-
1
-
-
79960914105
-
Inference of human population history from individual whole-genome sequences
-
Li H, Durbin R, (2011) Inference of human population history from individual whole-genome sequences. Nature 475: 493-496.
-
(2011)
Nature
, vol.475
, pp. 493-496
-
-
Li, H.1
Durbin, R.2
-
2
-
-
49749142953
-
Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors
-
Burgess R, Yang Z, (2008) Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol Biol Evol 25: 1979-1994.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 1979-1994
-
-
Burgess, R.1
Yang, Z.2
-
3
-
-
77749261628
-
Estimating divergence parameters with small samples from a large number of loci
-
Wang Y, Hey J, (2010) Estimating divergence parameters with small samples from a large number of loci. Genetics 184: 363-379.
-
(2010)
Genetics
, vol.184
, pp. 363-379
-
-
Wang, Y.1
Hey, J.2
-
4
-
-
77952294620
-
Isolation with migration models for more than two populations
-
Hey J, (2010) Isolation with migration models for more than two populations. Mol Biol Evol 27: 905-920.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 905-920
-
-
Hey, J.1
-
5
-
-
77957905707
-
A likelihood ratio test of speciation with gene ow using genomic sequence data
-
Yang Z, (2010) A likelihood ratio test of speciation with gene ow using genomic sequence data. Genome Biology and Evolution 2: 200-211.
-
(2010)
Genome Biology and Evolution
, vol.2
, pp. 200-211
-
-
Yang, Z.1
-
6
-
-
80053386624
-
Bayesian inference of ancient human demography from individual genome sequences
-
Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A, (2011) Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics 43: 1031-1034.
-
(2011)
Nature Genetics
, vol.43
, pp. 1031-1034
-
-
Gronau, I.1
Hubisz, M.J.2
Gulko, B.3
Danko, C.G.4
Siepel, A.5
-
7
-
-
84866889123
-
Maximum Likelihood Implementation of an Isolation-with-Migration Model with Three Species for Testing Speciation with Gene Flow
-
Zhu T, Yang Z, (2012) Maximum Likelihood Implementation of an Isolation-with-Migration Model with Three Species for Testing Speciation with Gene Flow. Mol Biol Evol.
-
(2012)
Mol Biol Evol
-
-
Zhu, T.1
Yang, Z.2
-
8
-
-
34948847222
-
A new approach to estimate parameters of speciation models with application to apes
-
Becquet C, Przeworski M, (2007) A new approach to estimate parameters of speciation models with application to apes. Genome Res 17: 1505-1519.
-
(2007)
Genome Res
, vol.17
, pp. 1505-1519
-
-
Becquet, C.1
Przeworski, M.2
-
9
-
-
0033150745
-
Recombination as a point process along sequences
-
Wiuf C, Hein J, (1999) Recombination as a point process along sequences. Theor Popul Biol 55: 248-59.
-
(1999)
Theor Popul Biol
, vol.55
, pp. 248-259
-
-
Wiuf, C.1
Hein, J.2
-
11
-
-
33646348730
-
Fast "coalescent" simulation
-
Marjoram P, Wall JD, (2006) Fast "coalescent" simulation. BMC genetics 7: 16.
-
(2006)
BMC Genetics
, vol.7
, pp. 16
-
-
Marjoram, P.1
Wall, J.D.2
-
12
-
-
61449135985
-
Fast and exible simulation of DNA sequence data
-
Chen GK, Marjoram P, Wall JD, (2009) Fast and exible simulation of DNA sequence data. Genome Research 19: 136-142.
-
(2009)
Genome Research
, vol.19
, pp. 136-142
-
-
Chen, G.K.1
Marjoram, P.2
Wall, J.D.3
-
13
-
-
33847253862
-
Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden markov model
-
Hobolth A, Christensen OF, Mailund T, Schierup MH, (2007) Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden markov model. PLoS Genet 3: e7.
-
(2007)
PLoS Genet
, vol.3
-
-
Hobolth, A.1
Christensen, O.F.2
Mailund, T.3
Schierup, M.H.4
-
14
-
-
70350139887
-
Ancestral population genomics: The coalescent hidden markov model approach
-
Dutheil JY, Ganapathy G, Hobolth A, Mailund T, Uyenoyama MK, et al. (2009) Ancestral population genomics: The coalescent hidden markov model approach. Genetics 183: 259-274.
-
(2009)
Genetics
, vol.183
, pp. 259-274
-
-
Dutheil, J.Y.1
Ganapathy, G.2
Hobolth, A.3
Mailund, T.4
Uyenoyama, M.K.5
-
15
-
-
79953744766
-
Estimating divergence time and ancestral effective population size of bornean and sumatran orangutan subspecies using a coalescent hidden markov model
-
Mailund T, Dutheil JY, Hobolth A, Lunter G, Schierup MH, (2011) Estimating divergence time and ancestral effective population size of bornean and sumatran orangutan subspecies using a coalescent hidden markov model. PLoS Genet 7: e1001319.
-
(2011)
PLoS Genet
, vol.7
-
-
Mailund, T.1
Dutheil, J.Y.2
Hobolth, A.3
Lunter, G.4
Schierup, M.H.5
-
16
-
-
79955434528
-
An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination
-
Paul JS, Steinrucken M, Song YS, (2011) An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination. Genetics 187: 1115-1128.
-
(2011)
Genetics
, vol.187
, pp. 1115-1128
-
-
Paul, J.S.1
Steinrucken, M.2
Song, Y.S.3
-
17
-
-
79952270485
-
Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
-
Hobolth A, Dutheil JY, Hawks J, Schierup MH, Mailund T, (2011) Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Research 21: 349-356.
-
(2011)
Genome Research
, vol.21
, pp. 349-356
-
-
Hobolth, A.1
Dutheil, J.Y.2
Hawks, J.3
Schierup, M.H.4
Mailund, T.5
-
18
-
-
78049354879
-
Fine-scale recombination rate differences between sexes, populations and individuals
-
Kong A, Thorleifsson G, Gudbjartsson DF, Masson G, Sigurdsson A, 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
-
19
-
-
84862980012
-
The bonobo genome compared with the chimpanzee and human genomes
-
Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, et al. (2012) The bonobo genome compared with the chimpanzee and human genomes. Nature 486: 527-531.
-
(2012)
Nature
, vol.486
, pp. 527-531
-
-
Prüfer, K.1
Munch, K.2
Hellmann, I.3
Akagi, K.4
Miller, J.R.5
-
20
-
-
84863230553
-
Insights into hominid evolution from the gorilla genome sequence
-
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, et al. (2012) Insights into hominid evolution from the gorilla genome sequence. Nature 483: 169-175.
-
(2012)
Nature
, vol.483
, pp. 169-175
-
-
Scally, A.1
Dutheil, J.Y.2
Hillier, L.W.3
Jordan, G.E.4
Goodhead, I.5
-
21
-
-
79251553493
-
Comparative and demographic analysis of orang-utan genomes
-
Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, et al. (2011) Comparative and demographic analysis of orang-utan genomes. Nature 469: 529-533.
-
(2011)
Nature
, vol.469
, pp. 529-533
-
-
Locke, D.P.1
Hillier, L.W.2
Warren, W.C.3
Worley, K.C.4
Nazareth, L.V.5
-
22
-
-
84865856910
-
Revising the human mutation rate: implications for understanding human evolution
-
Scally A, Durbin R, (2012) Revising the human mutation rate: implications for understanding human evolution. Nat Rev Genet 13: 745-753.
-
(2012)
Nat Rev Genet
, vol.13
, pp. 745-753
-
-
Scally, A.1
Durbin, R.2
-
23
-
-
84866856766
-
Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution
-
Langergraber KEK, Prüfer KK, Rowney CC, Boesch CC, Crockford CC, et al. (2012) Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. PNAS 109: 15716-15721.
-
(2012)
PNAS
, vol.109
, pp. 15716-15721
-
-
Langergraber, K.E.K.1
Prüfer, K.K.2
Rowney, C.C.3
Boesch, C.C.4
Crockford, C.C.5
-
24
-
-
84865208871
-
Rate of de novo mutations and the importance of father's age to disease risk
-
Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, et al. (2012) Rate of de novo mutations and the importance of father's age to disease risk. Nature 488: 471-475.
-
(2012)
Nature
, vol.488
, pp. 471-475
-
-
Kong, A.1
Frigge, M.L.2
Masson, G.3
Besenbacher, S.4
Sulem, P.5
-
25
-
-
33845899683
-
The complex evolutionary history of gorillas: insights from genomic data
-
Thalmann O, Fischer A, Lankester F, Pääbo S, Vigilant L, (2007) The complex evolutionary history of gorillas: insights from genomic data. Mol Biol Evol 24: 146-58.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 146-158
-
-
Thalmann, O.1
Fischer, A.2
Lankester, F.3
Pääbo, S.4
Vigilant, L.5
-
26
-
-
33646187369
-
Population history, biogeography, and taxonomy of orangutans (genus: Pongo) based on a population genetic meta-analysis of multiple loci
-
Steiper ME, (2006) Population history, biogeography, and taxonomy of orangutans (genus: Pongo) based on a population genetic meta-analysis of multiple loci. J Hum Evol 50: 509-22.
-
(2006)
J Hum Evol
, vol.50
, pp. 509-522
-
-
Steiper, M.E.1
-
27
-
-
12344265079
-
Divergence population genetics of chimpanzees
-
Won YJ, Hey J, (2005) Divergence population genetics of chimpanzees. Mol Biol Evol 22: 297-307.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 297-307
-
-
Won, Y.J.1
Hey, J.2
-
28
-
-
77952297997
-
The divergence of chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses
-
Hey J, (2010) The divergence of chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses. Mol Biol Evol 27: 921-933.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 921-933
-
-
Hey, J.1
-
29
-
-
0042008126
-
A model of the biogeographical journey from Proto-pan to Pan paniscus
-
Myers Thompson JA, (2003) A model of the biogeographical journey from Proto-pan to Pan paniscus. Primates; journal of primatology 44: 191-197.
-
(2003)
Primates; Journal of Primatology
, vol.44
, pp. 191-197
-
-
Myers Thompson, J.A.1
-
30
-
-
32044448476
-
A proposed drainage evolution model for Central Africa-Did the Congo ow east?
-
Stankiewicz J, de Wit MJ, (2006) A proposed drainage evolution model for Central Africa-Did the Congo ow east? Journal of African Earth Sciences 44: 75-84.
-
(2006)
Journal of African Earth Sciences
, vol.44
, pp. 75-84
-
-
Stankiewicz, J.1
de Wit, M.J.2
-
31
-
-
77952136530
-
A draft sequence of the Neandertal genome
-
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, et al. (2010) A draft sequence of the Neandertal genome. Science (New York, NY) 328: 710-722.
-
(2010)
Science (New York, NY)
, vol.328
, pp. 710-722
-
-
Green, R.E.1
Krause, J.2
Briggs, A.W.3
Maricic, T.4
Stenzel, U.5
-
32
-
-
78650850475
-
Genetic history of an archaic hominin group from Denisova Cave in Siberia
-
Reich D, Green RE, Kircher M, Krause J, Patterson N, et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468: 1053-1060.
-
(2010)
Nature
, vol.468
, pp. 1053-1060
-
-
Reich, D.1
Green, R.E.2
Kircher, M.3
Krause, J.4
Patterson, N.5
-
33
-
-
80053089069
-
Genetic evidence for archaic admixture in Africa
-
Hammer MF, Woerner AE, Mendez FL, Watkins JC, Wall JD, (2011) Genetic evidence for archaic admixture in Africa. Proceedings Of The National Academy Of Sciences Of The United States Of America 108: 15123-15128.
-
(2011)
Proceedings Of The National Academy Of Sciences Of The United States Of America
, vol.108
, pp. 15123-15128
-
-
Hammer, M.F.1
Woerner, A.E.2
Mendez, F.L.3
Watkins, J.C.4
Wall, J.D.5
-
34
-
-
80053899093
-
Denisova admixture and the first modern human dispersals into southeast Asia and oceania
-
Reich D, Patterson N, Kircher M, Delfin F, Nandineni MR, et al. (2011) Denisova admixture and the first modern human dispersals into southeast Asia and oceania. American journal of human genetics 89: 516-528.
-
(2011)
American Journal of Human Genetics
, vol.89
, pp. 516-528
-
-
Reich, D.1
Patterson, N.2
Kircher, M.3
Delfin, F.4
Nandineni, M.R.5
-
35
-
-
84868089030
-
The Date of Interbreeding between Neandertals and Modern Humans
-
Sankararaman SS, Patterson NN, Li HH, Pääbo SS, Reich DD, (2012) The Date of Interbreeding between Neandertals and Modern Humans. PLoS Genet 8: e1002947.
-
(2012)
PLoS Genet
, vol.8
-
-
Sankararaman, S.S.1
Patterson, N.N.2
Li, H.H.3
Pääbo, S.S.4
Reich, D.D.5
-
36
-
-
33745591114
-
Genetic evidence for complex speciation of humans and chimpanzees
-
Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D, (2006) Genetic evidence for complex speciation of humans and chimpanzees. Nature 441: 1103-1108.
-
(2006)
Nature
, vol.441
, pp. 1103-1108
-
-
Patterson, N.1
Richter, D.J.2
Gnerre, S.3
Lander, E.S.4
Reich, D.5
-
37
-
-
40749148589
-
Complex speciation of humans and chimpanzees
-
discussion E4
-
Wakeley J, (2008) Complex speciation of humans and chimpanzees. Nature 452: E3-4; discussion E4.
-
(2008)
Nature
, vol.452
-
-
Wakeley, J.1
-
38
-
-
69749102659
-
Doubts about complex speciation between humans and chimpanzees
-
Presgraves DC, Yi SV, (2009) Doubts about complex speciation between humans and chimpanzees. Trends in ecology and evolution 24: 533-540.
-
(2009)
Trends in Ecology and Evolution
, vol.24
, pp. 533-540
-
-
Presgraves, D.C.1
Yi, S.V.2
-
39
-
-
67449088152
-
Patterns of autosomal divergence between the human and chimpanzee genomes support an allopatric model of speciation
-
Webster MT, (2009) Patterns of autosomal divergence between the human and chimpanzee genomes support an allopatric model of speciation. Gene 443: 70-75.
-
(2009)
Gene
, vol.443
, pp. 70-75
-
-
Webster, M.T.1
-
40
-
-
84862845234
-
An autosomal analysis gives no genetic evidence for complex speciation of humans and chimpanzees
-
Yamamichi MM, Gojobori JJ, Innan HH, (2011) An autosomal analysis gives no genetic evidence for complex speciation of humans and chimpanzees. Mol Biol Evol 29: 145-156.
-
(2011)
Mol Biol Evol
, vol.29
, pp. 145-156
-
-
Yamamichi, M.M.1
Gojobori, J.J.2
Innan, H.H.3
-
41
-
-
84862491766
-
Using Colored Petri Nets to Construct Coalescent Hidden Markov Models: Automatic Translation from Demographic Specifications to Efficient Inference Methods
-
In: Haddad S, Pomello L, editors, Springer Berlin/Heidelberg
-
Mailund T, Halager A, Westergaard M (2012) Using Colored Petri Nets to Construct Coalescent Hidden Markov Models: Automatic Translation from Demographic Specifications to Efficient Inference Methods. In: Haddad S, Pomello L, editors, Application and Theory of Petri Nets. Springer Berlin/Heidelberg, pp. 32-50.
-
(2012)
Application and Theory of Petri Nets
, pp. 32-50
-
-
Mailund, T.1
Halager, A.2
Westergaard, M.3
-
43
-
-
84255162312
-
Genomic islands of divergence in hybridizing Heliconius butteries identified by large-scale targeted sequencing
-
Nadeau NJ, Whibley A, Jones RT, Davey JW, Dasmahapatra KK, et al. (2012) Genomic islands of divergence in hybridizing Heliconius butteries identified by large-scale targeted sequencing. Philosophical transactions of the Royal Society of London Series B, Biological sciences 367: 343-353.
-
(2012)
Philosophical Transactions of the Royal Society of London Series B, Biological Sciences
, vol.367
, pp. 343-353
-
-
Nadeau, N.J.1
Whibley, A.2
Jones, R.T.3
Davey, J.W.4
Dasmahapatra, K.K.5
-
44
-
-
84862005843
-
Genome-wide architecture of reproductive isolation in a naturally occurring hybrid zone between Mus musculus musculus and M. m. domesticus
-
Janoušek V, Wang L, Luzynski K, Dufková P, Vyskočilová MM, et al. (2012) Genome-wide architecture of reproductive isolation in a naturally occurring hybrid zone between Mus musculus musculus and M. m. domesticus. Molecular Ecology 21: 3032-3047.
-
(2012)
Molecular Ecology
, vol.21
, pp. 3032-3047
-
-
Janoušek, V.1
Wang, L.2
Luzynski, K.3
Dufková, P.4
Vyskočilová, M.M.5
-
46
-
-
0030772560
-
A Markov Chain Model of Coalescence with Recombination
-
Simonsen K, Churchill G, (1997) A Markov Chain Model of Coalescence with Recombination. Theor Popul Biol 52: 43-59.
-
(1997)
Theor Popul Biol
, vol.52
, pp. 43-59
-
-
Simonsen, K.1
Churchill, G.2
-
47
-
-
33645234370
-
The concordance of gene trees and species trees at two linked loci
-
Slatkin M, Pollack JL, (2006) The concordance of gene trees and species trees at two linked loci. Genetics 172: 1979-1984.
-
(2006)
Genetics
, vol.172
, pp. 1979-1984
-
-
Slatkin, M.1
Pollack, J.L.2
-
48
-
-
79955372694
-
On computing the coalescence time density in an isolation-with-migration model with few samples
-
Hobolth A, Andersen LN, Mailund T, (2011) On computing the coalescence time density in an isolation-with-migration model with few samples. Genetics 187: 1241-1243.
-
(2011)
Genetics
, vol.187
, pp. 1241-1243
-
-
Hobolth, A.1
Andersen, L.N.2
Mailund, T.3
-
49
-
-
0018611505
-
Note on finite homogeneous continuous-time Markov-chains
-
Tavare S, (1979) Note on finite homogeneous continuous-time Markov-chains. Biometrics 35: 831-834.
-
(1979)
Biometrics
, vol.35
, pp. 831-834
-
-
Tavare, S.1
-
51
-
-
27644455774
-
CoaSim: a exible environment for simulating genetic data under coalescent models
-
Mailund T, Schierup MH, Pedersen CNS, Mechlenborg PJM, Madsen JN, et al. (2005) CoaSim: a exible environment for simulating genetic data under coalescent models. BMC Bioinformatics 6: 252.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 252
-
-
Mailund, T.1
Schierup, M.H.2
Pedersen, C.N.S.3
Mechlenborg, P.J.M.4
Madsen, J.N.5
-
52
-
-
53249100490
-
Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs
-
Dutheil J, Boussau B, (2008) Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. BMC Evol Biol 8: 255.
-
(2008)
BMC Evol Biol
, vol.8
, pp. 255
-
-
Dutheil, J.1
Boussau, B.2
-
53
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
54
-
-
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.
-
(2011)
Genome Research
, vol.21
, pp. 936-939
-
-
Lunter, G.1
Goodson, M.2
-
55
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
-
57
-
-
0141815478
-
Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes
-
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D, (2003) Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proceedings of the National Academy of Sciences of the United States of America 100: 11484-9.
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, pp. 11484-11489
-
-
Kent, W.J.1
Baertsch, R.2
Hinrichs, A.3
Miller, W.4
Haussler, D.5
-
58
-
-
84859865967
-
The UCSC genome browser database: extensions and updates 2011
-
Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, et al. (2012) The UCSC genome browser database: extensions and updates 2011. Nucleic acids research 40: D918-923.
-
(2012)
Nucleic Acids Research
, vol.40
-
-
Dreszer, T.R.1
Karolchik, D.2
Zweig, A.S.3
Hinrichs, A.S.4
Raney, B.J.5
-
59
-
-
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 Research 14: 708-715.
-
(2004)
Genome Research
, vol.14
, pp. 708-715
-
-
Blanchette, M.1
Kent, W.J.2
Riemer, C.3
Elnitski, L.4
Smit, A.F.A.5
|