Publications

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Møllegaard Friborg, R., Bjørndalen, J. M. & Vinter, B. (2013). Scaling PyCSP. Paper presented at Communicating Process Architectures 2013, Edinburgh, United Kingdom.

Møllegaard Friborg, R., Jon Ison, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael Jimenez, Nick Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Mičetić & Sebastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vařeková, Silvio C.E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen Parkinson, Peter Løngreen, Søren Brunak (2015). Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research, 44(D1), D38-D47. https://doi.org/10.1093/nar/gkv1116

Moeskjær, S., Skovbjerg, C. K., Tausen, M., Wind, R., Roulund, N., Janss, L. & Andersen, S. U. (2022). Major effect loci for plant size before onset of nitrogen fixation allow accurate prediction of yield in white clover. Theoretical and Applied Genetics, 135(1), 125-143. https://doi.org/10.1007/s00122-021-03955-3

Mirarab, S., Rivas-González, I., Feng, S., Stiller, J., Fang, Q., Mai, U., Hickey, G., Chen, G., Brajuka, N., Fedrigo, O., Formenti, G., Wolf, J. B. W., Howe, K., Antunes, A., Schierup, M. H., Paten, B., Jarvis, E. D., Zhang, G. & Braun, E. L. (2024). A region of suppressed recombination misleads neoavian phylogenomics. Proceedings of the National Academy of Sciences (PNAS), 121(15), Article e2319506121. https://doi.org/10.1073/pnas.2319506121

Mineur, A., Mota, R., Gengler, N., Vanderick, S., Hammami, H. & GplusE Consortium (2018). Defining and using novel milk composition based heat stress resilience traits in the context of genomic selection for more robust dairy cows in Wallonia. In J. Bryant, M. Burke, R. Cook, B. Harris, C. Mosconi & B. Wickham (Eds.), Proceedings of the ICAR Conference (Vol. 23, pp. 229-234) https://www.icar.org/wp-content/uploads/2018/07/ICAR-Technical-Series-23-Auckland-2018-Proceedings.pdf

Miller, W., Schuster, S. C., Welch, A. J., Ratan, A., Bedoya-Reina, O. C., Zhao, F., Kim, H. L., Burhans, R. C., Drautz, D. I., Wittekindt, N. E., Tomsho, L. P., Ibarra-Laclette, E., Herrera-Estrella, L., Peacock, E., Farley, S., Sage, G. K., Rode, K., Obbard, M., Montiel, R. ... Lindqvist, C. (2012). Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proceedings of the National Academy of Sciences (PNAS). https://doi.org/10.1073/pnas.1210506109

Miles, A. E., Dos Santos, F. C., Byrne, E. M., Renteria, M. E., McIntosh, A. M., Adams, M. J., Pistis, G., Castelao, E., Preisig, M., Baune, B. T., Schubert, K. O., Lewis, C. M., Jones, L. A., Jones, I., Uher, R., Smoller, J. W., Perlis, R. H., Levinson, D. F., Potash, J. B. ... Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium (2021). Transcriptome-based polygenic score links depression-related corticolimbic gene expression changes to sex-specific brain morphology and depression risk. Neuropsychopharmacology, 46(13), 2304-2311. https://doi.org/10.1038/s41386-021-01189-x

Mikic, N., Poulsen, F. R., Kristoffersen, K. B., Laursen, R. J., Guldberg, T. L., Skjøth-Rasmussen, J., Wong, E. T., Møller, S., Dahlrot, R. H., Sørensen, J. C. H. & Korshøj, A. R. (2021). Study protocol for OptimalTTF-2: enhancing Tumor Treating Fields with skull remodeling surgery for first recurrence glioblastoma: a phase 2, multi-center, randomized, prospective, interventional trial. BMC Cancer, 21(1), Article 1010. https://doi.org/10.1186/s12885-021-08709-4

Mikalsen, S.-O., Tausen, M. & Kongsstovu, S. I. (2020). Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies. BMC Genomics, 21(1), Article 223. https://doi.org/10.1186/s12864-020-6620-2

Miege, C., Ruffio-Chable, V., Schierup, M. H., Cabrillac, D., Dumas, C., Gaude, T. & Cock, J. M. (2001). Intrahaplotype Polymorphism at the Brassica S Locus. Genetics, 159, 811-822.

Midzi, N., Mduluza, T., Mudenge, B., Foldager, L. & Leutscher, P. D. C. (2017). Decrease in Seminal HIV-1 RNA Load After Praziquantel Treatment of Urogenital Schistosomiasis Coinfection in HIV-Positive Men—An Observational Study. Open Forum Infectious Diseases, 4(4), Article ofx199. https://doi.org/10.1093/ofid/ofx199

Meier, S. M., Agerbo, E., Maier, R., Pedersen, C. B., Lang, M., Grove, J., Hollegaard, M. V., Demontis, D., Trabjerg, B. B., Hjorthøj, C., Ripke, S., Degenhardt, F., Nöthen, M. M., Rujescu, D., Maier, W., Werge, T., Mors, O., Hougaard, D. M., Børglum, A. D. ... MooDS SCZ Consortium (2015). High loading of polygenic risk in cases with chronic schizophrenia. Molecular Psychiatry, 1-6. https://doi.org/10.1038/mp.2015.130

McKhann, H. I., Camilleri, C., Bérard, A., Bataillon, T., David, J. L., Reboud, X., Le Corre, V., Caloustian, C., Gut, I. G. & Brunel, D. (2004). Nested core collections maximizing genetic diversity in Arabidopsis thaliana. Plant Journal, 38(1), 193-202. https://doi.org/10.1111/j.1365-313X.2004.02034.x

McFarland, K. N., Tiwari, A., Hashem, V., Zhang, L., Zeng, D., Vincent, J., Arredondo, M. J., Johnson, K. L., Gan, S. R., Yabe, I., Skov, L., Rasmussen, A. & Ashizawa, T. (2024). Extended haplotype with rs41524547-G defines the ancestral origin of SCA10. Human Molecular Genetics, 33(18), 1567-1574. https://doi.org/10.1093/hmg/ddae092

McCauley, S., de Groot, S., Mailund, T. & Hein, J. (2007). Annotation of selection strengths in viral genomes. Bioinformatics, 23(22), 2978-2986. https://doi.org/10.1093/bioinformatics/btm472

Mattila, T., Bechsgaard, J. S., Hansen, T., Schierup, M. H. & Bilde, T. (2012). Ortholog genes identified by transcriptome sequencing in the spider genus Stegodyphus. BMC Genomics, 13(70). https://doi.org/10.1186/1471-2164-13-70

Mattheisen, M., Grove, J., Als, T. D., Martin, J., Voloudakis, G., Meier, S., Demontis, D., Bendl, J., Walters, R., Carey, C. E., Rosengren, A., Strom, N. I., Hauberg, M. E., Zeng, B., Hoffman, G., Zhang, W., Bybjerg-Grauholm, J., Bækvad-Hansen, M., Agerbo, E. ... Børglum, A. D. (2022). Identification of shared and differentiating genetic architecture for autism spectrum disorder, attention-deficit hyperactivity disorder and case subgroups. Nature Genetics, 54(10), 1470-1478. https://doi.org/10.1038/s41588-022-01171-3

Matey-Hernandez, M. L., Brunak, S., Izarzugaza, J. M. G. & Danish Pan-Genome Consortium (Jakob Grove, member of -) (2018). Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios. BMC Bioinformatics, 19(1), Article 239. https://doi.org/10.1186/s12859-018-2239-6

Martins, H. & Villesen, P. (2009). Highly improved dating of primate ERV integrations. Poster session presented at Frontiers of Retrovirology: Complex retroviruses, retroelements and their hosts, Montpellier, France. https://doi.org/10.1186/1742-4690-6-S2-P54

Martins, H. & Villesen, P. (2011). Improved integration time estimation of endogenous retroviruses with phylogenetic data. PLoS One, 6(3), e14745. https://doi.org/10.1371/journal.pone.0014745

Martínez-Ruiz, C., Black, J. R. M., Puttick, C., Hill, M. S., Demeulemeester, J., Larose Cadieux, E., Thol, K., Jones, T. P., Veeriah, S., Naceur-Lombardelli, C., Toncheva, A., Prymas, P., Rowan, A., Ward, S., Cubitt, L., Athanasopoulou, F., Pich, O., Karasaki, T., Moore, D. A. ... TRACERx Consortium (2023). Genomic-transcriptomic evolution in lung cancer and metastasis. Nature, 616(7957), 543-552. https://doi.org/10.1038/s41586-023-05706-4

Maretty, L., Jensen, J. M., Petersen, B., Sibbesen, J. A., Liu, S., Villesen, P., Skov, L., Belling, K. C., Theil Have, C., Izarzugaza, J. M. G., Grosjean, M., Bork-Jensen, J., Grove, J., Als, T. D., Huang, S., Chang, Y., Xu, R., Ye, W., Rao, J. ... Schierup, M. H. (2017). Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nature, 548(7665), 87-91. https://doi.org/10.1038/nature23264

Mapendano, C. K., Preker, P., Villesen, P., Prokop, A., Piatkowski, J., Schierup, M. H. & Jensen, T. H. (2011). Depletion of the RNA exosome triggers hypermethylation of human promoters.. Abstract from Third EMBO meeting on 'Chromatin and Epigenetics, Heidelberg, Germany.

Mansilla, F., Lamy, P., Ørntoft, T. F. & Birkenkamp-Demtröder, K. (2008). Upregulation of genes involved in rRNA processing in colon cancer. Poster session presented at EACR Annual Meeting of the European Association of Cancer Research, Lyon, France.

Malolepszy, A., Mun, T., Sandal, N., Gupta, V., Dubin, M., Urbanski, D. F., Shah, N., Bachmann, A., Fukai, E., Hirakawa, H., Tabata, S., Nadzieja, M., Markmann, K., Su, J., Umehara, Y., Soyano, T., Miyahara, A., Sato, S., Hayashi, M. ... Andersen, S. U. (2016). The LORE1 insertion mutant resource. The Plant Journal, 88(2), 306-317. https://doi.org/10.1111/tpj.13243

Malmos, K., Dong, M., Besenbacher, F., Daasbjerg, K. & Pedersen, S. U. (2007). Formation with the use of Electrostatic Repulsion of Covalent Attached Thin Layer on Glassy Carbon Surface. Paper presented at Electrochemical Science and Technology, Aarhus, Denmark.

Malmkvist, J., Coutant, M. P., Foldager, L., Kaiser, M. Ø. & Herskin, M. S. (2022). Optimering af procedure for lokalbedøvelse af pattegrise forud for kastration. DCA - Nationalt Center for Fødevarer og Jordbrug. Rådgivningsrapport fra DCA - Nationalt Center for Fødevarer og Jordbrug

Malham, M., Vestergaard, M. V., Bataillon, T., Villesen, P., Dempfle, A., Bang, C., Engsbro, A. L., Jakobsen, C., Franke, A., Wewer, V., Thingholm, L. B. & Petersen, A. M. (2025). The Composition of the Fecal and Mucosa-adherent Microbiota Varies Based on Age and Disease Activity in Ulcerative Colitis. Inflammatory Bowel Diseases, 31(2), 501-513. https://doi.org/10.1093/ibd/izae179

Malaspinas, A.-S., Westaway, M. C., Muller, C., Sousa, V. C., Lao, O., Alves, I., Athanasiadis, G., Cheng, J. Y., Crawford, J. E., Heupink, T. H., Macholdt, E., Peischl, S., Schiffels, S., Subramanian, S., Wright, J. L., Albrechtsen, A., Barbieri, C., Dupanloup, I., Eriksson, A. ... Willerslev, E. (2016). A genomic history of Aboriginal Australia. Nature, 538(7624), 207-214. https://doi.org/10.1038/nature18299

Mailund & Lyngsø, R. B. (1998). Textual interchange format for high-level Petri nets. In Proceedings of the first workshop on practical use of coloured Petri nets and Design/CPN (pp. 47-64)

Mailund (1999). Parameterised coloured Petri nets. In Prorceedings of the second workshop on practical use of coloured Petri nets and Design/CPN (pp. 133-151)

Mailund (2000). Separation of style and content with XML in an interchange format for high-level Petri nets. In Proceedings on the XML/SGML based interchange formats for Petri nets (pp. 7-12)

Mailund (2006). Analysing Infinite-State Systems by Combining Equivalence Reduction and the Sweep-Line Method. In Proceedings of International Conference on Application and Theory of Petri Nets (ICATPN 2002) (pp. 314-333)

Mailund & Kristensen, L. M. (2002). A Generalised Sweep-Line Method for Safety Properties. In Proceedings of Formal Methods Europe (FME 2002) (pp. 549-567)

Mailund & Kristensen, L. M. (2002). A Compositional Sweep-Line State Space Exploration Method. In Proceedings of Formal Description Techniques for Distributed Systems and Communication Protocols (FORTE 2002) (pp. 327-343)

Mailund, T. & Westergaard, M. (2004). Obtaining Memory-Efficient Reachability Graph Representations Using the Sweep-Line Method. In Proceedings of Tools and Algorithms for the Construction and Analysis of Systems (TACAS 2004) (pp. 177-191)

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

Mailund & Pedersen, C. N. S. (2004). QDist—Quartet Distance Between Evolutionary Trees. Bioinformatics, 20(10), 1636-1637.

Mailund & Pedersen, C. N. S. (2004). QuickJoin—Fast Neighbour-Joining Tree Reconstruction. Bioinformatics, 20(17), 3261-3262.

Mailund , Schierup, M. H., Pedersen, C. N. S., Mechlenborg, P., Madsen, J. N. & Schauser, L. (2005). CoaSim: A Flexible Environment for Simulating Genetic Data under Coalescent Models. BMC Bioinformatics, 6(252). http://www.biomedcentral.com/1471-2105/6/252

Mailund , Brodal, G. S., Fagerberg, R., Pedersen, C. N. S. & Phillips, D. (2006). Recrafting the Neighbor-Joining Method. BMC Bioinformatics, 7(29).

Mailund, T. & Pedersen, C. N. S. (2004). QDist - Quartet Distance between Evolutionary Trees. Bioinformatics, 20(10), 1636-1637.

Mailund, T. (2004). SplitDist—Calculating Split-Distances for Sets of Trees.

Mailund, T. (2005). Getting Started with CoaSim — An Introduction to the Simulator CoaSim.

Mailund, T. (2006). CoaSim Guile Manual — Using the Guile-based CoaSim Simulator.

Mailund, T. & Schauser, L. (2006). Getting Started with GeneRecon — An Introduction to the Association Mapping Tool GeneRecon.

Mailund, T. (2006). GeneRecon Users' Manual — A coalescent based tool for fine-scale association mapping.

Mailund, T. (2006). Getting Started with Blossoc. http://www.daimi.au.dk/~mailund/Blossoc/download/getting-started-1.1.pdf

Mailund, T., Schierup, M. H., Pedersen, C. N. S., Madsen, J. N., Hein, J. & Schauser, L. (2006). GeneRecon—A coalescent based tool for fine-scale association mapping. Bioinformatics, 22(18), 2317–2318.