-
1
-
-
77955480278
-
Revisiting date and party hubs: Novel approaches to role assignment in protein interaction networks
-
Agarwal S, Deane CM, Porter MA, Jones NS. 2010. Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks. PLoS Comput Biol. 6:e1000817.
-
(2010)
PLoS Comput Biol.
, vol.6
-
-
Agarwal, S.1
Deane, C.M.2
Porter, M.A.3
Jones, N.S.4
-
2
-
-
77952697477
-
Experimental genomics of fitness in yeast
-
Bell G. 2010. Experimental genomics of fitness in yeast. Proc Biol Sci. 277: 1459-1467.
-
(2010)
Proc Biol Sci.
, vol.277
, pp. 1459-1467
-
-
Bell, G.1
-
3
-
-
80051558597
-
Putting genetic interactions in context through a global modular decomposition
-
Bellay J, et al. 2011. Putting genetic interactions in context through a global modular decomposition. Genome Res. 21:1375-1387.
-
(2011)
Genome Res.
, vol.21
, pp. 1375-1387
-
-
Bellay, J.1
-
4
-
-
31344474880
-
Complex networks: Structure and dynamics
-
Boccaletti S, Latora V, Moreno Y, Chavez M, Hwang DU. 2006. Complex networks: structure and dynamics. Phys Rep. 424:175-308.
-
(2006)
Phys Rep.
, vol.424
, pp. 175-308
-
-
Boccaletti, S.1
Latora, V.2
Moreno, Y.3
Chavez, M.4
Hwang, D.U.5
-
5
-
-
34249041230
-
Exploring genetic interactions and networks with yeast
-
Boone C, Bussey H, Andrews BJ. 2007. Exploring genetic interactions and networks with yeast. Nature Rev Genet. 8:437-449.
-
(2007)
Nature Rev Genet.
, vol.8
, pp. 437-449
-
-
Boone, C.1
Bussey, H.2
Andrews, B.J.3
-
6
-
-
13444306165
-
The landscape of genetic complexity across 5,700 gene expression traits in yeast
-
Brem R, Kruglyak L. 2005. The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci U S A. 102: 1572-1577.
-
(2005)
Proc Natl Acad Sci U S A.
, vol.102
, pp. 1572-1577
-
-
Brem, R.1
Kruglyak, L.2
-
7
-
-
0035149551
-
Remodeling of yeast genome expression in response to environmental changes
-
Causton HC, et al. 2001. Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell. 12:323-337.
-
(2001)
Mol Biol Cell.
, vol.12
, pp. 323-337
-
-
Causton, H.C.1
-
8
-
-
38649094557
-
Epigenetic regulation and the variability of gene expression
-
Choi JK, Kim YJ. 2008. Epigenetic regulation and the variability of gene expression. Nat Genet. 40:141-147.
-
(2008)
Nat Genet.
, vol.40
, pp. 141-147
-
-
Choi, J.K.1
Kim, Y.J.2
-
9
-
-
63449105244
-
Intrinsic variability of gene expression encoded in nucleosome positioning sequences
-
Choi JK, Kim YJ. 2009. Intrinsic variability of gene expression encoded in nucleosome positioning sequences. Nat Genet. 41:498-503.
-
(2009)
Nat Genet.
, vol.41
, pp. 498-503
-
-
Choi, J.K.1
Kim, Y.J.2
-
10
-
-
79957958115
-
Diminishing returns epistasis among beneficial mutations decelerates adaptation
-
Chou HH, Chiu HC, Delaney NF, Segre D, Marx CJ. 2011. Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 332:1190-1192.
-
(2011)
Science
, vol.332
, pp. 1190-1192
-
-
Chou, H.H.1
Chiu, H.C.2
Delaney, N.F.3
Segre, D.4
Marx, C.J.5
-
11
-
-
75649111192
-
The genetic landscape of a cell
-
Costanzo M, et al. 2010. The genetic landscape of a cell. Science 327: 425-431.
-
(2010)
Science
, vol.327
, pp. 425-431
-
-
Costanzo, M.1
-
12
-
-
18144405733
-
The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans
-
Denver DR, et al. 2005. The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nat Genet. 37:544-548.
-
(2005)
Nat Genet.
, vol.37
, pp. 544-548
-
-
Denver, D.R.1
-
13
-
-
73349095048
-
Systematic mapping of genetic interaction networks
-
Dixon SJ, Costanzo M, Baryshnikova A, Andrews B, Boone C. 2009. Systematic mapping of genetic interaction networks. Ann Rev Genet. 43:601-625.
-
(2009)
Ann Rev Genet.
, vol.43
, pp. 601-625
-
-
Dixon, S.J.1
Costanzo, M.2
Baryshnikova, A.3
Andrews, B.4
Boone, C.5
-
14
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch AP, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 11:4241-4257.
-
(2000)
Mol Biol Cell.
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
-
15
-
-
0037173615
-
Functional profiling of the Saccharomyces cerevisiae genome
-
Giaever G, et al. 2002. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387-391.
-
(2002)
Nature
, vol.418
, pp. 387-391
-
-
Giaever, G.1
-
16
-
-
80052266351
-
Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder
-
Gui Y, et al. 2011. Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet. 43:875-878.
-
(2011)
Nat Genet.
, vol.43
, pp. 875-878
-
-
Gui, Y.1
-
17
-
-
0842290925
-
Molecular evolution in large genetic networks: Does connectivity equal constraint
-
Hahn MW, Conant GC, Wagner A. 2004. Molecular evolution in large genetic networks: does connectivity equal constraint? J Mol Evol. 58: 203-211.
-
(2004)
J Mol Evol
, vol.58
, pp. 203-211
-
-
Hahn, M.W.1
Conant, G.C.2
Wagner, A.3
-
18
-
-
38049079362
-
Protein-protein interaction networks and biology-what's the connection?
-
Hakes L, Pinney JW, Robertson DL, Lovell SC. 2008. Protein-protein interaction networks and biology-what's the connection? Nat Biotechnol. 26:69-72.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 69-72
-
-
Hakes, L.1
Pinney, J.W.2
Robertson, D.L.3
Lovell, S.C.4
-
19
-
-
77649182884
-
Prevalent positive epistasis in Eschericia coli and Saccharomyces cerevisiae metabolic networks
-
He X, Qian W, Wang Z, Li Y, Zhang J. 2010. Prevalent positive epistasis in Eschericia coli and Saccharomyces cerevisiae metabolic networks. Nat Genet. 42:272-278.
-
(2010)
Nat Genet.
, vol.42
, pp. 272-278
-
-
He, X.1
Qian, W.2
Wang, Z.3
Li, Y.4
Zhang, J.5
-
20
-
-
65449187535
-
Evolutionary rates and centrality in the yeast gene regulatory network
-
Jovelin R, Phillips PC. 2009. Evolutionary rates and centrality in the yeast gene regulatory network. Genome Biol. 10:R35.
-
(2009)
Genome Biol.
, vol.10
-
-
Jovelin, R.1
Phillips, P.C.2
-
21
-
-
79957948242
-
Negative epistasis between beneficial mutations in an evolving bacterial population
-
Khan A, Dinh D, Schneider D, Lenski R, Cooper T. 2011. Negative epistasis between beneficial mutations in an evolving bacterial population. Science 332:1193-1196.
-
(2011)
Science
, vol.332
, pp. 1193-1196
-
-
Khan, A.1
Dinh, D.2
Schneider, D.3
Lenski, R.4
Cooper, T.5
-
22
-
-
34250785284
-
Genetic properties influencing the evolvability of gene expression
-
Landry CR, Lemos B, Rifkin SA, Dickinson WJ, Hartl DL. 2007. Genetic properties influencing the evolvability of gene expression. Science 317: 118-121.
-
(2007)
Science
, vol.317
, pp. 118-121
-
-
Landry, C.R.1
Lemos, B.2
Rifkin, S.A.3
Dickinson, W.J.4
Hartl, D.L.5
-
23
-
-
34748826166
-
A high-resolution atlas of nucleosome occupancy in yeast
-
Lee W, et al. 2007. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet. 39:1235-1244.
-
(2007)
Nat Genet.
, vol.39
, pp. 1235-1244
-
-
Lee, W.1
-
24
-
-
78649708844
-
Conflict between noise and plasticity in yeast
-
Lehner B, 2010a. Conflict between noise and plasticity in yeast. PLoS Genet. 6: e1001185.
-
(2010)
PLoS Genet.
, vol.6
-
-
Lehner, B.1
-
25
-
-
77949386270
-
Genes confer similar robustness to environmental, stochastic, and genetic perturbations in yeast
-
Lehner B, 2010b. Genes confer similar robustness to environmental, stochastic, and genetic perturbations in yeast. PLoS One 5: e9035.
-
(2010)
PLoS One
, vol.5
-
-
Lehner, B.1
-
26
-
-
69449106377
-
Robustness: Mechanisms and consequences
-
Masel J, Siegal ML. 2009. Robustness: mechanisms and consequences. Trends Genet. 25:395-403.
-
(2009)
Trends Genet.
, vol.25
, pp. 395-403
-
-
Masel, J.1
Siegal, M.L.2
-
27
-
-
79952474742
-
Protein complexes are central in the yeast genetic landscape
-
Michaut M, et al. 2011. Protein complexes are central in the yeast genetic landscape. PLoS Comput Biol. 7:e1001092.
-
(2011)
PLoS Comput Biol.
, vol.7
-
-
Michaut, M.1
-
28
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
Nagalakshmi U, et al. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344-1349.
-
(2008)
Science
, vol.320
, pp. 1344-1349
-
-
Nagalakshmi, U.1
-
29
-
-
33745220278
-
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
-
Newman JRS, et al. 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.S.1
-
30
-
-
54149088214
-
Epistasis-The essential role of gene interactions in the structure and evolution of genetic systems
-
Phillips PC. 2008. Epistasis-the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet. 9: 855-867.
-
(2008)
Nat Rev Genet.
, vol.9
, pp. 855-867
-
-
Phillips, P.C.1
-
31
-
-
0002854090
-
Beyond the average. The evolutionary importance of gene interactions and variability of epistatic effects
-
In: Wolf JB, Brodie ED III, Wade MJ, editors. Oxford (UK): Oxford University Press
-
Phillips PC, Otto SP, Whitlock MC. 2000. Beyond the average. The evolutionary importance of gene interactions and variability of epistatic effects. In: Wolf JB, Brodie ED III, Wade MJ, editors. Epistasis and the evolutionary process. Oxford (UK): Oxford University Press. p. 20-38.
-
(2000)
Epistasis and the Evolutionary Process
, pp. 20-38
-
-
Phillips, P.C.1
Otto, S.P.2
Whitlock, M.C.3
-
32
-
-
77952309062
-
Exploring the differences in evolutionary rates between monogenic and polygenic disease genes in human
-
Podder S, Ghosh TC. 2010. Exploring the differences in evolutionary rates between monogenic and polygenic disease genes in human. Mol Biol Evol. 27:934-941.
-
(2010)
Mol Biol Evol.
, vol.27
, pp. 934-941
-
-
Podder, S.1
Ghosh, T.C.2
-
33
-
-
41249104062
-
Direct selection on genetic robustness revealed in the yeast transcriptome
-
Proulx SR, Nuzhdin S, Promislow DEL. 2007. Direct selection on genetic robustness revealed in the yeast transcriptome. PLoS One 2:e911.
-
(2007)
PLoS One
, vol.2
-
-
Proulx, S.R.1
Nuzhdin, S.2
Promislow, D.E.L.3
-
36
-
-
27744499137
-
A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression
-
Rifkin S, Houle D, Kim J, White K. 2005. A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression. Nature 438:220-223.
-
(2005)
Nature
, vol.438
, pp. 220-223
-
-
Rifkin, S.1
Houle, D.2
Kim, J.3
White, K.4
-
37
-
-
51249121392
-
Estimating nonlinear selection gradients using quadratic regression coefficients: Double or nothing
-
Stinchcombe JR, Agrawal AF, Hohenlohe PA, Arnold SJ, BlowsMW. 2008. Estimating nonlinear selection gradients using quadratic regression coefficients: double or nothing? Evolution 62:2435-2440.
-
(2008)
Evolution
, vol.62
, pp. 2435-2440
-
-
Stinchcombe, J.R.1
Agrawal, A.F.2
Hohenlohe, P.A.3
Arnold, S.J.4
Blows, M.W.5
-
38
-
-
79959687662
-
An integrated approach to characterize genetic interaction networks in yeast metabolism
-
Szappanos B, et al. 2011. An integrated approach to characterize genetic interaction networks in yeast metabolism. Nat Genet. 43: 656-662.
-
(2011)
Nat Genet.
, vol.43
, pp. 656-662
-
-
Szappanos, B.1
-
39
-
-
39649122611
-
Evolution of gene sequence and gene expression are not correlated in yeast
-
Tirosh I, Barkai N. 2008a. Evolution of gene sequence and gene expression are not correlated in yeast. Trends Genet. 24:109-113.
-
(2008)
Trends Genet.
, vol.24
, pp. 109-113
-
-
Tirosh, I.1
Barkai, N.2
-
40
-
-
43749088127
-
Two strategies for gene regulation by promoter nucleosomes
-
Tirosh I, Barkai N. 2008b. Two strategies for gene regulation by promoter nucleosomes. Genome Res. 18: 1084-1091.
-
(2008)
Genome Res.
, vol.18
, pp. 1084-1091
-
-
Tirosh, I.1
Barkai, N.2
-
41
-
-
74549187509
-
Promoter architecture and the evolvability of gene expression
-
Tirosh I, Barkai N, Verstrepen K. 2009. Promoter architecture and the evolvability of gene expression. J Biol. 8:95.
-
(2009)
J Biol.
, vol.8
, pp. 95
-
-
Tirosh, I.1
Barkai, N.2
Verstrepen, K.3
-
42
-
-
65549086559
-
A yeast hybrid provides insight into the evolution of gene expression regulation
-
Tirosh I, Reikhav S, Levy A, 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.3
Barkai, N.4
-
43
-
-
78649829305
-
Chromatin regulators as capacitors of interspecies variations in gene expression
-
Tirosh I, Reikhav S, Sigal N, Assia Y, Barkai N. 2010. Chromatin regulators as capacitors of interspecies variations in gene expression. Mol Syst Biol. 6:1-9.
-
(2010)
Mol Syst Biol.
, vol.6
, pp. 1-9
-
-
Tirosh, I.1
Reikhav, S.2
Sigal, N.3
Assia, Y.4
Barkai, N.5
-
44
-
-
33745583768
-
A genetic signature of interspecies variations in gene expression
-
Tirosh I, Weinberger A, Carmi M, Barkai 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
-
45
-
-
77955045449
-
The role of nucleosome positioning in the evolution of gene regulation
-
Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ. 2010. The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol. 8:e1000414.
-
(2010)
PLoS Biol.
, vol.8
-
-
Tsankov, A.M.1
Thompson, D.A.2
Socha, A.3
Regev, A.4
Rando, O.J.5
-
46
-
-
67349199647
-
A picture is worth a thousand words: Genomics to phenomics in the yeast Saccharomyces cerevisiae
-
Vizeacoumar FJ, Chong Y, Boone C, Andrews BJ. 2009. A picture is worth a thousand words: genomics to phenomics in the yeast Saccharomyces cerevisiae. FEBS Lett. 583:1656-1661.
-
(2009)
FEBS Lett.
, vol.583
, pp. 1656-1661
-
-
Vizeacoumar, F.J.1
Chong, Y.2
Boone, C.3
Andrews, B.J.4
-
47
-
-
17244367886
-
Functional genomic analysis of the rates of protein evolution
-
Wall D, Hirsh A, Fraser H. 2005. Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci U S A. 102:5483-5488.
-
(2005)
Proc Natl Acad Sci U S A.
, vol.102
, pp. 5483-5488
-
-
Wall, D.1
Hirsh, A.2
Fraser, H.3
-
48
-
-
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
|