-
1
-
-
77951600170
-
What can we learn about the distribution of fitness effects of new mutations from DNA sequence data?
-
Keightley PD, Eyre-Walker A, (2010) What can we learn about the distribution of fitness effects of new mutations from DNA sequence data? Philos Trans R Soc Lond B Biol Sci 365: 1187–1193 doi:10.1098/rstb.2009.0266
-
(2010)
Philos Trans R Soc Lond B Biol Sci
, vol.365
, pp. 1187-1193
-
-
Keightley, P.D.1
Eyre-Walker, A.2
-
2
-
-
27144491328
-
Adaptive evolution of non-coding DNA in Drosophila
-
Andolfatto P, (2005) Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149–1152 doi:10.1038/nature04107
-
(2005)
Nature
, vol.437
, pp. 1149-1152
-
-
Andolfatto, P.1
-
3
-
-
70149100044
-
Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence
-
Torgerson DG, Boyko AR, Hernandez RD, Indap A, Hu X, et al. (2009) Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genet 5: e1000592 doi:10.1371/journal.pgen.1000592
-
(2009)
PLoS Genet
, vol.5
, pp. e1000592
-
-
Torgerson, D.G.1
Boyko, A.R.2
Hernandez, R.D.3
Indap, A.4
Hu, X.5
-
4
-
-
80054973803
-
A high-resolution map of human evolutionary constraint using 29 mammals
-
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, et al. (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478: 476–482 doi:10.1038/nature10530
-
(2011)
Nature
, vol.478
, pp. 476-482
-
-
Lindblad-Toh, K.1
Garber, M.2
Zuk, O.3
Lin, M.F.4
Parker, B.J.5
-
5
-
-
84879684637
-
Genome-wide inference of natural selection on human transcription factor binding sites
-
Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, et al. (2013) Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet 45: 723–729 doi:10.1038/ng.2658
-
(2013)
Nat Genet
, vol.45
, pp. 723-729
-
-
Arbiza, L.1
Gronau, I.2
Aksoy, B.A.3
Hubisz, M.J.4
Gulko, B.5
-
8
-
-
84892714881
-
Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents
-
Halligan DL, Kousathanas A, Ness RW, Harr B, Eőry L, et al. (2013) Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents. PLoS Genet 9: e1003995 doi:10.1371/journal.pgen.1003995
-
(2013)
PLoS Genet
, vol.9
, pp. e1003995
-
-
Halligan, D.L.1
Kousathanas, A.2
Ness, R.W.3
Harr, B.4
Eőry, L.5
-
9
-
-
33847057226
-
The evolutionary significance of cis-regulatory mutations
-
Wray GA, (2007) The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 8: 206–216 doi:10.1038/nrg2063
-
(2007)
Nat Rev Genet
, vol.8
, pp. 206-216
-
-
Wray, G.A.1
-
10
-
-
22744439568
-
Evolution at two levels: on genes and form
-
Carroll SB, (2005) Evolution at two levels: on genes and form. PLoS Biol 3: e245 doi:10.1371/journal.pbio.0030245
-
(2005)
PLoS Biol
, vol.3
, pp. e245
-
-
Carroll, S.B.1
-
11
-
-
34247855863
-
The locus of evolution: evo devo and the genetics of adaptation
-
Hoekstra HE, Coyne JA, (2007) The locus of evolution: evo devo and the genetics of adaptation. Evolution 61: 995–1016 doi:10.1111/j.1558-5646.2007.00105.x
-
(2007)
Evolution
, vol.61
, pp. 995-1016
-
-
Hoekstra, H.E.1
Coyne, J.A.2
-
12
-
-
0344824015
-
Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents
-
Keightley PD, Gaffney DJ, (2003) Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents. Proc Natl Acad Sci USA 100: 13402–13406 doi:10.1073/pnas.2233252100
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 13402-13406
-
-
Keightley, P.D.1
Gaffney, D.J.2
-
13
-
-
13144251179
-
Plant conserved non-coding sequences and paralogue evolution
-
Lockton S, Gaut BS, (2005) Plant conserved non-coding sequences and paralogue evolution. Trends Genet 21: 60–65 doi:10.1016/j.tig.2004.11.013
-
(2005)
Trends Genet
, vol.21
, pp. 60-65
-
-
Lockton, S.1
Gaut, B.S.2
-
14
-
-
84881028642
-
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
-
Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, et al. (2013) An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet 45: 891–898 doi:10.1038/ng.2684
-
(2013)
Nat Genet
, vol.45
, pp. 891-898
-
-
Haudry, A.1
Platts, A.E.2
Vello, E.3
Hoen, D.R.4
Leclercq, M.5
-
15
-
-
0034978556
-
Highly expressed genes in yeast evolve slowly
-
Pál C, Papp B, Hurst LD, (2001) Highly expressed genes in yeast evolve slowly. Genetics 158: 927–931.
-
(2001)
Genetics
, vol.158
, pp. 927-931
-
-
Pál, C.1
Papp, B.2
Hurst, L.D.3
-
16
-
-
5044252972
-
Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome
-
Subramanian S, Kumar S, (2004) Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 168: 373–381 doi:10.1534/genetics.104.028944
-
(2004)
Genetics
, vol.168
, pp. 373-381
-
-
Subramanian, S.1
Kumar, S.2
-
17
-
-
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 doi:10.1093/molbev/msj038
-
(2006)
Mol Biol Evol
, vol.23
, pp. 327-337
-
-
Drummond, D.A.1
Raval, A.2
Wilke, C.O.3
-
18
-
-
79961064486
-
Factors that contribute to variation in evolutionary rate among Arabidopsis genes
-
Yang L, Gaut BS, (2011) Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Mol Biol Evol 28: 2359–2369 doi:10.1093/molbev/msr058
-
(2011)
Mol Biol Evol
, vol.28
, pp. 2359-2369
-
-
Yang, L.1
Gaut, B.S.2
-
19
-
-
84859114543
-
Genomic determinants of protein evolution and polymorphism in Arabidopsis
-
Slotte T, Bataillon T, Hansen TT, St Onge K, Wright SI, et al. (2011) Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biol Evol 3: 1210–1219 doi:10.1093/gbe/evr094
-
(2011)
Genome Biol Evol
, vol.3
, pp. 1210-1219
-
-
Slotte, T.1
Bataillon, T.2
Hansen, T.T.3
St Onge, K.4
Wright, S.I.5
-
20
-
-
84879553718
-
Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula
-
Paape T, Bataillon T, Zhou P, J Y Kono T, Briskine R, et al. (2013) Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula. Mol Ecol 22: 3525–3538 doi:10.1111/mec.12329
-
(2013)
Mol Ecol
, vol.22
, pp. 3525-3538
-
-
Paape, T.1
Bataillon, T.2
Zhou, P.3
J Y Kono, T.4
Briskine, R.5
-
21
-
-
84878596895
-
The population genomics of sunflowers and genomic determinants of protein evolution revealed by RNAseq
-
Renaut S, Grassa CJ, Moyers BT, Kane NC, Rieseberg LH, (2012) The population genomics of sunflowers and genomic determinants of protein evolution revealed by RNAseq. Biology (Basel) 1: 575–596 doi:10.3390/biology1030575
-
(2012)
Biology (Basel)
, vol.1
, pp. 575-596
-
-
Renaut, S.1
Grassa, C.J.2
Moyers, B.T.3
Kane, N.C.4
Rieseberg, L.H.5
-
22
-
-
78650892229
-
The patterns and causes of variation in plant nucleotide substitution rates
-
Gaut B, Yang L, Takuno S, Eguiarte LE, (2011) The patterns and causes of variation in plant nucleotide substitution rates. Annu Rev Ecol Evol Syst 42: 245–266 doi:10.1146/annurev-ecolsys-102710-145119
-
(2011)
Annu Rev Ecol Evol Syst
, vol.42
, pp. 245-266
-
-
Gaut, B.1
Yang, L.2
Takuno, S.3
Eguiarte, L.E.4
-
23
-
-
84874250754
-
Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly
-
Park C, Chen X, Yang J-R, Zhang J, (2013) Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly. Proc Natl Acad Sci USA 110: E678–E686 doi:10.1073/pnas.1218066110
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, pp. E678-E686
-
-
Park, C.1
Chen, X.2
Yang, J.-R.3
Zhang, J.4
-
24
-
-
84859473329
-
Protein misinteraction avoidance causes highly expressed proteins to evolve slowly
-
Yang J-R, Liao B-Y, Zhuang S-M, Zhang J, (2012) Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. Proc Natl Acad Sci USA 109: E831–E840 doi:10.1073/pnas.1117408109
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. E831-E840
-
-
Yang, J.-R.1
Liao, B.-Y.2
Zhuang, S.-M.3
Zhang, J.4
-
25
-
-
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 doi:10.1016/j.cell.2008.05.042
-
(2008)
Cell
, vol.134
, pp. 341-352
-
-
Drummond, D.A.1
Wilke, C.O.2
-
26
-
-
77954969511
-
Genome wide analyses reveal little evidence for adaptive evolution in many plant species
-
Gossmann TI, Song B-H, Windsor AJ, Mitchell-Olds T, Dixon CJ, et al. (2010) Genome wide analyses reveal little evidence for adaptive evolution in many plant species. Mol Biol Evol 27: 1822–1832.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 1822-1832
-
-
Gossmann, T.I.1
Song, B.-H.2
Windsor, A.J.3
Mitchell-Olds, T.4
Dixon, C.J.5
-
27
-
-
80051669931
-
Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems
-
St Onge KR, Källman T, Slotte T, Lascoux M, Palmé AE, (2011) Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems. Mol Ecol 20: 3306–3320 doi:10.1111/j.1365-294X.2011.05189.x
-
(2011)
Mol Ecol
, vol.20
, pp. 3306-3320
-
-
St Onge, K.R.1
Källman, T.2
Slotte, T.3
Lascoux, M.4
Palmé, A.E.5
-
28
-
-
68949202924
-
Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change
-
Eyre-Walker A, Keightley PD, (2009) Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. Mol Biol Evol 26: 2097–2108 doi:10.1093/molbev/msp119
-
(2009)
Mol Biol Evol
, vol.26
, pp. 2097-2108
-
-
Eyre-Walker, A.1
Keightley, P.D.2
-
29
-
-
67651050074
-
Pervasive natural selection in the Drosophila genome?
-
Sella G, Petrov DA, Przeworski M, Andolfatto P, (2009) Pervasive natural selection in the Drosophila genome? PLoS Genet 5: e1000495 doi:10.1371/journal.pgen.1000495
-
(2009)
PLoS Genet
, vol.5
, pp. e1000495
-
-
Sella, G.1
Petrov, D.A.2
Przeworski, M.3
Andolfatto, P.4
-
30
-
-
84879686532
-
The Capsella rubella genome and the genomic consequences of rapid mating system evolution
-
Slotte T, Hazzouri KM, Agren JA, Koenig D, Maumus F, et al. (2013) The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet 45: 831–835 doi:10.1038/ng.2669
-
(2013)
Nat Genet
, vol.45
, pp. 831-835
-
-
Slotte, T.1
Hazzouri, K.M.2
Agren, J.A.3
Koenig, D.4
Maumus, F.5
-
31
-
-
77956295988
-
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
-
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297–1303 doi:10.1101/gr.107524.110
-
(2010)
Genome Res
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
Hanna, M.2
Banks, E.3
Sivachenko, A.4
Cibulskis, K.5
-
32
-
-
77954966377
-
Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size
-
Slotte T, Foxe JP, Hazzouri KM, Wright SI, (2010) Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size. Mol Biol Evol 27: 1813–1821.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 1813-1821
-
-
Slotte, T.1
Foxe, J.P.2
Hazzouri, K.M.3
Wright, S.I.4
-
33
-
-
34547108086
-
Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana
-
Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, et al. (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317: 338–342 doi:10.1126/science.1138632
-
(2007)
Science
, vol.317
, pp. 338-342
-
-
Clark, R.M.1
Schweikert, G.2
Toomajian, C.3
Ossowski, S.4
Zeller, G.5
-
34
-
-
33751351656
-
Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata
-
Wright SI, Foxe JP, DeRose-Wilson L, Kawabe A, Looseley M, et al. (2006) Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata. Genetics 174: 1421–1430 doi:10.1534/genetics.106.062588
-
(2006)
Genetics
, vol.174
, pp. 1421-1430
-
-
Wright, S.I.1
Foxe, J.P.2
Derose-Wilson, L.3
Kawabe, A.4
Looseley, M.5
-
35
-
-
49849105982
-
High DNA sequence diversity in pericentromeric genes of the plant Arabidopsis lyrata
-
Kawabe A, Forrest A, Wright SI, Charlesworth D, (2008) High DNA sequence diversity in pericentromeric genes of the plant Arabidopsis lyrata. Genetics 179: 985–995 doi:10.1534/genetics.107.085282
-
(2008)
Genetics
, vol.179
, pp. 985-995
-
-
Kawabe, A.1
Forrest, A.2
Wright, S.I.3
Charlesworth, D.4
-
36
-
-
80054797858
-
Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula
-
Branca A, Paape TD, Zhou P, Briskine R, Farmer AD, et al. (2011) Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proc Natl Acad Sci USA 108: E864–E870 doi:10.1073/pnas.1104032108
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. E864-E870
-
-
Branca, A.1
Paape, T.D.2
Zhou, P.3
Briskine, R.4
Farmer, A.D.5
-
37
-
-
84905126894
-
The impact of linked selection on plant genomic variation
-
Slotte T, (2014) The impact of linked selection on plant genomic variation. Brief Funct Genomics 13: 268–275 doi:10.1093/bfgp/elu009
-
(2014)
Brief Funct Genomics
, vol.13
, pp. 268-275
-
-
Slotte, T.1
-
38
-
-
48249142558
-
Sequence variation of MicroRNAs and their binding sites in Arabidopsis
-
Ehrenreich IM, Purugganan MD, (2008) Sequence variation of MicroRNAs and their binding sites in Arabidopsis. Plant Physiol 146: 1974–1982 doi:10.1104/pp.108.116582
-
(2008)
Plant Physiol
, vol.146
, pp. 1974-1982
-
-
Ehrenreich, I.M.1
Purugganan, M.D.2
-
39
-
-
79952263624
-
Pervasive adaptive protein evolution and diversity patterns around amino acid substitutions in Drosophila simulans
-
Sattath S, Elyashiv E, Kolodny O, Rinott Y, Sella G, (2011) Pervasive adaptive protein evolution and diversity patterns around amino acid substitutions in Drosophila simulans. PLoS Genet 7: e1001302.
-
(2011)
PLoS Genet
, vol.7
, pp. e1001302
-
-
Sattath, S.1
Elyashiv, E.2
Kolodny, O.3
Rinott, Y.4
Sella, G.5
-
40
-
-
55849144411
-
The hitch-hiking effect of a favourable gene
-
Smith JM, Haigh J, (1974) The hitch-hiking effect of a favourable gene. Genet Res 23: 23–35 doi:10.1017/S0016672308009579
-
(1974)
Genet Res
, vol.23
, pp. 23-35
-
-
Smith, J.M.1
Haigh, J.2
-
41
-
-
84891797628
-
The immediate upstream region of the 5′-UTR from the AUG start codon has a pronounced effect on the translational efficiency in Arabidopsis thaliana
-
Kim Y, Lee G, Jeon E, Sohn EJ, Lee Y, et al. (2013) The immediate upstream region of the 5′-UTR from the AUG start codon has a pronounced effect on the translational efficiency in Arabidopsis thaliana. Nucleic Acids Res 42: 485–498 doi:10.1093/nar/gkt864
-
(2013)
Nucleic Acids Res
, vol.42
, pp. 485-498
-
-
Kim, Y.1
Lee, G.2
Jeon, E.3
Sohn, E.J.4
Lee, Y.5
-
42
-
-
66049138497
-
Adaptive evolution of young gene duplicates in mammals
-
Han MV, Demuth JP, McGrath CL, Casola C, Hahn MW, (2009) Adaptive evolution of young gene duplicates in mammals. Genome Res 19: 859–867 doi:10.1101/gr.085951.108
-
(2009)
Genome Res
, vol.19
, pp. 859-867
-
-
Han, M.V.1
Demuth, J.P.2
McGrath, C.L.3
Casola, C.4
Hahn, M.W.5
-
43
-
-
84855751842
-
Reduced efficacy of natural selection on codon usage bias in selfing Arabidopsis and Capsella species
-
Qiu S, Zeng K, Slotte T, Wright S, Charlesworth D, (2011) Reduced efficacy of natural selection on codon usage bias in selfing Arabidopsis and Capsella species. Genome Biol Evol 3: 868–880 doi:10.1093/gbe/evr085
-
(2011)
Genome Biol Evol
, vol.3
, pp. 868-880
-
-
Qiu, S.1
Zeng, K.2
Slotte, T.3
Wright, S.4
Charlesworth, D.5
-
44
-
-
4143122090
-
Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata
-
Wright SI, Yau CBK, Looseley M, Meyers BC, (2004) Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol Biol Evol 21: 1719–1726 doi:10.1093/molbev/msh191
-
(2004)
Mol Biol Evol
, vol.21
, pp. 1719-1726
-
-
Wright, S.I.1
Yau, C.B.K.2
Looseley, M.3
Meyers, B.C.4
-
45
-
-
0033551151
-
Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis
-
Duret L, Mouchiroud D, (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc Natl Acad Sci USA 96: 4482–4487.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 4482-4487
-
-
Duret, L.1
Mouchiroud, D.2
-
46
-
-
0035826858
-
Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes
-
Marais G, Mouchiroud D, Duret L, (2001) Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc Natl Acad Sci USA 98: 5688–5692.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 5688-5692
-
-
Marais, G.1
Mouchiroud, D.2
Duret, L.3
-
47
-
-
79951829399
-
Classic selective sweeps were rare in recent human evolution
-
Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, et al. (2011) Classic selective sweeps were rare in recent human evolution. Science 331: 920–924 doi:10.1126/science.1198878
-
(2011)
Science
, vol.331
, pp. 920-924
-
-
Hernandez, R.D.1
Kelley, J.L.2
Elyashiv, E.3
Melton, S.C.4
Auton, A.5
-
48
-
-
33646592536
-
Soft sweeps II–molecular population genetics of adaptation from recurrent mutation or migration
-
Pennings PS, Hermisson J, (2006) Soft sweeps II–molecular population genetics of adaptation from recurrent mutation or migration. Mol Biol Evol 23: 1076–1084 doi:10.1093/molbev/msj117
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1076-1084
-
-
Pennings, P.S.1
Hermisson, J.2
-
49
-
-
33845971545
-
Soft sweeps III: the signature of positive selection from recurrent mutation
-
Pennings PS, Hermisson J, (2006) Soft sweeps III: the signature of positive selection from recurrent mutation. PLoS Genet 2: e186 doi:10.1371/journal.pgen.0020186
-
(2006)
PLoS Genet
, vol.2
, pp. e186
-
-
Pennings, P.S.1
Hermisson, J.2
-
50
-
-
18844439645
-
Soft sweeps: molecular population genetics of adaptation from standing genetic variation
-
Hermisson J, Pennings PS, (2005) Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169: 2335–2352 doi:10.1534/genetics.104.036947
-
(2005)
Genetics
, vol.169
, pp. 2335-2352
-
-
Hermisson, J.1
Pennings, P.S.2
-
51
-
-
84885911072
-
Population genomics of rapid adaptation by soft selective sweeps
-
Messer PW, Petrov DA, (2013) Population genomics of rapid adaptation by soft selective sweeps. Trends Ecol Evol 28: 659–669 doi:10.1016/j.tree.2013.08.003
-
(2013)
Trends Ecol Evol
, vol.28
, pp. 659-669
-
-
Messer, P.W.1
Petrov, D.A.2
-
52
-
-
84866134251
-
Selective sweeps in multilocus models of quantitative traits
-
Pavlidis P, Metzler D, Stephan W, (2012) Selective sweeps in multilocus models of quantitative traits. Genetics 192: 225–239 doi:10.1534/genetics.112.142547
-
(2012)
Genetics
, vol.192
, pp. 225-239
-
-
Pavlidis, P.1
Metzler, D.2
Stephan, W.3
-
53
-
-
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 doi:10.1093/molbev/msi122
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1345-1354
-
-
Lemos, B.1
Bettencourt, B.R.2
Meiklejohn, C.D.3
Hartl, D.L.4
-
54
-
-
47149117454
-
Evolution of genes and genomes on the Drosophila phylogeny
-
Clark AG, Eisen MB, Smith DR, Bergman CM, Drosophila 12 Genomes Consortium, et al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203–218 doi:10.1038/nature06341
-
(2007)
Nature
, vol.450
, pp. 203-218
-
-
Clark, A.G.1
Eisen, M.B.2
Smith, D.R.3
Bergman, C.M.4
-
55
-
-
84863585352
-
Evidence for widespread positive and purifying selection across the European rabbit (Oryctolagus cuniculus) Genome
-
Carneiro M, Albert FW, Melo-Ferreira J, Galtier N, Gayral P, et al. (2012) Evidence for widespread positive and purifying selection across the European rabbit (Oryctolagus cuniculus) Genome. Mol Biol Evol 29: 1837–1849 doi:10.1093/molbev/mss025
-
(2012)
Mol Biol Evol
, vol.29
, pp. 1837-1849
-
-
Carneiro, M.1
Albert, F.W.2
Melo-Ferreira, J.3
Galtier, N.4
Gayral, P.5
-
56
-
-
79956307251
-
Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads
-
Lunter G, Goodson M, (2011) Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Research 21: 936–939 doi:10.1101/gr.111120.110
-
(2011)
Genome Research
, vol.21
, pp. 936-939
-
-
Lunter, G.1
Goodson, M.2
-
57
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics 43: 491–498 doi:10.1038/ng.806
-
(2011)
Nature Genetics
, vol.43
, pp. 491-498
-
-
Depristo, M.A.1
Banks, E.2
Poplin, R.3
Garimella, K.V.4
Maguire, J.R.5
-
59
-
-
75549086594
-
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
-
Ostlund G, Schmitt T, Forslund K, Kostler T, Messina DN, et al. (2009) InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res 38: D196–D203 doi:10.1093/nar/gkp931
-
(2009)
Nucleic Acids Res
, vol.38
, pp. D196-D203
-
-
Ostlund, G.1
Schmitt, T.2
Forslund, K.3
Kostler, T.4
Messina, D.N.5
-
60
-
-
33747892409
-
Automatic clustering of orthologs and inparalogs shared by multiple proteomes
-
Alexeyenko A, Tamas I, Liu G, Sonnhammer ELL, (2006) Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 22: e9–e15 doi:10.1093/bioinformatics/btl213
-
(2006)
Bioinformatics
, vol.22
, pp. e9-e15
-
-
Alexeyenko, A.1
Tamas, I.2
Liu, G.3
Sonnhammer, E.L.L.4
-
61
-
-
45949105543
-
DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment
-
Subramanian AR, Kaufmann M, Morgenstern B, (2008) DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. Algorithms Mol Biol 3: 6 doi:10.1186/1748-7188-3-6
-
(2008)
Algorithms Mol Biol
, vol.3
, pp. 6
-
-
Subramanian, A.R.1
Kaufmann, M.2
Morgenstern, B.3
-
62
-
-
34547803197
-
PAML 4: phylogenetic analysis by maximum likelihood
-
Yang Z, (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586–1591 doi:10.1093/molbev/msm088
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
63
-
-
1542748076
-
Aligning multiple genomic sequences with the threaded blockset aligner
-
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14: 708–715 doi:10.1101/gr.1933104
-
(2004)
Genome Res
, vol.14
, pp. 708-715
-
-
Blanchette, M.1
Kent, W.J.2
Riemer, C.3
Elnitski, L.4
Smit, A.F.A.5
-
64
-
-
37249042614
-
Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies
-
Keightley PD, Eyre-Walker A, (2007) Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies. Genetics 177: 2251–2261 doi:10.1534/genetics.107.080663
-
(2007)
Genetics
, vol.177
, pp. 2251-2261
-
-
Keightley, P.D.1
Eyre-Walker, A.2
-
65
-
-
65449136284
-
TopHat: discovering splice junctions with RNA-Seq
-
Trapnell C, Pachter L, Salzberg SL, (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105–1111 doi:10.1093/bioinformatics/btp120
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
66
-
-
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, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511–515 doi:10.1038/nbt.1621
-
(2010)
Nat Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
|