-
1
-
-
84872519386
-
Sex-biased transcriptome evolution in Drosophila
-
Assis R, Zhou Q, Bachtrog D. 2012. Sex-biased transcriptome evolution in Drosophila. Genome Biol Evol. 4:1189-1200.
-
(2012)
Genome Biol Evol.
, vol.4
, pp. 1189-1200
-
-
Assis, R.1
Zhou, Q.2
Bachtrog, D.3
-
2
-
-
26444621352
-
Why highly expressed proteins evolve slowly
-
Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. 2005. Why highly expressed proteins evolve slowly. Proc Natl Acad Sci USA. 102:14338-14343.
-
(2005)
Proc Natl Acad Sci USA.
, vol.102
, pp. 14338-14343
-
-
Drummond, D.A.1
Bloom, J.D.2
Adami, C.3
Wilke, C.O.4
Arnold, F.H.5
-
3
-
-
30744441602
-
A single determinant dominates the rate of yeast protein evolution
-
Drummond DA, Raval A, Wilke CO. 2006. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol. 23:327-337.
-
(2006)
Mol Biol Evol.
, vol.23
, pp. 327-337
-
-
Drummond, D.A.1
Raval, A.2
Wilke, C.O.3
-
4
-
-
47549097539
-
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
-
Drummond DA, Wilke CO. 2008. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341-352.
-
(2008)
Cell
, vol.134
, pp. 341-352
-
-
Drummond, D.A.1
Wilke, C.O.2
-
5
-
-
0033977618
-
Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate
-
Duret L, Mouchiroud D. 2000. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol. 17:68-74.
-
(2000)
Mol Biol Evol.
, vol.17
, pp. 68-74
-
-
Duret, L.1
Mouchiroud, D.2
-
6
-
-
79551674254
-
Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast
-
Geiler-Samerotte KA, Dion MF, Budnik BA, Wang SM, Hartl DL, Drummond DA. 2011. Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast. Proc Natl Acad Sci USA. 108:680-685.
-
(2011)
Proc Natl Acad Sci USA.
, vol.108
, pp. 680-685
-
-
Geiler-Samerotte, K.A.1
Dion, M.F.2
Budnik, B.A.3
Wang, S.M.4
Hartl, D.L.5
Drummond, D.A.6
-
7
-
-
33645115481
-
Strength of purifying selection against different categories of the point mutations in the coding regions of the human genome
-
Gorlov IP, Kimmel M, Amos CI. 2006. Strength of purifying selection against different categories of the point mutations in the coding regions of the human genome. Hum Mol Genet. 15:1143-1150.
-
(2006)
Hum Mol Genet.
, vol.15
, pp. 1143-1150
-
-
Gorlov, I.P.1
Kimmel, M.2
Amos, C.I.3
-
8
-
-
0016197604
-
Amino acid difference formula to help explain protein evolution
-
Grantham R. 1974. Amino acid difference formula to help explain protein evolution. Science 185:862-864.
-
(1974)
Science
, vol.185
, pp. 862-864
-
-
Grantham, R.1
-
9
-
-
78751612067
-
Estimating the parameters of selection on nonsynonymous mutations in Drosophila pseudoobscura and D. Miranda
-
Haddrill PR, Loewe L, Charlesworth B. 2010. Estimating the parameters of selection on nonsynonymous mutations in Drosophila pseudoobscura and D. miranda. Genetics 185:1381-1396.
-
(2010)
Genetics
, vol.185
, pp. 1381-1396
-
-
Haddrill, P.R.1
Loewe, L.2
Charlesworth, B.3
-
10
-
-
24944526640
-
Converging on a general model of protein evolution
-
Herbeck HT, Wall DP. 2005. Converging on a general model of protein evolution. Trends Biotechnol. 23:485-487.
-
(2005)
Trends Biotechnol.
, vol.23
, pp. 485-487
-
-
Herbeck, H.T.1
Wall, D.P.2
-
11
-
-
0035963414
-
Protein dispensability and rate of evolution
-
Hirsh AE, Fraser HB. 2001. Protein dispensability and rate of evolution. Nature 411:1046-1049.
-
(2001)
Nature
, vol.411
, pp. 1046-1049
-
-
Hirsh, A.E.1
Fraser, H.B.2
-
12
-
-
0033565762
-
Do essential genes evolve slowly?
-
Hurst LD, Smith NG. 1999. Do essential genes evolve slowly? Curr Biol. 9: 747-750.
-
(1999)
Curr Biol.
, vol.9
, pp. 747-750
-
-
Hurst, L.D.1
Smith, N.G.2
-
13
-
-
0036078078
-
Essential genes aremore evolutionarily conserved than are nonessential genes in bacteria
-
Jordan IK, Rogozin IB,Wolf YI, Koonin EV. 2002. Essential genes aremore evolutionarily conserved than are nonessential genes in bacteria. Genome Res. 12:962-968.
-
(2002)
Genome Res.
, vol.12
, pp. 962-968
-
-
Jordan, I.K.1
Rogozin, I.B.2
Wolf, Y.I.3
Koonin, E.V.4
-
14
-
-
67650064592
-
Analysis of the genome sequence of three Drosophila melanogaster spontaneous mutation accumulation lines
-
Keightley PD, Trivedi U, Thomson M, Oliver F, Kumar S, Blaxter ML. 2009. Analysis of the genome sequence of three Drosophila melanogaster spontaneous mutation accumulation lines. Genome Res. 19: 1195-1201.
-
(2009)
Genome Res.
, vol.19
, pp. 1195-1201
-
-
Keightley, P.D.1
Trivedi, U.2
Thomson, M.3
Oliver, F.4
Kumar, S.5
Blaxter, M.L.6
-
15
-
-
33748980210
-
Evolutionary systems biology: Links between gene evolution and function
-
Koonin EV, Wolf YI. 2006. Evolutionary systems biology: links between gene evolution and function. Curr Opin Biotechnol. 17:481-487.
-
(2006)
Curr Opin Biotechnol.
, vol.17
, pp. 481-487
-
-
Koonin, E.V.1
Wolf, Y.I.2
-
16
-
-
0142124263
-
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
-
Krylov DM, Wolf YI, Rogozin IB, Koonin EV. 2003. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res. 13: 2229-2235.
-
(2003)
Genome Res.
, vol.13
, pp. 2229-2235
-
-
Krylov, D.M.1
Wolf, Y.I.2
Rogozin, I.B.3
Koonin, E.V.4
-
17
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25.
-
(2009)
Genome Biol.
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
18
-
-
39749084483
-
Evolution of protein-coding genes in Drosophila
-
Larracuente AM, Sackton TB, Greenberg AJ, Wong A, Singh ND, Sturgill D, Zhang Y, Oliver B, Clark AG. 2008. Evolution of protein-coding genes in Drosophila. Trends Genet. 24:114-123.
-
(2008)
Trends Genet.
, vol.24
, pp. 114-123
-
-
Larracuente, A.M.1
Sackton, T.B.2
Greenberg, A.J.3
Wong, A.4
Singh, N.D.5
Sturgill, D.6
Zhang, Y.7
Oliver, B.8
Clark, A.G.9
-
19
-
-
17744376961
-
Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions
-
Lemos B, Bettencourt BR, Meiklejohn CD, Hartl DL. 2005. Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions. Mol Biol Evol. 22:1345-1354.
-
(2005)
Mol Biol Evol.
, vol.22
, pp. 1345-1354
-
-
Lemos, B.1
Bettencourt, B.R.2
Meiklejohn, C.D.3
Hartl, D.L.4
-
20
-
-
84870901239
-
Cellular crowding imposes global constraints on the chemistry and evolution of proteomes
-
Levy ED, De S, Teichmann SA. 2012. Cellular crowding imposes global constraints on the chemistry and evolution of proteomes. Proc Natl Acad Sci USA. 109:20461-20466.
-
(2012)
Proc Natl Acad Sci USA.
, vol.109
, pp. 20461-20466
-
-
Levy, E.D.1
De S Teichmann, S.A.2
-
21
-
-
0034978556
-
Highly expressed genes in yeast evolve slowly
-
Pal C, Papp B, Hurst LD. 2001. Highly expressed genes in yeast evolve slowly. Genetics 158:927-931.
-
(2001)
Genetics
, vol.158
, pp. 927-931
-
-
Pal, C.1
Papp, B.2
Hurst, L.D.3
-
22
-
-
33646182934
-
An integrated view of protein evolution
-
Pal C, Papp B, Lercher MJ. 2006. An integrated view of protein evolution. Nat Rev Genet. 7:337-348.
-
(2006)
Nat Rev Genet.
, vol.7
, pp. 337-348
-
-
Pal, C.1
Papp, B.2
Lercher, M.J.3
-
23
-
-
70149113077
-
-
R Development Core Team Vienna (Austria): R Foundation for Statistical Computing
-
R Development Core Team. 2009. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing.
-
(2009)
R: A Language and Environment for Statistical Computing
-
-
-
24
-
-
80052824121
-
MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons
-
Ranwez V, Harispe S, Delsuc F, Douzery EJP. 2011. MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. PLoS One 6:e22594.
-
(2011)
PLoS One
, vol.6
-
-
Ranwez, V.1
Harispe, S.2
Delsuc, F.3
Douzery, E.J.P.4
-
25
-
-
84871946825
-
Streaming fragment assignment for real-time analysis of sequencing experiments
-
Roberts A, Pachter L. 2013. Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods. 10:71-73.
-
(2013)
Nat Methods.
, vol.10
, pp. 71-73
-
-
Roberts, A.1
Pachter, L.2
-
26
-
-
84865730325
-
Protein biophysics explains why highly abundant proteins evolve slowly
-
Serohijos AWR, Rimas Z, Shakhnovich EI. 2012. Protein biophysics explains why highly abundant proteins evolve slowly. Cell Rep. 2: 249-256.
-
(2012)
Cell Rep.
, vol.2
, pp. 249-256
-
-
Awr, S.1
Rimas, Z.2
Shakhnovich, E.I.3
-
27
-
-
0035869223
-
Prediction of deleterious human alleles
-
Sunyaev S, Ramensky V, Koch I, Lathe W 3rd, Kondrashov AS, Bork P. 2001. Prediction of deleterious human alleles. Hum Mol Genet. 10: 591-597.
-
(2001)
Hum Mol Genet.
, vol.10
, pp. 591-597
-
-
Sunyaev, S.1
Ramensky, V.2
Koch, I.3
Lathe Iii., W.4
Kondrashov, A.S.5
Bork, P.6
-
28
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 28: 511-515.
-
(2010)
Nat Biotechnol.
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
29
-
-
33745107471
-
Influence of metabolic network structure and function on enzyme evolution
-
Vitkup D, Kharchenko P, Wagner A. 2006. Influence of metabolic network structure and function on enzyme evolution. Genome Biol. 7: R39.
-
(2006)
Genome Biol.
, vol.7
-
-
Vitkup, D.1
Kharchenko, P.2
Wagner, A.3
-
30
-
-
17244367886
-
Functional genomic analysis of the rates of protein evolution
-
Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G, Eisen MB, Feldman MW. 2005. Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci USA. 102:5483-5488.
-
(2005)
Proc Natl Acad Sci USA.
, vol.102
, pp. 5483-5488
-
-
Wall, D.P.1
Hirsh, A.E.2
Fraser, H.B.3
Kumm, J.4
Giaever, G.5
Eisen, M.B.6
Feldman, M.W.7
-
32
-
-
0347766006
-
Elevated rates of protein secretion, evolution, and disease among tissue-specific genes
-
Winter EE, Goodstadt L, Ponting CP. 2004. Elevated rates of protein secretion, evolution, and disease among tissue-specific genes. Genome Res. 14:54-61.
-
(2004)
Genome Res.
, vol.14
, pp. 54-61
-
-
Winter, E.E.1
Goodstadt, L.2
Ponting, C.P.3
-
33
-
-
33745744354
-
Coping with the quantitative genomics 'elephant': The correlation between gene dispensability and evolution rate
-
Wolf YI. 2006. Coping with the quantitative genomics 'elephant': the correlation between gene dispensability and evolution rate. Trends Genet. 22: 354-357.
-
(2006)
Trends Genet.
, vol.22
, pp. 354-357
-
-
Wolf, Y.I.1
-
34
-
-
77958476428
-
Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes
-
Wolf YI, Gopich IV, Lipman DJ, Koonin EV. 2010. Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes. Genome Biol Evol. 2:90-199.
-
(2010)
Genome Biol Evol.
, vol.2
, pp. 90-199
-
-
Wolf, Y.I.1
Gopich, I.V.2
Lipman, D.J.3
Koonin, E.V.4
-
35
-
-
20144376345
-
Genomewide midrange transcription profiles reveal expression level relationships in human tissue specifications
-
(12 co-authors)
-
Yanai I, Benjamin H, Shmoish M, et al. (12 co-authors). 2005. Genomewide midrange transcription profiles reveal expression level relationships in human tissue specifications. Bioinformatics 21:650-659.
-
(2005)
Bioinformatics
, vol.21
, pp. 650-659
-
-
Yanai, I.1
Benjamin, H.2
Shmoish, M.3
-
36
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
-
(2007)
Mol Biol Evol.
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
37
-
-
84859473329
-
Proteinmisinteraction avoidance causes highly expressed proteins to evolve slowly
-
Yang J, Liao B, Zhuang S, Zhang J. 2012. Proteinmisinteraction avoidance causes highly expressed proteins to evolve slowly. Proc Natl Acad Sci USA. 109:5158-5159.
-
(2012)
Proc Natl Acad Sci USA.
, vol.109
, pp. 5158-5159
-
-
Yang, J.1
Liao, B.2
Zhuang, S.3
Zhang, J.4
-
38
-
-
77958577844
-
Impact of translational error-induced and error-free misfolding on the rate of protein evolution
-
Yang J, Zhuang S, Zhang J. 2010. Impact of translational error-induced and error-free misfolding on the rate of protein evolution. Mol Syst Biol. 6:421.
-
(2010)
Mol Syst Biol.
, vol.6
, pp. 421
-
-
Yang, J.1
Zhuang, S.2
Zhang, J.3
-
39
-
-
36049027813
-
Protein stability imposes limits on organism complexity and speed of molecular evolution
-
Zeldovich KB, Chen P, Shakhnovich EI. 2007. Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc Natl Acad Sci USA. 104:16152-16157.
-
(2007)
Proc Natl Acad Sci USA.
, vol.104
, pp. 16152-16157
-
-
Zeldovich, K.B.1
Chen, P.2
Shakhnovich, E.I.3
-
40
-
-
1542286776
-
Mammalian housekeeping genes evolve more slowly than tissue-specific genes
-
Zhang L, Li WH. 2004. Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol Biol Evol. 21:236-239.
-
(2004)
Mol Biol Evol.
, vol.21
, pp. 236-239
-
-
Zhang, L.1
Li, W.H.2
|