Publications

Textbooks

2021

• Introduction to Computational Thinking: Problem Solving, Algorithms, Data Structures, and More Thomas Mailund Apress, July 17, 2021, ISBN-10: 1484270762, ISBN-13: 978-1484270769

• Pointers in C programming: A modern approach to memory management, recursive data structures, strings, and arrays Thomas Mailund Apress, April 23, 2021, ISBN-10: 1484269268, ISBN-13: 978-1484269268

2020

• String Algorithms in C: Efficient text representation and search Thomas Mailund Apress, Sep 30, ISBN-10: 148425919X, ISBN-13: 978-1484259191

2019

• Introducing Markdown and Pandoc Thomas Mailund Apress, August 20, 2019,

• R Data Science Quick Reference: A Pocket Guide to APIs, Libraries, and Packages Thomas Mailund Apress, August 8, 2019, ISBN-10: 1484248937, ISBN-13: 978-1484248935

• The Joys of Hashing: Hash Table Programming with C Thomas Mailund Apress, May 14, 2019, ISBN-10: 1484240650, ISBN-13: 978-1484240656

2018

• Domain-Specific Languages in R: Advanced Statistical Programming Thomas Mailund Apress, June 23, 2018, ISBN-10: 1484240049, ISBN-13: 978-1484240045

2017

• Functional Data Structures in R: Advanced Statistical Programming in R Thomas Mailund Apress, November 18, 2017, ISBN-10: 1484231430, ISBN-13: 978-1484231432

• Advanced Object-Oriented Programming in R: Statistical Programming for Data Science, Analysis, and Finance Thomas Mailund Apress, August 2, 2017, ISBN-10: 1484229185, ISBN-13: 978-1484229187

• Metaprogramming in R: Advanced Statistical Programming for Data Science, Analysis and Finance Thomas Mailund Apress, June 30, 2017, ISBN-10: 1484228804, ISBN-13: 978-1484228807

• Functional Programming in R: Advanced Statistical Programming for Data Science, Analysis and Finance Thomas Mailund Apress, March 29, 2017, ISBN-10: 148422745X, ISBN-13: 978-1484227459

• Beginning Data Science in R: Data Analysis, Visualization, and Modelling for the Data Scientist Thomas Mailund Apress, March 13, 2017, ISBN-10: 1484226704, ISBN-13: 978-1484226704

Peer-reviewed publications

2022

• Insights into bear evolution from a Pleistocene polar bear genome T Lan, K Leppälä, C Tomlin, SL Talbot, GK Sage, SD Farley, RT Shideler, L Bachmann, Ø Wiig, VA Albert, J Salojärvi, T Mailund, DI Drautz-Moses, SC Schuster, L Herrera-Estrella, and C Lindqvist PNAS 119(24) 2022.

2020

• Targeted conservation genetics of the endangered chimpanzee P Frandsen, C Fontsere, SV Nielsen, K Hanghøj, N Castejon-Fernandez, E Lizano, D Hughes, J Hernandez-Rodriguez, TS Korneliussen, FC, HR Siegismund, T Mailund, T Marques-Bonet & C Hvilsom Heredity, 2020

• Ancestral population genomics with Jocx, a coalescent hidden markov model JY Cheng & T Mailund Statistical Population Genomics pp 167-189, 2020

2019

• Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry JA Walker, VE Jordan, JM Storer, CJ Steely, P Gonzalez-Quiroga, TO Beckstrom, LC Rewerts, CP St. Romain, CE Rockwell, J Rogers, CJ Jolly, MK Konkel, The Baboon Genome Analysis Consortium & MA Batzer Mobile DNA volume 10, Article number: 46, 2019

• The comparative genomics and complex population history of Papio baboons J Rogers, M Raveendran, RA Harris, T Mailund, K Leppälä, G Athanasiadis, MH Schierup, J Cheng, K Munch, JA Walker, MK Konkel, V Jordan, CJ Steely, TO Beckstrom, C Bergey, A Burrell, D Schrempf, A Noll, M Kothe, GH Kopp, Y Liu, S Murali, K Billis, FJ Martin, M Muffato, L Cox, J Else, T Disotell, DM Muzny, J Phillips-Conroy, B Aken, EE Eichler, T Marques-Bonet, C Kosiol, MA Batzer, MW Hahn, J Tung, D Zinner, C Roos, CJ Jolly, RA Gibbs, KC Worley Science Advances, 2019

• Direct estimation of mutations in great apes reconciles phylogenetic dating S Besenbacher, C Hvilsom, T Marques-Bonet, T Mailund and MH Schierup Nature Ecology and Evolution, 2019

• Identifying loci under positive selection in complex population histories, A Refoyo-Martinez, RR de Fonseca, K Halldorsdottir, E Arnason, T Mailund, F Racimo, Genome Research 26(9) pp 1506-1520, 2019

• Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover AG Griffiths, R Moraga, M Tausen, V Gupta, TP Bilton, MA Campbell, R Ashby, I Nagy, A Khan, A Larking, C Anderson, B Franzmayr, K Hancock, A Scott, NW Ellison, MP Cox, T Asp, T Mailund, MH Schierup, SU Andersen Plant Cell 31(7) pp 1466-1487, 2019

2018

• A comprehensive genomic history of extinct and living elephants E Palkopoulou, M Lipson, S Mallick, S Nielsen, N Rohland, S Baleka, E Karpinski, AM Ivancevic, T-H To, RD Kortschak, JM Raison, Z Qu, T-J Chin, KW Alt, S Claesson, L Dalén, RDE MacPhee, H Meller, AL Roca, OA Ryder, D Heiman, S Young, M Breen, C Williams, BL Aken, M Ruffier, E Karlsson, J Johnson, F Di Palma, J Alfoldi, DL Adelson, T Mailund, K Munch, K Lindblad-Toh, M Hofreiter, H Poinar and D Reich PNAS (2018). doi.org/10.1073/pnas.1720554115

2017

• Assembly and analysis of 100 full MHC haplotypes from the Danish population JM Jensen, P Villesen, RM Friborg, The Danish Pan-Genome Consortium, T Mailund, S Besenbacher and MH Schierup Genome Res. (2017). 27: 1597-1607 doi:10.1101/gr.218891.116

• Sequencing and de novo assembly of 150 genomes from Denmark as a population reference L Maretty, JM Jensen, B Petersen, JA Sibbesen, S Liu, P Villesen, L Skov, K Belling, CT Have, JMG Izarzugaza, M Grosjean, J Bork-Jensen, J Grove, TD Als, S Huang, Y Chang, R Xu, W Ye, J Rao, X Guo, J Sun, H Cao, C Ye, J van Beusekom, T Espeseth, E Flindt, RM Friborg, AE Halager, SL Hellard, CM Hultman, F Lescai, S Li, O Lund, P Løngren, T Mailund, ML Matey-Hernandez, O Mors, CNS Pedersen, T Sicheritz-Pontén, P Sullivan, A Syed, D Westergaard, R Yadav, N Li, X Xu, T Hansen, A Krogh, L Bolund, TIA Sørensen, O Pedersen, R Gupta, S Rasmussen, S Besenbacher, AD Børglum, J Wang, H Eiberg, K Kristiansen, S Brunak and MH Schierup Nature (2017) doi:10.1038/nature23264

• Fast admixture analysis and population tree estimation for SNP and NGS data JY Cheng, T Mailund and R Nielsen Bioinformatics (2017) DOI: https://doi.org/10.1093/bioinformatics/btx098.

• Evidence that the rate of strong selective sweeps increases with population size in the great apes K Nam, K Munch, T Mailund, A Nater, MP Greminger, M Krützenc, T Marquès-Bonet, and MH Schierup PNAS (2017) doi: 10.1073/pnas.1605660114

• admixturegraph: An R Package for Admixture Graph Manipulation and Fitting K Leppälä, SV Nielsen, and T Mailund Bioinformatics (2017) DOI: https://doi.org/10.1093/bioinformatics/btx048

2016

• Measurement Units in R Edzer Pebesma, Thomas Mailund, James Hiebert The R Journal, 8 (2), 486-494 (2016)

• Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx F Abascal, A Corvelo, F Cruz, JL Villanueva-Cañas, A Vlasova, M Marcet-Houben, B Martínez-Cruz, JY Cheng, P Prieto, V Quesada, J Quilez, G Li, F García, M Rubio-Camarillo, L Frias, P Ribeca, S Capella-Gutiérrez, JM Rodríguez, F Câmara, E Lowy, L Cozzuto, IE, ML Tress, JL Rodriguez-Ales, J Ruiz-Orera, F Reverter, M Casas-Marce, L Soriano, JR Arango, S Derdak, B Galán, J Blanc, M Gut, B Lorente-Galdos, M Andrés-Nieto, C López-Otín, A Valencia, I Gut, JL García, R Guigó, WJ Murphy, A Ruiz-Herrera, T Marques-Bonet, G Roma, C Notredame, T Mailund, MM Albà, T Gabaldón, T Alioto and JA Godoy Genome Biology201617:251 DOI: 10.1186/s13059-016-1090-1

• Selective sweeps across twenty millions years of primate evolution K Munch, K Nam, MH Schierup and T Mailund Mol Biol Evol (2016) doi: 10.1093/molbev/msw199

• A genomic history of Aboriginal Australia A-S Malaspinas, MC Westaway, C Muller, VC Sousa, O Lao, I Alves, A Bergström, G Athanasiadis, JY Cheng, JE Crawford, TH Heupink, E Macholdt, S Peischl, S Rasmussen, S Schiffels, S Subramanian, JL Wright, A Albrechtsen, C Barbieri, I Dupanloup, A Eriksson, A Margaryan, I Moltke, I Pugach, TS Korneliussen, IP Levkivskyi, JV Moreno-Mayar, S Ni, F Racimo, M Sikora, Y Xue, FA Aghakhanian, N Brucato, S Brunak, PF Campos, W Clark, S Ellingvåg, G Fourmile, P Gerbault, D Injie, G Koki, M Leavesley, B Logan, A Lynch, EA Matisoo-Smith, PJ McAllister, AJ Mentzer, M Metspalu, AB Migliano, L Murgha, ME Phipps, W Pomat, D Reynolds, F-X Ricaut, P Siba, MG Thomas, T Wales, CM Wall, SJ Oppenheimer, C Tyler-Smith, R Durbin, J Dortch, A Manica, MH Schierup, RA Foley, MM Lahr, C Bowern, JD Wall, T Mailund, M Stoneking, R Nielsen, MS Sandhu, L Excoffier, DM Lambert and E Willerslev Nature 2016. doi:10.1038/nature18299

• Spitting for Science: Danish High School Students Commit to a Large-Scale Self-Reported Genetic Study G Athanasiadis, FG Jørgensen, JY Cheng, PC Kjærgaard, MH Schierup, and T Mailund PLoS ONE 11(8): e0161822. doi:10.1371/journal.pone.0161822

• Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity G Athanasiadis, JY Cheng, BJ Vilhjálmsson, FG Jørgensen, TD Als, SL Hellard, T Espeseth, PF Sullivan, CM Hultman, PC Kjærgaard, MH Schierup, and T Mailund Genetics, DOI: 10.1534/genetics.116.189241 (2016)

• The ecological niche and distribution of Neanderthals during the Last Interglacial BM Benito, J-C Svenning, T Kellberg-Nielsen, F Riede, G Gil-Romera, T Mailund, PC Kjaergaard, and BS Sandel Journal of Biogeography, DOI: 10.1111/jbi.12845 (2016)

2015

• Strong selective sweeps on the X chromosome in the human-chimpanzee ancestor explain its low divergence JY Dutheil, K Munch, K Nam, T Mailund and MH Schierup PLOS Genetics, 11(8): e1005451. DOI: 10.1371/journal.pgen.1005451 (2015)

• Extreme selective sweeps independently targeted the X chromosomes of the great apes K Nam, K Munch, A Hobolth, JY Dutheil, K Veeramah, A Woerner, MF Hammer, Great Ape Genome Diversity Project, T Mailund, and MH Schierup In PNAS 112(20); 6413–6418, doi: 10.1073/pnas.1419306112 (2015)

• Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing T Bataillon, J Duan, C Hvilsom, X Jin, Y Li, L Skov, S Glemin, K Munch, T Jiang, Y Qian, A Hobolth, J Wang, T Mailund, HR Siegismund and MH Schierup Genome Biology and Evolution, 7(4):1122–1132 2015

• Ancestral population genomics using coalescence hidden Markov models and heuristic optimisation algorithms J Cheng and T Mailund Computational Biology and Chemistry; doi:10.1016/j.compbiolchem.2015.02.001

• Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios S Besenbacher, S Liu, JMG Izarzugaza, J Grove, K Belling, J Bork-Jensen, S Huang, TD Als, S Li, R Yadav, A Rubio-García, F Lescai, D Demontis, J Rao, W Ye, T Mailund, RM Friborg, CNS Pedersen, R Xu, J Sun, H Liu, O Wang, X Cheng, D Flores, E Rydza, K Rapacki, JD Sørensen, P Chmura, D Westergaard, P Dworzynski, TIA Sørensen, O Lund, T Hansen, X Xu, N Li, L Bolund, O Pedersen, H Eiberg, A Krogh, AD Børglum, S Brunak, K Kristiansen, MH Schierup, J Wang, R Gupta, P Villesen and S Rasmussen Nature Communications 6 (5969) doi:10.1038/ncomms6969

2014

• Lineage sorting in apes T Mailund, K Munch and MH Schierup Annual Review of Genetics 48 (1) 519-535; doi:10.1146/annurev-genet-120213-092532 (2014)

• Unraveling recombination rate evolution using ancestral recombination maps K Munch, MH Schierup and T Mailund BioEssays 36 (9): 892–900 (2014)

• tqDist: A Library for Computing the Quartet and Triplet Distances Between Binary or General Trees A Sand, MK Holt, J Johansen, GS Brodal, T Mailund and CNS Pedersen Bioinformatics 30 (14): 2079-2080 (2014)

• Inferring the process of human-chimpanzee speciation T Mailund, K Munch and MH Schierup Encyclopedia of Life Sciences (2014)

• 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 K Munch, JY Dutheil, T Mailund and MH Schierup Genome Research 24 467-474 (2014)

• Identifying disease associated genes by network propagation Y Qian, S Besenbacher, T Mailund and MH Schierup BMC Systems Biology, 8(Suppl 1):S6; doi:10.1186/1752-0509-8-S1-S6 (2014)

2013

• zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm A Sand, M Kristiansen, CNS Pedersen and T Mailund BMC Bioinformatics 2013, 14(339); doi:10.1186/1471-2105-14-339

• Algorithms for Hidden Markov Models Restricted to Occurrences of Regular Expressions P Tataru, A Sand, A Hobolth, T Mailund and CNS Pedersen Biology 2013, 2(4), 1282-1295; doi:10.3390/biology2041282

• Algorithms for Computing the Triplet and Quartet Distances for Binary and General Trees A Sand, MK Holt, J Johansen, R Fagerberg, GS Brodal, CNS Pedersen and T Mailund Biology 2013, 2(4), 1189-1209; doi:10.3390/biology2041189

• Efficient computation in the IM model LN Andersen, T Mailund and A Hobolth Journal of Mathematical Biology doi:10.1007/s00285-013-0671-9

• Great ape genetic diversity and population history J Prado-Martinez, PH Sudmant, JM Kidd, H Li, JL Kelley, B Lorente-Galdos, KR Veeramah, AE Woerner, TD O’Connor, G Santpere, A Cagan, C Theunert, F Casals, H Laayouni, K Munch, A Hobolth, AE Halager, M Malig, J Hernandez-Rodriguez, I Hernando-Herraez, K Prüfer, M Pybus, L Johnstone, M Lachmann, C Alkan, D Twigg, N Petit, C Baker, F Hormozdiari, M Fernandez-Callejo, M Dabad, ML Wilson, L Stevison, C Camprubí, T Carvalho, A Ruiz-Herrera, L Vives, M Mele, T Abello, I Kondova, RE Bontrop, A Pusey, F Lankester, JA Kiyang, RA Bergl, E Lonsdorf, S Myers, M Ventura, P Gagneux, D Comas, H Siegismund, J Blanc, L Agueda-Calpena, M Gut, L Fulton, SA Tishkoff, JC Mullikin, RK Wilson, IG Gut, MK Gonder, OA Ryder, BH Hahn, A Navarro, JM Akey, J Bertranpetit, D Reich, T Mailund, MH Schierup, C Hvilsom, AM Andrés, JD Wall, CD Bustamante, MF Hammer, EE Eichler and T Marques-Bonet Nature doi:10.1038/nature12228 (2013)

• Efficient algorithms for computing the triplet and quartet distance between trees of arbitrary degree GS Brodal, R Fagerberg, T Mailund, CNS Pedersen and A Sand ACM-SIAM Symposium on Discrete Algorithms (SODA) 1814-1832 (2013)

• A practical O(n log2 n) time algorithm for computing the triplet distance on binary trees A Sand, GS Brodal, R Fagerberg, CNS Pedersen, and T Mailund BMC Bioinformatics 14 Suppl 2 1-9 (2013)

2012

• A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species T Mailund, AE Halager, M Westergaard, JY Dutheil, K Munch, LN Andersen, G Lunter, Kay Prüfer, A Scally, A Hobolth, and MH Schierup PLoS Genetics 8(12):e1003125. doi:10.1371/journal.pgen.1003125 (2012)

• Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change W Miller, SC Schuster, AJ Welch, A Ratan, OC Bedoya-Reina, F Zhao, HL Kim RC Burhans, DI Drautz, NE Wittekindt, LP Tomsho, E Ibarra-Laclette, L Herrera-Estrella, E Peacock, S Farley, GK Sage, K Rode, M Obbard, R Montiel, L Bachmann, O Ingolfsson, J Aars, T Mailund, Ø Wiig, SL Talbot and C Lindqvist PNAS 109(36) E2382–E2390 (2012)

• An effort to use human based exome capture chip to analyze chimpanzee and macaque exomes X. Jin, M. He, B. Ferguson, Y. Meng, L. Ouyang, J. Ren, T. Mailund, F. Sun, L. Sun, J. Shen, M. Zhuo, L. Song, J. Wang, F. Ling, Y. Zhu, C. Hvilsom, H. Siegismund, H. Kang, X. Liu, Z. Gong, F. Ji, X. Wang, B. Liu, Y. Zhang, J. Hou, J. Wang, X. Fang, G. Zhang, J. Wang, X. Zhang, MH. Schierup, H. Du, J. Wang, X. Wang PLoS ONE 7(7): e40637. doi:10.1371/journal.pone.0040637 (2012)

• The bonobo genome compared with the chimpanzee and human genomes K. Prüfer, K. Munch, I. Hellmann, K. Akagi, J.R. Miller, B. Walenz, S. Koren, G. Sutton, C. Kodira, R. Winer, J.R. Knight, J.C. Mullikin, S.J. Meader, C.P. Ponting, G. Lunter, S. Higashino, A. Hobolth, J. Dutheil, E. Karakoç, C. Alkan, S. Sajjadian, C. R. Catacchio, M. Ventura, T. Marques-Bonet, E. E. Eichler, C. André, R. Atencia, L. Mugisha, J. Junhold, N. Patterson, M. Siebauer, J.M. Good, A. Fischer, S. E. Ptak, M. Lachmann, D.E. Symer, T. Mailund, M. H. Schierup, A. M. Andrés, J. Kelso and S. Pääbo Nature 486 527–531 (2012)

• Cultural phylogenetics of the Tupi language family in lowland South America R.S. Walker, S. Wichmann, T. Mailund and C.J. Atkisson PLoS ONE 7(4): e35025. doi:10.1371/journal.pone.0035025 (2012)

• The sweep-line state space exploration method K. Jensen, L.M. Kristensen and T. Mailund Theoretical Computer Science 429 169–179 (2012)

• Insights into the hominid evolution from the gorilla genome sequence A. Scally, J.Y. Dutheil, L.W. Hillier, G.E. Jordan, I. Goodhead, J. Herrero, A. Hobolth, T. Lappalainen, T. Mailund, T. Marques-Bonet, S. McCarthy, S. H. Montgomery, P. C. Schwalie, Y. A. Tang, M. C. Ward, Y. Xue, B. Yngvadottir, C. Alkan, L.N. Andersen, Q. Ayub, E.V. Ball, K. Beal, B.J. Bradley, Y. Chen, C. M. Clee, S. Fitzgerald, T. A. Graves, Y. Gu, P. Heath, A. Heger, E. Karakoc, A. Kolb-Kokocinski, G. K. Laird, G. Lunger, S. Meader, M. Mort, J.C. Mullikin, K. Munch, T.D. OConnor, A.D. Phillips, J. Prado-Martinez, A.S. Rogers, S. Sajjadian, D. Schmidt, K. Shaw, J.T. Simpson, P.D. Stenson, D.J. Turner, L. Vigilant, A.J. Vilella, W. Whitener, B. Zhu, D.N. Cooper, P. de Jong, E.T. Dermitzakis, E.E. Eichler, P. Flicek, N. Goldman, N. I. Mundy, Z. Ning, D.T. Odom, C.P. Ponting, M.A. Quail, O.A. Ryder, S.M. Searle, W.C. Warren, R.K. Wilson, M.H.Schierup, J. Rogers, C. Tyler-Smith and R. Durbin Nature 483 169–175 (2012)

• Extensive X-linked adaptive evolution in central chimpanzees C. Hvilsom, Y. Qian, T. Bataillon, Y. Li, T. Mailund, B. Salle, F. Carlsen, R. Li, H. Zhang, T. Jiang, H. Jiang, X. Jin, K. Munch, A. Hobolth, H.R. Siegismund, J. Wang, and M.H. Schierup PNAS 109(6) 2054–2059 (2012)

• Using colored Petri nets to construct coalescent hidden Markov models: Automatic translation from demopgrahic specifications to efficient inference methods T. Mailund, A.E. Halager, and M. Westergaard Proceedings of International Conference on Application and Theory of Petri Nets (PETRI NETS 2012), LNCS 7347 30–25 Springer-Verlag (2012)

2011

• Local genealogies in a linear mixed model for genome-wide association mapping in complex pedigreed populations G. Sahana, T. Mailund, M.S. Lund and B. Guldbrandtsen PLoS ONE 6(11): e27061. doi:10.1371/journal.pone.0027061 (2011)

• A sub-cubic time algorithm for computing the quartet distance between two general trees J. Nielsen, A.K. Kristensen, T. Mailund and C.N.S. Pedersen Algorithms for Molecular Biology 6(15) doi:10.1186/1748-7188-6-15 (2011)

• On computing the coalescence time density in an isolation-with-migration model with few samples A. Hobolth, L.N. Andersen and T. Mailund Genetics 187 1241–1243 (2011)

• Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies using a Coalescent Hidden Markov Model T. Mailund, J.Y. Dutheil, A. Hobolth, G. Lunter and M.H. Schierup PLoS Genetics 7(3): e1001319. doi:10.1371/journal.pgen.1001319 (2011)

• Incomplete lineage sorting patterns among human, chimpanzee and orangutan suggest recent orangutan speciation and widespread natural selection A. Hobolth, J.Y. Dutheil, J. Hawks, M.H. Schierup and T. Mailund Genome Research 21 349-356 (2011)

• Comparative and demographic analysis of orangutan genomes D. P. Locke, L. W. Hillier, W. C. Warren, K. C. Worley, L. V. Nazareth, D. M. Muzny, S-P. Yang, Z. Wang, A.T. Chinwalla, P. Minx, M. Mitreva, L. Cook, K.D. Delehaunty, C. Fronick, H. Scmidt, L.A. Fulton, R.S. Fulton, J.O. Nelson, V. Magrini, C. Pohl, T.A. Graves, C. Markovic, A. Cree, H.H. Dinh, J. Hume, C.L. Kovar, G.R. Fowler, G. Lunter, S. Meader, A. Heger, C.P. Ponting, T. Marques-Bonet, C. Alkan, L. Chen, Z, Cheng, J.M. Kidd, E.E. Eichler, S. White, S. Searle, A.J. Vilella, Y. Chen, P. Flicek, J. Ma, B. Raney, B. Suh, R. Burhans, J. Herrero, D. Haussler, R. Faria, O. Fernando, Fl. Darré, D. Farré, E. Gazave, M. Oliva, A. Navarro, R. Roberto, O. Capozzi, N. Archidiacono, G.D. Valle, S. Purgato, M. Rocchi, M.K. Konkel, J.A. Walker, B. Ullmer, M.A. Batzer, A.F.A. Smit, R. Hubley, C. Casola, D.R. Schrider, M.W. Hahn, V. Quesada, X.S. Puente, G.R. Ordoñez, C. López-Otín, T. Vinar, B. Brejova, A. Ratan, R.S. Harris, W. Miller, C. Kosiol, H.A. Lawson, V. Taliwal, A.L. Martins, A. Siepel, A. RoyChoudhury, X. Ma, J. Degenhardt, C.D. Bustamante, R.N. Gutenkunst,, T. Mailund, J.Y. Dutheil, A. Hobolth, M.H. Schierup, O.A. Ryder, Y. Yoshinaga, P.J. de Jong, G.M. Weinstock, J. Rogers, E.R. Mardis, R.A. Gibbs and R.K. Wilson Nature 469 529–533 doi:10.1038/nature09687 (2011)

• Inference of large phylogenies using neighbour-joining M. Simonsen, T. Mailund and C.N.S. Pedersen Biomedical Engineering Systems and Technologies 127 334–344 Springer-Verlag (2011)

2010

• HMMlib: A C++ library for general hidden Markov models exploiting modern CPUs A. Sand, A.T. Brask, C.N.S. Pedersen and T. Mailund Proceedings of HiBi (2010)

• A new powerful method for genome-wide association mapping using local phylogenies in a mixed model G. Sahana, T. Mailund, M.S. Lund and B. Guldbrandtsen Proceedings of WCGALP (2010)

• Building very large neighbour-joining trees M. Simonsen, T. Mailund and C.N.S. Pedersen Proceedings of Bioinformatics (2010)

2009

• Ancestral population genomics: the coalescent hidden Markov model approach J.Y. Dutheil, G. Ganapathy, A. Hobolth, T. Mailund, M.K. Uyenoyama, and M.H. Schierup Genetics 183 259–274 doi:10.1534/genetics.109.103010 (2009)

• Using biological networks to search for interacting loci in genomewide association studies M. Emily, T. Mailund, J. Hein, L. Schauser and M.H. Schierup European Journal of Human Genetics; doi: 10.1038/ejhg.2009.15 (2009)

• Haplotype frequencies in a sub-region of chromosome 19q13.3, related to risk and prognosis of cancer, differ dramatically between ethnic groups M.H. Schierup, T. Mailund, H. Li, J. Wang, A. A. Tjønneland, U. Vogel, L. Bolund and B. Nexø BMC Evolutionary Biology, 10(20); doi:10.1186/1471-2350-10-20 (2009)

• Local phylogeny mapping of quantitative traits: Higher accuracy and better ranking than single marker association in genomewide scans S. Besenbacher, T. Mailund and M.H. Schierup Genetics 181 747–753; doi:10.1534/genetics.108.092643 (2009)

• A fast algorithm for genome wide haplotype pattern mining S. Besenbacher, C.N.S. Pedersen and T. Mailund BMC Bioinformatics, 10(Suppl 1): S74 doi:10.1186/1471-2105-10-S1-S74 (2009)

• A sub-cubic time algorithm for computing the quartet distance between two general trees T. Mailund, J. Nielsen, and C.N.S. Pedersen Proc. of IJCBS (2009)

• A fast algorithm for genome wide haplotype pattern mining S. Besenbacher, C.N.S. Pedersen and T. Mailund In the Proc of APBC 2009, Tsinghua University Press, 772–780 (2009)

2008

• SNPFile - A software library and file format for large scale association mapping and population genetics studies J. Nielsen and T. Mailund BMC Bioinformatics 9(526) doi:10.1186/1471-2105-9-526 (2008)

• Efficient Whole-Genome Association Mapping using Local Phylogenies for Unphased Genome Data Z. Ding, T. Mailund and Y.S. Song Bioinformatics 24(19):2215–2221; doi:10.1093/bioinformatics/btn406 (2008)

• Investigating Selection on Viruses: A Statisical Alignment Approach S. de Groot, T. Mailund, G.A. Lunter and J. Hein BMC Bioinformatics 9(304) doi:10.1186/1471-2105-9-304 (2008)

• Computing the All-Pairs Quartet Distance on a Set of Evolutionary Trees M. Stissing, T. Mailund, C.N.S. Pedersen, G.S. Brodal, and R. Fagerberg Journal of Bioinformatics and Computational Biology 6(1) 37–50 (2008)

• Rapid neighbour-joining M. Simonsen, T. Mailund and C.N.S. Pedersen Proceedings of the Workshop on Algorithms in Bioinformatics (WABI) 2008, LNBI 5251 Springer, 113–122 doi:10.1007/978-3-540-87361-7_10 (2008)

2007

• On Recombination Induced Multiple and Simultaneous Coalescent Events J. Davies, F. Simancik, R. Lyngsø, T. Mailund, and J. Hein Genetics 177: 2151–2160. doi:10.1534/genetics.107.071126 (2007)

• Annotation of Selection Strengths in Viral Genomes S. McCauley, S. de Groot, T. Mailund, and J. Hein Bioinformatics 23(22): 2978–2986. doi:10.1093/bioinformatics/btm472 (2007)

• Comparative Annotation of Viral Genomes with Non-Conserved Gene Structure S. de Groot, T. Mailund, and J. Hein Bioinformatics 23(9):1080–1089. doi:10.1093/bioinformatics/btm078 (2007)

• Genomic relationships and speciation times of human, chimpanzee and gorilla inferred from a coalescent hidden Markov model A. Hobolth, O.F. Christensen, T. Mailund and M.H. Schierup PLoS Genetics, 3(2) 2007; doi:10.1371/journal.pgen.0030007 (2007)

• Computing the All-Pairs Quartet Distance on a Set of Evolutionary Trees M. Stissing, T. Mailund, C.N.S. Pedersen, G.S. Brodal, and R. Fagerberg Proceedings of the Asia-Pacific Bioinformatics Conference (APBC) 2007, 91–100, Series on Advances in Bioinformatics and Computational Biology, vol. 5, Imperial College Press (2007)

• Computing the Quartet Distance between Evolutionary Trees of Bounded Degree M. Stissing, C.N.S. Pedersen, T. Mailund, G.S. Brodal, and R. Fagerberg Proceedings of the Asia-Pacific Bioinformatics Conference (APBC) 2007, 101–110, Series on Advances in Bioinformatics and Computational Biology, vol. 5, Imperial College Press (2007)

• Experiences with GeneRecon on MiG T. Mailund, C.N.S. Pedersen, J. Bardino, B. Vinter, and H.H. Karlsen In Future Generation Computer Systems 23 580–586. doi:10.1016/j.future.2006.09.003 (2007)

2006

• Whole genome association mapping by incompatibilities and local perfect phylogenies T. Mailund, S. Besenbacher, and M.H. Schierup BMC Bioinformatics 7(454). doi:10.1186/1471-2105-7-454 (2006)

• Fast Calculation of the Quartet Distance Between Trees of Arbitrary Degrees C. Christiansen, T. Mailund, C.N.S. Pedersen, M. Randers, and M. Stissing Algorithms for Molecular Biology 1(16); doi:10.1186/1748-7188-1-16 (2006)

• GeneRecon—A coalescent based tool for fine-scale association mapping T. Mailund, M.H. Schierup, C.N.S. Pedersen, J.N. Madsen, J. Hein, and L. Schauser Bioinformatics 22(18): 2317–2318; doi:10.1093/bioinformatics/btl153 (2006)

• The effective size of the Icelandic population and the prospects for LD mapping: inference from unphased microsatellite markers T. Bataillon, T. Mailund, S. Thorlacius, E. Steingrimsson, T. Rafnar, M.M. Halldorsson, V. Calian, and M.H. Schierup European Journal of Human Genetics 14 1044–1053. doi:10.1038/sj.ejhg.5201669 (2006)

• Recrafting the Neighbor-Joining Method T. Mailund, G.S. Brodal, R. Fagerberg, C.N.S. Pedersen, and D. Phillips BMC Bioinformatics 7(29). doi:10.1186/1471-2105-7-29 (2006)

2005

• CoaSim: A Flexible Environment for Simulating Genetic Data under Coalescent Models T. Mailund, M.H. Schierup, C.N.S. Pedersen, P.J.M. Mechlenborg, J.N. Madsen, and L. Schauser BMC Bioinformatics 6(252). doi:10.1186/1471-2105-6-252 (2005)

• Pigs in Sequence Space: A 0.66X Coverage Pig Genome Survey based on Shotgun Sequencing R.Wernersson, M.H. Schierup, F.G. Jørgensen, J. Gorodkin, F. Panitz, H.H. Staerfeldt, O.F. Christensen, T. Mailund, H. Hornshøj, A. Klein, W. Jun, B. Liu, S. Hu, W. Dong, W. Li, G.K.-S. Wong, J. Yu, J. Wang, C. Bendixen, M. Fredholm, S. Brunak, H. Yang and L. Bolund BMC Genomics 6(70). doi:10.1186/1471-2164-6-70 (2006)

• Algorithms for Computing the Quartet Distance between Trees of Arbitrary Degree C. Christiansen, T. Mailund, C.N.S. Pedersen, and M. Randers Proceedings of Workshop on Algorithms in Bioinformatics (WABI) 2005, LNBI 3692 77–88 Springer-Verlag (2005)

• Quartet Distance between General Trees C. Christiansen, T. Mailund, C.N.S. Pedersen, and M. Randers Proceedings of International Conference on Numerical Analysis and Applied Mathematics (ICNAAM) 2005, 796–799 Wiley-VCH Verlag GmbH & Co (2005)

• RBT—A Tool for Building Refined Buneman Trees S. Besenbacher, T. Mailund, L. Westh-Nielsen, C.N.S. Pedersen Bioinformatics 21(8) 1711–1712 (2005)

• Initial experiences with GeneRecon on MiG T. Mailund, C.N.S. Pedersen, J. Bardino, B. Vinter, and H.H. Karlsen Proceedings of The 2005 International Conference on Grid Computing and Applications (2005)

2004

• QuickJoin—Fast Neighbour-Joining Tree Reconstruction T. Mailund and C.N.S. Pedersen Bioinformatics 20(17): 3261–3262 (2004)

• QDist—Quartet Distance Between Evolutionary Trees T. Mailund and C.N.S. Pedersen Bioinformatics 20(10): 1636–1637 (2004)

• Exploiting Equivalence Reduction and the Sweep-Line Method for Detecting Terminal States J. Billington, G.E. Gallasch, L.M. Kristensen, and T. Mailund IEEE Transactions on Systems, Man, and Cybernetics, Part A: Systems and Humans. 34(1): 23–37 (2004)

• Obtaining Memory-Efficient Reachability Graph Representations Using the Sweep-Line Method T. Mailund and M. Westergaard Proceedings of Tools and Algorithms for the Construction and Analysis of Systems (TACAS 2004), LNCS 2988 177–191 Springer-Verlag (2004)

2003

• Efficient Path Finding with the Sweep-Line Method using External Storage L.M. Kristensen and T. Mailund Proceedings of International Conference on Formal Engineering Methods (ICFEM 2003) LNCS 2885 319–337 Springer-Verlag (2003)

2002

• A Compositional Sweep-Line State Space Exploration Method L.M. Kristensen and T. Mailund Proceedings of Formal Description Techniques for Distributed Systems and Communication Protocols (FORTE), LNCS 2529 327–343 Springer-Verlag (2002)

• A Generalised Sweep-Line Method for Safety Properties L.M. Kristensen and T. Mailund Proceedings of Formal Methods Europe (FME 2002), LNCS 2391 549–567 Springer-Verlag

• Analysing Infinite-State Systems by Combining Equivalence Reduction and the Sweep-Line Method T. Mailund Proceedings of International Conference on Application and Theory of Petri Nets (ICATPN), LNCS 2360 314–333 Springer-Verlag (2002)

• Sweep-Line State Space Exploration for Coloured Petri Nets G.E. Gallasch, L.M. Kristensen, and T. Mailund Proceedings of Fourth Workshop on Practical Use of Coloured Petri Nets and the CPN Tools (CPN 2002). DAIMI PB-560 pp. 101-119, Aarhus, Denmark, (2002)

2001

• Condensed State Spaces for Timed Petri Nets S. Christensen, L.M. Kristensen and T. Mailund Proceedings of International Conference on Application and Theory of Petri Nets (ICATPN), LNCS 2075 101–120 Springer-Verlag (2001)

• A Sweep-Line Method for State Space Exploration S. Christensen, L.M. Kristensen and T. Mailund Proceedings of Tools and Algorithms for the Construction and Analysis of Systems (TACAS), LNCS 2031 450–464 Springer-Verlag (2001)

• State Space Methods for Timed Coloured Petri Nets S. Christensen, K. Jensen, T. Mailund and L.M. Kristensen Proceedings of 2nd International Colloquium on Petri Net Technologies for Modelling Communication Based Systems. pp. 14-15, Berlin Germany (2001)

2000

• Separation of Style and Content with XML in an Interchange Format for High-level Petri Nets T. Mailund and K.H. Mortensen Proceedings of the Meeting on XML/SGML based Interchange Formats for Petri Nets, pp. 7-12, Aarhus, Denmark (2000)

1999

• Parameterised Coloured Petri Nets T. Mailund Proceedings of Second Workshop on Practical Use of Coloured Petri Nets and Design/CPN, DAIMI PB-541 pp. 133-151, Aarhus, Denmark (1999)

1998

• Textual Interchange Format for High-Level Petri Nets R.B. Lyngsø and T. Mailund Proceedings of First Workshop on Practical Use of Coloured Petri Nets and Design/CPN, DAIMI PB-532 pp. 47-64 Aarhus, Denmark (1998)

Other publications

• Associaton Mapping and Disease: Evolutionary Perspectives S. Besenbacher, T. Mailund and M.H. Schierup Evolutionary Genomics Methods in Molecular Biology 856 275–291 (2012)

• Et genom – mange historier T. Mailund, K. Munch, A. Hobolth, MH. Schierup and P.F. Gammelby Aktuel Naturvidenskab 3 (2012)

• DNA-statistik gør mennesket yngre MH. Schierup, T. Mailund, A. Hobolth and A. Vollertsen Aktuel Naturvidenskab 3 (2007)