-
1
-
-
33846978695
-
Relative impact of nucleotide and copy number variation on gene expression phenotypes
-
Stranger, B. E., Forrest, M. S., Dunning, M., Ingle, C. E. et al., Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007, 315, 848-853.
-
(2007)
Science
, vol.315
, pp. 848-853
-
-
Stranger, B.E.1
Forrest, M.S.2
Dunning, M.3
Ingle, C.E.4
-
2
-
-
63149198301
-
Copy number variants, diseases and gene expression
-
Henrichsen, C. N., Chaignat, E., Reymond, A., Copy number variants, diseases and gene expression. Hum. Mol. Genet. 2009, 18, R1-R8.
-
(2009)
Hum. Mol. Genet
, vol.18
-
-
Henrichsen, C.N.1
Chaignat, E.2
Reymond, A.3
-
3
-
-
33745287724
-
Noise in protein expression scales with natural protein abundance
-
Bar-Even, A., Paulsson, J., Maheshri, N., Carmi, M. et al., Noise in protein expression scales with natural protein abundance. Nat. Genet. 2006, 38, 636-643.
-
(2006)
Nat. Genet
, vol.38
, pp. 636-643
-
-
Bar-Even, A.1
Paulsson, J.2
Maheshri, N.3
Carmi, M.4
-
4
-
-
33745220278
-
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
-
Newman, J. R., Ghaemmaghami, S., Ihmels, J., Breslow, D. K. et al., Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 2006, 441, 840-846.
-
(2006)
Nature
, vol.441
, pp. 840-846
-
-
Newman, J.R.1
Ghaemmaghami, S.2
Ihmels, J.3
Breslow, D.K.4
-
5
-
-
57349097152
-
Dynamic proteomics of individual cancer cells in response to a drug
-
Cohen, A. A., Geva-Zatorsky, N., Eden, E., Frenkel-Morgenstern, M. et al., Dynamic proteomics of individual cancer cells in response to a drug. Science 2008, 322, 1511-1516.
-
(2008)
Science
, vol.322
, pp. 1511-1516
-
-
Cohen, A.A.1
Geva-Zatorsky, N.2
Eden, E.3
Frenkel-Morgenstern, M.4
-
6
-
-
19344372220
-
A neutral model of transcriptome evolution
-
Khaitovich, P., Weiss, G., Lachmann, M., Hellmann, I. et al., A neutral model of transcriptome evolution. PLoS Biol. 2004, 2, E132.
-
(2004)
PLoS Biol
, vol.2
-
-
Khaitovich, P.1
Weiss, G.2
Lachmann, M.3
Hellmann, I.4
-
7
-
-
59049088893
-
Optimization of gene expression by natural selection
-
Bedford, T., Hartl, D. L., Optimization of gene expression by natural selection. Proc. Natl. Acad. Sci. USA 2009, 106, 1133-1138.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 1133-1138
-
-
Bedford, T.1
Hartl, D.L.2
-
8
-
-
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
-
9
-
-
38549084066
-
Evaluating the role of natural selection in the evolution of gene regulation
-
Fay, J. C., Wittkopp, P. J., Evaluating the role of natural selection in the evolution of gene regulation. Heredity 2008, 100, 191-199.
-
(2008)
Heredity
, vol.100
, pp. 191-199
-
-
Fay, J.C.1
Wittkopp, P.J.2
-
10
-
-
23144432213
-
Optimality and evolutionary tuning of the expression level of a protein
-
Dekel, E., Alon, U., Optimality and evolutionary tuning of the expression level of a protein. Nature 2005, 436, 588-592.
-
(2005)
Nature
, vol.436
, pp. 588-592
-
-
Dekel, E.1
Alon, U.2
-
11
-
-
0142215475
-
Global analysis of protein expression in yeast
-
Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W. et al., Global analysis of protein expression in yeast. Nature 2003, 425, 737-741.
-
(2003)
Nature
, vol.425
, pp. 737-741
-
-
Ghaemmaghami, S.1
Huh, W.K.2
Bower, K.3
Howson, R.W.4
-
12
-
-
33644524918
-
Mass spectrometry-based proteomics turns quantitative
-
Ong, S. E., Mann, M., Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 2005, 1, 252-262.
-
(2005)
Nat. Chem. Biol
, vol.1
, pp. 252-262
-
-
Ong, S.E.1
Mann, M.2
-
13
-
-
61849105469
-
Mass spectrometry based targeted protein quantification: Methods and applications
-
Pan, S., Aebersold, R., Chen, R., Rush, J. et al., Mass spectrometry based targeted protein quantification: methods and applications. J. Proteome Res. 2009, 8, 787-797.
-
(2009)
J. Proteome Res
, vol.8
, pp. 787-797
-
-
Pan, S.1
Aebersold, R.2
Chen, R.3
Rush, J.4
-
14
-
-
34748916981
-
Quantitative mass spectrometry in proteomics: A critical review
-
Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., Kuster, B., Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 2007, 389, 1017-1031.
-
(2007)
Anal. Bioanal. Chem
, vol.389
, pp. 1017-1031
-
-
Bantscheff, M.1
Schirle, M.2
Sweetman, G.3
Rick, J.4
Kuster, B.5
-
15
-
-
68449102172
-
Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans
-
Malmstrom, J., Beck, M., Schmidt, A., Lange, V. et al., Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature 2009, 460, 762-765.
-
(2009)
Nature
, vol.460
, pp. 762-765
-
-
Malmstrom, J.1
Beck, M.2
Schmidt, A.3
Lange, V.4
-
16
-
-
57449099865
-
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
-
Cox, J., Mann, M., MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008, 26, 1367-1372.
-
(2008)
Nat. Biotechnol
, vol.26
, pp. 1367-1372
-
-
Cox, J.1
Mann, M.2
-
17
-
-
34249717879
-
A high-quality catalog of the Drosophila melanogaster proteome
-
Brunner, E., Ahrens, C. H., Mohanty, S., Baetschmann, H. et al., A high-quality catalog of the Drosophila melanogaster proteome. Nat. Biotechnol. 2007, 25, 576-583.
-
(2007)
Nat. Biotechnol
, vol.25
, pp. 576-583
-
-
Brunner, E.1
Ahrens, C.H.2
Mohanty, S.3
Baetschmann, H.4
-
18
-
-
44249091879
-
Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics
-
Baerenfaller, K., Grossmann, J., Grobei, M. A., Hull, R. et al., Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 2008, 320, 938-941.
-
(2008)
Science
, vol.320
, pp. 938-941
-
-
Baerenfaller, K.1
Grossmann, J.2
Grobei, M.A.3
Hull, R.4
-
19
-
-
65949096636
-
Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes
-
Schrimpf, S. P., Weiss, M., Reiter, L., Ahrens, C. H. et al., Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol. 2009, 7, e48.
-
(2009)
PLoS Biol
, vol.7
-
-
Schrimpf, S.P.1
Weiss, M.2
Reiter, L.3
Ahrens, C.H.4
-
20
-
-
0348142993
-
Changes in the protein expression of yeast as a function of carbon source
-
Gao, J., Opiteck, G. J., Friedrichs, M. S., Dongre, A. R., Hefta, S. A., Changes in the protein expression of yeast as a function of carbon source. J. Proteome Res. 2003, 2, 643-649.
-
(2003)
J. Proteome Res
, vol.2
, pp. 643-649
-
-
Gao, J.1
Opiteck, G.J.2
Friedrichs, M.S.3
Dongre, A.R.4
Hefta, S.A.5
-
21
-
-
3242731195
-
-
Liu, H., Sadygov, R. G., Yates,J. R., 3rd, A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
-
Liu, H., Sadygov, R. G., Yates,J. R., 3rd, A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
-
-
-
-
22
-
-
26844559000
-
Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
-
Ishihama, Y., Oda, Y., Tabata, T., Sato, T. et al., Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 2005, 4, 1265-1272.
-
(2005)
Mol. Cell. Proteomics
, vol.4
, pp. 1265-1272
-
-
Ishihama, Y.1
Oda, Y.2
Tabata, T.3
Sato, T.4
-
23
-
-
33846165487
-
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
-
Lu, P., Vogel, C., Wang, R., Yao, X., Marcotte, E. M., Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 2007, 25, 117-124.
-
(2007)
Nat. Biotechnol
, vol.25
, pp. 117-124
-
-
Lu, P.1
Vogel, C.2
Wang, R.3
Yao, X.4
Marcotte, E.M.5
-
24
-
-
33846133955
-
Computational prediction of proteotypic peptides for quantitative proteomics
-
Mallick, P., Schirle, M., Chen, S. S., Flory, M. R. et al., Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 2007, 25, 125-131.
-
(2007)
Nat. Biotechnol
, vol.25
, pp. 125-131
-
-
Mallick, P.1
Schirle, M.2
Chen, S.S.3
Flory, M.R.4
-
25
-
-
33748319353
-
Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae
-
Zybailov, B., Mosley, A. L., Sardiu, M. E., Coleman, M. K. et al., Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J. Proteome Res. 2006, 5, 2339-2347.
-
(2006)
J. Proteome Res
, vol.5
, pp. 2339-2347
-
-
Zybailov, B.1
Mosley, A.L.2
Sardiu, M.E.3
Coleman, M.K.4
-
26
-
-
43049127826
-
PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows
-
Deutsch, E. W., Lam, H., Aebersold, R., PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 2008, 9, 429-434.
-
(2008)
EMBO Rep
, vol.9
, pp. 429-434
-
-
Deutsch, E.W.1
Lam, H.2
Aebersold, R.3
-
27
-
-
58149193234
-
STRING 8 - a global view on proteins and their functional interactions in 630 organisms
-
Jensen, L. J., Kuhn, M., Stark, M., Chaffron, S. et al., STRING 8 - a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 2009, 37, D412-D416.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Jensen, L.J.1
Kuhn, M.2
Stark, M.3
Chaffron, S.4
-
28
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov, R. L., Koonin, E. V., Lipman, D. J., A genomic perspective on protein families. Science 1997, 278, 631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
29
-
-
38549177928
-
eggNOG: Automated construction and annotation of orthologous groups of genes
-
Jensen, L. J., Julien, P., Kuhn, M., von Mering, C. et al., eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res. 2008, 36, D250-D254.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Jensen, L.J.1
Julien, P.2
Kuhn, M.3
von Mering, C.4
-
30
-
-
38549123363
-
Gene Ontology annotations at SGD: New data sources and annotation methods
-
Hong, E. L., Balakrishnan, R., Dong, Q., Christie, K. R. et al., Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008, 36, D577-D581.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Hong, E.L.1
Balakrishnan, R.2
Dong, Q.3
Christie, K.R.4
-
31
-
-
63349085550
-
Up-to-date catalogues of yeast protein complexes
-
Pu, S., Wong, J., Turner, B., Cho, E., Wodak, S. J., Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res. 2009, 37, 825-831.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 825-831
-
-
Pu, S.1
Wong, J.2
Turner, B.3
Cho, E.4
Wodak, S.J.5
-
32
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y., Hochberg, Y., Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 1995, 57, 289-300.
-
(1995)
J. R. Stat. Soc. Ser. B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
33
-
-
55249096894
-
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
-
de Godoy, L. M., Olsen, J. V., Cox, J., Nielsen, M. L. et al., Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 2008, 455, 1251-1254.
-
(2008)
Nature
, vol.455
, pp. 1251-1254
-
-
de Godoy, L.M.1
Olsen, J.V.2
Cox, J.3
Nielsen, M.L.4
-
34
-
-
0033016717
-
Correlation between protein and mRNA abundance in yeast
-
Gygi, S. P., Rochon, Y., Franza, B. R., Aebersold, R., Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 1999, 19, 1720-1730.
-
(1999)
Mol. Cell. Biol
, vol.19
, pp. 1720-1730
-
-
Gygi, S.P.1
Rochon, Y.2
Franza, B.R.3
Aebersold, R.4
-
35
-
-
65649083411
-
Estimating accuracy of RNA-Seq and microarrays with proteomics
-
Fu, X., Fu, N., Guo, S., Yan, Z. et al., Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics 2009, 10, 161.
-
(2009)
BMC Genomics
, vol.10
, pp. 161
-
-
Fu, X.1
Fu, N.2
Guo, S.3
Yan, Z.4
-
36
-
-
0346801873
-
The Gene Ontology (GO) database and informatics resource
-
Harris, M. A., Clark, J., Ireland, A., Lomax, J. et al., The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004, 32, D258-D261.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Harris, M.A.1
Clark, J.2
Ireland, A.3
Lomax, J.4
-
37
-
-
0037173615
-
Functional profiling of the Saccharomyces cerevisiae genome
-
Giaever, G., Chu, A. M., Ni, L., Connelly, C. et al., Functional profiling of the Saccharomyces cerevisiae genome. Nature 2002, 418, 387-391.
-
(2002)
Nature
, vol.418
, pp. 387-391
-
-
Giaever, G.1
Chu, A.M.2
Ni, L.3
Connelly, C.4
-
38
-
-
25444468618
-
Noise in gene expression: Origins, consequences, and control
-
Raser, J. M., O'Shea, E. K., Noise in gene expression: origins, consequences, and control. Science 2005, 309, 2010-2013.
-
(2005)
Science
, vol.309
, pp. 2010-2013
-
-
Raser, J.M.1
O'Shea, E.K.2
-
39
-
-
25144450143
-
Contributions of low molecule number and chromosomal positioning to stochastic gene expression
-
Becskei, A., Kaufmann, B. B., van Oudenaarden, A., Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat. Genet. 2005, 37, 937-944.
-
(2005)
Nat. Genet
, vol.37
, pp. 937-944
-
-
Becskei, A.1
Kaufmann, B.B.2
van Oudenaarden, A.3
-
40
-
-
43349090699
-
Comparison of protein and mRNA expression evolution in humans and chimpanzees
-
Fu, N., Drinnenberg, I., Kelso, J., Wu, J. R. et al., Comparison of protein and mRNA expression evolution in humans and chimpanzees. PLoS ONE 2007, 2, e216.
-
(2007)
PLoS ONE
, vol.2
-
-
Fu, N.1
Drinnenberg, I.2
Kelso, J.3
Wu, J.R.4
-
41
-
-
58149354386
-
Protein material costs: Single atoms can make an evolutionary difference
-
Bragg, J. G., Wagner, A., Protein material costs: single atoms can make an evolutionary difference. Trends Genet. 2009, 25, 5-8.
-
(2009)
Trends Genet
, vol.25
, pp. 5-8
-
-
Bragg, J.G.1
Wagner, A.2
-
42
-
-
65349162170
-
Conservation of core gene expression in vertebrate tissues
-
Chan, E. T., Quon, G. T., Chua, G., Babak, T. et al., Conservation of core gene expression in vertebrate tissues. J. Biol. 2009, 8, 33.
-
(2009)
J. Biol
, vol.8
, pp. 33
-
-
Chan, E.T.1
Quon, G.T.2
Chua, G.3
Babak, T.4
-
43
-
-
73249116559
-
Comparison of diverse developmental transcriptomes reveals that co-expression of gene neighbors is not evolutionarily conserved
-
Yanai, I., Hunter, C. P., Comparison of diverse developmental transcriptomes reveals that co-expression of gene neighbors is not evolutionarily conserved. Genome Res. 2009, 12, 2214-2220.
-
(2009)
Genome Res
, vol.12
, pp. 2214-2220
-
-
Yanai, I.1
Hunter, C.P.2
-
44
-
-
34548076977
-
Assessing the conservation of mammalian gene expression using high-density exon arrays
-
Xing, Y., Ouyang, Z., Kapur, K., Scott, M. P., Wong, W. H., Assessing the conservation of mammalian gene expression using high-density exon arrays. Mol. Biol. Evol. 2007, 24, 1283-1285.
-
(2007)
Mol. Biol. Evol
, vol.24
, pp. 1283-1285
-
-
Xing, Y.1
Ouyang, Z.2
Kapur, K.3
Scott, M.P.4
Wong, W.H.5
-
45
-
-
33746265259
-
Natural selection on gene expression
-
Gilad, Y., Oshlack, A., Rifkin, S. A., Natural selection on gene expression. Trends Genet. 2006, 22, 456-461.
-
(2006)
Trends Genet
, vol.22
, pp. 456-461
-
-
Gilad, Y.1
Oshlack, A.2
Rifkin, S.A.3
-
46
-
-
42049108914
-
Protein abundance profiling of the Escherichia coli cytosol
-
Ishihama, Y., Schmidt, T., Rappsilber, J., Mann, M. et al., Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics 2008, 9, 102.
-
(2008)
BMC Genomics
, vol.9
, pp. 102
-
-
Ishihama, Y.1
Schmidt, T.2
Rappsilber, J.3
Mann, M.4
-
47
-
-
33847081243
-
Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe
-
Schmidt, M. W., Houseman, A., Ivanov, A. R., Wolf, D. A., Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe. Mol. Syst. Biol. 2007, 3, 79.
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 79
-
-
Schmidt, M.W.1
Houseman, A.2
Ivanov, A.R.3
Wolf, D.A.4
-
48
-
-
47549097539
-
Mistranslation-induced protein misfolding as a dominant constraint on codingsequence evolution
-
Drummond, D. A., Wilke, C. O., Mistranslation-induced protein misfolding as a dominant constraint on codingsequence evolution. Cell 2008, 134, 341-352.
-
(2008)
Cell
, vol.134
, pp. 341-352
-
-
Drummond, D.A.1
Wilke, C.O.2
-
49
-
-
47549108636
-
Costly mistakes: Translational infidelity and protein homeostasis
-
Powers, E. T., Balch, W. E., Costly mistakes: translational infidelity and protein homeostasis. Cell 2008, 134, 204-206.
-
(2008)
Cell
, vol.134
, pp. 204-206
-
-
Powers, E.T.1
Balch, W.E.2
|