-
1
-
-
20444430245
-
A scan for positively selected genes in the genomes of humans and chimpanzees
-
Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, et al. (2005) A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 3: e170.
-
(2005)
PLoS Biol
, vol.3
-
-
Nielsen, R.1
Bustamante, C.2
Clark, A.G.3
Glanowski, S.4
Sackton, T.B.5
-
2
-
-
0034708444
-
Comparative genomics of the eukaryotes
-
Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, et al. (2000) Comparative genomics of the eukaryotes. Science 287: 2204-2215.
-
(2000)
Science
, vol.287
, pp. 2204-2215
-
-
Rubin, G.M.1
Yandell, M.D.2
Wortman, J.R.3
Gabor, M.G.L.4
Nelson, C.R.5
-
3
-
-
2542542256
-
Ultraconserved elements in the human genome
-
Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, et al. (2004) Ultraconserved elements in the human genome. Science 304: 1321-1325.
-
(2004)
Science
, vol.304
, pp. 1321-1325
-
-
Bejerano, G.1
Pheasant, M.2
Makunin, I.3
Stephen, S.4
Kent, W.J.5
-
4
-
-
22344454794
-
Ultraconserved elements in insect genomes: A highly conserved intronic sequence implicated in the control of homothorax mRNA splicing
-
Glazov EA, Pheasant M, McGraw EA, Bejerano G, Mattick JS (2005) Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Res 15: 800-808.
-
(2005)
Genome Res
, vol.15
, pp. 800-808
-
-
Glazov, E.A.1
Pheasant, M.2
McGraw, E.A.3
Bejerano, G.4
Mattick, J.S.5
-
5
-
-
0037158715
-
Molecular evolution of FOXP2, a gene involved in speech and language
-
Enard W, Przeworski M, Fisher SE, Lai CS, Wiebe V, et al. (2002) Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418: 869-872.
-
(2002)
Nature
, vol.418
, pp. 869-872
-
-
Enard, W.1
Przeworski, M.2
Fisher, S.E.3
Lai, C.S.4
Wiebe, V.5
-
6
-
-
2942737273
-
Molecular evolution of microcephalin, a gene determining human brain size
-
Wang YQ, Su B (2004) Molecular evolution of microcephalin, a gene determining human brain size. Hum Mol Genet 13: 1131-1137.
-
(2004)
Hum Mol Genet
, vol.13
, pp. 1131-1137
-
-
Wang, Y.Q.1
Su, B.2
-
7
-
-
22144447840
-
Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees
-
Khaitovich P, Hellmann I, Enard W, Nowick K, Leinweber M, et al. (2005) Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 309: 1850-1854.
-
(2005)
Science
, vol.309
, pp. 1850-1854
-
-
Khaitovich, P.1
Hellmann, I.2
Enard, W.3
Nowick, K.4
Leinweber, M.5
-
8
-
-
0037313182
-
Evolution of gene expression in the Drosophila melanogaster subgroup
-
Rifkin SA, Kim J, White KP (2003) Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet 33: 138-144.
-
(2003)
Nat Genet
, vol.33
, pp. 138-144
-
-
Rifkin, S.A.1
Kim, J.2
White, K.P.3
-
9
-
-
19344374050
-
Similarities and differences in genomewide expression data of six organisms
-
Bergmann S, Ihmels J, Barkai N (2004) Similarities and differences in genomewide expression data of six organisms. PLoS Biol 2: E9.
-
(2004)
PLoS Biol
, vol.2
-
-
Bergmann, S.1
Ihmels, J.2
Barkai, N.3
-
10
-
-
0037941585
-
Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
-
Segal E, Shapira M, Regev A, Péer D, Botstein D, et al. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 34: 166-176.
-
(2003)
Nat Genet
, vol.34
, pp. 166-176
-
-
Segal, E.1
Shapira, M.2
Regev, A.3
Péer, D.4
Botstein, D.5
-
11
-
-
23944458138
-
A general framework for weighted gene coexpression network analysis
-
Article
-
Zhang B, Horvath S (2005) A general framework for weighted gene coexpression network analysis. Stat Appl Genet Mol Biol 4: Article17.
-
(2005)
Stat Appl Genet Mol Biol
, vol.4
, pp. 17
-
-
Zhang, B.1
Horvath, S.2
-
12
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL (2002) Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555.
-
(2002)
Science
, vol.297
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
13
-
-
33749991402
-
Global similarity and local divergence in human and mouse gene co-expression networks
-
Tsaparas P, Marino-Ramirez L, Bodenreider O, Koonin EV, Jordan IK (2006) Global similarity and local divergence in human and mouse gene co-expression networks. BMC Evol Biol 6: 70.
-
(2006)
BMC Evol Biol
, vol.6
, pp. 70
-
-
Tsaparas, P.1
Marino-Ramirez, L.2
Bodenreider, O.3
Koonin, E.V.4
Jordan, I.K.5
-
14
-
-
34249818182
-
Tissue-specific transcriptional regulation has diverged significantly between human and mouse
-
Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, et al. (2007) Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet 39: 730-732.
-
(2007)
Nat Genet
, vol.39
, pp. 730-732
-
-
Odom, D.T.1
Dowell, R.D.2
Jacobsen, E.S.3
Gordon, W.4
Danford, T.W.5
-
15
-
-
0033028596
-
Systematic determination of genetic network architecture
-
Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM (1999) Systematic determination of genetic network architecture. Nat Genet 22: 281-285.
-
(1999)
Nat Genet
, vol.22
, pp. 281-285
-
-
Tavazoie, S.1
Hughes, J.D.2
Campbell, M.J.3
Cho, R.J.4
Church, G.M.5
-
16
-
-
0033027794
-
Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
-
Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, et al. (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 96: 2907-2912.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 2907-2912
-
-
Tamayo, P.1
Slonim, D.2
Mesirov, J.3
Zhu, Q.4
Kitareewan, S.5
-
18
-
-
0036699526
-
Revealing modular organization in the yeast transcriptional network
-
Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, et al. (2002) Revealing modular organization in the yeast transcriptional network. Nat Genet 31: 370-377.
-
(2002)
Nat Genet
, vol.31
, pp. 370-377
-
-
Ihmels, J.1
Friedlander, G.2
Bergmann, S.3
Sarig, O.4
Ziv, Y.5
-
19
-
-
4544339167
-
Defining transcription modules using large-scale gene expression data
-
Ihmels J, Bergmann S, Barkai N (2004) Defining transcription modules using large-scale gene expression data. Bioinformatics 20: 1993-2003.
-
(2004)
Bioinformatics
, vol.20
, pp. 1993-2003
-
-
Ihmels, J.1
Bergmann, S.2
Barkai, N.3
-
20
-
-
84864994884
-
Iterative signature algorithm for the analysis of large-scale gene expression data
-
Bergmann S, Ihmels J, Barkai N (2003) Iterative signature algorithm for the analysis of large-scale gene expression data. Phys Rev E Stat Nonlin Soft Matter Phys 67: 031902.
-
(2003)
Phys Rev E Stat Nonlin Soft Matter Phys
, vol.67
, pp. 031902
-
-
Bergmann, S.1
Ihmels, J.2
Barkai, N.3
-
21
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes
-
Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101: 6062-6067.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 6062-6067
-
-
Su, A.I.1
Wiltshire, T.2
Batalov, S.3
Lapp, H.4
Ching, K.A.5
-
22
-
-
35748937331
-
Construction, visualisation, and clustering of transcription networks from microarray expression data
-
Freeman TC, Goldovsky L, Brosch M, van Dongen S, Maziere P, et al. (2007) Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol 3: 2032-2042.
-
(2007)
PLoS Comput Biol
, vol.3
, pp. 2032-2042
-
-
Freeman, T.C.1
Goldovsky, L.2
Brosch, M.3
van Dongen, S.4
Maziere, P.5
-
23
-
-
33748352373
-
Multiple knockout analysis of genetic robustness in the yeast metabolic network
-
Deutscher D, Meilijson I, Kupiec M, Ruppin E (2006) Multiple knockout analysis of genetic robustness in the yeast metabolic network. Nat Genet 38: 993-998.
-
(2006)
Nat Genet
, vol.38
, pp. 993-998
-
-
Deutscher, D.1
Meilijson, I.2
Kupiec, M.3
Ruppin, E.4
-
24
-
-
7644238181
-
Biological robustness
-
Kitano H (2004) Biological robustness. Nat Rev Genet 5: 826-837.
-
(2004)
Nat Rev Genet
, vol.5
, pp. 826-837
-
-
Kitano, H.1
-
25
-
-
33751327438
-
Comparative gene expression analysis by differential clustering approach: Application to the Candida albicans transcription program
-
Ihmels J, Bergmann S, Berman J, Barkai N (2005) Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program. PLoS Genet 1: e39.
-
(2005)
PLoS Genet
, vol.1
-
-
Ihmels, J.1
Bergmann, S.2
Berman, J.3
Barkai, N.4
-
26
-
-
0346095291
-
Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae
-
Ihmels J, Levy R, Barkai N (2004) Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat Biotechnol 22: 86-92.
-
(2004)
Nat Biotechnol
, vol.22
, pp. 86-92
-
-
Ihmels, J.1
Levy, R.2
Barkai, N.3
-
27
-
-
0035733690
-
Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae
-
Ge H, Liu Z, Church GM, Vidal M (2001) Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 29: 482-486.
-
(2001)
Nat Genet
, vol.29
, pp. 482-486
-
-
Ge, H.1
Liu, Z.2
Church, G.M.3
Vidal, M.4
-
28
-
-
35349024501
-
Network modeling links breast cancer susceptibility and centrosome dysfunction
-
Pujana MA, Han JD, Starita LM, Stevens KN, Tewari M, et al. (2007) Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet 39: 1338-1349.
-
(2007)
Nat Genet
, vol.39
, pp. 1338-1349
-
-
Pujana, M.A.1
Han, J.D.2
Starita, L.M.3
Stevens, K.N.4
Tewari, M.5
-
29
-
-
34347329333
-
In search of the biological significance of modular structures in protein networks
-
Wang Z, Zhang J (2007) In search of the biological significance of modular structures in protein networks. PLoS Comput Biol 3: e107.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Wang, Z.1
Zhang, J.2
-
30
-
-
0037177560
-
Evolutionary rate in the protein interaction network
-
Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW (2002) Evolutionary rate in the protein interaction network. Science 296: 750-752.
-
(2002)
Science
, vol.296
, pp. 750-752
-
-
Fraser, H.B.1
Hirsh, A.E.2
Steinmetz, L.M.3
Scharfe, C.4
Feldman, M.W.5
-
31
-
-
16844363315
-
Modularity and evolutionary constraint on proteins
-
Fraser HB (2005) Modularity and evolutionary constraint on proteins. Nat Genet 37: 351-352.
-
(2005)
Nat Genet
, vol.37
, pp. 351-352
-
-
Fraser, H.B.1
-
33
-
-
52949087576
-
A genomewide functional network for the laboratory mouse
-
Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, et al. (2008) A genomewide functional network for the laboratory mouse. PLoS Comput Biol 4: e1000165.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Guan, Y.1
Myers, C.L.2
Lu, R.3
Lemischka, I.R.4
Bult, C.J.5
-
34
-
-
65349169643
-
The correlation of evolutionary rate with pathway position in plant terpenoid biosynthesis
-
Ramsay H, Rieseberg LH, Ritland K (2009) The correlation of evolutionary rate with pathway position in plant terpenoid biosynthesis. Mol Biol Evol 26(5):1045-1053.
-
(2009)
Mol Biol Evol
, vol.26
, Issue.5
, pp. 1045-1053
-
-
Ramsay, H.1
Rieseberg, L.H.2
Ritland, K.3
-
35
-
-
33749579409
-
Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins
-
Liao BY, Scott NM, Zhang J (2006) Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins. Mol Biol Evol 23: 2072-2080.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 2072-2080
-
-
Liao, B.Y.1
Scott, N.M.2
Zhang, J.3
-
36
-
-
41149119083
-
The role of disorder in interaction networks: A structural analysis
-
Kim PM, Sboner A, Xia Y, Gerstein M (2008) The role of disorder in interaction networks: a structural analysis. Mol Syst Biol 4: 179.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 179
-
-
Kim, P.M.1
Sboner, A.2
Xia, Y.3
Gerstein, M.4
-
37
-
-
12344269924
-
TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
-
Boyle EI, Weng S, Gollub J, Jin H, Botstein D, et al. (2004) GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20: 3710-3715.
-
(2004)
Bioinformatics
, vol.20
, pp. 3710-3715
-
-
Boyle, E.I.1
Weng, S.2
Gollub, J.3
Jin, H.4
Botstein, D.5
-
38
-
-
54249099196
-
Species-specific transcription in mice carrying human chromosome 21
-
Wilson MD, Barbosa-Morais NL, Schmidt D, Conboy CM, Vanes L, et al. (2008) Species-specific transcription in mice carrying human chromosome 21. Science 322: 434-438.
-
(2008)
Science
, vol.322
, pp. 434-438
-
-
Wilson, M.D.1
Barbosa-Morais, N.L.2
Schmidt, D.3
Conboy, C.M.4
Vanes, L.5
-
39
-
-
33750964227
-
Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup
-
Yu XJ, Zheng HK, Wang J, Wang W, Su B (2006) Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup. Genomics 88: 745-751.
-
(2006)
Genomics
, vol.88
, pp. 745-751
-
-
Yu, X.J.1
Zheng, H.K.2
Wang, J.3
Wang, W.4
Su, B.5
-
40
-
-
0036947892
-
Robust estimators for expression analysis
-
Hubbell E, Liu WM, Mei R (2002) Robust estimators for expression analysis. Bioinformatics 18: 1585-1592.
-
(2002)
Bioinformatics
, vol.18
, pp. 1585-1592
-
-
Hubbell, E.1
Liu, W.M.2
Mei, R.3
-
41
-
-
10844290766
-
Model-Based Background Adjustment for Oligonucleotide Expression Arrays
-
Wu Z, Irizarry R, Gentleman R, Martinez-Murillo F, Spencer FA (2004) Model-Based Background Adjustment for Oligonucleotide Expression Arrays. Journal of the American Statistical Association 99: 909.
-
(2004)
Journal of The American Statistical Association
, vol.99
, pp. 909
-
-
Wu, Z.1
Irizarry, R.2
Gentleman, R.3
Martinez-Murillo, F.4
Spencer, F.A.5
-
42
-
-
24744438019
-
Gene expression evolves faster in narrowly than in broadly expressed mammalian genes
-
Yang J, Su AI, Li WH (2005) Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Mol Biol Evol 22: 2113-2118.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 2113-2118
-
-
Yang, J.1
Su, A.I.2
Li, W.H.3
-
43
-
-
33646882591
-
Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution
-
Liao BY, Zhang J (2006) Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution. Mol Biol Evol 23: 1119-1128.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1119-1128
-
-
Liao, B.Y.1
Zhang, J.2
-
45
-
-
0037172779
-
Metal ion requirements for structure and catalysis of an RNA ligase ribozyme
-
Glasner ME, Bergman NH, Bartel DP (2002) Metal ion requirements for structure and catalysis of an RNA ligase ribozyme. Biochemistry 41: 8103-8112.
-
(2002)
Biochemistry
, vol.41
, pp. 8103-8112
-
-
Glasner, M.E.1
Bergman, N.H.2
Bartel, D.P.3
-
46
-
-
61649083057
-
BioMart-biological queries made easy
-
Smedley D, Haider S, Ballester B, Holland R, London D, et al. (2009) BioMart-biological queries made easy. BMC Genomics 10: 22.
-
(2009)
BMC Genomics
, vol.10
, pp. 22
-
-
Smedley, D.1
Haider, S.2
Ballester, B.3
Holland, R.4
London, D.5
-
47
-
-
25444472044
-
TransAlign: Using amino acids to facilitate the multiple alignment of protein-coding DNA sequences
-
Bininda-Emonds OR (2005) TransAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. BMC Bioinformatics 6: 156.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 156
-
-
Bininda-Emonds, O.R.1
-
48
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
49
-
-
0028820333
-
A new method of inference of ancestral nucleotide and amino acid sequences
-
Yang Z, Kumar S, Nei M (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141: 1641-1650.
-
(1995)
Genetics
, vol.141
, pp. 1641-1650
-
-
Yang, Z.1
Kumar, S.2
Nei, M.3
-
50
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556.
-
(1997)
Comput Appl Biosci
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
51
-
-
0027533924
-
Evolution of the Zfx and Zfy genes: Rates and interdependence between the genes
-
Pamilo P, Bianchi NO (1993) Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol Biol Evol 10: 271-281.
-
(1993)
Mol Biol Evol
, vol.10
, pp. 271-281
-
-
Pamilo, P.1
Bianchi, N.O.2
-
52
-
-
0033979433
-
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
-
Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17: 32-43.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 32-43
-
-
Yang, Z.1
Nielsen, R.2
-
53
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, 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
|