-
1
-
-
0031021132
-
Mouse models of human disease. Part I: Techniques and resources for genetic analysis in mice
-
Bedell MA, Jenkins NA, Copeland NG. Mouse models of human disease. Part I: techniques and resources for genetic analysis in mice. Genes and Dev. 1997;11:1-10.
-
(1997)
Genes and Dev
, vol.11
, pp. 1-10
-
-
Bedell, M.A.1
Jenkins, N.A.2
Copeland, N.G.3
-
2
-
-
15444374561
-
Mouse models for human lung cancer
-
Meuwissen R, Berns A. Mouse models for human lung cancer. Genes and Dev. 2005;19:643-64.
-
(2005)
Genes and Dev
, vol.19
, pp. 643-664
-
-
Meuwissen, R.1
Berns, A.2
-
3
-
-
0345275881
-
Models to Study the Interaction of Risk Factors for Human Liver Cancer
-
Sell S. Mouse Models to Study the Interaction of Risk Factors for Human Liver Cancer. Cancer Res. 2003;63:7553-62.
-
(2003)
Cancer Res
, vol.63
, pp. 7553-7562
-
-
Mouse, S.S.1
-
4
-
-
33746664765
-
-
Gerlt JA, Babbitt PC. Can sequence determine function? Genome Biol. 2000;1:reviews0005.1-0005.10.
-
Gerlt JA, Babbitt PC. Can sequence determine function? Genome Biol. 2000;1:reviews0005.1-0005.10.
-
-
-
-
5
-
-
45549083763
-
Functional diversification of duplicate genes through subcellular adaptation of encoded proteins
-
Marques AC, Vinckenbosh N, Brawand D, Kaessmann H. Functional diversification of duplicate genes through subcellular adaptation of encoded proteins. Genome Biol. 2008;9:R54.
-
(2008)
Genome Biol
, vol.9
-
-
Marques, A.C.1
Vinckenbosh, N.2
Brawand, D.3
Kaessmann, H.4
-
6
-
-
0034612214
-
Decoupled evolution of coding region and mRNA expression patterns after gene duplication: Implications for the neutralist-selectionist debate
-
Wagner A. Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debate. Proc Natl Acad Sci U S A. 2000;97:6579-84.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 6579-6584
-
-
Wagner, A.1
-
7
-
-
0033569406
-
Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring
-
Golub TR, Slonim DK, Tamayo P, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999;286:531-7.
-
(1999)
Science
, vol.286
, pp. 531-537
-
-
Golub, T.R.1
Slonim, D.K.2
Tamayo, P.3
-
8
-
-
18244409687
-
Gene expression profiling predicts clinical outcome of breast cancer
-
van't Veer LJ, Dai H, van de Vijver MJ, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature. 2002; 415:530-6.
-
(2002)
Nature
, vol.415
, pp. 530-536
-
-
van't Veer, L.J.1
Dai, H.2
van de Vijver, M.J.3
-
9
-
-
0033536012
-
Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
-
Alon U, Barkai N, Notterman DA, et al. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci U S A. 1999;96:6745-50.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 6745-6750
-
-
Alon, U.1
Barkai, N.2
Notterman, D.A.3
-
10
-
-
4344598209
-
Cross-species comparison of genome-wide expression patterns
-
Zhou XJ, Gibson G. Cross-species comparison of genome-wide expression patterns. Genome Biol. 2004;5:232.
-
(2004)
Genome Biol
, vol.5
, pp. 232
-
-
Zhou, X.J.1
Gibson, G.2
-
11
-
-
19344374050
-
Similarities and differences in genomewide expression data of six orgamisms
-
Bergman S, Ihmels J, Barkai N. Similarities and differences in genomewide expression data of six orgamisms. Plos Biol. 2004;2:E9.
-
(2004)
Plos Biol
, vol.2
-
-
Bergman, S.1
Ihmels, J.2
Barkai, N.3
-
12
-
-
33745627082
-
Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms
-
Lelandais G, Vincens P, Badel-Chagnon A, Vialette S, Jacq C, Hazout S. Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms. Bioinformatics. 2006;22:1359-66.
-
(2006)
Bioinformatics
, vol.22
, pp. 1359-1366
-
-
Lelandais, G.1
Vincens, P.2
Badel-Chagnon, A.3
Vialette, S.4
Jacq, C.5
Hazout, S.6
-
13
-
-
19344366754
-
Lineage-specific gene duplication and loss in human and great ape evolution
-
Fortna A, Kim Y, MacLaren E, et al. Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol. 2004;2:E207.
-
(2004)
PLoS Biol
, vol.2
-
-
Fortna, A.1
Kim, Y.2
MacLaren, E.3
-
15
-
-
3042591076
-
Common pattern of evolution of gene expression level and protein sequence in Drosophila
-
Nuzhdin SV, Wayne ML, Harmon KL, McIntyre LM. Common pattern of evolution of gene expression level and protein sequence in Drosophila. Mol Biol Evol. 2004;21:1308-17.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 1308-1317
-
-
Nuzhdin, S.V.1
Wayne, M.L.2
Harmon, K.L.3
McIntyre, L.M.4
-
16
-
-
22144447840
-
Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees
-
Khaitovich P, Hellmann I, Enard W, et al. Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science. 2005;309:1850-4.
-
(2005)
Science
, vol.309
, pp. 1850-1854
-
-
Khaitovich, P.1
Hellmann, I.2
Enard, W.3
-
17
-
-
34447336411
-
Using DNA microarrays to study gene expression in closely related species
-
Oshlack A, Chabot AE, Smyth GK, Gilad Y. Using DNA microarrays to study gene expression in closely related species. Bioinformatics. 2007;23:1235-42.
-
(2007)
Bioinformatics
, vol.23
, pp. 1235-1242
-
-
Oshlack, A.1
Chabot, A.E.2
Smyth, G.K.3
Gilad, Y.4
-
18
-
-
19844365733
-
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles
-
Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP. Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res. 2005;15:674-80.
-
(2005)
Genome Res
, vol.15
, pp. 674-680
-
-
Gilad, Y.1
Rifkin, S.A.2
Bertone, P.3
Gerstein, M.4
White, K.P.5
-
19
-
-
33745483813
-
Derivation of species-specific hybridization-like knowledge out of cross-species hybridization results
-
Bar-Or C, Bar-Eyal M, Gal TZ, Kapulnik Y, Czosnek H, Koltai H. Derivation of species-specific hybridization-like knowledge out of cross-species hybridization results. BMC Genomics. 2006;7:110.
-
(2006)
BMC Genomics
, vol.7
, pp. 110
-
-
Bar-Or, C.1
Bar-Eyal, M.2
Gal, T.Z.3
Kapulnik, Y.4
Czosnek, H.5
Koltai, H.6
-
20
-
-
1842631448
-
Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control
-
Yanai I, Graur D, Ophir R. Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. OMICS. 2004;8:15-24.
-
(2004)
OMICS
, vol.8
, pp. 15-24
-
-
Yanai, I.1
Graur, D.2
Ophir, R.3
-
21
-
-
13444251367
-
Evolutionary significance of gene expression divergence
-
Jordan IK, Marino-Ramirez L, Koonin EV. Evolutionary significance of gene expression divergence. Gene. 2005;345:119-26.
-
(2005)
Gene
, vol.345
, pp. 119-126
-
-
Jordan, I.K.1
Marino-Ramirez, L.2
Koonin, E.V.3
-
22
-
-
33244455951
-
Evolutionary conservation of expression profiles between human and mouse orthologous genes
-
Liao B, Zhang J. Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol. 2006;23:530-40.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 530-540
-
-
Liao, B.1
Zhang, J.2
-
23
-
-
17744380974
-
Making very similar embryos with divergent genomes: Conservation of regulatory mechanisms of Otx between the ascidians Halocynthia roretzi and Ciona intestinalis
-
Oda-Ishii I, Betrand V, Matsuo I, Lemaire P, Saiga H. Making very similar embryos with divergent genomes: conservation of regulatory mechanisms of Otx between the ascidians Halocynthia roretzi and Ciona intestinalis. Development. 2005;132:1663-74.
-
(2005)
Development
, vol.132
, pp. 1663-1674
-
-
Oda-Ishii, I.1
Betrand, V.2
Matsuo, I.3
Lemaire, P.4
Saiga, H.5
-
24
-
-
33645833857
-
Conservation of RET regulatory function from human to zebrafish without sequence similarity
-
Fisher S, Grice EA, Vinton RM, Bessling SL, McCallion AS. Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science. 2006;312:276-9.
-
(2006)
Science
, vol.312
, pp. 276-279
-
-
Fisher, S.1
Grice, E.A.2
Vinton, R.M.3
Bessling, S.L.4
McCallion, A.S.5
-
25
-
-
34147170895
-
Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons
-
Wang QF, Prabhakar S, Chanan S, Cheng JF, Rubin EM, Boffelli D. Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons. Genome Biol. 2007;8:R1.
-
(2007)
Genome Biol
, vol.8
-
-
Wang, Q.F.1
Prabhakar, S.2
Chanan, S.3
Cheng, J.F.4
Rubin, E.M.5
Boffelli, D.6
-
26
-
-
38349018723
-
On the relation between promoter divergence and gene expression evolution
-
Tirosh I, Weinberger A, Bezalel D, Kaganovich M, Barkai N. On the relation between promoter divergence and gene expression evolution. Mol Syst Biol. 2008;4:159.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 159
-
-
Tirosh, I.1
Weinberger, A.2
Bezalel, D.3
Kaganovich, M.4
Barkai, N.5
-
27
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
Stuart JM, Segal E, Koller D, Kim SK. A gene-coexpression network for global discovery of conserved genetic modules. Science. 2003;302: 249-55.
-
(2003)
Science
, vol.302
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
28
-
-
33751327438
-
Comparative gene expression analysis by a differential clustering approach: Application to the Candida albicans transcription program
-
Ihmels J, Bergmann S, Berman J, Barkai N. Comparative gene expression analysis by a differential clustering approach: application to the Candida albicans transcription program. Plos Genet. 2005;1:e39.
-
(2005)
Plos Genet
, vol.1
-
-
Ihmels, J.1
Bergmann, S.2
Berman, J.3
Barkai, N.4
-
29
-
-
33845231723
-
Conservation and evolution of gene coexpression networks in human and chimpanzee brains
-
Oldham MC, Horvath S, Geschwind DH. Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci U S A. 2006;103:17973-8.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 17973-17978
-
-
Oldham, M.C.1
Horvath, S.2
Geschwind, D.H.3
-
30
-
-
14544301584
-
Clusters of co-expressed genes in mammalian genomes are conserved by natural selection
-
Singer GA, Lloyd AT, Huminiecki LB, Wolfe KH. Clusters of co-expressed genes in mammalian genomes are conserved by natural selection. Mol Biol Evol. 2005;22:767-75.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 767-775
-
-
Singer, G.A.1
Lloyd, A.T.2
Huminiecki, L.B.3
Wolfe, K.H.4
-
31
-
-
33644598453
-
A global definition of gene expression context is conserved between orthologs, but does not correlate with sequence conservation
-
Dutihl BE, Huynen MA, Snel B. A global definition of gene expression context is conserved between orthologs, but does not correlate with sequence conservation. BMC Genomics. 2006;7:10.
-
(2006)
BMC Genomics
, vol.7
, pp. 10
-
-
Dutihl, B.E.1
Huynen, M.A.2
Snel, B.3
-
32
-
-
34548527460
-
Comparative analysis indicates regulatory neofunctionalization of yeast duplicates
-
Tirosh I, Barkai N. Comparative analysis indicates regulatory neofunctionalization of yeast duplicates. Genome Biol. 2007a; 8:R50.
-
(2007)
Genome Biol
, vol.8
-
-
Tirosh, I.1
Barkai, N.2
-
33
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes
-
Su AI, Wiltshire T, Batalov S, et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 2004;101: 6062-7.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 6062-6067
-
-
Su, A.I.1
Wiltshire, T.2
Batalov, S.3
-
34
-
-
24744438019
-
Gene expression evolves faster in narrowly than in broadly expressed mammalian genes
-
Yang J, Su AI, Li WH. Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Mol Biol Evol. 2005;22:2113-8.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 2113-2118
-
-
Yang, J.1
Su, A.I.2
Li, W.H.3
-
35
-
-
44349173103
-
Null mutations in human and mouse orthologs frequently result in different phenotypes
-
Liao B, Zhang J. Null mutations in human and mouse orthologs frequently result in different phenotypes. Proc Natl Acad Sci U S A. 2008;105:6987-92.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 6987-6992
-
-
Liao, B.1
Zhang, J.2
-
36
-
-
0036947892
-
Robust estimators for expression analysis
-
Hubbell E, Liu WM, Mei R. Robust estimators for expression analysis. Bioinformatics. 2002;18:1585-92.
-
(2002)
Bioinformatics
, vol.18
, pp. 1585-1592
-
-
Hubbell, E.1
Liu, W.M.2
Mei, R.3
-
37
-
-
0142121516
-
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
-
Irizarry RA, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4:249-64.
-
(2003)
Biostatistics
, vol.4
, pp. 249-264
-
-
Irizarry, R.A.1
Hobbs, B.2
Collin, F.3
-
38
-
-
0035793042
-
Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
-
Li C, Wong WH. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A. 2001;98:31-6.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 31-36
-
-
Li, C.1
Wong, W.H.2
-
39
-
-
0037007048
-
Large-scale analysis of the human and mouse transcriptomes
-
Su AI, Cooke MP, Ching KA, et al. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A. 2002;99:4465-70.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 4465-4470
-
-
Su, A.I.1
Cooke, M.P.2
Ching, K.A.3
-
40
-
-
0031742022
-
Comprehensive identification of cell cycle regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
Spellman PT, Sherlock G, Zhang MQ, et al. Comprehensive identification of cell cycle regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell. 1998;9:3273-97.
-
(1998)
Mol Biol Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.T.1
Sherlock, G.2
Zhang, M.Q.3
-
41
-
-
3142665525
-
GOstat: Find statistically overrepresented Gene Ontologies within a group of genes
-
Beissbarth T, Speed TP. GOstat: Find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics. 2004; 20:1464-5.
-
(2004)
Bioinformatics
, vol.20
, pp. 1464-1465
-
-
Beissbarth, T.1
Speed, T.P.2
-
42
-
-
4143118944
-
How much expression divergence after yeast gene duplication could be explained by regulatory motif evolution?
-
Zhang Z, Gu J, Gu X. How much expression divergence after yeast gene duplication could be explained by regulatory motif evolution? Trends Genet. 2004;20:403-7.
-
(2004)
Trends Genet
, vol.20
, pp. 403-407
-
-
Zhang, Z.1
Gu, J.2
Gu, X.3
-
43
-
-
39649122611
-
Evolution of gene sequence and gene expression are not correlated in yeast
-
Tirosh I, Barkai N. Evolution of gene sequence and gene expression are not correlated in yeast. Trends Genet. 2007b;24:109-13.
-
(2007)
Trends Genet
, vol.24
, pp. 109-113
-
-
Tirosh, I.1
Barkai, N.2
-
44
-
-
33748526495
-
Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication
-
Johnson R, Gamblin RJ, Ooi L, et al. Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication. Nucleic Acids Res. 2006;34:3862-77.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3862-3877
-
-
Johnson, R.1
Gamblin, R.J.2
Ooi, L.3
-
45
-
-
34250894949
-
Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1
-
Kim JD, Faulk C, Kim J. Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1. Nucleic Acids Res. 2007;35:3442-52.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 3442-3452
-
-
Kim, J.D.1
Faulk, C.2
Kim, J.3
-
46
-
-
63449135035
-
Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization
-
Field Y, Fondufe-Mittendorf Y, Moore IK, et al. Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nat Genet. 2009;41:438-45.
-
(2009)
Nat Genet
, vol.41
, pp. 438-445
-
-
Field, Y.1
Fondufe-Mittendorf, Y.2
Moore, I.K.3
-
47
-
-
60849098170
-
Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes
-
Park C, Makova KD. Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes. Genome Biol. 2009;10:R10.
-
(2009)
Genome Biol
, vol.10
-
-
Park, C.1
Makova, K.D.2
|