Publications by authors named "Thomas Mailund"

71Publications

Ancestral Population Genomics with Jocx, a Coalescent Hidden Markov Model.

Methods Mol Biol 2020 ;2090:167-189

Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.

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http://dx.doi.org/10.1007/978-1-0716-0199-0_8DOI Listing
January 2020

Identifying loci under positive selection in complex population histories.

Genome Res 2019 09 30;29(9):1506-1520. Epub 2019 Jul 30.

Lundbeck GeoGenetics Centre, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1350, Denmark.

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http://dx.doi.org/10.1101/gr.246777.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6724678PMC
September 2019

Association Mapping and Disease: Evolutionary Perspectives.

Methods Mol Biol 2019 ;1910:533-553

Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.

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http://link.springer.com/10.1007/978-1-4939-9074-0_17
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http://dx.doi.org/10.1007/978-1-4939-9074-0_17DOI Listing
January 2020

Direct estimation of mutations in great apes reconciles phylogenetic dating.

Nat Ecol Evol 2019 02 21;3(2):286-292. Epub 2019 Jan 21.

Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.

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http://dx.doi.org/10.1038/s41559-018-0778-xDOI Listing
February 2019

Assembly and analysis of 100 full MHC haplotypes from the Danish population.

Genome Res 2017 09 3;27(9):1597-1607. Epub 2017 Aug 3.

Bioinformatics Research Centre, Aarhus University, 8000 Aarhus C., Denmark.

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http://dx.doi.org/10.1101/gr.218891.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5580718PMC
September 2017

Fast admixture analysis and population tree estimation for SNP and NGS data.

Bioinformatics 2017 Jul;33(14):2148-2155

Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA, USA.

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https://academic.oup.com/bioinformatics/article/33/14/2148/3
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http://dx.doi.org/10.1093/bioinformatics/btx098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6543773PMC
July 2017

admixturegraph: an R package for admixture graph manipulation and fitting.

Bioinformatics 2017 Jun;33(11):1738-1740

Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btx048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5447235PMC
June 2017

Evidence that the rate of strong selective sweeps increases with population size in the great apes.

Proc Natl Acad Sci U S A 2017 02 30;114(7):1613-1618. Epub 2017 Jan 30.

Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark;

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http://dx.doi.org/10.1073/pnas.1605660114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320968PMC
February 2017

Selective Sweeps across Twenty Millions Years of Primate Evolution.

Mol Biol Evol 2016 12 22;33(12):3065-3074. Epub 2016 Sep 22.

Bioinformatics Research Centre, Aarhus University, C. F. Møllers Alle, Denmark.

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http://dx.doi.org/10.1093/molbev/msw199DOI Listing
December 2016

A genomic history of Aboriginal Australia.

Nature 2016 Oct 21;538(7624):207-214. Epub 2016 Sep 21.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.

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http://dx.doi.org/10.1038/nature18299DOI Listing
October 2016

Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity.

Genetics 2016 Oct 17;204(2):711-722. Epub 2016 Aug 17.

Bioinformatics Research Centre, Aarhus University, 8000, Denmark Centre for Biocultural History, Aarhus University, 8000, Denmark.

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http://dx.doi.org/10.1534/genetics.116.189241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068857PMC
October 2016

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

PLoS Genet 2015 Aug 14;11(8):e1005451. Epub 2015 Aug 14.

Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark; Department of Bioscience, Aarhus University, Aarhus, Denmark.

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http://dx.doi.org/10.1371/journal.pgen.1005451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537231PMC
August 2015

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

Proc Natl Acad Sci U S A 2015 May 4;112(20):6413-8. Epub 2015 May 4.

Bioinformatics Research Centre and Department of Bioscience, Aarhus University, Aarhus 8000, Denmark;

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http://dx.doi.org/10.1073/pnas.1419306112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443357PMC
May 2015

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

Comput Biol Chem 2015 Aug 5;57:80-92. Epub 2015 Mar 5.

Bioinformatics Research Centre, Aarhus University, C.F. Møllers Allé 8, 8000 Aarhus, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.compbiolchem.2015.02.001DOI Listing
August 2015

Lineage sorting in apes.

Annu Rev Genet 2014 19;48:519-35. Epub 2014 Sep 19.

Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark; email: , ,

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http://dx.doi.org/10.1146/annurev-genet-120213-092532DOI Listing
July 2015

Unraveling recombination rate evolution using ancestral recombination maps.

Bioessays 2014 Sep 14;36(9):892-900. Epub 2014 Jul 14.

Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.

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http://dx.doi.org/10.1002/bies.201400047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4314685PMC
September 2014

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

Bioinformatics 2014 Jul 20;30(14):2079-80. Epub 2014 Mar 20.

Bioinformatics Research Centre, Department of Computer Science and MADALGO, Center for Massive Data Algorithms, a Center of the Danish National Research Foundation, Aarhus University, DK-8000 Aarhus C, DenmarkBioinformatics Research Centre, Department of Computer Science and MADALGO, Center for Massive Data Algorithms, a Center of the Danish National Research Foundation, Aarhus University, DK-8000 Aarhus C, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btu157DOI Listing
July 2014

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

BMC Bioinformatics 2013 Nov 22;14:339. Epub 2013 Nov 22.

Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.

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http://dx.doi.org/10.1186/1471-2105-14-339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4222747PMC
November 2013

Great ape genetic diversity and population history.

Nature 2013 Jul 3;499(7459):471-5. Epub 2013 Jul 3.

Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.

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http://dx.doi.org/10.1038/nature12228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3822165PMC
July 2013

Efficient computation in the IM model.

J Math Biol 2014 May 16;68(6):1423-51. Epub 2013 Apr 16.

Bioinformatics Research Centre, Aarhus University, C.F. Møllers Allé 8, Aarhus C, 8000 , Aarhus, Denmark,

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http://users-birc.au.dk/mailund/ps/IM-2013.pdf
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http://link.springer.com/10.1007/s00285-013-0671-9
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http://dx.doi.org/10.1007/s00285-013-0671-9DOI Listing
May 2014

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

BMC Bioinformatics 2013 21;14 Suppl 2:S18. Epub 2013 Jan 21.

Bioinformatics Research Center, Aarhus University, Denmark.

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http://dx.doi.org/10.1186/1471-2105-14-S2-S18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549851PMC
September 2013

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

Biology (Basel) 2013 Nov 8;2(4):1282-95. Epub 2013 Nov 8.

Bioinformatics Research Centre, Aarhus University, C. F. Møllers Allé 8, DK-8000 Aarhus C, Denmark.

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http://dx.doi.org/10.3390/biology2041282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009796PMC
November 2013

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

Biology (Basel) 2013 Sep 26;2(4):1189-209. Epub 2013 Sep 26.

Bioinformatics Research Centre, Aarhus University, C.F. Møllers Allé 8, DK-8000 Aarhus C, Denmark.

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http://pure.au.dk/portal/files/52122446/soda13.pdf
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http://www.mdpi.com/2079-7737/2/4/1189/
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http://dx.doi.org/10.3390/biology2041189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009797PMC
September 2013

Cultural phylogenetics of the Tupi language family in lowland South America.

PLoS One 2012 10;7(4):e35025. Epub 2012 Apr 10.

Department of Anthropology, University of Missouri, Columbia, Missouri, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0035025PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3323632PMC
October 2012

Association mapping and disease: evolutionary perspectives.

Methods Mol Biol 2012 ;856:275-91

deCODE Genetics, Reykjavik, Iceland.

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http://dx.doi.org/10.1007/978-1-61779-585-5_11DOI Listing
July 2012

Local genealogies in a linear mixed model for genome-wide association mapping in complex pedigreed populations.

PLoS One 2011 2;6(11):e27061. Epub 2011 Nov 2.

Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Tjele, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027061PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3206889PMC
March 2012

A sub-cubic time algorithm for computing the quartet distance between two general trees.

Algorithms Mol Biol 2011 Jun 3;6:15. Epub 2011 Jun 3.

Bioinformatics Research Centre (BiRC), Aarhus University, C, F, Møllers Alle 8, DK-8000 Aarhus C, Denmark.

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http://dx.doi.org/10.1186/1748-7188-6-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141660PMC
June 2011

Comparative and demographic analysis of orang-utan genomes.

Authors:
Devin P Locke LaDeana W Hillier Wesley C Warren Kim C Worley Lynne V Nazareth Donna M Muzny Shiaw-Pyng Yang Zhengyuan Wang Asif T Chinwalla Pat Minx Makedonka Mitreva Lisa Cook Kim D Delehaunty Catrina Fronick Heather Schmidt Lucinda A Fulton Robert S Fulton Joanne O Nelson Vincent Magrini Craig Pohl Tina A Graves Chris Markovic Andy Cree Huyen H Dinh Jennifer Hume Christie L Kovar Gerald R Fowler Gerton Lunter Stephen Meader Andreas Heger Chris P Ponting Tomas Marques-Bonet Can Alkan Lin Chen Ze Cheng Jeffrey M Kidd Evan E Eichler Simon White Stephen Searle Albert J Vilella Yuan Chen Paul Flicek Jian Ma Brian Raney Bernard Suh Richard Burhans Javier Herrero David Haussler Rui Faria Olga Fernando Fleur Darré Domènec Farré Elodie Gazave Meritxell Oliva Arcadi Navarro Roberta Roberto Oronzo Capozzi Nicoletta Archidiacono Giuliano Della Valle Stefania Purgato Mariano Rocchi Miriam K Konkel Jerilyn A Walker Brygg Ullmer Mark A Batzer Arian F A Smit Robert Hubley Claudio Casola Daniel R Schrider Matthew W Hahn Victor Quesada Xose S Puente Gonzalo R Ordoñez Carlos López-Otín Tomas Vinar Brona Brejova Aakrosh Ratan Robert S Harris Webb Miller Carolin Kosiol Heather A Lawson Vikas Taliwal André L Martins Adam Siepel Arindam Roychoudhury Xin Ma Jeremiah Degenhardt Carlos D Bustamante Ryan N Gutenkunst Thomas Mailund Julien Y Dutheil Asger Hobolth Mikkel H Schierup Oliver A Ryder Yuko Yoshinaga Pieter J de Jong George M Weinstock Jeffrey Rogers Elaine R Mardis Richard A Gibbs Richard K Wilson

Nature 2011 Jan;469(7331):529-33

The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature09687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778PMC
January 2011

Ancestral population genomics: the coalescent hidden Markov model approach.

Genetics 2009 Sep 6;183(1):259-74. Epub 2009 Jul 6.

Bioinformatics Research Center, Aarhus University, C. F. Møllers Alle 8, Bldg. 1110, DK-8000 Aarhus C, Denmark.

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http://dx.doi.org/10.1534/genetics.109.103010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746150PMC
September 2009

Using biological networks to search for interacting loci in genome-wide association studies.

Eur J Hum Genet 2009 Oct 11;17(10):1231-40. Epub 2009 Mar 11.

Bioinformatics Research Center, University of Aarhus, C. F. Møllers Alle, Aarhus C, Denmark.

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http://dx.doi.org/10.1038/ejhg.2009.15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2986645PMC
October 2009

A fast algorithm for genome-wide haplotype pattern mining.

BMC Bioinformatics 2009 Jan 30;10 Suppl 1:S74. Epub 2009 Jan 30.

Bioinformatics Research Center, University of Aarhus, Denmark.

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http://dx.doi.org/10.1186/1471-2105-10-S1-S74DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648728PMC
January 2009

Local phylogeny mapping of quantitative traits: higher accuracy and better ranking than single-marker association in genomewide scans.

Genetics 2009 Feb 8;181(2):747-53. Epub 2008 Dec 8.

Bioinformatics Research Center, University of Aarhus, DK-8000 Arhus C, Denmark.

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http://dx.doi.org/10.1534/genetics.108.092643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2644962PMC
February 2009

SNPFile--a software library and file format for large scale association mapping and population genetics studies.

BMC Bioinformatics 2008 Dec 8;9:526. Epub 2008 Dec 8.

Bioinformatics Research Center, University of Aarhus, Denmark.

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http://dx.doi.org/10.1186/1471-2105-9-526DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2633306PMC
December 2008

Efficient whole-genome association mapping using local phylogenies for unphased genotype data.

Bioinformatics 2008 Oct 30;24(19):2215-21. Epub 2008 Jul 30.

Department of Computer Science, University of California, Davis, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553438PMC
October 2008

On recombination-induced multiple and simultaneous coalescent events.

Genetics 2007 Dec 18;177(4):2151-60. Epub 2007 Oct 18.

Department of Statistics, University of Oxford, Oxford, OX1 3TG, United Kingdom.

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http://dx.doi.org/10.1534/genetics.107.071126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2219491PMC
December 2007

Annotation of selection strengths in viral genomes.

Bioinformatics 2007 Nov 5;23(22):2978-86. Epub 2007 Oct 5.

Department of Statistics, University of Oxford, 1 South Parks Road, OX1 3TG, UK.

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http://dx.doi.org/10.1093/bioinformatics/btm472DOI Listing
November 2007

Comparative annotation of viral genomes with non-conserved gene structure.

Bioinformatics 2007 May 6;23(9):1080-9. Epub 2007 Mar 6.

Department of Statistics, University of Oxford, UK.

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http://dx.doi.org/10.1093/bioinformatics/btm078DOI Listing
May 2007

Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model.

PLoS Genet 2007 Feb 30;3(2):e7. Epub 2006 Nov 30.

Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America.

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https://dx.plos.org/10.1371/journal.pgen.0030007
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http://dx.doi.org/10.1371/journal.pgen.0030007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1802818PMC
February 2007

Whole genome association mapping by incompatibilities and local perfect phylogenies.

BMC Bioinformatics 2006 Oct 16;7:454. Epub 2006 Oct 16.

Department of Statistics, University of Oxford, UK.

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http://dx.doi.org/10.1186/1471-2105-7-454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1624851PMC
October 2006

Fast calculation of the quartet distance between trees of arbitrary degrees.

Algorithms Mol Biol 2006 Sep 25;1:16. Epub 2006 Sep 25.

Department of Computer Science, University of Aarhus, Aabogade 34, DK-8200 Arhus N, Denmark.

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http://dx.doi.org/10.1186/1748-7188-1-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1592098PMC
September 2006

The effective size of the Icelandic population and the prospects for LD mapping: inference from unphased microsatellite markers.

Eur J Hum Genet 2006 Sep 31;14(9):1044-53. Epub 2006 May 31.

Bioinformatics Research Center, University of Aarhus, Høegh-Guldbergs Gade 10, DK-8000 Aarhus C, Denmark.

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http://dx.doi.org/10.1038/sj.ejhg.5201669DOI Listing
September 2006

GeneRecon--a coalescent based tool for fine-scale association mapping.

Bioinformatics 2006 Sep 21;22(18):2317-8. Epub 2006 Apr 21.

Bioinformatics Research Center, University of Aarhus Høegh-Guldbergs Gade 10, DK-8000 Arhus C, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btl153DOI Listing
September 2006

Recrafting the neighbor-joining method.

BMC Bioinformatics 2006 Jan 19;7:29. Epub 2006 Jan 19.

Bioinformatics Research Center, University of Aarhus, Denmark.

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http://dx.doi.org/10.1186/1471-2105-7-29DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271233PMC
January 2006

CoaSim: a flexible environment for simulating genetic data under coalescent models.

BMC Bioinformatics 2005 Oct 14;6:252. Epub 2005 Oct 14.

Bioinformatics Research Center, University of Aarhus, Høegh Guldbergsgade 10, 8000 Arhus C, Denmark.

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http://dx.doi.org/10.1186/1471-2105-6-252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1274299PMC
October 2005

RBT--a tool for building refined Buneman trees.

Bioinformatics 2005 Apr 7;21(8):1711-2. Epub 2004 Dec 7.

Bioinformatics Research Center, Department of Computer Science, University of Aarhus, Høegh-Guldbergs Gade 10, Building 090, DK-8000 Arhus C, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/bti195DOI Listing
April 2005

QuickJoin--fast neighbour-joining tree reconstruction.

Bioinformatics 2004 Nov 16;20(17):3261-2. Epub 2004 Jun 16.

Bioinformatics Research Center (BiRC), University of Aarhus, Høegh-Guldbergs Grade 10, Bldg. 090, DK-8000 Arhus C, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/bth359DOI Listing
November 2004

QDist--quartet distance between evolutionary trees.

Bioinformatics 2004 Jul 12;20(10):1636-7. Epub 2004 Feb 12.

Bioinformatics Research Center (BiRC), University of Aarhus, Ny Munkegade, Building 540, DK-8000 Arhus C, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/bth097DOI Listing
July 2004