Publications

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Kjeldgaard, M., Nissen, P., Thirup, S. & Nyborg, J. (1993). The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation. Structure, 1(1), 35-50.

Borbye-Lorenzen, N., Zhu, Z., Agerbo, E., Albiñana, C., Benros, M. E., Bian, B., Børglum, A. D., Bulik, C. M., Debost, J.-C. P. G., Grove, J., Hougaard, D. M., McRae, A. F., Mors, O., Mortensen, P. B., Musliner, K. L., Nordentoft, M., Petersen, L. V., Privé, F., Sidorenko, J. ... McGrath, J. J. (2023). The correlates of neonatal complement component 3 and 4 protein concentrations with a focus on psychiatric and autoimmune disorders. Cell Genomics, 3(12), 100457. Article 100457. https://doi.org/10.1016/j.xgen.2023.100457

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

Brodal, G. S., Fagerberg, R., Pedersen, C. N. S., Östlin, A., Orejas, F. (Ed.), Spirakis, P. G. (Ed.) & Leeuwen, J. V. (Ed.) (2001). The Complexity of Constructing Evolutionary Trees Using Experiments. In Lecture Notes In Computer Science; Vol. 2076: Proceedings of the 28th International Colloquium on Automata, Languages and Programming (2076 of Lecture Notes in Computer Science ed., Vol. 2076/2001, pp. 140-151). Springer.

Rogers, J., Raveendran, M., Alan Harris, R., Mailund, T., Leppälä, K., Athanasiadis, G., Schierup, M. H., Cheng, J., Munch, K., Walker, J. A., Konkel, M. K., Jordan, V., Steely, C. J., Beckstrom, T. O., Bergey, C., Burrell, A., Schrempf, D., Noll, A., Kothe, M. ... Baboon Genome Analysis Consortium (2019). The comparative genomics and complex population history of Papio baboons. Science Advances, 5(1), Article 6947. https://doi.org/10.1126/sciadv.aau6947

Wiuf, C. & Hein, J. (2000). The coalescent with gene conversion. Genetics, 155, 451-462.

Schierup, M. H. & Wiuf, C. H. (2010). The coalescent in bacterial populations. In D. A. Robinson, D. Falush & E. J. Feil (Eds.), Bacterial population genetics in infectious disease (pp. 3-19). Wiley-Blackwell.

Knudsen, M. & Wiuf, C. H. (2010). The CATH Database. Human Genomics (Online).

Nielsen, S. M., de Gier, C., Dimopoulou, C., Gupta, V., Hansen, L. H. & Nørskov-Lauritsen, N. (2015). The capsule biosynthesis locus of Haemophilus influenzae show conspicuous similarity to the corresponding locus in Haemophilus sputorum and may have been recruited from this species by horizontal gene transfer. Microbiology, 161(6), 1182-1188. https://doi.org/10.1099/mic.0.000081

Munch, D., Gupta, V., Bachmann, A., Busch, W., Kelly, S., Mun, T. & Andersen, S. U. (2018). The Brassicaceae family displays divergent, shoot-skewed NLR resistance gene expression. Plant Physiology, 176(2), 1598-1609. https://doi.org/10.1104/pp.17.01606

Prüfer, K., Munch, K., Hellmann, I., Akagi, K., Miller, J. R., Walenz, B., Koren, S., Sutton, G., Kodira, C., Winer, R., Knight, J. R., Mullikin, J. C., Meader, S. J., Ponting, C. P., Lunter, G., Higashino, S., Hobolth, A., Dutheil, J., Karakoç, E. ... Pääbo, S. (2012). The bonobo genome compared with the chimpanzee and human genomes. Nature, 486(7404), 527-31. https://doi.org/10.1038/nature11128

Høst, S., Olsen, J., Jansik, B., Thøgersen, L., Jørgensen, P. & Helgaker, T. (2008). The augmented Roothaan-Hall method for optimizing Hartree-Fock and Kohn-Sham density matrices. Journal of Chemical Physics, 129, 124106.

Christensen, L. L., Wikman, F., Wiuf, C., Madsen, B. E., Overvad, K., Tjønnland, A., Koed, K. & Ørntoft, T. F. (2006). The Association of Missense and Silent Mutations with the Development of sporadic and Familial Breast Cancer in the Danish Population. Poster session presented at 19th Meeting of the European Association for Cancer Research, Budapest, Hungary.

Østergaard, S. D. & Foldager, L. (2011). The association between physical illness and major depressive episode in general practice. Acta Psychiatrica Scandinavica, 123(4), 290-296. https://doi.org/10.1111/j.1600-0447.2010.01668.x

Christensen, L. L., Madsen, B. E., Wikman, F. P., Wiuf, C., Koed, K., Tjønneland, A., Olsen, A. V., Syvänen, A.-C., Andersen, C. L. & Orntoft, T. F. (2008). The association between genetic variants in hMLH1 and hMSH2 and the development of sporadic colorectal cancer in the Danish population. BMC Medical Genetics, 9, 52. https://doi.org/10.1186/1471-2350-9-52

Thornton, L. M., Munn-Chernoff, M. A., Baker, J. H., Juréus, A., Parker, R., Henders, A. K., Larsen, J. T., Petersen, L., Watson, H. J., Yilmaz, Z., Kirk, K. M., Gordon, S., Leppä, V. M., Martin, F. C., Whiteman, D. C., Olsen, C. M., Werge, T. M., Pedersen, N. L., Kaye, W. ... Bulik, C. M. (2018). The anorexia nervosa genetics initiative (ANGI): Overview and methods. Contemporary Clinical Trials, 74, 61-69. https://doi.org/10.1016/j.cct.2018.09.015

Wiuf, C. & Hein, J. (1999). The ancestry of a sample of sequences subject to recombination. Genetics, 151, 1217-1228.

Wiuf, C. (2003). The age of a rare mutation. In PJ. Green, NL. Hjort & S. Richardson (Eds.), Highly Structured Stochastic Systems (Vol. 27, pp. 417-422). Oxford University Press.

Aagaard, L., Villesen, P., Kjeldbjerg, A. L. & Pedersen, F. S. (2005). The ~30-million-year-old ERVPb1 envelope gene is evolutionarily conserved among hominoids and Old World monkeys. Genomics, 86(6).

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)

Liljas, A., Liljas, L., Piskur, J., Lindblom, G., Nissen, P. & Kjeldgaard, M. (2009). Textbook on Structural Biology. (1 ed.) World Scientific.

Christensen, O. F., Frydenberg, M., Jensen, J. L. & Pedersen, J. G. (2005). Tests and Confidence Intervals for an Extended Variance Component Using the Modified Likelihood Ratio Statistic.

Christensen, O. F., Frydenberg, M., Jensen, J. L. & Pedersen, J. G. (2007). Tests and confidence intervals for an extended variance component using the modified likelihood ratio statistic. Scandinavian Journal of Statistics, 34(2), 347-364. https://doi.org/10.1111/j.1467-9469.2006.00520.x

Pradal, C., Olesen, J. M. & Wiuf, C. H. (2009). Temporal development and collapse of an Arctic plant-pollinator network. BMC Ecology, 9. https://doi.org/10.1186/1472-6785-9-24

Thodberg, K., Foldager, L., Fogsgaard, K. K., Gaillard, C. & Herskin, M. S. (2022). Temperature conditions during commercial transportation of cull sows to slaughter. Computers and Electronics in Agriculture, 192, Article 106626. https://doi.org/10.1016/j.compag.2021.106626

Foldager, L., Trenel, P., Munksgaard, L. & Thomsen, P. T. (2020). Technical note: Random forests prediction of daily eating time of dairy cows from 3-dimensional accelerometer and radiofrequency identification. Journal of Dairy Science, 103(7), 6271–6275. https://doi.org/10.3168/jds.2019-17613

Fredslund, J. (2000). Teaching a new dog old tricks – the Assumption Architecture. Poster session presented at Learning'00 Workshop, Madrid, Spain.

Frandsen, P., Fontsere, C., Nielsen, S. V., Hanghøj, K., Castejon-Fernandez, N., Lizano, E., Hughes, D., Hernandez-Rodriguez, J., Korneliussen, T. S., Carlsen, F., Siegismund, H. R., Mailund, T., Marques-Bonet, T. & Hvilsom, C. (2020). Targeted conservation genetics of the endangered chimpanzee. Heredity, 125(1-2), 15-27. https://doi.org/10.1038/s41437-020-0313-0

Gengler, N. & GplusE Consortium (2017). Targeted combination of estimated breeding values for lower accuracy mid-infrared biomarkers increases their usefulness in genetic evaluation of dairy cattle. Abstract from ICAR 2017, United Kingdom. http://www.icar.org/wp-content/uploads/2017/06/5.-Nicolas-Gengler-1.pdf

Sall, K., Gessler, F., Foldager, L. & Simonic, M. (2021). Tannins to control Clostridium perfringens in vitro. Poster session presented at Annual Congress of The Danish Microbiological Society, Frederiksberg, Denmark.

Kongsted, H., Foldager, L. & Sørensen, J. T. (2019). Tail bites in free-range based finisher pig systems: prevalence and risk factors. Abstract from 11th symposium of porcine health management, Utrecht, Netherlands.

Luo, X.-J., Mattheisen, M., Li, M., Huang, L., Rietschel, M., Børglum, A. D., Als, T. D., van den Oord, E. J., Aberg, K. A., Mors, O., Mortensen, P. B., Luo, Z., Degenhardt, F., Cichon, S., Schulze, T. G., Nöthen, M. M., Su, B., Zhao, Z., Gan, L. ... iPSYCH-GEMS SCZ working group (Jakob Grove, member) (2015). Systematic Integration of Brain eQTL and GWAS Identifies ZNF323 as a Novel Schizophrenia Risk Gene and Suggests Recent Positive Selection Based on Compensatory Advantage on Pulmonary Function. Schizophrenia Bulletin. https://doi.org/10.1093/schbul/sbv017

Penner, R., Andersen, J. E., Wiuf, C. H. & Knudsen, M. (2008). System and method for modelling a molecule with a graph. (Patent No. PA 2008 01009).

Balslev, H., Arge, L. A., Svenning, J.-C., Schierup, M. H. & Jensen, C. S. (Eds.) (2011). Symposium on Biodiversity in the Silicon Age - Abstracts. The Royal Danish Academy of Sciences and Letters.

Cavassim, M. I. A., Moeskjær, S., Moslemi, C., Fields, B., Bachmann, A., Vilhjálmsson, B. J., Schierup, M. H., W Young, J. P. & Andersen, S. U. (2020). Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex. Microbial Genomics, 6(4), Article 000351. https://doi.org/10.1099/mgen.0.000351

Kongsted, H., Foldager, L. & Sørensen, J. T. (2018). Sygdomsproblemer hos økologiske grise og frilandsgrise. DCA - Nationalt Center for Fødevarer og Jordbrug. DCA rapport No. 128 http://web.agrsci.dk/djfpublikation/index.asp?action=show&id=1271

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

Fredslund, J. & Andersen, E. S. (2005). Superjordnøddernes hemmelighed. Aktuel Naturvidenskab, (6), 12-15.

Hobolth, A. & Jensen, J. L. (2011). Summary statistics for endpoint-conditioned continuous-time Markov chains. Journal of Applied Probability, 48(4), 911-924. https://doi.org/10.1239/jap/1324046009

Hobolth, A. & Jensen, J. L. (2010). Summary statistics for end-point conditioned continuous-time Markov chains. Thiele Centre, Institut for Matematiske Fag, Aarhus Universitet.

Lasry, C., Guillemot, V., Lechat, P., Menager, H., Vilhjalmsson, B. J. & Aschard, H. (2017). Summary Statistic GWAS Joint Re-Analyses Across 30+Traits. Genetic Epidemiology, 41(7), 652-652.

Villesen, P. (2001). Summary of "Mating System Evolution, Worker Reproduction and Symbiont Diversity in Attine Ants. In Doctorates and PhDs 2001, Faculty of Science, University of Aarhus (pp. 616-618)

Dai, N., Foldager, L., Gallego, J. A., Hack, L. M., Ji, Y., Lett, T. A. P., Liu, B., Loken, E. K., Mandelli, L., Mehta, D., Power, R. A., Sprooten, E., Stephens, S. H., Paska, A. V., Yan, J., Zai, C. C., Zai, G., Zhang-James, Y., O'Shea, A. & DeLisi, L. E. (2012). Summaries from the XIX World Congress of Psychiatric Genetics, Washington, DC, September 10-14 2011. American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 159B(1), 128-129. https://doi.org/10.1002/ajmg.b.32017

Speed, D. & Balding, D. J. (2019). SumHer better estimates the SNP heritability of complex traits from summary statistics. Nature Genetics, 51(2), 277-284. https://doi.org/10.1038/s41588-018-0279-5

Stumpf, MPH., Wiuf, C. & May, RM. (2005). Subnets of scale-free networks are not scale-free: Sampling properties of networks. Proceedings of the National Academy of Sciences (PNAS), 102, 4221-4224.

Andersen, L. N. (2011). Subexponential loss rate asymptotics for Lévy processes. Mathematical Methods of Operations Research, 73(1), 91-108. https://doi.org/10.1007/s00186-010-0335-0

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

Bergeron, L. A., Besenbacher, S., Schierup, M. H. & Zhang, G. (2021). Studying mutation rate evolution in primates-a need for systematic comparison of computational pipelines. GigaScience, 10(10), Article giab072. https://doi.org/10.1093/gigascience/giab072

Christiansen, F. (1980). Studies on selection components in natural populations using population samples of mother-offspring combinations. Hereditas, 92, 199-203.

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Palle Villesen