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Results: 1 to 20 of 53

1.

Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence.

Dutheil JY, Munch K, Nam K, Mailund T, Schierup MH.

PLoS Genet. 2015 Aug 14;11(8):e1005451. doi: 10.1371/journal.pgen.1005451. eCollection 2015 Aug.

2.

Extreme selective sweeps independently targeted the X chromosomes of the great apes.

Nam K, Munch K, Hobolth A, Dutheil JY, Veeramah KR, Woerner AE, Hammer MF; Great Ape Genome Diversity Project, Mailund T, Schierup MH.

Proc Natl Acad Sci U S A. 2015 May 19;112(20):6413-8. doi: 10.1073/pnas.1419306112. Epub 2015 May 4.

3.

Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing.

Bataillon T, Duan J, Hvilsom C, Jin X, Li Y, Skov L, Glemin S, Munch K, Jiang T, Qian Y, Hobolth A, Wang J, Mailund T, Siegismund HR, Schierup MH.

Genome Biol Evol. 2015 Mar 30;7(4):1122-32. doi: 10.1093/gbe/evv058.

4.

Ancestral population genomics using coalescence hidden Markov models and heuristic optimisation algorithms.

Cheng JY, Mailund T.

Comput Biol Chem. 2015 Aug;57:80-92. doi: 10.1016/j.compbiolchem.2015.02.001. Epub 2015 Mar 5.

5.

Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios.

Besenbacher S, Liu S, Izarzugaza JM, Grove J, Belling K, Bork-Jensen J, Huang S, Als TD, Li S, Yadav R, Rubio-García A, Lescai F, Demontis D, Rao J, Ye W, Mailund T, Friborg RM, Pedersen CN, Xu R, Sun J, Liu H, Wang O, Cheng X, Flores D, Rydza E, Rapacki K, Damm Sørensen J, Chmura P, Westergaard D, Dworzynski P, Sørensen TI, Lund O, Hansen T, Xu X, Li N, Bolund L, Pedersen O, Eiberg H, Krogh A, Børglum AD, Brunak S, Kristiansen K, Schierup MH, Wang J, Gupta R, Villesen P, Rasmussen S.

Nat Commun. 2015 Jan 19;6:5969. doi: 10.1038/ncomms6969.

6.

Lineage sorting in apes.

Mailund T, Munch K, Schierup MH.

Annu Rev Genet. 2014;48:519-35. doi: 10.1146/annurev-genet-120213-092532. Epub 2014 Sep 19. Review.

PMID:
25251849
7.

Unraveling recombination rate evolution using ancestral recombination maps.

Munch K, Schierup MH, Mailund T.

Bioessays. 2014 Sep;36(9):892-900. doi: 10.1002/bies.201400047. Epub 2014 Jul 14. Review.

8.

tqDist: a library for computing the quartet and triplet distances between binary or general trees.

Sand A, Holt MK, Johansen J, Brodal GS, Mailund T, Pedersen CN.

Bioinformatics. 2014 Jul 15;30(14):2079-80. doi: 10.1093/bioinformatics/btu157. Epub 2014 Mar 20.

9.

Identifying disease associated genes by network propagation.

Qian Y, Besenbacher S, Mailund T, Schierup MH.

BMC Syst Biol. 2014;8 Suppl 1:S6. doi: 10.1186/1752-0509-8-S1-S6. Epub 2014 Jan 24.

10.

zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.

Sand A, Kristiansen M, Pedersen CN, Mailund T.

BMC Bioinformatics. 2013 Nov 22;14:339. doi: 10.1186/1471-2105-14-339.

11.

A fine-scale recombination map of the human-chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion.

Munch K, Mailund T, Dutheil JY, Schierup MH.

Genome Res. 2014 Mar;24(3):467-74. doi: 10.1101/gr.158469.113. Epub 2013 Nov 4.

12.

Great ape genetic diversity and population history.

Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T.

Nature. 2013 Jul 25;499(7459):471-5. doi: 10.1038/nature12228. Epub 2013 Jul 3.

13.

Efficient computation in the IM model.

Andersen LN, Mailund T, Hobolth A.

J Math Biol. 2014 May;68(6):1423-51. doi: 10.1007/s00285-013-0671-9. Epub 2013 Apr 16.

PMID:
23588350
14.

A practical O(n log2 n) time algorithm for computing the triplet distance on binary trees.

Sand A, Brodal GS, Fagerberg R, Pedersen CN, Mailund T.

BMC Bioinformatics. 2013;14 Suppl 2:S18. doi: 10.1186/1471-2105-14-S2-S18. Epub 2013 Jan 21.

15.

A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species.

Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K, Andersen LN, Lunter G, Prüfer K, Scally A, Hobolth A, Schierup MH.

PLoS Genet. 2012;8(12):e1003125. doi: 10.1371/journal.pgen.1003125. Epub 2012 Dec 20.

16.

Algorithms for hidden markov models restricted to occurrences of regular expressions.

Tataru P, Sand A, Hobolth A, Mailund T, Pedersen CN.

Biology (Basel). 2013 Nov 8;2(4):1282-95. doi: 10.3390/biology2041282.

17.

Algorithms for computing the triplet and quartet distances for binary and general trees.

Sand A, Holt MK, Johansen J, Fagerberg R, Brodal GS, Pedersen CN, Mailund T.

Biology (Basel). 2013 Sep 26;2(4):1189-209. doi: 10.3390/biology2041189.

18.

An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes.

Jin X, He M, Ferguson B, Meng Y, Ouyang L, Ren J, Mailund T, Sun F, Sun L, Shen J, Zhuo M, Song L, Wang J, Ling F, Zhu Y, Hvilsom C, Siegismund H, Liu X, Gong Z, Ji F, Wang X, Liu B, Zhang Y, Hou J, Wang J, Zhao H, Wang Y, Fang X, Zhang G, Wang J, Zhang X, Schierup MH, Du H, Wang J, Wang X.

PLoS One. 2012;7(7):e40637. doi: 10.1371/journal.pone.0040637. Epub 2012 Jul 27.

19.

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change.

Miller W, Schuster SC, Welch AJ, Ratan A, Bedoya-Reina OC, Zhao F, Kim HL, Burhans RC, Drautz DI, Wittekindt NE, Tomsho LP, Ibarra-Laclette E, Herrera-Estrella L, Peacock E, Farley S, Sage GK, Rode K, Obbard M, Montiel R, Bachmann L, Ingólfsson O, Aars J, Mailund T, Wiig O, Talbot SL, Lindqvist C.

Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):E2382-90. doi: 10.1073/pnas.1210506109. Epub 2012 Jul 23.

20.

The bonobo genome compared with the chimpanzee and human genomes.

Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoç E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, André C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andrés AM, Kelso J, Pääbo S.

Nature. 2012 Jun 28;486(7404):527-31. doi: 10.1038/nature11128.

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