Thomas Mailund

  1. 2017
  2. Published

    Assembly and analysis of 100 full MHC haplotypes from the Danish population. / Jensen, Jacob Malte; Villesen, Palle; Friborg, Rune M; Mailund, Thomas; Besenbacher, Søren; Schierup, Mikkel H; Danish Pan-Genome Consortium.

    In: Genome Research, 09.2017, p. 1597-1607.

    Research output: Research - peer-reviewJournal article

  3. Published

    Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. / Maretty, Lasse; Jensen, Jacob Malte; Petersen, Bent; Sibbesen, Jonas Andreas; Liu, Siyang; Villesen, Palle; Skov, Laurits; Belling, Kirstine Christensen; Theil Have, Christian; Izarzugaza, José M G; Grosjean, Marie; Bork-Jensen, Jette; Grove, Jakob; Als, Thomas D; Huang, Shujia; Chang, Yuqi; Xu, Ruiqi; Ye, Weijian; Rao, Junhua; Guo, Xiaosen; Sun, Jihua; Cao, Hongzhi; Ye, Chen; van Beusekom, Johan; Espeseth, Thomas; Flindt, Esben Nørgaard; Friborg, Rune M; Halager, Anders E; Le Hellard, Stephanie; Hultman, Christina M; Lescai, Francesco; Li, Shengting; Lund, Ole; Løngren, Peter; Mailund, Thomas; Matey-Hernandez, Maria Luisa; Mors, Ole; Pedersen, Christian N S; Sicheritz-Ponten, Thomas; Sullivan, Patrick F; Syed, Ali; Westergaard, David; Yadav, Rachita; Li, Ning; Xu, Xun; Hansen, Torben; Krogh, Anders; Bolund, Lars; Sørensen, Thorkild I A; Pedersen, Oluf; Gupta, Ramneek; Rasmussen, Simon; Besenbacher, Søren; Børglum, Anders D; Wang, Jun; Eiberg, Hans; Kristiansen, Karsten; Brunak, Søren; Schierup, Mikkel Heide.

    In: Nature, Vol. 548, 03.08.2017, p. 87-91.

    Research output: Research - peer-reviewJournal article

  4. Published

    Fast admixture analysis and population tree estimation for SNP and NGS data. / Cheng, Jade Yu; Mailund, Thomas; Nielsen, Rasmus.

    In: Bioinformatics (Online), Vol. 33, No. 14, 15.07.2017, p. 2148–2155.

    Research output: Research - peer-reviewJournal article

  5. Published

    admixturegraph : an R package for admixture graph manipulation and fitting. / Leppälä, Kalle; Nielsen, Svend V; Mailund, Thomas.

    In: Bioinformatics (Online), Vol. 33, No. 11, 01.06.2017, p. 1738-1740.

    Research output: Research - peer-reviewJournal article

  6. Published

    Evidence that the rate of strong selective sweeps increases with population size in the great apes. / Nam, Kiwoong; Munch, Kasper; Mailund, Thomas; Nater, Alexander; Greminger, Maja Patricia; Krützen, Michael; Marquès-Bonet, Tomàs; Schierup, Mikkel Heide.

    In: National Academy of Sciences. Proceedings, Vol. 114, No. 7, 02.2017, p. 1613-1618.

    Research output: Research - peer-reviewJournal article

  7. Published

    The ecological niche and distribution of Neanderthals during the Last Interglacial. / Benito, Blas M.; Svenning, Jens-Christian; Kellberg-Nielsen, Trine; Riede, Felix; Gil-Romera, Graciela; Mailund, Thomas; Kjaergaard, Peter C.; Sandel, Brody S.

    In: Journal of Biogeography, Vol. 44, No. 1, 01.2017, p. 51–61.

    Research output: Research - peer-reviewJournal article

  8. Published
  9. Published
  10. Published
  11. Published
  12. 2016
  13. Published

    Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. / Abascal, Federico; Corvelo, André; Cruz, Fernando; Villanueva-Cañas, José L; Vlasova, Anna; Marcet-Houben, Marina; Martínez-Cruz, Begoña; Cheng, Jade Yu; Prieto, Pablo; Quesada, Víctor; Quilez, Javier; Li, Gang; García, Francisca; Rubio-Camarillo, Miriam; Frias, Leonor; Ribeca, Paolo; Capella-Gutiérrez, Salvador; Rodríguez, José M; Câmara, Francisco; Lowy, Ernesto; Cozzuto, Luca; Erb, Ionas; Tress, Michael L; Rodriguez-Ales, Jose L; Ruiz-Orera, Jorge; Reverter, Ferran; Casas-Marce, Mireia; Soriano, Laura; Arango, Javier R; Derdak, Sophia; Galán, Beatriz; Blanc, Julie; Gut, Marta; Lorente-Galdos, Belen; Andrés-Nieto, Marta; López-Otín, Carlos; Valencia, Alfonso; Gut, Ivo; García, José L; Guigó, Roderic; Murphy, William J; Ruiz-Herrera, Aurora; Marques-Bonet, Tomas; Roma, Guglielmo; Notredame, Cedric; Mailund, Thomas; Albà, M Mar; Gabaldón, Toni; Alioto, Tyler; Godoy, José A.

    In: Genome Biology (Online), Vol. 17, No. 1, 14.12.2016, p. 251.

    Research output: Research - peer-reviewJournal article

  14. Published

    Selective sweeps across twenty millions years of primate evolution. / Munch, Kasper; Nam, Kiwoong; Schierup, Mikkel Heide; Mailund, Thomas.

    In: Molecular Biology and Evolution, Vol. 33, No. 12, 22.09.2016, p. 3065-3074.

    Research output: Research - peer-reviewJournal article

  15. Published

    Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity. / Athanasiadis, Georgios; Cheng, Jade Y; Vilhjálmsson, Bjarni J; Jørgensen, Frank G; Als, Thomas D; Le Hellard, Stephanie; Espeseth, Thomas; Sullivan, Patrick F; Hultman, Christina M; Kjærgaard, Peter C; Schierup, Mikkel H; Mailund, Thomas.

    In: Genetics, Vol. 204, No. 2, 17.08.2016, p. 711-722.

    Research output: Research - peer-reviewJournal article

  16. Published

    A genomic history of Aboriginal Australia. / Malaspinas, Anna-Sapfo; Westaway, Michael C; Muller, Craig; Sousa, Vitor C; Lao, Oscar; Alves, Isabel; Athanasiadis, Georgios; Cheng, Jade Y; Crawford, Jacob E; Heupink, Tim H; Macholdt, Enrico; Peischl, Stephan; Schiffels, Stephan; Subramanian, Sankar; Wright, Joanne L; Albrechtsen, Anders; Barbieri, Chiara; Dupanloup, Isabelle; Eriksson, Anders; Margaryan, Ashot; Moltke, Ida; Pugach, Irina; Korneliussen, Thorfinn S; Levkivskyi, Ivan P; Moreno-Mayar, J Víctor; Ni, Shengyu; Racimo, Fernando; Sikora, Martin; Xue, Yali; Aghakhanian, Farhang A; Brucato, Nicolas; Brunak, Søren; Campos, Paula F; Clark, Warren; Ellingvåg, Sturla; Fourmile, Gudjugudju; Gerbault, Pascale; Injie, Darren; Koki, George; Leavesley, Matthew; Logan, Betty; Lynch, Aubrey; Matisoo-Smith, Elizabeth A; McAllister, Peter J; Mentzer, Alexander J; Metspalu, Mait; Migliano, Andrea B; Murgha, Les; Phipps, Maude E; Pomat, William; Reynolds, Doc; Ricaut, Francois-Xavier; Siba, Peter; Thomas, Mark G; Wales, Thomas; Wall, Colleen Ma'run; Oppenheimer, Stephen J; Tyler-Smith, Chris; Durbin, Richard; Dortch, Joe; Manica, Andrea; Schierup, Mikkel H; Foley, Robert A; Lahr, Marta Mirazón; Bowern, Claire; Wall, Jeffrey D; Mailund, Thomas; Stoneking, Mark; Sandhu, Manjinder S; Excoffier, Laurent; Lambert, David M; Willerslev, Eske.

    In: Nature, Vol. 538, No. 7624, 2016, p. 207-214.

    Research output: Research - peer-reviewJournal article

  17. Published

    Measurement units in R. / Pebesma, Edzer; Mailund, Thomas; Hiebert, James.

    In: The R Journal, Vol. 8, No. 2, 2016, p. 486-494.

    Research output: Research - peer-reviewJournal article

  18. Published

    Spitting for Science : Danish High School Students Commit to a Large-Scale Self-Reported Genetic Study. / Athanasiadis, Georgios; Jorgensen, Frank G.; Cheng, Jade Y.; Kjaergaard, Peter C.; Schierup, Mikkel H.; Mailund, Thomas.

    In: P L o S One, Vol. 11, No. 8, e0161822, 2016.

    Research output: Research - peer-reviewJournal article

  19. 2015
  20. Published

    Ancestral population genomics using coalescence hidden Markov models and heuristic optimisation algorithms. / Cheng, Jade Yu; Mailund, Thomas.

    In: Computational Biology and Chemistry, Vol. 57, 08.2015, p. 80-92.

    Research output: Research - peer-reviewJournal article

  21. Published

    Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence. / Dutheil, Julien Y; Munch, Kasper; Nam, Kiwoong; Mailund, Thomas; Schierup, Mikkel H.

    In: P L o S Genetics, Vol. 11, No. 8, 08.2015, p. e1005451.

    Research output: Research - peer-reviewJournal article

  22. Published

    Extreme selective sweeps independently targeted the X chromosomes of the great apes. / Nam, Kiwoong; Munch, Kasper; Hobolth, Asger; Dutheil, Julien Yann; Veeramah, Krishna R; Woerner, August E; Hammer, Michael F; Mailund, Thomas; Schierup, Mikkel Heide; Great Ape Genome Diversity Project.

    In: National Academy of Sciences. Proceedings, Vol. 112, No. 20, 04.05.2015.

    Research output: Research - peer-reviewJournal article

  23. Published

    Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing. / Bataillon, Thomas; Duan, Jinjie; Hvilsom, Christina; Jin, Xin; Li, Yingrui; Skov, Laurits; Glemin, Sylvain; Munch, Kasper; Jiang, Tao; Qian, Yu; Hobolth, Asger; Wang, Jun; Mailund, Thomas; Siegismund, Hans R; Schierup, Mikkel H.

    In: Genome Biology and Evolution, Vol. 7, No. 4, 04.2015, p. 1122-32.

    Research output: Research - peer-reviewJournal article

  24. Published

    Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios. / Besenbacher, Søren; Liu, Siyang; Izarzugaza, José M G; Grove, Jakob; Belling, Kirstine; Bork-Jensen, Jette; Huang, Shujia; Als, Thomas D; Li, Shengting; Yadav, Rachita; Rubio-García, Arcadio; Lescai, Francesco; Demontis, Ditte; Rao, Junhua; Ye, Weijian; Mailund, Thomas; Møllegaard Friborg, Rune; Pedersen, Christian N S; Xu, Ruiqi; Sun, Jihua; Liu, Hao; Wang, Ou; Cheng, Xiaofang; Flores, David; Rydza, Emil; Rapacki, Kristoffer; Damm Sørensen, John; Chmura, Piotr; Westergaard, David; Dworzynski, Piotr; Sørensen, Thorkild I A; Lund, Ole; Hansen, Torben; Xu, Xun; Li, Ning; Bolund, Lars; Pedersen, Oluf; Eiberg, Hans; Krogh, Anders; Børglum, Anders D; Brunak, Søren; Kristiansen, Karsten; Schierup, Mikkel H; Wang, Jun; Gupta, Ramneek; Villesen, Palle; Rasmussen, Simon.

    In: Nature Communications, Vol. 6, 5969, 2015.

    Research output: Research - peer-reviewJournal article

  25. 2014
  26. Published

    Unraveling recombination rate evolution using ancestral recombination maps. / Munch, Kasper; Schierup, Mikkel H; Mailund, Thomas.

    In: BioEssays, Vol. 36, No. 9, 14.07.2014, p. 892-900.

    Research output: Research - peer-reviewJournal article

  27. Published

    Strong selective sweeps associated with ampliconic regions in great ape X chromosomes. / Nam, Kiwoong; Munch, Kasper; Hobolth, Asger; Y. Dutheil, Julien; Veeramah, Krishna; Woerner, August; F. Hammer, Michael; Ape Genome Diversity Project, Great; Mailund, Thomas; H. Schierup, Mikkel.

    In: arXiv, 24.02.2014.

    Research output: ResearchJournal article

  28. Published

    Lineage sorting in apes. / Mailund, Thomas; Munch, Kasper; Schierup, Mikkel Heide.

    In: Annual Review of Genetics, Vol. 48, 01.01.2014, p. 519-535.

    Research output: Research - peer-reviewJournal article

  29. Published
  30. Published

    Efficient computation in the IM model. / Andersen, Lars Nørvang; Mailund, Thomas; Hobolth, Asger.

    In: Journal of Mathematical Biology, Vol. 68, No. 6, 2014, p. 1423-1451.

    Research output: Research - peer-reviewJournal article

  31. Published

    Identifying disease associated genes by network propagation. / Qian, Yu; Besenbacher, Soren; Mailund, Thomas; Schierup, Mikkel Heide.

    In: B M C Systems Biology, Vol. 8, No. Suppl 1, 2014, p. S6.

    Research output: ResearchConference abstract in journal

  32. Published

    Inferring the Process of Human–Chimpanzee Speciation. / Mailund, Thomas; Munch, Kasper; Schierup, Mikkel Heide.

    Encyclopedia of Life Sciences. Wiley, 2014.

    Research output: ResearchReview

  33. Published

    tqDist: A Library for Computing the Quartet and Triplet Distances Between Binary and General Trees. / Sand, Andreas; Holt, Morten Kragelund; Johansen, Jens; Brodal, Gerth Stølting; Mailund, Thomas; Pedersen, Christian Nørgaard Storm.

    In: Bioinformatics, Vol. 30, No. 4, 2014, p. 2079-2080.

    Research output: Research - peer-reviewJournal article

  34. 2013
  35. Published

    zipHMMlib: : a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm. / Sand, Andreas; Kristiansen, Martin; Pedersen, Christian Nørgaard Storm; Mailund, Thomas.

    In: BMC Bioinformatics , Vol. 14, No. 339, 12.2013, p. 339-348.

    Research output: Research - peer-reviewJournal article

  36. Published

    Algorithms for Hidden Markov Models Restricted to Occurrences of Regular Expressions. / Tataru, Paula; Sand, Andreas; Hobolth, Asger; Mailund, Thomas; Pedersen, Christian Nørgaard Storm.

    In: Biology, Vol. 2, No. 4, 08.11.2013, p. 1282-1295.

    Research output: Research - peer-reviewJournal article

  37. Published

    Hvor kommer du fra? : En undersøgelse af danskernes genetiske historie. / Jørgensen, Frank Grønlund; Mailund, Thomas; Schierup, Mikkel Heide; Kjærgaard, Peter C.

    In: Biofag, Vol. 3, 08.2013, p. 18-20.

    Research output: CommunicationJournal article

  38. Published

    A practical O(n log2 n) time algorithm for computing the triplet distance on binary trees. / Sand, Andreas; Pedersen, Christian Nørgaard Storm; Mailund, Thomas; Brodal, Gerth Stølting; Fagerberg, Rolf.

    In: B M C Bioinformatics, Vol. 14, No. Suppl 2, 2013, p. S18.

    Research output: Research - peer-reviewConference article

  39. Published

    Algorithms for Computing the Triplet and Quartet Distances for Binary and General Trees. / Sand, Andreas; Holt, Morten Kragelund; Johansen, Jens; Fagerberg, Rolf; Pedersen, Christian Nørgaard Storm; Brodal, Gerth Stølting; Mailund, Thomas.

    In: Biology, Vol. 2, No. 4, 2013, p. 1189-1209.

    Research output: Research - peer-reviewJournal article

  40. Published

    Efficient Algorithms for Computing the Triplet and Quartet Distance Between Trees of Arbitrary Degree. / Brodal, Gerth Stølting; Fagerberg, Rolf; Mailund, Thomas; Pedersen, Christian Nørgaard Storm; Sand, Andreas.

    In: The Annual A C M - S I A M Symposium on Discrete Algorithms. Proceedings, Vol. 24, 2013, p. 1814-1832.

    Research output: Research - peer-reviewConference article

  41. Published

    Great ape genetic diversity and population history. / Prado-Martinez, Javier; Sudmant, Peter H; Kidd, Jeffrey M; Li, Heng; Kelley, Joanna L; Lorente-Galdos, Belen; Veeramah, Krishna R; Woerner, August E; O'Connor, Timothy D; Santpere, Gabriel; Cagan, Alexander; Theunert, Christoph; Casals, Ferran; Laayouni, Hafid; Munch, Kasper; Hobolth, Asger; Halager, Anders E; Malig, Maika; Hernandez-Rodriguez, Jessica; Hernando-Herraez, Irene; Prüfer, Kay; Pybus, Marc; Johnstone, Laurel; Lachmann, Michael; Alkan, Can; Twigg, Dorina; Petit, Natalia; Baker, Carl; Hormozdiari, Fereydoun; Fernandez-Callejo, Marcos; Dabad, Marc; Wilson, Michael L; Stevison, Laurie; Camprubí, Cristina; Carvalho, Tiago; Ruiz-Herrera, Aurora; Vives, Laura; Mele, Marta; Abello, Teresa; Kondova, Ivanela; Bontrop, Ronald E; Pusey, Anne; Lankester, Felix; Kiyang, John A; Bergl, Richard A; Lonsdorf, Elizabeth; Myers, Simon; Ventura, Mario; Gagneux, Pascal; Comas, David; Siegismund, Hans; Blanc, Julie; Agueda-Calpena, Lidia; Gut, Marta; Fulton, Lucinda; Tishkoff, Sarah A; Mullikin, James C; Wilson, Richard K; Gut, Ivo G; Gonder, Mary Katherine; Ryder, Oliver A; Hahn, Beatrice H; Navarro, Arcadi; Akey, Joshua M; Bertranpetit, Jaume; Reich, David; Mailund, Thomas; Schierup, Mikkel H; Hvilsom, Christina; Andrés, Aida M; Wall, Jeffrey D; Bustamante, Carlos D; Hammer, Michael F; Eichler, Evan E; Marques-Bonet, Tomas.

    In: Nature, Vol. 499, 2013, p. 471–475.

    Research output: Research - peer-reviewJournal article

  42. 2012
  43. Published

    Using colored Petri nets to construct coalescent hidden markov models : Automatic translation from demographic specifications to efficient inference methods. / Mailund, Thomas; Halager, A.E.; Westergaard, M.

    In: Lecture Notes in Computer Science, Vol. 7347, 01.01.2012, p. 32-50.

    Research output: Research - peer-reviewJournal article

  44. Published

    A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species. / Mailund, Thomas; Halager, Anders E; Westergaard, Michael; Dutheil, Julien Y; Munch, Kasper; Andersen, Lars N; Lunter, Gerton; Prüfer, Kay; Scally, Aylwyn; Hobolth, Asger; Schierup, Mikkel H.

    In: P L o S Genetics, Vol. 8, No. 12, 2012, p. e1003125.

    Research output: Research - peer-reviewJournal article

  45. Published

    An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes. / Jin, Xin; He, Mingze; Ferguson, Betsy; Meng, Yuhuan; Ouyang, Limei; Ren, Jingjing; Mailund, Thomas; Sun, Fei; Sun, Liangdan; Shen, Juan; Zhuo, Min; Song, Li; Wang, Jufang; Ling, Fei; Zhu, Yuqi; Hvilsom, Christina; Siegismund, Hans; Liu, Xiaoming; Gong, Zhuolin; Ji, Fang; Wang, Xinzhong; Liu, Boqing; Zhang, Yu; Hou, Jianguo; Wang, Jing; Zhao, Hua; Wang, Yanyi; Fang, Xiaodong; Zhang, Guojie; Wang, Jian; Zhang, Xuejun; Schierup, Mikkel H; Du, Hongli; Wang, Jun; Wang, Xiaoning.

    In: P L o S One, Vol. 7, No. 7, 2012, p. e40637.

    Research output: Research - peer-reviewJournal article

  46. Published

    Association mapping and disease : evolutionary perspectives. / Besenbacher, Søren; Mailund, Thomas; Schierup, Mikkel H.

    In: Methods in Molecular Biology, Vol. 856, 2012, p. 275-91.

    Research output: Research - peer-reviewJournal article

  47. Published

    Cultural phylogenetics of the tupi language family in lowland South america. / Walker, Robert S; Wichmann, Søren; Mailund, Thomas; Atkisson, Curtis J.

    In: P L o S One, Vol. 7, No. 4, 2012, p. e35025.

    Research output: Research - peer-reviewJournal article

  48. Published

    Extensive X-linked adaptive evolution in central chimpanzees. / Hvilsom, Christina; Qian, Yu; Bataillon, Thomas; Li, Yingrui; Mailund, Thomas; Sallé, Bettina; Carlsen, Frands; Li, Ruiqiang; Zheng, Hancheng; Jiang, Tao; Jiang, Hui; Jin, Xin; Munch, Kasper; Hobolth, Asger; Siegismund, Hans R; Wang, Jun; Schierup, Mikkel Heide.

    In: National Academy of Sciences. Proceedings, 2012.

    Research output: Research - peer-reviewJournal article

  49. Published

    Insights into hominid evolution from the gorilla genome sequence. / Scally, Aylwyn; Dutheil, Julien Y; Hillier, LaDeana W; Jordan, Gregory E; Goodhead, Ian; Herrero, Javier; Hobolth, Asger; Lappalainen, Tuuli; Mailund, Thomas; Marques-Bonet, Tomas; McCarthy, Shane; Montgomery, Stephen H; Schwalie, Petra C; Tang, Y Amy; Ward, Michelle C; Xue, Yali; Yngvadottir, Bryndis; Alkan, Can; Andersen, Lars N; Ayub, Qasim; Ball, Edward V; Beal, Kathryn; Bradley, Brenda J; Chen, Yuan; Clee, Chris M; Fitzgerald, Stephen; Graves, Tina A; Gu, Yong; Heath, Paul; Heger, Andreas; Karakoc, Emre; Kolb-Kokocinski, Anja; Laird, Gavin K; Lunter, Gerton; Meader, Stephen; Mort, Matthew; Mullikin, James C; Munch, Kasper; O'Connor, Timothy D; Phillips, Andrew D; Prado-Martinez, Javier; Rogers, Anthony S; Sajjadian, Saba; Schmidt, Dominic; Shaw, Katy; Simpson, Jared T; Stenson, Peter D; Turner, Daniel J; Vigilant, Linda; Vilella, Albert J; Whitener, Weldon; Zhu, Baoli; Cooper, David N; de Jong, Pieter; Dermitzakis, Emmanouil T; Eichler, Evan E; Flicek, Paul; Goldman, Nick; Mundy, Nicholas I; Ning, Zemin; Odom, Duncan T; Ponting, Chris P; Quail, Michael A; Ryder, Oliver A; Searle, Stephen M; Warren, Wesley C; Wilson, Richard K; Schierup, Mikkel H; Rogers, Jane; Tyler-Smith, Chris; Durbin, Richard.

    In: Nature, Vol. 483, No. 7388, 2012, p. 169-75.

    Research output: Research - peer-reviewJournal article

  50. Published

    Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. / Miller, Webb; Schuster, Stephan C; Welch, Andreanna J; Ratan, Aakrosh; Bedoya-Reina, Oscar C; Zhao, Fangqing; Kim, Hie Lim; Burhans, Richard C; Drautz, Daniela I; Wittekindt, Nicola E; Tomsho, Lynn P; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Peacock, Elizabeth; Farley, Sean; Sage, George K; Rode, Karyn; Obbard, Martyn; Montiel, Rafael; Bachmann, Lutz; Ingólfsson, Olafur; Aars, Jon; Mailund, Thomas; Wiig, Oystein; Talbot, Sandra L; Lindqvist, Charlotte.

    In: National Academy of Sciences. Proceedings, 2012.

    Research output: Research - peer-reviewJournal article

  51. Published

    The bonobo genome compared with the chimpanzee and human genomes. / Prüfer, Kay; Munch, Kasper; Hellmann, Ines; Akagi, Keiko; Miller, Jason R; Walenz, Brian; Koren, Sergey; Sutton, Granger; Kodira, Chinnappa; Winer, Roger; Knight, James R; Mullikin, James C; Meader, Stephen J; Ponting, Chris P; Lunter, Gerton; Higashino, Saneyuki; Hobolth, Asger; Dutheil, Julien; Karakoç, Emre; Alkan, Can; Sajjadian, Saba; Catacchio, Claudia Rita; Ventura, Mario; Marques-Bonet, Tomas; Eichler, Evan E; André, Claudine; Atencia, Rebeca; Mugisha, Lawrence; Junhold, Jörg; Patterson, Nick; Siebauer, Michael; Good, Jeffrey M; Fischer, Anne; Ptak, Susan E; Lachmann, Michael; Symer, David E; Mailund, Thomas; Schierup, Mikkel H; Andrés, Aida M; Kelso, Janet; Pääbo, Svante.

    In: Nature, Vol. 486, No. 7404, 2012, p. 527-31.

    Research output: Research - peer-reviewJournal article

  52. Published

    The sweep-line state space exploration method. / Jensen, Kurt; Kristensen, Lars M.; Mailund, Thomas.

    In: Theoretical Computer Science, Vol. 429, 2012, p. 169–179.

    Research output: Research - peer-reviewJournal article

  53. 2011
  54. Published
  55. Published

    A sub-cubic time algorithm for computing the quartet distance between two general trees. / Nielsen, Jesper; Kristensen, Anders Kabell; Mailund, Thomas; Pedersen, Christian Nørgaard Storm.

    In: Algorithms for Molecular Biology, Vol. 6, No. 15, 03.06.2011.

    Research output: Research - peer-reviewJournal article

  56. Published

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

    In: Nature, Vol. 469, 2011, p. 529-533.

    Research output: Research - peer-reviewJournal article

  57. Published

    Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model. / Mailund, Thomas; Dutheil, Julien; Hobolth, Asger; Lunter, Gerton; Schierup, Mikkel Heide.

    In: P L o S Genetics, Vol. 7, No. 3, 2011.

    Research output: Research - peer-reviewJournal article

  58. Published

    Incomplete lineage sorting patterns among human, chimpanzee and orangutan suggest recent orangutan speciation and widespread selection. / Hobolth, Asger; Dutheil, Julien; Hawks, John; Schierup, Mikkel Heide; Mailund, Thomas.

    In: Genome Research, Vol. 21, No. 3, 2011, p. 349-356.

    Research output: Research - peer-reviewJournal article

  59. Published

    Inference of Large Phylogenies Using Neighbour-Joining. / Simonsen, Martin; Mailund, Thomas; Pedersen, Christian Nørgaard Storm.

    In: Biomedical Engineering Systems and Technologies, Vol. 127, No. 5, 2011, p. 334-344.

    Research output: Research - peer-reviewJournal article

  60. Published
  61. 2010
  62. Published

    Using the Power of Modern Processors in Bioformatics. / Simonsen, Martin; Sand, Andreas; Mailund, Thomas; Pedersen, Christian Nørgaard Storm.

    2010. Poster session presented at Conference on IT research at AU, Århus, Denmark.

    Research output: ResearchPoster

  63. Published

    A new powerful method for genome-wide association mapping using local phylogenies in a mixed model. / Sahana, Goutam; Lund, Mogens Sandø; Mailund, Thomas; Guldbrandtsen, Bernt.

    2010. Paper presented at 9th World Congress on Genetics Applied to Livestock Production, Leipzig, Germany.

    Research output: Research - peer-reviewPaper

  64. Published

    Building Very Large Neighbour-Joining Trees. / Simonsen, Martin; Mailund, Thomas; Pedersen, Christian Nørgaard Storm.

    BIOINFORMATICS 2010: Proceedings of the First International Conference on Bioinformatics (part of the 3rd International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2010). ed. / Ana Fred; Joaquim Filipe; Hugo Gamboa. Institute for Systems and Technologies of Information, Control and Communication, 2010. p. 26.

    Research output: Research - peer-reviewArticle in proceedings

  65. Published

    HMMlib: A C++ Library for General Hidden Markov Models Exploiting Modern CPUs. / Sand, Andreas; Brask, Asbjørn Tølbøl; Pedersen, Christian Nørgaard Storm; Mailund, Thomas; Brask, Asbjørn Tølbøl.

    2010 Ninth International Workshop on Parallel and Distributed Methods in Verification and Second International Workshop on High Performance Computational Systems Biology. IEEE, 2010. p. 126 - 134 .

    Research output: Research - peer-reviewArticle in proceedings

  66. 2009
  67. Published

    A Quadratic Time Algorithm for Computing the Quartet Distance between Two General Trees. / Mailund, Thomas; Nielsen, Jesper; Pedersen, Christian Storm.

    Proceedings of IJCBS 2009. IEEE Computer Society Press, 2009. p. 565-568.

    Research output: Research - peer-reviewArticle in proceedings

  68. Published

    A fast algorithm for genome wide haplotype pattern mining. / Besenbacher, Søren; Mailund, Thomas; Pedersen, Christian Storm.

    In: B M C Bioinformatics, No. suppl. 1, 2009, p. 772.

    Research output: Research - peer-reviewConference article

  69. Published

    A fast algorithm for genome wide haplotype pattern mining. / Besenbacher, Søren; Mailund, Thomas; Pedersen, Christian Storm.

    In: B M C Bioinformatics, Vol. 10, No. S1, 2009.

    Research output: Research - peer-reviewJournal article

  70. Published

    Ancestral population genomics : the coalescent hidden Markov model approach. / Dutheil, Julien; Ganapathy, Ganesh; Hobolth, Asger; Mailund, Thomas; Uyenoyama, Marcy; Schierup, Mikkel Heide.

    In: Genetics, Vol. 183, No. 1, 2009, p. 259–274.

    Research output: Research - peer-reviewJournal article

  71. Published

    Building very large neighbour-joining trees. / Simonsen, Martin; Mailund, Thomas; Pedersen, Christian Storm.

    2009. Poster session presented at 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden.

    Research output: ResearchPoster

  72. Published

    Haplotype frequencies in a sub-region of chromosome 19q13.3, related to risk and prognosis of cancer, differ dramatically between ethnic groups. / Schierup, Mikkel H; Mailund, Thomas; Li, Heng; Wang, Jun; Tjønneland, Anne; Vogel, Ulla; Bolund, Lars; Nexø, Bjørn A.

    In: B M C Medical Genetics, Vol. 10, 2009, p. 20.

    Research output: Research - peer-reviewJournal article

  73. Published
  74. Published

    Using biological networks to search for interacting loci in genomewide association studies. / Emily, Mathieu; Mailund, Thomas; Hein, Jotun; Schauser, Leif; Schierup, Mikkel Heide.

    In: European Journal of Human Genetics, 2009.

    Research output: Research - peer-reviewJournal article

  75. 2008
  76. Published

    SNPFile - A software library and file format for large scale association mapping and population genetics studies. / Nielsen, Jesper; Mailund, Thomas.

    In: B M C Bioinformatics, Vol. 9, No. 526, 08.12.2008, p. 1-11.

    Research output: Research - peer-reviewJournal article

  77. Published

    Computing the all-pairs quartet distance on a set of evolutionary trees. / Stissing, Martin; Mailund, Thomas; Pedersen, Christian Storm; Brodal, Gerth Stølting; Fagerberg, Rolf.

    In: Journal of Bioinformatics and Computational Biology, Vol. 6, No. 1, 2008, p. 37-50.

    Research output: Research - peer-reviewJournal article

  78. Published

    Efficient Whole-Genome Association Mapping using Local Phylogenies for Unphased Genome Data. / Ding, Zhihong; Mailund, Thomas; Song, Yun.

    In: Bioinformatics, 2008, p. 2215-2221.

    Research output: Research - peer-reviewJournal article

  79. Published

    Investigating Selection on Viruses: A Statistical Alignment Approach. / de Groot, Saskia; Mailund, Thomas; Lunter, Gerton; Hein, Jotun.

    In: B M C Bioinformatics, Vol. 9, No. 308, 2008.

    Research output: Research - peer-reviewJournal article

  80. Published
  81. Published

    Rapid Neighbour-Joining. / Simonsen, Martin; Mailund, Thomas; Pedersen, Christian Storm.

    Proceedings of the 8th International Workshop on Algorithms in Bioinformatics (WABI). 2008. p. 113-122.

    Research output: Research - peer-reviewArticle in proceedings

  82. 2007
  83. Published

    Annotation of selection strengths in viral genomes. / McCauley, Stephen; de Groot, Saskia; Mailund, Thomas; Hein, Jotun.

    In: Bioinformatics, Vol. 23, No. 22, 2007, p. 2978-2986.

    Research output: Research - peer-reviewJournal article

  84. Published

    Comparative Annotation of Viral Genomes with Non-Conserved Gene Structure. / de Groot, Saskia; Mailund, Thomas; Hein, Jotun.

    In: Bioinformatics, Vol. 23, No. 9, 2007, p. 1080-1089.

    Research output: Research - peer-reviewJournal article

  85. Published

    Computing the All-Pairs Quartet Distance on a Set of Evolutionary Trees. / Stissing, Martin; Mailund, Thomas; Pedersen, Christian Nørgaard Storm; Brodal, Gerth Stølting; Fagerberg, Rolf.

    Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC). 2007. p. 91-100.

    Research output: Research - peer-reviewArticle in proceedings

  86. Published

    Computing the Quartet Distance between Evolutionary Trees of Bounded Degree. / Stissing, Martin; Pedersen, Christian Nørgaard Storm; Mailund, Thomas; Brodal, Gerth Stølting.

    Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC). 2007. p. 101-110.

    Research output: Research - peer-reviewArticle in proceedings

  87. Published

    Experiences with GeneRecon on MiG. / Mailund, Thomas; Pedersen, Christian Nørgaard Storm; Bardino, Jonas; Vinter, Brian; Karlsen, Henrik.

    In: Future Generation Computer Systems, Vol. 23, 2007, p. 580-586.

    Research output: Research - peer-reviewJournal article

  88. Published

    Genomic Relationships and Speciation Times of Human, Chimpanzee and Gorilla inferred from a Coalescent Hidden Markov Model. / Hobolth, Asger; Christensen, Ole Fredslund; Mailund, Thomas; Schierup, Mikkel Heide.

    2007. Poster session presented at Beyond the HapMap, Boston, United States.

    Research output: ResearchPoster

  89. Published

    Genomic relationships and speciation times of human, chimpanzee and gorilla inferred from a coalescent hidden Markov model. / Hobolth, Asger; Christensen, Ole Fredslund; Mailund, Thomas; Schierup, Mikkel Heide.

    In: P L o S Genetics, Vol. 3, No. 2, 2007.

    Research output: Research - peer-reviewJournal article

  90. Published

    On Recombination-Induced Multiple and Simultaneous Coalescent Events. / Davies, Joanna; Simancik, Frantisek; Lyngsø, Rune; Mailund, Thomas; Hein, Jotun.

    In: Genetics, Vol. 177, 2007, p. 2151-2160.

    Research output: Research - peer-reviewJournal article

  91. 2006
  92. Published

    Analysing Infinite-State Systems by Combining Equivalence Reduction and the Sweep-Line Method. / Mailund.

    Proceedings of International Conference on Application and Theory of Petri Nets (ICATPN 2002). 2006. p. 314-333.

    Research output: ResearchArticle in proceedings

  93. Published

    CoaSim Guile Manual — Using the Guile-based CoaSim Simulator. / Mailund, T.

    2006.

    Research output: ResearchWorking paper

  94. Published

    Fast Calculation of the Quartet Distance Between Trees of Arbitrary Degrees. / Christiansen, Chris; Mailund, Thomas; Pedersen, Christian Nørgaard Storm; Randers, Martin; Stissing, Martin.

    In: Algorithms for Molecular Biology, Vol. 1, No. 16, 2006.

    Research output: Research - peer-reviewJournal article

  95. Published
  96. Published

    GeneRecon—A coalescent based tool for fine-scale association mapping. / Mailund, Thomas; Schierup, Mikkel Heide; Pedersen, Christian Nørgaard Storm; Madsen, Jesper Nymann; Hein, Jotun; Schauser, Leif.

    In: Bioinformatics, Vol. 22, No. 18, 2006, p. 2317–2318.

    Research output: Research - peer-reviewJournal article

  97. Published

    Getting Started with Blossoc. / Mailund, Thomas.

    2006.

    Research output: ResearchWorking paper

  98. Published

    Getting Started with GeneRecon — An Introduction to the Association Mapping Tool GeneRecon. / Mailund, T; Schauser, Leif.

    2006.

    Research output: ResearchWorking paper

  99. Published
  100. Published

    Recrafting the Neighbor-Joining Method. / Mailund, ; Brodal, Gerth Stølting; Fagerberg, Rolf; Pedersen, Christian Nørgaard Storm; Phillips, Derek.

    In: B M C Bioinformatics, Vol. 7, No. 29, 2006.

    Research output: Research - peer-reviewJournal article

  101. Published

    The effective size of the Icelandic population and the prospects for LD mapping: inference from unphased microsatellite markers. / Bataillon, Thomas; Mailund, Thomas; Thorlacius, Steinunn; Steingrimsson, Eirikur; Rafnar, Thorunn; Halldorsson, Magnus; Calian, Violeta; Schierup, Mikkel Heide.

    In: European Journal of Human Genetics, Vol. 14, 2006, p. 1044–1053.

    Research output: Research - peer-reviewJournal article

  102. Published

    Whole genome association mapping by incompatibilities and local perfect phylogenies. / Mailund, Thomas; Besenbacher, Søren; Schierup, Mikkel Heide.

    In: B M C Bioinformatics, Vol. 7, No. 454, 2006.

    Research output: Research - peer-reviewJournal article

  103. 2005
  104. Published

    CoaSim: A Flexible Environment for Simulating Genetic Data under Coalescent Models. / Mailund, ; Schierup, Mikkel Heide; Pedersen, Christian Nørgaard Storm; Mechlenborg, Peter; Madsen, Jesper N; Schauser, Leif.

    In: B M C Bioinformatics, Vol. 6, No. 252, 2005.

    Research output: Research - peer-reviewJournal article

  105. Published

    Computing the Quartet Distance between Trees of Arbitrary Degree. / Christiansen, Chris; Mailund, ; Pedersen, Christian Nørgaard Storm; Randers, Martin.

    Proceedings of the 5th International Workshop on Algorithms in Bioinformatics (WABI). 2005. p. 77-88.

    Research output: Research - peer-reviewArticle in proceedings

  106. Published
  107. Published

    Initial experiences with GeneRecon on MiG. / Mailund, ; Pedersen, Christian Nørgaard Storm; Bardino, Jonas; Vinter, Brian; Karlsen, Henrik H.

    Proceedings of The 2005 International Conference on Grid Computing and Applications (GCA). 2005.

    Research output: Research - peer-reviewArticle in proceedings

  108. Published

    Pigs in Sequence Space: A 0.66X Coverage Pig Genome Survey based on Shotgun Sequencing. / Wernersson, R; Schierup, Mikkel Heide; Jørgensen, Frank Grønlund; Gorodkin, J; Panitz, F; Staerfeldt, HH; Christensen, Ole Fredslund; Mailund, T; Hornshøj, H; Klein, A; Jun, W; Liu, B; Hu, S; Dong, W; Li, W; Wong, G.K.-S.; Yu, J; Wang, J; Bendixen, C; Fredholm, M; Brunak, S; Yang, H; Bolund, Lars.

    In: B M C Genomics, Vol. 6, No. 70, 2005.

    Research output: Research - peer-reviewJournal article

  109. Published

    Quartet Distance between General Trees. / Christiansen, Chris; Mailund, ; Pedersen, Christian Nørgaard Storm; Randers, Martin.

    Proceedings of International Conference on Numerical Analysis and Applied Mathematics (ICNAAM). 2005. p. 796-799.

    Research output: Research - peer-reviewArticle in proceedings

  110. Published

    RBT—A Tool for Building Refined Buneman Trees. / Besenbacher, Søren; Mailund; Westh-Nielsen, Lasse; Pedersen, Christian N. Storm.

    In: Bioinformatics, Vol. 21, No. 8, 2005, p. 1711-1712.

    Research output: Research - peer-reviewJournal article

  111. Published

    The effect of a single recombination event. / Schierup, Mikkel Heide; Jensen, Thomas Mailund; Wiuf, Carsten.

    2005. Poster session presented at Genomic Studies and the HapMap, Oxford, United Kingdom.

    Research output: ResearchPoster

  112. 2004
  113. Published

    Exploiting Equivalence Reduction and the Sweep-Line Method for Detecting Terminal States. / Billington, Jonathan; Gallasch, Guy E; Kristensen, Lars Michael; Mailund.

    In: I E E E Transactions on Systems, Man and Cybernetics, Part A: Systems & Humans, Vol. 34, No. 1, 2004, p. 23-37.

    Research output: Research - peer-reviewJournal article

  114. Published

    Obtaining Memory-Efficient Reachability Graph Representations Using the Sweep-Line Method. / Mailund, Thomas; Westergaard, Michael.

    Proceedings of Tools and Algorithms for the Construction and Analysis of Systems (TACAS 2004). 2004. p. 177-191.

    Research output: Research - peer-reviewArticle in proceedings

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