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Items: 50

1.

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

Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N; PCAWG Drivers and Functional Interpretation Working Group; PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G; PCAWG Consortium.

Nature. 2020 Feb;578(7793):102-111. doi: 10.1038/s41586-020-1965-x. Epub 2020 Feb 5.

PMID:
32025015
2.

Ancestral Population Genomics.

Dutheil JY, Hobolth A.

Methods Mol Biol. 2019;1910:555-589. doi: 10.1007/978-1-4939-9074-0_18. Review.

PMID:
31278677
3.

Phase-type distributions in population genetics.

Hobolth A, Siri-Jégousse A, Bladt M.

Theor Popul Biol. 2019 Jun;127:16-32. doi: 10.1016/j.tpb.2019.02.001. Epub 2019 Feb 26.

PMID:
30822431
4.

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

Speed MS, Balding DJ, Hobolth A.

J Math Biol. 2019 May;78(6):1727-1769. doi: 10.1007/s00285-018-01325-0. Epub 2019 Jan 28.

PMID:
30734077
5.

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

Nielsen MM, Tataru P, Madsen T, Hobolth A, Pedersen JS.

Algorithms Mol Biol. 2018 Dec 8;13:17. doi: 10.1186/s13015-018-0135-2. eCollection 2018.

6.

Detecting archaic introgression using an unadmixed outgroup.

Skov L, Hui R, Shchur V, Hobolth A, Scally A, Schierup MH, Durbin R.

PLoS Genet. 2018 Sep 18;14(9):e1007641. doi: 10.1371/journal.pgen.1007641. eCollection 2018 Sep.

7.

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

Juul M, Madsen T, Guo Q, Bertl J, Hobolth A, Kellis M, Pedersen JS.

Bioinformatics. 2019 Jan 15;35(2):189-199. doi: 10.1093/bioinformatics/bty511.

8.

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

Waltoft BL, Hobolth A.

Stat Appl Genet Mol Biol. 2018 Jun 11;17(3). pii: /j/sagmb.2018.17.issue-3/sagmb-2017-0061/sagmb-2017-0061.xml. doi: 10.1515/sagmb-2017-0061.

PMID:
29886455
9.

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

Bertl J, Guo Q, Juul M, Besenbacher S, Nielsen MM, Hornshøj H, Pedersen JS, Hobolth A.

BMC Bioinformatics. 2018 Apr 19;19(1):147. doi: 10.1186/s12859-018-2141-2.

10.

Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival.

Hornshøj H, Nielsen MM, Sinnott-Armstrong NA, Świtnicki MP, Juul M, Madsen T, Sallari R, Kellis M, Ørntoft T, Hobolth A, Pedersen JS.

NPJ Genom Med. 2018 Jan 11;3:1. doi: 10.1038/s41525-017-0040-5. eCollection 2018.

11.

Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate.

Juul M, Bertl J, Guo Q, Nielsen MM, Świtnicki M, Hornshøj H, Madsen T, Hobolth A, Pedersen JS.

Elife. 2017 Mar 31;6. pii: e21778. doi: 10.7554/eLife.21778.

12.

Significance evaluation in factor graphs.

Madsen T, Hobolth A, Jensen JL, Pedersen JS.

BMC Bioinformatics. 2017 Mar 31;18(1):199. doi: 10.1186/s12859-017-1614-z.

13.

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

Tataru P, Simonsen M, Bataillon T, Hobolth A.

Syst Biol. 2017 Jan 1;66(1):e30-e46. doi: 10.1093/sysbio/syw056. Review.

14.
15.

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

Hobolth A, Siren J.

Theor Popul Biol. 2016 Apr;108:36-50. doi: 10.1016/j.tpb.2015.11.001. Epub 2015 Nov 29.

PMID:
26612605
16.

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

Waltoft BL, Pedersen CB, Nyegaard M, Hobolth A.

BMC Med Genet. 2015 Aug 30;16:71. doi: 10.1186/s12881-015-0210-1.

17.

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

Tataru P, Bataillon T, Hobolth A.

Genetics. 2015 Nov;201(3):1133-41. doi: 10.1534/genetics.115.179606. Epub 2015 Aug 26.

18.

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.

19.

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.

20.

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

Wilton PR, Carmi S, Hobolth A.

Genetics. 2015 May;200(1):343-55. doi: 10.1534/genetics.114.173898. Epub 2015 Mar 17.

21.

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

Hobolth A, Jensen JL.

Theor Popul Biol. 2014 Dec;98:48-58. doi: 10.1016/j.tpb.2014.01.002. Epub 2014 Jan 28.

PMID:
24486389
22.

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.

23.

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
24.

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.

25.

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.

26.

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.

27.

Ancestral population genomics.

Dutheil JY, Hobolth A.

Methods Mol Biol. 2012;856:293-313. doi: 10.1007/978-1-61779-585-5_12. Review.

PMID:
22399464
28.

Insights into hominid evolution from the gorilla genome sequence.

Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R.

Nature. 2012 Mar 7;483(7388):169-75. doi: 10.1038/nature10842.

29.

Extensive X-linked adaptive evolution in central chimpanzees.

Hvilsom C, Qian Y, Bataillon T, Li Y, Mailund T, Sallé B, Carlsen F, Li R, Zheng H, Jiang T, Jiang H, Jin X, Munch K, Hobolth A, Siegismund HR, Wang J, Schierup MH.

Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):2054-9. doi: 10.1073/pnas.1106877109. Epub 2012 Jan 23.

30.

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

Tataru P, Hobolth A.

BMC Bioinformatics. 2011 Dec 5;12:465. doi: 10.1186/1471-2105-12-465.

31.

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.

PLoS Genet. 2011 Mar;7(3):e1001319. doi: 10.1371/journal.pgen.1001319. Epub 2011 Mar 3.

32.

On computing the coalescence time density in an isolation-with-migration model with few samples.

Hobolth A, Andersen LN, Mailund T.

Genetics. 2011 Apr;187(4):1241-3. doi: 10.1534/genetics.110.124164. Epub 2011 Feb 14. No abstract available.

33.

Comparative and demographic analysis of orang-utan genomes.

Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK.

Nature. 2011 Jan 27;469(7331):529-33. doi: 10.1038/nature09687.

34.

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.

Genome Res. 2011 Mar;21(3):349-56. doi: 10.1101/gr.114751.110. Epub 2011 Jan 26.

36.

Ancestral population genomics: the coalescent hidden Markov model approach.

Dutheil JY, Ganapathy G, Hobolth A, Mailund T, Uyenoyama MK, Schierup MH.

Genetics. 2009 Sep;183(1):259-74. doi: 10.1534/genetics.109.103010. Epub 2009 Jul 6.

37.

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

Hobolth A, Wiuf C.

Theor Popul Biol. 2009 Jun;75(4):260-5. doi: 10.1016/j.tpb.2009.02.001. Epub 2009 Feb 26.

PMID:
19249321
38.

Importance sampling for the infinite sites model.

Hobolth A, Uyenoyama MK, Wiuf C.

Stat Appl Genet Mol Biol. 2008;7(1):Article32. doi: 10.2202/1544-6115.1400. Epub 2008 Oct 30.

39.

Quantifying the impact of protein tertiary structure on molecular evolution.

Choi SC, Hobolth A, Robinson DM, Kishino H, Thorne JL.

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

PMID:
17522088
40.

Bayesian regularization of diffusion tensor images.

Frandsen J, Hobolth A, Ostergaard L, Vestergaard-Poulsen P, Vedel Jensen EB.

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

PMID:
17429105
41.

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.

PLoS Genet. 2007 Feb 23;3(2):e7. Epub 2006 Nov 30.

42.

On error prediction in circular systematic sampling.

Jónsdóttir KY, Hoffmann LM, Hobolth A, Vedel Jensen EB.

J Microsc. 2006 Jun;222(Pt 3):212-6.

43.

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

Hobolth A, Jensen JL.

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

PMID:
16646835
44.

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

Hobolth A, Nielsen R, Wang Y, Wu F, Tanksley SD.

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

PMID:
16600999
45.

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

Christensen OF, Hobolth A, Jensen JL.

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

PMID:
16305327
46.
47.

Comparative analysis of protein coding sequences from human, mouse and the domesticated pig.

Jørgensen FG, Hobolth A, Hornshøj H, Bendixen C, Fredholm M, Schierup MH.

BMC Biol. 2005 Jan 28;3:2.

48.

Shape discrimination by total curvature, with a view to cancer diagnostics.

Gardner RJ, Hobolth A, Jensen EB, Sørensen FB.

J Microsc. 2005 Jan;217(Pt 1):49-59.

49.

Shape modelling of spatial particles from planar central sections -- a case study.

Hannila ML, Vedel Jensen EB, Hobolth A, Nyengaard JR.

J Microsc. 2004 Aug;215(Pt 2):183-90.

50.

The spherical deformation model.

Hobolth A.

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

PMID:
14557113

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