-
1
-
-
84975795680
-
An integrated map of genetic variation from 1,092 human genomes
-
The 1000 Genomes Project Consortium
-
The 1000 Genomes Project Consortium. 2012. An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65.
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
-
2
-
-
77951640946
-
A method and server for predicting damaging missense mutations
-
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. 2010. A method and server for predicting damaging missense mutations. Nat Methods 7: 248-249.
-
(2010)
Nat Methods
, vol.7
, pp. 248-249
-
-
Adzhubei, I.A.1
Schmidt, S.2
Peshkin, L.3
Ramensky, V.E.4
Gerasimova, A.5
Bork, P.6
Kondrashov, A.S.7
Sunyaev, S.R.8
-
3
-
-
65149103048
-
Constructing genomic maps of positive selection in humans: Where do we go from here?
-
Akey JM. 2009. Constructing genomic maps of positive selection in humans: Where do we go from here? Genome Res 19: 711-722.
-
(2009)
Genome Res
, vol.19
, pp. 711-722
-
-
Akey, J.M.1
-
4
-
-
38849194141
-
Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome
-
DOI 10.1101/gr.6691007
-
Andolfatto P. 2007. Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome. Genome Res 17: 1755-1762. (Pubitemid 351359999)
-
(2007)
Genome Research
, vol.17
, Issue.12
, pp. 1755-1762
-
-
Andolfatto, P.1
-
5
-
-
44949129000
-
Assessing the evolutionary impact of amino acid mutations in the human genome
-
Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez RD, Lohmueller KE, Adams MD, Schmidt S, Sninsky JJ, Sunyaev SR, et al. 2008. Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet 4: e1000083.
-
(2008)
PLoS Genet
, vol.4
-
-
Boyko, A.R.1
Williamson, S.H.2
Indap, A.R.3
Degenhardt, J.D.4
Hernandez, R.D.5
Lohmueller, K.E.6
Adams, M.D.7
Schmidt, S.8
Sninsky, J.J.9
Sunyaev, S.R.10
-
7
-
-
0027305597
-
The effect of deleterious mutations on neutral molecular variation
-
Charlesworth B, Morgan MT, Charlesworth D. 1993. The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303. (Pubitemid 23220050)
-
(1993)
Genetics
, vol.134
, Issue.4
, pp. 1289-1303
-
-
Charlesworth, B.1
Morgan, M.T.2
Charlesworth, D.3
-
8
-
-
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.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 2097-2108
-
-
Eyre-Walker, A.1
Keightley, P.D.2
-
9
-
-
77957233773
-
The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection
-
Fletcher W, Yang Z. 2010. The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol 27: 2257-2267.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 2257-2267
-
-
Fletcher, W.1
Yang, Z.2
-
10
-
-
84858221706
-
Ensembl 2012
-
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, et al. 2012. Ensembl 2012. Nucleic Acids Res 40: D84-D90.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Brent, S.5
Carvalho-Silva, D.6
Clapham, P.7
Coates, G.8
Fairley, S.9
Fitzgerald, S.10
-
11
-
-
84880076219
-
Gene expression drives local adaptation in humans
-
Fraser HB. 2013. Gene expression drives local adaptation in humans. Genome Res 23: 1089-1096.
-
(2013)
Genome Res
, vol.23
, pp. 1089-1096
-
-
Fraser, H.B.1
-
12
-
-
84865739425
-
Architecture of thehuman regulatory network derived from ENCODE data
-
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, et al. 2012. Architecture of thehuman regulatory network derived from ENCODE data. Nature 489: 91-100.
-
(2012)
Nature
, vol.489
, pp. 91-100
-
-
Gerstein, M.B.1
Kundaje, A.2
Hariharan, M.3
Landt, S.G.4
Yan, K.K.5
Cheng, C.6
Mu, X.J.7
Khurana, E.8
Rozowsky, J.9
Alexander, R.10
-
13
-
-
84874069538
-
Identifying recent adaptations in large-scale genomic data
-
Grossman SR, Andersen KG, Shlyakhter I, Tabrizi S, Winnicki S, Yen A, Park DJ, Griesemer D, Karlsson EK, Wong SH, et al. 2013. Identifying recent adaptations in large-scale genomic data. Cell 152: 703-713.
-
(2013)
Cell
, vol.152
, pp. 703-713
-
-
Grossman, S.R.1
Andersen, K.G.2
Shlyakhter, I.3
Tabrizi, S.4
Winnicki, S.5
Yen, A.6
Park, D.J.7
Griesemer, D.8
Karlsson, E.K.9
Wong, S.H.10
-
14
-
-
79951829399
-
Classic selective sweeps were rare in recent human evolution
-
Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, Sella G, Przeworski M. 2011. Classic selective sweeps were rare in recent human evolution. Science 331: 920-924.
-
(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
McVean, G.6
Sella, G.7
Przeworski, M.8
-
15
-
-
37249042614
-
Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies
-
DOI 10.1534/genetics.107.080663
-
Keightley PD, Eyre-Walker A. 2007. Joint inference of the distribution of fitness effects of deleteriousmutations and population demography based on nucleotide polymorphism frequencies. Genetics 177: 2251-2261. (Pubitemid 350277004)
-
(2007)
Genetics
, vol.177
, Issue.4
, pp. 2251-2261
-
-
Keightley, P.D.1
Eyre-Walker, A.2
-
16
-
-
0036226603
-
BLAT: The BLAST-like alignment tool
-
Kent WJ. 2002. BLAT: the BLAST-like alignment tool. Genome Res 12: 656-664.
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
17
-
-
0016669094
-
Evolution at two levels in humans and chimpanzees
-
King MC, Wilson AC. 1975. Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
-
(1975)
Science
, vol.188
, pp. 107-116
-
-
King, M.C.1
Wilson, A.C.2
-
18
-
-
78049354879
-
Fine-scale recombination rate differences between sexes, populations and individuals
-
Kong A, Thorleifsson G, Gudbjartsson DF, Masson G, Sigurdsson A, Jonasdottir A, Walters GB, Gylfason A, Kristinsson KT, Gudjonsson SA, et al. 2010. Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467: 1099-1103.
-
(2010)
Nature
, vol.467
, pp. 1099-1103
-
-
Kong, A.1
Thorleifsson, G.2
Gudbjartsson, D.F.3
Masson, G.4
Sigurdsson, A.5
Jonasdottir, A.6
Walters, G.B.7
Gylfason, A.8
Kristinsson, K.T.9
Gudjonsson, S.A.10
-
19
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
Linton, L.M.2
Birren, B.3
Nusbaum, C.4
Zody, M.C.5
Baldwin, J.6
Devon, K.7
Dewar, K.8
Doyle, M.9
FitzHugh, W.10
-
20
-
-
80055095261
-
Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome
-
Lohmueller KE, Albrechtsen A, Li Y, Kim SY, Korneliussen T, Vinckenbosch N, Tian G, Huerta-Sanchez E, Feder AF, Grarup N, et al. 2011. Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genet 7: e1002326.
-
(2011)
PLoS Genet
, vol.7
-
-
Lohmueller, K.E.1
Albrechtsen, A.2
Li, Y.3
Kim, S.Y.4
Korneliussen, T.5
Vinckenbosch, N.6
Tian, G.7
Huerta-Sanchez, E.8
Feder, A.F.9
Grarup, N.10
-
21
-
-
46249095233
-
Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
-
DOI 10.1126/science.1158395
-
Löytynoja A, Goldman N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320: 1632-1635. (Pubitemid 351931252)
-
(2008)
Science
, vol.320
, Issue.5883
, pp. 1632-1635
-
-
Loytynoja, A.1
Goldman, N.2
-
22
-
-
37249036929
-
Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila
-
DOI 10.1534/genetics.107.080226
-
Macpherson JM, Sella G, Davis JC, Petrov DA. 2007. Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila. Genetics 177: 2083-2099. (Pubitemid 350276990)
-
(2007)
Genetics
, vol.177
, Issue.4
, pp. 2083-2099
-
-
Macpherson, J.M.1
Sella, G.2
Davis, J.C.3
Petrov, D.A.4
-
23
-
-
67149096366
-
Widespread genomic signatures of natural selection in hominid evolution
-
McVicker G, Gordon D, Davis C, Green P. 2009. Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet 5: e1000471.
-
(2009)
PLoS Genet
, vol.5
-
-
McVicker, G.1
Gordon, D.2
Davis, C.3
Green, P.4
-
24
-
-
84881041428
-
SLiM: Simulating evolution with selection and linkage
-
Messer PW. 2013. SLiM: simulating evolution with selection and linkage. Genetics 194: 1037-1039.
-
(2013)
Genetics
, vol.194
, pp. 1037-1039
-
-
Messer, P.W.1
-
25
-
-
84878147503
-
Frequent adaptation and the McDonald-Kreitman test
-
Messer PW, Petrov DA. 2013. Frequent adaptation and the McDonald-Kreitman test. Proc Natl Acad Sci 110: 8615-8620.
-
(2013)
Proc Natl Acad Sci
, vol.110
, pp. 8615-8620
-
-
Messer, P.W.1
Petrov, D.A.2
-
26
-
-
26844482093
-
Genetics: A fine-scale map of recombination rates and hotspots across the human genome
-
DOI 10.1126/science.1117196
-
Myers S, Bottolo L, Freeman C, McVean G, Donnelly P. 2005. A fine-scale map of recombination rates and hotspots across the human genome. Science 310: 321-324. (Pubitemid 41457199)
-
(2005)
Science
, vol.310
, Issue.5746
, pp. 321-324
-
-
Myers, S.1
Bottolo, L.2
Freeman, C.3
McVean, G.4
Donnelly, P.5
-
27
-
-
66049157487
-
Signals of recent positive selection in a worldwide sample of human populations
-
Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ, Absher D, Srinivasan BS, Barsh GS, Myers RM, Feldman MW, et al. 2009. Signals of recent positive selection in a worldwide sample of human populations. Genome Res 19: 826-837.
-
(2009)
Genome Res
, vol.19
, pp. 826-837
-
-
Pickrell, J.K.1
Coop, G.2
Novembre, J.3
Kudaravalli, S.4
Li, J.Z.5
Absher, D.6
Srinivasan, B.S.7
Barsh, G.S.8
Myers, R.M.9
Feldman, M.W.10
-
28
-
-
0037167852
-
Detecting recent positive selection in the human genome from haplotype structure
-
DOI 10.1038/nature01140
-
Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, et al. 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837. (Pubitemid 35238568)
-
(2002)
Nature
, vol.419
, Issue.6909
, pp. 832-837
-
-
Sabeti, P.C.1
Reich, D.E.2
Higgins, J.M.3
Levine, H.Z.P.4
Richter, D.J.5
Schaffner, S.F.6
Gabriel, S.B.7
Platko, J.V.8
Patterson, N.J.9
McDonald, G.J.10
Ackerman, H.C.11
Campbell, S.J.12
Altshuler, D.13
Cooper, R.14
Kwiatkowski, D.15
Ward, R.16
Lander, E.S.17
-
29
-
-
33745121154
-
Positive natural selection in the human lineage
-
DOI 10.1126/science.1124309
-
Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, Shamovsky O, Palma A, Mikkelsen TS, Altshuler D, Lander ES. 2006. Positive natural selection in the human lineage. Science 312: 1614-1620. (Pubitemid 43902654)
-
(2006)
Science
, vol.312
, Issue.5780
, pp. 1614-1620
-
-
Sabeti, P.C.1
Schaffner, S.F.2
Fry, B.3
Lohmueller, J.4
Varilly, P.5
Shamovsky, O.6
Palma, A.7
Mikkelsen, T.S.8
Altshuler, D.9
Lander, E.S.10
-
30
-
-
35349012592
-
Genome-wide detection and characterization of positive selection in human populations
-
Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, et al. 2007. Genome-wide detection and characterization of positive selection in human populations. Nature 449: 913-918.
-
(2007)
Nature
, vol.449
, pp. 913-918
-
-
Sabeti, P.C.1
Varilly, P.2
Fry, B.3
Lohmueller, J.4
Hostetter, E.5
Cotsapas, C.6
Xie, X.7
Byrne, E.H.8
McCarroll, S.A.9
Gaudet, R.10
-
31
-
-
79952263624
-
Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans
-
Sattath S, Elyashiv E, Kolodny O, Rinott Y, Sella G. 2011. Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans . PLoS Genet 7: e1001302.
-
(2011)
PLoS Genet
, vol.7
-
-
Sattath, S.1
Elyashiv, E.2
Kolodny, O.3
Rinott, Y.4
Sella, G.5
-
32
-
-
0037267806
-
Human-mouse alignments with BLASTZ
-
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. 2003. Human-mouse alignments with BLASTZ. Genome Res 13: 103-107.
-
(2003)
Genome Res
, vol.13
, pp. 103-107
-
-
Schwartz, S.1
Kent, W.J.2
Smit, A.3
Zhang, Z.4
Baertsch, R.5
Hardison, R.C.6
Haussler, D.7
Miller, W.8
-
33
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
DOI 10.1101/gr.3715005
-
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050. (Pubitemid 41126859)
-
(2005)
Genome Research
, vol.15
, Issue.8
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
Hinrichs, A.S.4
Hou, M.5
Rosenbloom, K.6
Clawson, H.7
Spieth, J.8
Hillier, L.W.9
Richards, S.10
Weinstock, G.M.11
Wilson, R.K.12
Gibbs, R.A.13
Kent, W.J.14
Miller, W.15
Haussler, D.16
-
35
-
-
34347336584
-
Localizing recent adaptive evolution in the human genome
-
Williamson SH, Hubisz MJ, Clark AG, Payseur BA, Bustamante CD, Nielsen R. 2007. Localizing recent adaptive evolution in the human genome. PLoS Genet 3: e90.
-
(2007)
PLoS Genet
, vol.3
-
-
Williamson, S.H.1
Hubisz, M.J.2
Clark, A.G.3
Payseur, B.A.4
Bustamante, C.D.5
Nielsen, R.6
|