Genet.
, vol.38
, pp. 830-834
-
-
Tirosh, I.1
Weinberger, A.2
Carmi, M.3
Barkai, N.4
-
63
-
-
0141626909
-
Detecting putative orthologs
-
Wall, D. P., Fraser, H. B., andHirsh, A. E. (2003). Detecting putative orthologs. Bioinformatics 19, 1710-1711.
-
(2003)
Bioinformatics
, vol.19
, pp. 1710-1711
-
-
Wall, D.P.1
Fraser, H.B.2
Hirsh, A.E.3
-
64
-
-
34548501747
-
Natural history and evolutionary principles of gene duplication in fungi
-
DOI 10.1038/nature06107, PII NATURE06107
-
Wapinski, I., Pfeffer, A., Friedman, N., andRegev, A. (2007a). Natural history and evolutionary principles of gene duplication in fungi. Nature 449, 54-61. (Pubitemid 47373776)
-
(2007)
Nature
, vol.449
, Issue.7158
, pp. 54-61
-
-
Wapinski, I.1
Pfeffer, A.2
Friedman, N.3
Regev, A.4
-
65
-
-
34547844121
-
Automatic genome-wide reconstruction of phylogenetic gene trees
-
DOI 10.1093/bioinformatics/btm193
-
Wapinski, I., Pfeffer, A., Friedman, N., andRegev, A. (2007b). Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics 23, i549-i558. (Pubitemid 47244442)
-
(2007)
Bioinformatics
, vol.23
, Issue.13
-
-
Wapinski, I.1
Pfeffer, A.2
Friedman, N.3
Regev, A.4
-
66
-
-
0034791426
-
A simple algorithm to infer gene duplication and speciation events on a gene tree
-
Zmasek, C. M., andEddy, S. R. (2001). A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17, 821-828.
-
(2001)
Bioinformatics
, vol.17
, pp. 821-828
-
-
Zmasek, C.M.1
Eddy, S.R.2
|