-
1
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181: 223-230.
-
(1973)
Science
, vol.181
, pp. 223-230
-
-
Anfinsen, C.B.1
-
2
-
-
0014958491
-
Darwinian evolution of proteins
-
Clarke B (1970) Darwinian evolution of proteins. Science 168: 1009-1011.
-
(1970)
Science
, vol.168
, pp. 1009-1011
-
-
Clarke, B.1
-
3
-
-
0019474499
-
Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes
-
Ikemura T (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol 146: 1-21.
-
(1981)
J Mol Biol
, vol.146
, pp. 1-21
-
-
Ikemura, T.1
-
5
-
-
0036889468
-
Evolution of synonymous codon usage in metazoans
-
Duret L (2002) Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev 12: 640-649.
-
(2002)
Curr Opin Genet Dev
, vol.12
, pp. 640-649
-
-
Duret, L.1
-
6
-
-
4143122090
-
Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata
-
DOI 10.1093/molbev/msh191
-
Wright SI, Yau CB, Looseley M, Meyers BC (2004) Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol Biol Evol 21: 1719-1726. (Pubitemid 39096888)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.9
, pp. 1719-1726
-
-
Wright, S.I.1
Yau, C.B.K.2
Looseley, M.3
Meyers, B.C.4
-
7
-
-
79954456859
-
Determinants of translation efficiency and accuracy
-
Gingold H, Pilpel Y (2011) Determinants of translation efficiency and accuracy. Mol Syst Biol 7: 481.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 481
-
-
Gingold, H.1
Pilpel, Y.2
-
8
-
-
84857715986
-
Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels
-
Frenkel-Morgenstern M, Danon T, Christian T, Igarashi T, Cohen L, et al. (2012) Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels. Mol Syst Biol 8: 572.
-
(2012)
Mol Syst Biol
, vol.8
, pp. 572
-
-
Frenkel-Morgenstern, M.1
Danon, T.2
Christian, T.3
Igarashi, T.4
Cohen, L.5
-
9
-
-
31144465926
-
Hearing silence: Non-neutral evolution at synonymous sites in mammals
-
DOI 10.1038/nrg1770, PII NRG1770
-
Chamary JV, Parmley JL, Hurst LD (2006) Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 7: 98-108. (Pubitemid 43128905)
-
(2006)
Nature Reviews Genetics
, vol.7
, Issue.2
, pp. 98-108
-
-
Chamary, J.V.1
Parmley, J.L.2
Hurst, L.D.3
-
10
-
-
0037047644
-
Predictive identification of exonic splicing enhancers in human genes
-
DOI 10.1126/science.1073774
-
Fairbrother WG, Yeh RF, Sharp PA, Burge CB (2002) Predictive identification of exonic splicing enhancers in human genes. Science 297: 1007-1013. (Pubitemid 34856033)
-
(2002)
Science
, vol.297
, Issue.5583
, pp. 1007-1013
-
-
Fairbrother, W.G.1
Yeh, R.-F.2
Sharp, P.A.3
Burge, C.B.4
-
11
-
-
10944256767
-
Systematic identification and analysis of exonic splicing silencers
-
DOI 10.1016/j.cell.2004.11.010, PII S0092867404010566
-
Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, et al. (2004) Systematic identification and analysis of exonic splicing silencers. Cell 119: 831-845. (Pubitemid 40017689)
-
(2004)
Cell
, vol.119
, Issue.6
, pp. 831-845
-
-
Wang, Z.1
Rolish, M.E.2
Yeo, G.3
Tung, V.4
Mawson, M.5
Burge, C.B.6
-
12
-
-
2942596145
-
Natural selection affects frequencies of AG and GT dinucleotides at the 59 and 39 ends of exons
-
DOI 10.1534/genetics.167.1.543
-
Eskesen ST, Eskesen FN, Ruvinsky A (2004) Natural selection affects frequencies of AG and GT dinucleotides at the 59 and 39 ends of exons. Genetics 167: 543-550. (Pubitemid 38736409)
-
(2004)
Genetics
, vol.167
, Issue.1
, pp. 543-550
-
-
Eskesen, S.T.1
Eskesen, F.N.2
Ruvinsky, A.3
-
13
-
-
0035252561
-
Evidence for purifying selection acting on silent sites in BRCA1
-
DOI 10.1016/S0168-9525(00)02173-9, PII S0168952500021739
-
Hurst LD, Pal C (2001) Evidence for purifying selection acting on silent sites in BRCA1. Trends Genet 17: 62-65. (Pubitemid 32140772)
-
(2001)
Trends in Genetics
, vol.17
, Issue.2
, pp. 62-65
-
-
Hurst, L.D.1
Pal, C.2
-
14
-
-
0035340508
-
Purifying selection on silent sites - A constraint from splicing regulation?
-
Orban TI, Olah E (2001) Purifying selection on silent sites - a constraint from splicing regulation? Trends Genet 17: 252-253.
-
(2001)
Trends Genet
, vol.17
, pp. 252-253
-
-
Orban, T.I.1
Olah, E.2
-
15
-
-
0034736528
-
A test of translational selection at 'silent' sites in the human genome: Base composition comparisons in alternatively spliced genes
-
DOI 10.1016/S0378-1119(00)00482-0, PII S0378111900004820
-
Iida K, Akashi H (2000) A test of translational selection at 'silent' sites in the human genome: base composition comparisons in alternatively spliced genes. Gene 261: 93-105. (Pubitemid 32103527)
-
(2000)
Gene
, vol.261
, Issue.1
, pp. 93-105
-
-
Iida, K.1
Akashi, H.2
-
16
-
-
74549226523
-
Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments
-
Lu H, Lin L, Sato S, Xing Y, Lee CJ (2009) Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments. PLoS Comput Biol 5: e1000608.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Lu, H.1
Lin, L.2
Sato, S.3
Xing, Y.4
Lee, C.J.5
-
17
-
-
33745394130
-
Alternative splicing and RNA selection pressure - Evolutionary consequences for eukaryotic genomes
-
DOI 10.1038/nrg1896, PII N1896
-
Xing Y, Lee C (2006) Alternative splicing and RNA selection pressure-evolutionary consequences for eukaryotic genomes. Nat Rev Genet 7: 499-509. (Pubitemid 43943568)
-
(2006)
Nature Reviews Genetics
, vol.7
, Issue.7
, pp. 499-509
-
-
Xing, Y.1
Lee, C.2
-
18
-
-
0037320652
-
Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor
-
DOI 10.1093/hmg/ddg055
-
Duan J, Wainwright MS, Comeron JM, Saitou N, Sanders AR, et al. (2003) Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum Mol Genet 12: 205-216. (Pubitemid 36204418)
-
(2003)
Human Molecular Genetics
, vol.12
, Issue.3
, pp. 205-216
-
-
Duan, J.1
Wainwright, M.S.2
Comeron, J.M.3
Saitou, N.4
Sanders, A.R.5
Gelernter, J.6
Gejman, P.V.7
-
19
-
-
33845899137
-
Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure
-
DOI 10.1126/science.1131262
-
Nackley AG, Shabalina SA, Tchivileva IE, Satterfield K, Korchynskyi O, et al. (2006) Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science 314: 1930-1933. (Pubitemid 46026115)
-
(2006)
Science
, vol.314
, Issue.5807
, pp. 1930-1933
-
-
Nackley, A.G.1
Shabalina, S.A.2
Tchivileva, I.E.3
Satterfield, K.4
Korchynskyi, O.5
Makarov, S.S.6
Maixner, W.7
Diatchenko, L.8
-
20
-
-
19544391975
-
A synonymous SNP of the corneodesmosin gene leads to increased mRNA stability and demonstrates association with psoriasis across diverse ethnic groups
-
DOI 10.1093/hmg/ddh273
-
Capon F, Allen MH, Ameen M, Burden AD, Tillman D, et al. (2004) A synonymous SNP of the corneodesmosin gene leads to increased mRNA stability and demonstrates association with psoriasis across diverse ethnic groups. Hum Mol Genet 13: 2361-2368. (Pubitemid 39377840)
-
(2004)
Human Molecular Genetics
, vol.13
, Issue.20
, pp. 2361-2368
-
-
Capon, F.1
Allen, M.H.2
Ameen, M.3
Burden, A.D.4
Tillman, D.5
Barker, J.N.6
Trembath, R.C.7
-
21
-
-
33846504706
-
A "silent" polymorphism in the MDR1 gene changes substrate specificity
-
DOI 10.1126/science.1135308
-
Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, et al. (2007) A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science 315: 525-528. (Pubitemid 46175758)
-
(2007)
Science
, vol.315
, Issue.5811
, pp. 525-528
-
-
Kimchi-Sarfaty, C.1
Oh, J.M.2
Kim, I.-W.3
Sauna, Z.E.4
Calcagno, A.M.5
Ambudkar, S.V.6
Gottesman, M.M.7
-
22
-
-
0030018101
-
Ribosome-mediated translational pause and protein domain organization
-
Thanaraj TA, Argos P (1996) Ribosome-mediated translational pause and protein domain organization. Protein Sci 5: 1594-1612. (Pubitemid 26257223)
-
(1996)
Protein Science
, vol.5
, Issue.8
, pp. 1594-1612
-
-
Thanaraj, T.A.1
Argos, P.2
-
23
-
-
0032493780
-
Specific correlations between relative synonymous codon usage and protein secondary structure
-
DOI 10.1006/jmbi.1998.1921
-
Oresic M, Shalloway D (1998) Specific correlations between relative synonymous codon usage and protein secondary structure. J Mol Biol 281: 31-48. (Pubitemid 28360669)
-
(1998)
Journal of Molecular Biology
, vol.281
, Issue.1
, pp. 31-48
-
-
Oresic, M.1
Shalloway, D.2
-
24
-
-
35448992847
-
Silent polymorphisms speak: How they affect pharmacogenomics and the treatment of cancer
-
DOI 10.1158/0008-5472.CAN-07-2377
-
Sauna ZE, Kimchi-Sarfaty C, Ambudkar SV, Gottesman MM (2007) Silent polymorphisms speak: how they affect pharmacogenomics and the treatment of cancer. Cancer Res 67: 9609-9612. (Pubitemid 47621204)
-
(2007)
Cancer Research
, vol.67
, Issue.20
, pp. 9609-9612
-
-
Sauna, Z.E.1
Kimchi-Sarfaty, C.2
Ambudkar, S.V.3
Gottesman, M.M.4
-
25
-
-
80052964856
-
Understanding the contribution of synonymous mutations to human disease
-
Sauna ZE, Kimchi-Sarfaty C (2011) Understanding the contribution of synonymous mutations to human disease. Nat Rev Genet 12: 683-691.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 683-691
-
-
Sauna, Z.E.1
Kimchi-Sarfaty, C.2
-
26
-
-
67650264293
-
The price of silent mutations
-
Chamary JV, Hurst LD (2009) The price of silent mutations. Sci Am 300: 46-53.
-
(2009)
Sci Am
, vol.300
, pp. 46-53
-
-
Chamary, J.V.1
Hurst, L.D.2
-
27
-
-
78149437703
-
Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association
-
Chen R, Davydov EV, Sirota M, Butte AJ (2010) Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. PLoS One 5: e13574.
-
(2010)
PLoS One
, vol.5
-
-
Chen, R.1
Davydov, E.V.2
Sirota, M.3
Butte, A.J.4
-
28
-
-
84938534717
-
Detecting and understanding natural selection
-
Cannarozzi G, Schneider A, editors. Oxford University Press
-
Anisimova M, Liberles D (2012) Detecting and understanding natural selection. In: Cannarozzi G, Schneider A, editors. Codon Evolution: mechanisms and models: Oxford University Press.
-
(2012)
Codon Evolution: Mechanisms and Models
-
-
Anisimova, M.1
Liberles, D.2
-
29
-
-
34547739034
-
Widespread positive selection in synonymous sites of mammalian genes
-
DOI 10.1093/molbev/msm100
-
Resch AM, Carmel L, Marino-Ramirez L, Ogurtsov AY, Shabalina SA, et al. (2007) Widespread positive selection in synonymous sites of mammalian genes. Mol Biol Evol 24: 1821-1831. (Pubitemid 47236700)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.8
, pp. 1821-1831
-
-
Resch, A.M.1
Carmel, L.2
Marino-Ramirez, L.3
Ogurtsov, A.Y.4
Shabalina, S.A.5
Rogozin, I.B.6
Koonin, E.V.7
-
30
-
-
0033639150
-
Statistical methods for detecting molecular adaptation
-
Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15: 496-503.
-
(2000)
Trends Ecol Evol
, vol.15
, pp. 496-503
-
-
Yang, Z.1
Bielawski, J.P.2
-
31
-
-
77954988795
-
Detecting Positive and Purifying Selection at Synonymous Sites in Yeast and Worm
-
Zhou T, Gu WJ, Wilke CO (2010) Detecting Positive and Purifying Selection at Synonymous Sites in Yeast and Worm. Molecular Biology and Evolution 27: 1912-1922.
-
(2010)
Molecular Biology and Evolution
, vol.27
, pp. 1912-1922
-
-
Zhou, T.1
Gu, W.J.2
Wilke, C.O.3
-
32
-
-
33644878388
-
PANDIT: An evolution-centric database of protein and associated nucleotide domains with inferred trees
-
Whelan S, de Bakker PI, Quevillon E, Rodriguez N, Goldman N (2006) PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Res 34: D327-331.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Whelan, S.1
De Bakker, P.I.2
Quevillon, E.3
Rodriguez, N.4
Goldman, N.5
-
33
-
-
84858077472
-
The Pfam protein families database
-
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, et al. (2012) The Pfam protein families database. Nucleic Acids Res 40: D290-301.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Punta, M.1
Coggill, P.C.2
Eberhardt, R.Y.3
Mistry, J.4
Tate, J.5
-
34
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
-
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321.
-
(2010)
Syst Biol
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
-
35
-
-
79957622917
-
PANDITplus: Toward better integration of evolutionary view on molecular sequences with supplementary bioinformatics resources
-
Dimitrieva S, Anisimova M (2010) PANDITplus: toward better integration of evolutionary view on molecular sequences with supplementary bioinformatics resources. Trends in Evol Biol 2.
-
(2010)
Trends in Evol Biol
, vol.2
-
-
Dimitrieva, S.1
Anisimova, M.2
-
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
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure at amino acid sites
-
Yang Z, Nielsen R, Goldman N, Pedersen AM (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449. (Pubitemid 30257141)
-
(2000)
Genetics
, vol.155
, Issue.1
, pp. 431-449
-
-
Yang, Z.1
Nielsen, R.2
Goldman, N.3
Pedersen, A.-M.K.4
-
38
-
-
0034897709
-
Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
-
Anisimova M, Bielawski JP, Yang Z (2001) Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Molecular biology and evolution 18: 1585-1592. (Pubitemid 32735106)
-
(2001)
Molecular Biology and Evolution
, vol.18
, Issue.8
, pp. 1585-1592
-
-
Anisimova, M.1
Bielawski, J.P.2
Yang, Z.3
-
39
-
-
0036272936
-
Accuracy and power of Bayes prediction of amino acid sites under positive selection
-
Anisimova M, Bielawski JP, Yang Z (2002) Accuracy and power of bayes prediction of amino acid sites under positive selection. Molecular biology and evolution 19: 950-958. (Pubitemid 34602964)
-
(2002)
Molecular Biology and Evolution
, vol.19
, Issue.6
, pp. 950-958
-
-
Anisimova, M.1
Bielawski, J.P.2
Yang, Z.3
-
40
-
-
8544225780
-
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
-
DOI 10.1534/genetics.104.031153
-
Wong WSW, Yang Z, Goldman N, Nielsen R (2004) Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168: 1041-1051. (Pubitemid 39491478)
-
(2004)
Genetics
, vol.168
, Issue.2
, pp. 1041-1051
-
-
Wong, W.S.W.1
Yang, Z.2
Goldman, N.3
Nielsen, R.4
-
41
-
-
15844406550
-
HyPhy: Hypothesis testing using phylogenies
-
DOI 10.1093/bioinformatics/bti079
-
Pond SLK, Frost SDW, Muse SV (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics (Oxford, England) 21: 676-679. (Pubitemid 40424796)
-
(2005)
Bioinformatics
, vol.21
, Issue.5
, pp. 676-679
-
-
Kosakovsky, P.S.L.1
Frost, S.D.W.2
Muse, S.V.3
-
42
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B 57: 289-300.
-
(1995)
J R Statist Soc B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
44
-
-
0025318864
-
The Effective Number of Codons Used in a Gene
-
Wright F (1990) The Effective Number of Codons Used in a Gene. Gene 87: 23-29.
-
(1990)
Gene
, vol.87
, pp. 23-29
-
-
Wright, F.1
-
45
-
-
77954148069
-
-
PhD Thesis, University of Nottingham
-
Peden J (1999) CodonW. PhD Thesis, University of Nottingham.
-
(1999)
CodonW
-
-
Peden, J.1
-
46
-
-
33750258647
-
Measures of codon bias in yeast, the tRNA pairing index and possible DNA repair mechanisms
-
Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings
-
Friberg MT, Gonnet P, Barral Y, Schraudolph NN, Gonnet GH (2006) Measures of codon bias in yeast, the tRNA Pairing Index and possible DNA repair mechanisms. Algorithms in Bioinformatics, Proceedings 4175: 1-11. (Pubitemid 44609652)
-
(2006)
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
, vol.4175 LNBI
, pp. 1-11
-
-
Friberg, M.T.1
Gonnet, P.2
Barral, Y.3
Schraudolph, N.N.4
Gonnet, G.H.5
-
47
-
-
77951734603
-
A role for codon order in translation dynamics
-
Cannarozzi G, Schraudolph NN, Faty M, von Rohr P, Friberg MT, et al. (2010) A role for codon order in translation dynamics. Cell 141: 355-367.
-
(2010)
Cell
, vol.141
, pp. 355-367
-
-
Cannarozzi, G.1
Schraudolph, N.N.2
Faty, M.3
Von Rohr, P.4
Friberg, M.T.5
-
48
-
-
0034073452
-
Darwin v. 2.0: An interpreted computer language for the biosciences
-
Gonnet GH, Hallett MT, Korostensky C, Bernardin L (2000) Darwin v. 2.0: an interpreted computer language for the biosciences. Bioinformatics 16: 101-103. (Pubitemid 30248584)
-
(2000)
Bioinformatics
, vol.16
, Issue.2
, pp. 101-103
-
-
Gonnet, G.H.1
Hallett, M.T.2
Korostensky, C.3
Bernardin, L.4
-
50
-
-
58149202157
-
Human Proteinpedia: A unified discovery resource for proteomics research
-
Kandasamy K, Keerthikumar S, Goel R, Mathivanan S, Patankar N, et al. (2009) Human Proteinpedia: a unified discovery resource for proteomics research. Nucleic Acids Res 37: D773-781.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Kandasamy, K.1
Keerthikumar, S.2
Goel, R.3
Mathivanan, S.4
Patankar, N.5
-
51
-
-
70450157442
-
Monoallelic expression and tissue specificity are associated with high crossover rates
-
Necsulea A, Semon M, Duret L, Hurst LD (2009) Monoallelic expression and tissue specificity are associated with high crossover rates. Trends Genet 25: 519-522.
-
(2009)
Trends Genet
, vol.25
, pp. 519-522
-
-
Necsulea, A.1
Semon, M.2
Duret, L.3
Hurst, L.D.4
-
52
-
-
78651289449
-
Ensembl 2011
-
Flicek P, Amode MR, Barrell D, Beal K, Brent S, et al. (2011) Ensembl 2011. Nucleic Acids Res 39: D800-806.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Brent, S.5
-
53
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes
-
DOI 10.1073/pnas.0400782101
-
Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101: 6062-6067. (Pubitemid 38520528)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.16
, pp. 6062-6067
-
-
Su, A.I.1
Wiltshire, T.2
Batalov, S.3
Lapp, H.4
Ching, K.A.5
Block, D.6
Zhang, J.7
Soden, R.8
Hayakawa, M.9
Kreiman, G.10
Cooke, M.P.11
Walker, J.R.12
Hogenesch, J.B.13
-
54
-
-
12344283074
-
Determinants of adaptive evolution at the molecular level: The extended complexity hypothesis
-
Aris-Brosou S (2005) Determinants of adaptive evolution at the molecular level: the extended complexity hypothesis. Mol Biol Evol 22: 200-209.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 200-209
-
-
Aris-Brosou, S.1
-
55
-
-
17644370601
-
Biased codon usage near intron-exon junctions: Selection on splicing enhancers, splice-site recognition or something else?
-
Chamary JV, Hurst LD (2005) Biased codon usage near intron-exon junctions: selection on splicing enhancers, splice-site recognition or something else? Trends Genet 21: 256-259.
-
(2005)
Trends Genet
, vol.21
, pp. 256-259
-
-
Chamary, J.V.1
Hurst, L.D.2
-
56
-
-
0033018384
-
Evidence of selection on silent site base composition in mammals: Potential implications for the evolution of isochores and junk DNA
-
Eyre-Walker A (1999) Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA. Genetics 152: 675-683.
-
(1999)
Genetics
, vol.152
, pp. 675-683
-
-
Eyre-Walker, A.1
-
57
-
-
0030845926
-
Comparative evolutionary rates of introns and exons in murine rodents
-
DOI 10.1007/PL00006211
-
Hughes AL, Yeager M (1997) Comparative evolutionary rates of introns and exons in murine rodents. J Mol Evol 45: 125-130. (Pubitemid 27323517)
-
(1997)
Journal of Molecular Evolution
, vol.45
, Issue.2
, pp. 125-130
-
-
Hughes, A.L.1
Yeager, M.2
-
58
-
-
84861694712
-
Differential GC content between exons and introns establishes distinct strategies of splice-site recognition
-
May 31
-
Amit M, Donyo M, Hollander D, Goren A, Kim E, Gelfman S, Lev-Maor G, Burstein D, Schwartz S, Postolsky B, Pupko T, Ast G. Differential GC content between exons and introns establishes distinct strategies of splice-site recognition. Cell Rep. 2012 May 31;1(5): 543-56.
-
(2012)
Cell Rep
, vol.1
, Issue.5
, pp. 543-556
-
-
Amit, M.1
Donyo, M.2
Hollander, D.3
Goren, A.4
Kim, E.5
Gelfman, S.6
Lev-Maor, G.7
Burstein, D.8
Schwartz, S.9
Postolsky, B.10
Pupko, T.11
Ast, G.12
-
59
-
-
47149115729
-
Sequence-based prediction of protein-protein interactions by means of codon usage
-
Najafabadi HS, Salavati R (2008) Sequence-based prediction of protein-protein interactions by means of codon usage. Genome Biol 9: R87.
-
(2008)
Genome Biol
, vol.9
-
-
Najafabadi, H.S.1
Salavati, R.2
-
60
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
DOI 10.1038/75556
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29. (Pubitemid 30257031)
-
(2000)
Nature Genetics
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
61
-
-
50849122974
-
Patterns of positive selection in six Mammalian genomes
-
Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, et al. (2008) Patterns of positive selection in six Mammalian genomes. PLoS Genet 4: e1000144.
-
(2008)
PLoS Genet
, vol.4
-
-
Kosiol, C.1
Vinar, T.2
Da Fonseca, R.R.3
Hubisz, M.J.4
Bustamante, C.D.5
-
62
-
-
20444430245
-
A scan for positively selected genes in the genomes of humans and chimpanzees
-
Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, et al. (2005) A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 3: e170.
-
(2005)
PLoS Biol
, vol.3
-
-
Nielsen, R.1
Bustamante, C.2
Clark, A.G.3
Glanowski, S.4
Sackton, T.B.5
-
63
-
-
1542286776
-
Mammalian housekeeping genes evolve more slowly than tissue-specific genes
-
Zhang LQ, Li WH (2004) Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Molecular Biology and Evolution 21: 236-239.
-
(2004)
Molecular Biology and Evolution
, vol.21
, pp. 236-239
-
-
Zhang, L.Q.1
Li, W.H.2
-
64
-
-
77955223565
-
Expression breadth and expression abundance behave differently in correlations with evolutionary rates
-
Park SG, Choi SS (2010) Expression breadth and expression abundance behave differently in correlations with evolutionary rates. Bmc Evolutionary Biology 10.
-
(2010)
Bmc Evolutionary Biology
, vol.10
-
-
Park, S.G.1
Choi, S.S.2
-
65
-
-
0037177560
-
Evolutionary rate in the protein interaction network
-
DOI 10.1126/science.1068696
-
Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW (2002) Evolutionary rate in the protein interaction network. Science 296: 750-752. (Pubitemid 34442006)
-
(2002)
Science
, vol.296
, Issue.5568
, pp. 750-752
-
-
Fraser, H.B.1
Hirsh, A.E.2
Steinmetz, L.M.3
Scharfe, C.4
Feldman, M.W.5
-
66
-
-
1842580761
-
Functional and topological characterization of protein interaction networks
-
DOI 10.1002/pmic.200300636
-
Yook SH, Oltvai ZN, Barabasi AL (2004) Functional and topological characterization of protein interaction networks. Proteomics 4: 928-942. (Pubitemid 38445953)
-
(2004)
Proteomics
, vol.4
, Issue.4
, pp. 928-942
-
-
Yook, S.-H.1
Oltvai, Z.N.2
Barabasi, A.-L.3
-
67
-
-
58149199728
-
A pause for thought along the co-translational folding pathway
-
Komar AA (2009) A pause for thought along the co-translational folding pathway. Trends Biochem Sci 34: 16-24.
-
(2009)
Trends Biochem Sci
, vol.34
, pp. 16-24
-
-
Komar, A.A.1
-
68
-
-
79960672524
-
Complex Interplay of Evolutionary Forces in the ladybird Homeobox Genes of Drosophila melanogaster
-
Balakirev ES, Anisimova M, Ayala FJ (2011) Complex Interplay of Evolutionary Forces in the ladybird Homeobox Genes of Drosophila melanogaster. PLoS ONE 6: e22613.
-
(2011)
PLoS ONE
, vol.6
-
-
Balakirev, E.S.1
Anisimova, M.2
Ayala, F.J.3
-
69
-
-
33845884309
-
Pervasive adaptive evolution among interactors of the Drosophila hybrid inviability gene, Nup96
-
DOI 10.1093/molbev/msl157
-
Presgraves DC, Stephan W (2007) Pervasive adaptive evolution among interactors of the Drosophila hybrid inviability gene, Nup96. Molecular Biology and Evolution 24: 306-314. (Pubitemid 46026303)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.1
, pp. 306-314
-
-
Presgraves, D.C.1
Stephan, W.2
-
70
-
-
81055155799
-
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
-
Ingolia NT, Lareau LF, Weissman JS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147: 789-802.
-
(2011)
Cell
, vol.147
, pp. 789-802
-
-
Ingolia, N.T.1
Lareau, L.F.2
Weissman, J.S.3
-
71
-
-
84859219968
-
Balanced codon usage optimizes eukaryotic translational efficiency
-
Qian W, Yang J-R, Pearson NM, Maclean C, Zhang J (2012) Balanced codon usage optimizes eukaryotic translational efficiency. PLoS Genet 8: e1002603.
-
(2012)
PLoS Genet
, vol.8
-
-
Qian, W.1
Yang, J.-R.2
Pearson, N.M.3
Maclean, C.4
Zhang, J.5
-
72
-
-
84860231100
-
The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
-
Li GW, Oh E, Weissman JS (2012) The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 484: 538-541.
-
(2012)
Nature
, vol.484
, pp. 538-541
-
-
Li, G.W.1
Oh, E.2
Weissman, J.S.3
-
73
-
-
84875465945
-
Positively Charged Residues Are the Major Determinants of Ribosomal Velocity
-
Charneski CA, Hurst LD (2013) Positively Charged Residues Are the Major Determinants of Ribosomal Velocity. PLoS Biol 11(3): e1001508.
-
(2013)
PLoS Biol
, vol.11
, Issue.3
-
-
Charneski, C.A.1
Hurst, L.D.2
-
75
-
-
33846588874
-
Genetics. SNPs, silent but not invisible
-
Komar AA (2007) Genetics. SNPs, silent but not invisible. Science 315: 466-467.
-
(2007)
Science
, vol.315
, pp. 466-467
-
-
Komar, A.A.1
-
76
-
-
34548726841
-
Silent SNPs: Impact on gene function and phenotype
-
Komar AA (2007) Silent SNPs: impact on gene function and phenotype. Pharmacogenomics 8: 1075-1080.
-
(2007)
Pharmacogenomics
, vol.8
, pp. 1075-1080
-
-
Komar, A.A.1
-
77
-
-
34250639871
-
The sounds of silence: Synonymous mutations affect functions
-
DOI 10.2217/14622416.8.6.527
-
Sauna ZE, Kimchi-Sarfaty C, Ambudkar SV, Gottesman MM (2007) The sounds of silence: synonymous mutations affect function. Pharmacogenomics 8: 527-532. (Pubitemid 46939578)
-
(2007)
Pharmacogenomics
, vol.8
, Issue.6
, pp. 527-532
-
-
Sauna, Z.E.1
Kimchi-Sarfaty, C.2
Ambudkar, S.V.3
Gottesman, M.M.4
-
78
-
-
62449284683
-
Prion sequence polymorphisms and chronic wasting disease resistance in Illinois white-tailed deer (Odocoileus virginianus)
-
Kelly AC, Mateus-Pinilla NE, Diffendorfer J, Jewell E, Ruiz MO, et al. (2008) Prion sequence polymorphisms and chronic wasting disease resistance in Illinois white-tailed deer (Odocoileus virginianus). Prion 2: 28-36.
-
(2008)
Prion
, vol.2
, pp. 28-36
-
-
Kelly, A.C.1
Mateus-Pinilla, N.E.2
Diffendorfer, J.3
Jewell, E.4
Ruiz, M.O.5
-
79
-
-
52949137359
-
Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima
-
Tsai CJ, Sauna ZE, Kimchi-Sarfaty C, Ambudkar SV, Gottesman MM, et al. (2008) Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. J Mol Biol 383: 281-291.
-
(2008)
J Mol Biol
, vol.383
, pp. 281-291
-
-
Tsai, C.J.1
Sauna, Z.E.2
Kimchi-Sarfaty, C.3
Ambudkar, S.V.4
Gottesman, M.M.5
|