-
1
-
-
0037435030
-
Mass spectrometry-based proteomics
-
DOI 10.1038/nature01511
-
Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422: 198-207 (Pubitemid 36362757)
-
(2003)
Nature
, vol.422
, Issue.6928
, pp. 198-207
-
-
Aebersold, R.1
Mann, M.2
-
2
-
-
77950388941
-
Polygenic and directional regulatory evolution across pathways in Saccharomyces
-
Bullard JH, Mostovoy Y, Dudoit S, Brem RB (2010) Polygenic and directional regulatory evolution across pathways in Saccharomyces. Proc Natl Acad Sci 107: 5058-5063
-
(2010)
Proc Natl Acad Sci
, vol.107
, pp. 5058-5063
-
-
Bullard, J.H.1
Mostovoy, Y.2
Dudoit, S.3
Brem, R.B.4
-
3
-
-
0036843938
-
Detection of regulatory variation in mouse genes
-
DOI 10.1038/ng992
-
Cowles CR, Hirschhorn JN, Altshuler D, Lander ES (2002) Detection of regulatory variation in mouse genes. Nat Genet 32: 432-437 (Pubitemid 35266121)
-
(2002)
Nature Genetics
, vol.32
, Issue.3
, pp. 432-437
-
-
Cowles, C.R.1
Hirschhorn, J.N.2
Altshuler, D.3
Lander, E.S.4
-
4
-
-
0028285005
-
Quantitative trait loci underlying gene product variation: A novel perspective for analyzing regulation of genome expression
-
Damerval C, Maurice A, Josse JM, de-Vienne D (1994) Quantitative trait loci underlying gene product variation: A novel perspective for analyzing regulation of genome expression. Genetics 137: 289-301 (Pubitemid 24129295)
-
(1994)
Genetics
, vol.137
, Issue.1
, pp. 289-301
-
-
Damerval, C.1
Maurice, A.2
Josse, J.M.3
De Vienne, D.4
-
5
-
-
84859256941
-
Critical evaluation of imprinted gene expression by RNA-Seq: A new perspective
-
DeVeale B, van der Kooy D, Babak T (2012) Critical evaluation of imprinted gene expression by RNA-Seq: A new perspective. PLoS Genet 8: e1002600
-
(2012)
PLoS Genet
, vol.8
-
-
Deveale, B.1
Van Der Kooy, D.2
Babak, T.3
-
6
-
-
33847630405
-
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
-
DOI 10.1038/nmeth1019, PII NMETH1019
-
Elias JE, Gygi SP (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 4: 207-214 (Pubitemid 46358868)
-
(2007)
Nature Methods
, vol.4
, Issue.3
, pp. 207-214
-
-
Elias, J.E.1
Gygi, S.P.2
-
7
-
-
77952982347
-
Natural selection on cis and trans regulation in yeasts
-
Emerson JJ, Hsieh L-C, Sung H-M, Wang T-Y, Huang C-J, Lu HH-S, Lu M-YJ, Wu S-H, Li W-H (2010) Natural selection on cis and trans regulation in yeasts. Genome Res 20: 826-836
-
(2010)
Genome Res
, vol.20
, pp. 826-836
-
-
Emerson, J.J.1
Hsieh, L.-C.2
Sung, H.-M.3
Wang, T.-Y.4
Huang, C.-J.5
Hh-S, L.6
M-Yj, L.7
Wu, S.-H.8
Li, W.-H.9
-
8
-
-
80053337795
-
Genetic variation shapes protein networks mainly through non-transcriptional mechanisms
-
Foss EJ, Radulovic D, Shaffer SA, Goodlett DR, Kruglyak L, Bedalov A (2011) Genetic variation shapes protein networks mainly through non-transcriptional mechanisms. PLoS Biol 9: e1001144
-
(2011)
PLoS Biol
, vol.9
-
-
Foss, E.J.1
Radulovic, D.2
Shaffer, S.A.3
Goodlett, D.R.4
Kruglyak, L.5
Bedalov, A.6
-
9
-
-
35648969195
-
Genetic basis of proteome variation in yeast
-
DOI 10.1038/ng.2007.22, PII NG200722
-
Foss EJ, Radulovic D, Shaffer SA, Ruderfer DM, Bedalov A, Goodlett DR, Kruglyak L (2007) Genetic basis of proteome variation in yeast. Nat Genet 39: 1369-1375 (Pubitemid 350035001)
-
(2007)
Nature Genetics
, vol.39
, Issue.11
, pp. 1369-1375
-
-
Foss, E.J.1
Radulovic, D.2
Shaffer, S.A.3
Ruderfer, D.M.4
Bedalov, A.5
Goodlett, D.R.6
Kruglyak, L.7
-
10
-
-
67650690613
-
Genome-wide allele-and strand-specific expressionprofiling
-
Gagneur J, Sinha H, Perocchi F, Bourgon R, Huber W, Steinmetz LM (2009) Genome-wide allele-and strand-specific expressionprofiling. Mol Syst Biol 5: 274
-
(2009)
Mol Syst Biol
, vol.5
, pp. 274
-
-
Gagneur, J.1
Sinha, H.2
Perocchi, F.3
Bourgon, R.4
Huber, W.5
Steinmetz, L.M.6
-
11
-
-
0037173615
-
Functional profiling of the Saccharomyces cerevisiae genome
-
DOI 10.1038/nature00935
-
Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A et al (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 41 8: 387-391 (Pubitemid 34826834)
-
(2002)
Nature
, vol.418
, Issue.6896
, pp. 387-391
-
-
Giaever, G.1
Chu, A.M.2
Ni, L.3
Connelly, C.4
Riles, L.5
Veronneau, S.6
Dow, S.7
Lucau-Danila, A.8
Anderson, K.9
Andre, B.10
Arkin, A.P.11
Astromoff, A.12
El Bakkoury, M.13
Bangham, R.14
Benito, R.15
Brachat, S.16
Campanaro, S.17
Curtiss, M.18
Davis, K.19
Deutschbauer, A.20
Entian, K.-D.21
Flaherty, P.22
Foury, F.23
Garfinkel, D.J.24
Gerstein, M.25
Gotte, D.26
Guldener, U.27
Hegemann, J.H.28
Hempel, S.29
Herman, Z.30
Jaramillo, D.F.31
Kelly, D.E.32
Kelly, S.L.33
Kotter, P.34
LaBonte, D.35
Lamb, D.C.36
Lan, N.37
Liang, H.38
Liao, H.39
Liu, L.40
Luo, C.41
Lussier, M.42
Mao, R.43
Menard, P.44
Ooi, S.L.45
Revuelta, J.L.46
Roberts, C.J.47
Rose, M.48
Ross-Macdonald, P.49
Scherens, B.50
Schimmack, G.51
Shafer, B.52
Shoemaker, D.D.53
Sookhai-Mahadeo, S.54
Storms, R.K.55
Strathern, J.N.56
Valle, G.57
Voet, M.58
Volckaert, G.59
Wang, C.-Y.60
Ward, T.R.61
Wilhelmy, J.62
Winzeler, E.A.63
Yang, Y.64
Yen, G.65
Youngman, E.66
Yu, K.67
Bussey, H.68
Boeke, J.D.69
Snyder, M.70
Philippsen, P.71
Davis, R.W.72
Johnston, M.73
more..
-
12
-
-
47249142778
-
Revealing the architecture of gene regulation: The promise of eQTL studies
-
Gilad Y, Rifkin SA, Pritchard JK (2008) Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet 24: 408-415
-
(2008)
Trends Genet
, vol.24
, pp. 408-415
-
-
Gilad, Y.1
Rifkin, S.A.2
Pritchard, J.K.3
-
13
-
-
55249096894
-
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
-
de Godoy LM, Olsen JV, Cox J, Nielsen ML, Hubner NC, Frohlich F, Walther TC, Mann M (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 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
Hubner, N.C.5
Frohlich, F.6
Walther, T.C.7
Mann, M.8
-
14
-
-
77955285002
-
Sex-specific parent-of-origin allelic expression in the mouse brain
-
Gregg C, Zhang J, Butler JE, Haig D, Dulac C (2010) Sex-specific parent-of-origin allelic expression in the mouse brain. Science 329: 682-685
-
(2010)
Science
, vol.329
, pp. 682-685
-
-
Gregg, C.1
Zhang, J.2
Butler, J.E.3
Haig, D.4
Dulac, C.5
-
15
-
-
78149478886
-
RNA polymerase II subunits link transcription and mRNA decay to translation
-
Harel-Sharvit L, Eldad N, Haimovich G, Barkai O, Duek L, Choder M (2010) RNA polymerase II subunits link transcription and mRNA decay to translation. Cell 143: 552-563
-
(2010)
Cell
, vol.143
, pp. 552-563
-
-
Harel-Sharvit, L.1
Eldad, N.2
Haimovich, G.3
Barkai, O.4
Duek, L.5
Choder, M.6
-
16
-
-
83655203194
-
15N mass spectra
-
15N mass spectra. Genome Biol 12: R122
-
(2011)
Genome Biol
, vol.12
-
-
Khan, Z.1
Amini, S.2
Bloom, J.3
Ruse, C.4
Caudy, A.5
Kruglyak, L.6
Singh, M.7
Perlman, D.8
Tavazoie, S.9
-
17
-
-
70349436819
-
Protein quantification across hundreds of experimental conditions
-
Khan Z, Bloom JS, Garcia BA, Singh M, Kruglyak L (2009) Protein quantification across hundreds of experimental conditions. Proc Natl Acad Sci 106: 15544-15548
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 15544-15548
-
-
Khan, Z.1
Bloom, J.S.2
Garcia, B.A.3
Singh, M.4
Kruglyak, L.5
-
18
-
-
18544382234
-
Genetic analysis of the mouse brain proteome
-
Klose J, Nock C, Herrmann M, Stühler K, Marcus K, Blüggel M, Krause E, Schalkwyk LC, Rastan S, Brown SD, Büssow K, Himmelbauer H, Lehrach H (2002) Genetic analysis of the mouse brain proteome. Nat Genet 30: 385-393
-
(2002)
Nat Genet
, vol.30
, pp. 385-393
-
-
Klose, J.1
Nock, C.2
Herrmann, M.3
Stühler, K.4
Marcus, K.5
Blüggel, M.6
Krause, E.7
Schalkwyk, L.C.8
Rastan, S.9
Brown, S.D.10
Büssow, K.11
Himmelbauer, H.12
Lehrach, H.13
-
19
-
-
33847305359
-
Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species
-
DOI 10.1038/ng1967, PII NG1967
-
Man O, Pilpel Y (2007) Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species. Nat Genet 39: 415-421 (Pubitemid 46328488)
-
(2007)
Nature Genetics
, vol.39
, Issue.3
, pp. 415-421
-
-
Man, O.1
Pilpel, Y.2
-
20
-
-
77953010033
-
Regulatory divergence in Drosophila revealed by mRNA-seq
-
McManus CJ, Coolon JD, Duff MO, Eipper-Mains J, Graveley BR, Wittkopp PJ (2010) Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Res 20: 816-825
-
(2010)
Genome Res
, vol.20
, pp. 816-825
-
-
McManus, C.J.1
Coolon, J.D.2
Duff, M.O.3
Eipper-Mains, J.4
Graveley, B.R.5
Wittkopp, P.J.6
-
21
-
-
33745220278
-
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
-
Newman JRS, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS (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
-
-
Jrs, N.1
Ghaemmaghami, S.2
Ihmels, J.3
Breslow, D.K.4
Noble, M.5
Derisi, J.L.6
Weissman, J.S.7
-
22
-
-
70249111091
-
Targeted capture and massively parallel sequencing of 12 human exomes
-
Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, Shendure J (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461: 272-276
-
(2009)
Nature
, vol.461
, pp. 272-276
-
-
Ng, S.B.1
Turner, E.H.2
Robertson, P.D.3
Flygare, S.D.4
Bigham, A.W.5
Lee, C.6
Shaffer, T.7
Wong, M.8
Bhattacharjee, A.9
Eichler, E.E.10
Bamshad, M.11
Nickerson, D.A.12
Shendure, J.13
-
23
-
-
33644524918
-
Mass spectrometry-based proteomics turns quantitative
-
Ong S, Mann M (2005) Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol 1: 252-262
-
(2005)
Nat Chem Biol
, vol.1
, pp. 252-262
-
-
Ong, S.1
Mann, M.2
-
24
-
-
33644662511
-
Analysis of allelic differential expression in human white blood cells
-
DOI 10.1101/gr.4559106
-
Pant PVK, Tao H, Beilharz EJ, Ballinger DG, Cox DR, Frazer KA (2006) Analysis of allelic differential expression in human white blood cells. Genome Res 16: 331-339 (Pubitemid 43327503)
-
(2006)
Genome Research
, vol.16
, Issue.3
, pp. 331-339
-
-
Pant, P.V.K.1
Tao, H.2
Beilharz, E.J.3
Ballinger, D.G.4
Cox, D.R.5
Frazer, K.A.6
-
25
-
-
77954763156
-
Genome-wide allele-specific analysis: Insights into regulatory variation
-
Pastinen T (2010) Genome-wide allele-specific analysis: insights into regulatory variation. Nat Rev Genet 11: 533-538
-
(2010)
Nat Rev Genet
, vol.11
, pp. 533-538
-
-
Pastinen, T.1
-
26
-
-
7444235907
-
Cis-acting regulatory variation in the human genome
-
DOI 10.1126/science.1101659
-
Pastinen T, Hudson TJ (2004) Cis-acting regulatory variation in the human genome. Science 306: 647-650 (Pubitemid 39440905)
-
(2004)
Science
, vol.306
, Issue.5696
, pp. 647-650
-
-
Pastinen, T.1
Hudson, T.J.2
-
27
-
-
77950460661
-
Understanding mechanisms underlying human gene expression variation with RNA sequencing
-
Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras J-B, Stephens M, Gilad Y, Pritchard JK (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768-772
-
(2010)
Nature
, vol.464
, pp. 768-772
-
-
Pickrell, J.K.1
Marioni, J.C.2
Pai, A.A.3
Degner, J.F.4
Engelhardt, B.E.5
Nkadori, E.6
Veyrieras, J.-B.7
Stephens, M.8
Gilad, Y.9
Pritchard, J.K.10
-
28
-
-
63349085550
-
Up-to-date catalogues of yeast protein complexes
-
Pu S, Wong J, Turner B, Cho E, Wodak SJ (2009) Up-to-date catalogues of yeast protein complexes. Nucl Acids Res 37: 825-831
-
(2009)
Nucl Acids Res
, vol.37
, pp. 825-831
-
-
Pu, S.1
Wong, J.2
Turner, B.3
Cho, E.4
Wodak, S.J.5
-
29
-
-
0037317228
-
Stop And Go Extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics
-
DOI 10.1021/ac026117i
-
Rappsilber J, Ishihama Y, Mann M (2003) Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal Chem 75: 663-670 (Pubitemid 36176744)
-
(2003)
Analytical Chemistry
, vol.75
, Issue.3
, pp. 663-670
-
-
Rappsilber, J.1
Ishihama, Y.2
Mann, M.3
-
30
-
-
33750204290
-
Genetics of global gene expression
-
DOI 10.1038/nrg1964, PII NRG1964
-
Rockman MV, Kruglyak L (2006) Genetics of global gene expression. Nat Rev Genet 7: 862-872 (Pubitemid 44607102)
-
(2006)
Nature Reviews Genetics
, vol.7
, Issue.11
, pp. 862-872
-
-
Rockman, M.V.1
Kruglyak, L.2
-
32
-
-
40149090710
-
Differential allelic expression in the human genome: A robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression
-
Serre D, Gurd S, Ge B, Sladek R, Sinnett D, Harmsen E, Bibikova M, Chudin E, Barker DL, Dickinson T, Fan J-B, Hudson TJ (2008) Differential allelic expression in the human genome: A robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet 4: 1000006
-
(2008)
PLoS Genet
, vol.4
, pp. 1000006
-
-
Serre, D.1
Gurd, S.2
Ge, B.3
Sladek, R.4
Sinnett, D.5
Harmsen, E.6
Bibikova, M.7
Chudin, E.8
Barker, D.L.9
Dickinson, T.10
Fan, J.-B.11
Hudson, T.J.12
-
33
-
-
53949098609
-
Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation
-
Shalem O, Dahan O, Levo M, Martinez MR, Furman I, Segal E, Pilpel Y (2008) Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol Syst Biol 4: 223
-
(2008)
Mol Syst Biol
, vol.4
, pp. 223
-
-
Shalem, O.1
Dahan, O.2
Levo, M.3
Martinez, M.R.4
Furman, I.5
Segal, E.6
Pilpel, Y.7
-
34
-
-
0036020892
-
A direct approach to false discovery rates
-
Storey JD (2002) A direct approach to false discovery rates. JR Stat Soc Series B Stat Methodol 64: 479-498
-
(2002)
JR Stat Soc Series B Stat Methodol
, vol.64
, pp. 479-498
-
-
Storey, J.D.1
-
35
-
-
56149086397
-
Decision tree-driven tandem mass spectrometry for shotgun proteomics
-
Swaney DL, McAlister GC, Coon JJ (2008) Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat Methods 5: 959-964
-
(2008)
Nat Methods
, vol.5
, pp. 959-964
-
-
Swaney, D.L.1
McAlister, G.C.2
Coon, J.J.3
-
36
-
-
77949786295
-
Value of using multiple proteases for large-scale mass spectrometry-based proteomics
-
Swaney DL, Wenger CD, Coon JJ (2010) Value of using multiple proteases for large-scale mass spectrometry-based proteomics. JProteome Res 9: 1323-1329
-
(2010)
JProteome Res
, vol.9
, pp. 1323-1329
-
-
Swaney, D.L.1
Wenger, C.D.2
Coon, J.J.3
-
37
-
-
65549086559
-
A yeast hybrid provides insight into the evolution of gene expression regulation
-
Tirosh I, Reikhav S, Levy AA, Barkai N (2009) A yeast hybrid provides insight into the evolution of gene expression regulation. Science 324: 659-662
-
(2009)
Science
, vol.324
, pp. 659-662
-
-
Tirosh, I.1
Reikhav, S.2
Levy, A.A.3
Barkai, N.4
-
38
-
-
78049259700
-
Computational analysis of whole-genome differential allelic expression data in human
-
Wagner JR, Ge B, Pokholok D, Gunderson KL, Pastinen T, Blanchette M (2010) Computational analysis of whole-genome differential allelic expression data in human. PLoS Comput Biol 6: 1000849
-
(2010)
PLoS Comput Biol
, vol.6
, pp. 1000849
-
-
Wagner, J.R.1
Ge, B.2
Pokholok, D.3
Gunderson, K.L.4
Pastinen, T.5
Blanchette, M.6
-
39
-
-
77954866704
-
Paternally biased X inactivation in mouse neonatal brain
-
Wang X, Soloway P, Clark A (2010) Paternally biased X inactivation in mouse neonatal brain. Genome Biol 11: R79
-
(2010)
Genome Biol
, vol.11
-
-
Wang, X.1
Soloway, P.2
Clark, A.3
-
41
-
-
3042722019
-
Evolutionary changes in cis and trans gene regulation
-
DOI 10.1038/nature02698
-
Wittkopp PJ, Haerum BK, Clark AG (2004) Evolutionary divergence of cis and trans gene regulation. Nature 430: 85-88 (Pubitemid 38915229)
-
(2004)
Nature
, vol.430
, Issue.6995
, pp. 85-88
-
-
Wittkopp, P.J.1
Haerum, B.K.2
Clark, A.G.3
-
42
-
-
39749116219
-
Regulatory changes underlying expression differences within and between Drosophila species
-
DOI 10.1038/ng.77, PII NG77
-
Wittkopp PJ, Haerum BK, Clark AG (2008) Genetic basis of regulatory variation within and between Drosophila species. Nat Genet 40: 346-350 (Pubitemid 351311764)
-
(2008)
Nature Genetics
, vol.40
, Issue.3
, pp. 346-350
-
-
Wittkopp, P.J.1
Haerum, B.K.2
Clark, A.G.3
-
43
-
-
0042697343
-
The evolution of transcriptional regulation in eukaryotes
-
DOI 10.1093/molbev/msg140
-
Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV, Romano LA (2003) The evolution of transcriptional regulation in Eukaryotes. Mol Biol Evol 20: 1377-1419 (Pubitemid 37086669)
-
(2003)
Molecular Biology and Evolution
, vol.20
, Issue.9
, pp. 1377-1419
-
-
Wray, G.A.1
Hahn, M.W.2
Abouheif, E.3
Balhoff, J.P.4
Pizer, M.5
Rockman, M.V.6
Romano, L.A.7
-
44
-
-
0037119584
-
Allelic variation in human gene expression
-
Yan H, Yuan W, Velculescu VE, Vogelstein B, Kinzler KW (2002) Allelic variation in human gene expression. Science 297: 1143-1143
-
(2002)
Science
, vol.297
, pp. 1143-1143
-
-
Yan, H.1
Yuan, W.2
Velculescu, V.E.3
Vogelstein, B.4
Kinzler, K.W.5
|