Publications by authors named "Asger Hobolth"

47Publications

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Nature 2020 02 5;578(7793):102-111. Epub 2020 Feb 5.

The Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41586-020-1965-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7054214PMC
February 2020

Ancestral Population Genomics.

Methods Mol Biol 2019 ;1910:555-589

Bioinformatics Research Center (BiRC), Aarhus University, Aarhus, Denmark.

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http://dx.doi.org/10.1007/978-1-4939-9074-0_18DOI Listing
January 2020

Phase-type distributions in population genetics.

Theor Popul Biol 2019 06 26;127:16-32. Epub 2019 Feb 26.

University of Copenhagen, Department of Mathematical Sciences, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.tpb.2019.02.001DOI Listing
June 2019

A general framework for moment-based analysis of genetic data.

J Math Biol 2019 05 28;78(6):1727-1769. Epub 2019 Jan 28.

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

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http://dx.doi.org/10.1007/s00285-018-01325-0DOI Listing
May 2019

Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments.

Algorithms Mol Biol 2018 8;13:17. Epub 2018 Dec 8.

1Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8000 Aarhus C, Denmark.

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http://dx.doi.org/10.1186/s13015-018-0135-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6286601PMC
December 2018

Detecting archaic introgression using an unadmixed outgroup.

PLoS Genet 2018 09 18;14(9):e1007641. Epub 2018 Sep 18.

Department of Genetics, University of Cambridge, Cambridge United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1007641DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161914PMC
September 2018

ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation.

Bioinformatics 2019 01;35(2):189-199

Department of Molecular Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus N, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/bty511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330011PMC
January 2019

Non-parametric estimation of population size changes from the site frequency spectrum.

Stat Appl Genet Mol Biol 2018 06 11;17(3). Epub 2018 Jun 11.

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

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http://dx.doi.org/10.1515/sagmb-2017-0061DOI Listing
June 2018

A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data.

BMC Bioinformatics 2018 04 19;19(1):147. Epub 2018 Apr 19.

Department of Molecular Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus N, DK-8200, Denmark.

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http://dx.doi.org/10.1186/s12859-018-2141-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909259PMC
April 2018

Significance evaluation in factor graphs.

BMC Bioinformatics 2017 Mar 31;18(1):199. Epub 2017 Mar 31.

Department of Molecular Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus, Denmark.

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http://dx.doi.org/10.1186/s12859-017-1614-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374669PMC
March 2017

Statistical Inference in the Wright-Fisher Model Using Allele Frequency Data.

Syst Biol 2017 01;66(1):e30-e46

Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.

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http://dx.doi.org/10.1093/sysbio/syw056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5837693PMC
January 2017

The multivariate Wright-Fisher process with mutation: Moment-based analysis and inference using a hierarchical Beta model.

Theor Popul Biol 2016 Apr 29;108:36-50. Epub 2015 Nov 29.

Department of Biosciences, University of Helsinki, Finland. Electronic address:

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http://dx.doi.org/10.1016/j.tpb.2015.11.001DOI Listing
April 2016

The importance of distinguishing between the odds ratio and the incidence rate ratio in GWAS.

BMC Med Genet 2015 Aug 30;16:71. Epub 2015 Aug 30.

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

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http://dx.doi.org/10.1186/s12881-015-0210-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593225PMC
August 2015

Inference Under a Wright-Fisher Model Using an Accurate Beta Approximation.

Genetics 2015 Nov 26;201(3):1133-41. Epub 2015 Aug 26.

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

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http://dx.doi.org/10.1534/genetics.115.179606DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649640PMC
November 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

The SMC' is a highly accurate approximation to the ancestral recombination graph.

Genetics 2015 May 17;200(1):343-55. Epub 2015 Mar 17.

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

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http://dx.doi.org/10.1534/genetics.114.173898DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423375PMC
May 2015

Markovian approximation to the finite loci coalescent with recombination along multiple sequences.

Theor Popul Biol 2014 Dec 28;98:48-58. Epub 2014 Jan 28.

Department of Mathematics, Aarhus University, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.tpb.2014.01.002DOI Listing
December 2014

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

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

Ancestral population genomics.

Methods Mol Biol 2012 ;856:293-313

Institut des Sciences de l'Évolution Montpellier (ISE-M), UMR 5554, CNRS, Unversité Montpellier, Montpellier, France.

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http://dx.doi.org/10.1007/978-1-61779-585-5_12DOI Listing
July 2012

Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains.

BMC Bioinformatics 2011 Dec 5;12:465. Epub 2011 Dec 5.

Bioinformatics Research Center, Aarhus University, Aarhus, Denmark.

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http://dx.doi.org/10.1186/1471-2105-12-465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329461PMC
December 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

The genealogy, site frequency spectrum and ages of two nested mutant alleles.

Theor Popul Biol 2009 Jun 26;75(4):260-5. Epub 2009 Feb 26.

Bioinformatics Research Center, Aarhus University, Aarhus, Denmark.

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http://linkinghub.elsevier.com/retrieve/pii/S004058090900019
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http://dx.doi.org/10.1016/j.tpb.2009.02.001DOI Listing
June 2009

Importance sampling for the infinite sites model.

Stat Appl Genet Mol Biol 2008 30;7(1):Article32. Epub 2008 Oct 30.

Aarhus University.

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http://dx.doi.org/10.2202/1544-6115.1400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832804PMC
December 2008

Quantifying the impact of protein tertiary structure on molecular evolution.

Mol Biol Evol 2007 Aug 23;24(8):1769-82. Epub 2007 May 23.

Bioinformatics Research Center, North Carolina State University, NC, USA.

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ftp://statgen.ncsu.edu/pub/thorne/mypapers/ChoiEtAlMBE2007.p
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http://mbe.oxfordjournals.org/cgi/doi/10.1093/molbev/msm097
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http://dx.doi.org/10.1093/molbev/msm097DOI Listing
August 2007

Bayesian regularization of diffusion tensor images.

Biostatistics 2007 Oct 11;8(4):784-99. Epub 2007 Apr 11.

Department of Neuroradiology, Centre for Functionally Integrative Neuroscience, Arhus University Hospital, Arhus, Denmark.

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http://dx.doi.org/10.1093/biostatistics/kxm005DOI Listing
October 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

Statistical inference in evolutionary models of DNA sequences via the EM algorithm.

Stat Appl Genet Mol Biol 2005 12;4:Article18. Epub 2005 Aug 12.

Bioinformatics Research Center, University of Aarhus, Denmark.

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http://dx.doi.org/10.2202/1544-6115.1127DOI Listing
May 2006

CpG + CpNpG analysis of protein-coding sequences from tomato.

Mol Biol Evol 2006 Jun 6;23(6):1318-23. Epub 2006 Apr 6.

Bioinformatics Research Center, North Carolina State University, USA.

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http://cteg.berkeley.edu/~nielsen/wordpress/wp-content/uploa
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http://mbe.oxfordjournals.org/cgi/doi/10.1093/molbev/msk017
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http://dx.doi.org/10.1093/molbev/msk017DOI Listing
June 2006

Pseudo-likelihood analysis of codon substitution models with neighbor-dependent rates.

J Comput Biol 2005 Nov;12(9):1166-82

Bioinformatics Research Center, University of Aarhus, Denmark.

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http://dx.doi.org/10.1089/cmb.2005.12.1166DOI Listing
November 2005

Applications of hidden Markov models for characterization of homologous DNA sequences with a common gene.

J Comput Biol 2005 Mar;12(2):186-203

Bioinformatics Research Center, University of Aarhus, Aarhus, Denmark.

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http://dx.doi.org/10.1089/cmb.2005.12.186DOI Listing
March 2005

The spherical deformation model.

Authors:
Asger Hobolth

Biostatistics 2003 Oct;4(4):583-95

Department of Mathematical Sciences, University of Aarhus, Ny Munkegade, 8000 Aarhus C, Denmark.

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http://dx.doi.org/10.1093/biostatistics/4.4.583DOI Listing
October 2003