-
1
-
-
0001895697
-
Evolutionary divergence and convergence of proteins
-
New York: Academic Press Bryson V, Vogel HJ
-
Zuckerkandl E Pauling L Evolutionary divergence and convergence of proteins Evolving Gene and Proteins New York: Academic Press Bryson V, Vogel HJ 1965, 97-166.
-
(1965)
Evolving Gene and Proteins
, pp. 97-166
-
-
Zuckerkandl, E.1
Pauling, L.2
-
3
-
-
24944526640
-
Converging on a general model of protein evolution
-
16054255
-
Herbeck JT Wall DP Converging on a general model of protein evolution Trends Biotechnol 2005, 23(10):485-487. 16054255
-
(2005)
Trends Biotechnol
, vol.23
, Issue.10
, pp. 485-487
-
-
Herbeck, J.T.1
Wall, D.P.2
-
4
-
-
33748980210
-
Evolutionary systems biology: Links between gene evolution and function
-
16962765
-
Koonin EV Wolf YI Evolutionary systems biology: Links between gene evolution and function Curr Opin Biotechnol 2006, 17(5):481-487. 16962765
-
(2006)
Curr Opin Biotechnol
, vol.17
, Issue.5
, pp. 481-487
-
-
Koonin, E.V.1
Wolf, Y.I.2
-
5
-
-
54949095966
-
Evolutionary Systems Biology
-
Sunderland, MA: Sinauer Associates, Inc Pagel M, Pomiankowski A
-
Koonin EV Wolf YI Evolutionary Systems Biology Evolutionary Genomics and Proteomics Sunderland, MA: Sinauer Associates, Inc Pagel M, Pomiankowski A 2008, 11-25.
-
(2008)
Evolutionary Genomics and Proteomics
, pp. 11-25
-
-
Koonin, E.V.1
Wolf, Y.I.2
-
6
-
-
33646182934
-
An integrated view of protein evolution
-
16619049
-
Pal C Papp B Lercher MJ An integrated view of protein evolution Nat Rev Genet 2006, 7(5):337-348. 16619049
-
(2006)
Nat Rev Genet
, vol.7
, Issue.5
, pp. 337-348
-
-
Pal, C.1
Papp, B.2
Lercher, M.J.3
-
7
-
-
33745107471
-
Influence of metabolic network structure and function on enzyme evolution
-
1779518 16684370
-
Vitkup D Kharchenko P Wagner A Influence of metabolic network structure and function on enzyme evolution Genome Biol 2006, 7(5):R39. 1779518 16684370
-
(2006)
Genome Biol
, vol.7
, Issue.6
-
-
Vitkup, D.1
Kharchenko, P.2
Wagner, A.3
-
8
-
-
0033565762
-
Do essential genes evolve slowly?
-
10421576
-
Hurst LD Smith NG Do essential genes evolve slowly? Curr Biol 1999, 9(14):747-750. 10421576
-
(1999)
Curr Biol
, vol.9
, Issue.14
, pp. 747-750
-
-
Hurst, L.D.1
Smith, N.G.2
-
9
-
-
0035963414
-
Protein dispensability and rate of evolution
-
1049 11429604
-
Hirsh AE Fraser HB Protein dispensability and rate of evolution Nature 2001, 411:6841-1046. 1049 11429604
-
(2001)
Nature
, vol.411
, pp. 1046-1049
-
-
Hirsh, A.E.1
Fraser, H.B.2
-
10
-
-
0036078078
-
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
-
1383730 12045149
-
Jordan IK Rogozin IB Wolf YI Koonin EV Essential genes are more evolutionarily conserved than are nonessential genes in bacteria Genome Res 2002, 12(6):962-968 1383730 12045149
-
(2002)
Genome Res
, vol.12
, Issue.6
, pp. 962-968
-
-
Jordan, I.K.1
Rogozin, I.B.2
Wolf, Y.I.3
Koonin, E.V.4
-
11
-
-
0142124263
-
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
-
403683 14525925
-
Krylov DM Wolf YI Rogozin IB Koonin EV Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution Genome Res 2003, 13(10);2229-2235. 403683 14525925
-
(2003)
Genome Res
, vol.13
, Issue.10
, pp. 2229-2235
-
-
Krylov, D.M.1
Wolf, Y.I.2
Rogozin, I.B.3
Koonin, E.V.4
-
12
-
-
17244367886
-
Functional genomic analysis of the rates of protein evolution
-
555735 15800036
-
Wall DP Hirsh AE Fraser HB Kumm J Giaever G Eisen MB Feldman MW Functional genomic analysis of the rates of protein evolution Proc Natl Acad Sci USA 2005, 102(15):5483-5488. 555735 15800036
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.15
, 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
-
13
-
-
33745744354
-
Coping with the quantitative genomics 'elephant': The correlation between the gene dispensability and evolution rate
-
16697070
-
Wolf YI Coping with the quantitative genomics 'elephant': The correlation between the gene dispensability and evolution rate Trends Genet 2006, 16697070.
-
(2006)
Trends Genet
-
-
Wolf, Y.I.1
-
14
-
-
0034978556
-
Highly expressed genes in yeast evolve slowly
-
1461684 11430355
-
Pal C Papp B Hurst LD Highly expressed genes in yeast evolve slowly Genetics 2001, 158(2):927-931. 1461684 11430355
-
(2001)
Genetics
, vol.158
, Issue.2
, pp. 927-931
-
-
Pal, C.1
Papp, B.2
Hurst, L.D.3
-
16
-
-
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
-
15746013
-
Lemos B Bettencourt BR Meiklejohn CD Hartl DL 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 2005, 22(5):1345-1354. 15746013
-
(2005)
Mol Biol Evol
, vol.22
, Issue.5
, pp. 1345-1354
-
-
Lemos, B.1
Bettencourt, B.R.2
Meiklejohn, C.D.3
Hartl, D.L.4
-
17
-
-
0035799707
-
Lethality and centrality in protein networks
-
11333967
-
Jeong H Mason SP Barabasi AL Oltvai ZN Lethality and centrality in protein networks Nature 2001, 411(6833):41-42. 11333967
-
(2001)
Nature
, vol.411
, Issue.6833
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabasi, A.L.3
Oltvai, Z.N.4
-
18
-
-
2942678187
-
Evolutionary rate depends on number of protein-protein interactions independently of gene expression level
-
420460 15165289
-
Fraser HB Hirsh AE Evolutionary rate depends on number of protein-protein interactions independently of gene expression level BMC Evol Biol 2004, 4(1):13. 420460 15165289
-
(2004)
BMC Evol Biol
, vol.4
, Issue.1
, pp. 13
-
-
Fraser, H.B.1
Hirsh, A.E.2
-
20
-
-
0242284421
-
A simple dependence between protein evolution rate and the number of protein-protein interactions
-
166126 12769820
-
Fraser HB Wall DP Hirsh AE A simple dependence between protein evolution rate and the number of protein-protein interactions BMC Evol Biol 2003, 3(1):11. 166126 12769820
-
(2003)
BMC Evol Biol
, vol.3
, Issue.1
, pp. 11
-
-
Fraser, H.B.1
Wall, D.P.2
Hirsh, A.E.3
-
21
-
-
6344241652
-
Conservation and coevolution in the scale-free human gene coexpression network
-
15282333
-
Jordan IK Marino-Ramirez L Wolf YI Koonin EV Conservation and coevolution in the scale-free human gene coexpression network Mol Biol Evol 2004, 21(11):2058-2070. 15282333
-
(2004)
Mol Biol Evol
, vol.21
, Issue.11
, pp. 2058-2070
-
-
Jordan, I.K.1
Marino-Ramirez, L.2
Wolf, Y.I.3
Koonin, E.V.4
-
22
-
-
16844363315
-
Modularity and evolutionary constraint on proteins
-
15750592
-
Fraser HB Modularity and evolutionary constraint on proteins Nat Genet 2005, 37(4):351-352. 15750592
-
(2005)
Nat Genet
, vol.37
, Issue.4
, pp. 351-352
-
-
Fraser, H.B.1
-
23
-
-
33746192317
-
Unifying measures of gene function and evolution
-
1560323 16777745
-
Wolf YI Carmel L Koonin EV Unifying measures of gene function and evolution Proc Biol Sci 2006, 273:1507-1515. 1560323 16777745
-
(2006)
Proc Biol Sci
, vol.273
, pp. 1507-1515
-
-
Wolf, Y.I.1
Carmel, L.2
Koonin, E.V.3
-
24
-
-
30744441602
-
A single determinant dominates the rate of yeast protein evolution
-
16237209
-
Drummond DA Raval A Wilke CO A single determinant dominates the rate of yeast protein evolution Mol Biol Evol 2006, 23(2):327-337. 16237209
-
(2006)
Mol Biol Evol
, vol.23
, Issue.2
, pp. 327-337
-
-
Drummond, D.A.1
Raval, A.2
Wilke, C.O.3
-
25
-
-
47549097539
-
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
-
186625481
-
Drummond DA Wilke CO Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution Cell 2008, 134(2):341-352. 18662548
-
(2008)
Cell
, vol.134
, Issue.1
, pp. 341-352
-
-
Drummond, D.A.1
Wilke, C.O.2
-
26
-
-
33646904645
-
Population genetics of translational robustness
-
1461446 16489231
-
Wilke CO Drummond DA Population genetics of translational robustness Genetics 2006, 173(1):473-481. 1461446 16489231
-
(2006)
Genetics
, vol.173
, Issue.1
, pp. 473-481
-
-
Wilke, C.O.1
Drummond, D.A.2
-
27
-
-
31044448435
-
A simple physical model for scaling in protein-protein interaction networks
-
1326177 16384916
-
Deeds EJ Ashenberg O Shakhnovich EI A simple physical model for scaling in protein-protein interaction networks Proc Natl Acad Sci USA 2006, 103(2):311-316. 1326177 16384916
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.2
, pp. 311-316
-
-
Deeds, E.J.1
Ashenberg, O.2
Shakhnovich, E.I.3
-
28
-
-
26244442102
-
Modules, multidomain proteins and organismic complexity
-
16176277
-
Tordai H Nagy A Farkas K Banyai L Patthy L Modules, multidomain proteins and organismic complexity Febs J 2005, 272(19):50645078. 16176277
-
(2005)
Febs J
, vol.272
, Issue.19
, pp. 5064-5078
-
-
Tordai, H.1
Nagy, A.2
Farkas, K.3
Banyai, L.4
Patthy, L.5
-
29
-
-
40449095056
-
Evolution of protein domain promiscuity in eukaryotes
-
2259109 18230802
-
Basu MK Carmel L Rogozin IB Koonin EV Evolution of protein domain promiscuity in eukaryotes Genome Res 2008, 18(3):449-461. 2259109 18230802
-
(2008)
Genome Res
, vol.18
, Issue.3
, pp. 449-461
-
-
Basu, M.K.1
Carmel, L.2
Rogozin, I.B.3
Koonin, E.V.4
-
30
-
-
0345316714
-
Increase of functional diversity by alternative splicing
-
12615003
-
Kriventseva EV Koch I Apweiler R Vingron M Bork P Gelfand MS Sunyaev S Increase of functional diversity by alternative splicing Trends Genet 2003, 19(3):124-128. 12615003
-
(2003)
Trends Genet
, vol.19
, Issue.3
, pp. 124-128
-
-
Kriventseva, E.V.1
Koch, I.2
Apweiler, R.3
Vingron, M.4
Bork, P.5
Gelfand, M.S.6
Sunyaev, S.7
-
31
-
-
34250813107
-
Alternative splicing of pre-messenger RNAs in plants in the genomic era
-
17222076
-
Reddy AS Alternative splicing of pre-messenger RNAs in plants in the genomic era Annu Rev Plant Biol 2007, 58:267-294. 17222076
-
(2007)
Annu Rev Plant Biol
, vol.58
, pp. 267-294
-
-
Reddy, A.S.1
-
32
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
7723011
-
Murzin AG Brenner SE Hubbard T Chothia C SCOP: A structural classification of proteins database for the investigation of sequences and structures J Mol Biol, 1995, 247(4):536-540. 7723011
-
(1995)
J Mol Biol
, vol.247
, Issue.4
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
33
-
-
0033858110
-
From complete genomes to measures of substitution rate variability within and between proteins
-
310923 10899148
-
Grishin NV Wolf YI Koonin EV From complete genomes to measures of substitution rate variability within and between proteins Genome Res 2000, 10(7):991-1000. 310923 10899148
-
(2000)
Genome Res
, vol.10
, Issue.7
, pp. 991-1000
-
-
Grishin, N.V.1
Wolf, Y.I.2
Koonin, E.V.3
-
34
-
-
16444381885
-
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
-
395751 14759257
-
Koonin EV Fedorova ND Jackson JD Jacobs AR Krylov DM Makarova KS Mazumder R Mekhedov SL Nikolskaya AN Rao BS et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes Genome Biol 2004, 5(2):R7. 395751 14759257
-
(2004)
Genome Biol
, vol.5
, Issue.2
-
-
Koonin, E.V.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Krylov, D.M.5
Makarova, K.S.6
Mazumder, R.7
Mekhedov, S.L.8
Nikolskaya, A.N.9
Rao, B.S.10
-
35
-
-
0041673352
-
Structural determinant of protein designability
-
12786593
-
England JL Shakhnovich EI Structural determinant of protein designability Phys Rev Lett 2003, 90(21):218101. 12786593
-
(2003)
Phys Rev Lett
, vol.90
, Issue.21
, pp. 218101
-
-
England, J.L.1
Shakhnovich, E.I.2
-
36
-
-
33748143748
-
Structural determinants of the rate of protein evolution in yeast
-
16782762
-
Bloom JD Drummond DA Arnold FH Wilke CO Structural determinants of the rate of protein evolution in yeast Mol Biol Evol 2006, 23(9):1751-1761. 16782762
-
(2006)
Mol Biol Evol
, vol.23
, Issue.9
, pp. 1751-1761
-
-
Bloom, J.D.1
Drummond, D.A.2
Arnold, F.H.3
Wilke, C.O.4
-
37
-
-
43149112799
-
Contact density affects protein evolutionary rate from bacteria to animals
-
18379715
-
Zhou T Drummond DA Wilke CO Contact density affects protein evolutionary rate from bacteria to animals J Mol Evol 2008, 66(4):395-404. 18379715
-
(2008)
J Mol Evol
, vol.66
, Issue.4
, pp. 395-404
-
-
Zhou, T.1
Drummond, D.A.2
Wilke, C.O.3
-
38
-
-
33845895536
-
The frequency of translational misreading errors in E. coli is largely determined by tRNA competition
-
1705757 17095544
-
Kramer EB Farabaugh PJ The frequency of translational misreading errors in E. coli is largely determined by tRNA competition Rna 2007, 13(1):87-96. 1705757 17095544
-
(2007)
Rna
, vol.13
, Issue.1
, pp. 87-96
-
-
Kramer, E.B.1
Farabaugh, P.J.2
-
39
-
-
0346727127
-
Protein degradation and protection against misfolded or damaged proteins
-
14685250
-
Goldberg AL Protein degradation and protection against misfolded or damaged proteins Nature 2003, 426(6968):895-899. 14685250
-
(2003)
Nature
, vol.426
, Issue.6968
, pp. 895-899
-
-
Goldberg, A.L.1
-
40
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
146917 9254694
-
Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997, 25(17):3389-3402. 146917 9254694
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
43
-
-
0030660581
-
A genomic perspective on protein families
-
9381173
-
Tatusov RL Koonin EV Lipman DJ A genomic perspective on protein families Science 1997, 278(5338):631-637. 9381173
-
(1997)
Science
, vol.278
, Issue.5338
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
44
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
390337 15034147
-
Edgar RC MUSCLE: Multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res 2004, 32(5):1792-1797. 390337 15034147
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
-
45
-
-
0029901637
-
Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods
-
8743697
-
Felsenstein J Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods Methods Enzymol 1996, 266:418-427. 8743697
-
(1996)
Methods Enzymol
, vol.266
, pp. 418-427
-
-
Felsenstein, J.1
-
46
-
-
0001473437
-
On estimation of a probability density function and mode
-
Parzen E On estimation of a probability density function and mode Ann Math Stat 1962, 33:1065-1076.
-
(1962)
Ann Math Stat
, vol.33
, pp. 1065-1076
-
-
Parzen, E.1
|