Publications

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Bechsgaard, J., Schou, M. F., Vanthournout, B., Hendrickx, F., Knudsen, B., Settepani, V., Schierup, M. H. & Bilde, T. (2019). Evidence for Faster X Chromosome Evolution in Spiders. Molecular Biology and Evolution, 36(6), 1281-1293. https://doi.org/10.1093/molbev/msz074

Bechsgaard, J., Jorgensen, T. H. & Schierup, M. H. (2017). Evidence for Adaptive Introgression of Disease Resistance Genes Among Closely Related Arabidopsis Species. G3: Genes, Genomes, Genetics (Bethesda), 7(8), 2677-2683. https://doi.org/10.1534/g3.117.043984

Schendel, D., Munk Laursen, T., Albiñana, C., Vilhjalmsson, B., Ladd-Acosta, C., Fallin, M. D., Benke, K., Lee, B., Grove, J., Kalkbrenner, A., Ejlskov, L., Hougaard, D., Bybjerg-Grauholm, J., Baekvad-Hansen, M., Børglum, A. D., Werge, T., Nordentoft, M., Mortensen, P. B. & Agerbo, E. (2022). Evaluating the interrelations between the autism polygenic score and psychiatric family history in risk for autism. Autism Research, 15(1), 171-182. https://doi.org/10.1002/aur.2629

Sükösd, Z., Swenson, M. S., Kjems, J. & Heitsch, C. E. (2013). Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions. Nucleic Acids Research, 41(5), 2807-2816. https://doi.org/10.1093/nar/gks1283

Hebsgaard, MB., Wiuf, C., Gilbert, MTP., Glenner, H. & Willerslev, E. (2007). Evaluating Neandertal genetics and phylogeny. J. Mol. Evol., 64, 50-60. https://doi.org/10.1007/s00239-006-0017-y

Soraggi, S., Riera Belles, M., Rajpert-De Meyts, E., Schierup, M. H. & Almstrup, K. (2021). Evaluating genetic causes of azoospermia: What can we learn from a complex cellular structure and single-cell transcriptomics of the human testis? Human Genetics, 140(1), 183-201. https://doi.org/10.1007/s00439-020-02116-8

Lin, Y., Rasmussen, M. H., Christensen, M. H., Frydendahl, A., Maretty, L., Andersen, C. L. & Besenbacher, S. (2024). Evaluating Bioinformatics Processing of Somatic Variant Detection in cfDNA Using Targeted Sequencing with UMIs. International Journal of Molecular Sciences , 25(21), Article 11439. https://doi.org/10.3390/ijms252111439

Speed, D., Holmes, J. & Balding, D. J. (2020). Evaluating and improving heritability models using summary statistics. Nature Genetics, 52(4), 458-462. https://doi.org/10.1038/s41588-020-0600-y

Rafnar, T., Vermeulen, S. H., Sulem, P., Thorleifsson, G., Aben, K. K., Witjes, J. A., Grotenhuis, A. J., Verhaegh, G. W., Hulsbergen-van de Kaa, C. A., Besenbacher, S., Gudbjartsson, D., Stacey, S. N., Gudmundsson, J., Johannsdottir, H., Bjarnason, H., Zanon, C., Helgadottir, H., Jonasson, J. G., Tryggvadottir, L. ... Kiemeney, L. A. (2011). European genome-wide association study identifies SLC14A1 as a new urinary bladder cancer susceptibility gene. Human Molecular Genetics, 20(21), 4268-4281. https://doi.org/10.1093/hmg/ddr303

Wang, K., Li, J., Li, S., Bolund, L. & Wiuf, C. (2009). Estimation of tumor heterogeneity using CGH array data. BMC Bioinformatics, 10(1), 12. https://doi.org/10.1186/1471-2105-10-12

Jimenez Mena, B. (2016). Estimation of the effective population size (Ne) and its application in the management of small populations.

Bataillon, T. (2000). Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity, 84 ( Pt 5), 497-501. https://doi.org/10.1046/j.1365-2540.2000.00727.x

Barker, J. S. F., East, P. D. & Christiansen, F. (1989). Estimation of migration from a perturbation experiment in natural populations of Drosophila buzzatii Patterson & Wheeler. Biological Journal of the Linnean Society, 37, 311-334.

Chen, Y., Vanderick, S., Mota, R. R., Grelet, C., GplusE Consortium & Gengler, N. (2021). Estimation of genetic parameters for predicted nitrogen use efficiency and losses in early lactation of Holstein cows. Journal of Dairy Science, 104(4), 4413-4423. https://doi.org/10.3168/jds.2020-18849

Stumpf, M. PH., Thorne, T., Silva, E., Stewart, R., An, HJ., Lappe, M. & Wiuf, C. H. (2008). Estimating the size of the human interactome. Proceedings of the National Academy of Sciences (PNAS), 105, 6059.

Mable, B. K., Schierup, M. H. & Charlesworth, D. (2003). Estimating the number, frequency, and dominance of S-alleles in a natural population of Arabidopsis lyrata (Brassicaceae) with sporophytic control of self-incompatibility. Heredity, 90, 422-431. http://www.nature.com/hdy

Athanasiadis, G., Speed, D., Andersen, M. K., Appel, E. V. R., Grarup, N., Brandslund, I., Jørgensen, M. E., Larsen, C. V. L., Bjerregaard, P., Hansen, T. & Albrechtsen, A. (2020). Estimating narrow-sense heritability using family data from admixed populations. Heredity, 124(6), 751-762. https://doi.org/10.1038/s41437-020-0311-2

Charmouh, A. P., Porsborg, P. S., Hansen, L. T., Besenbacher, S., Boeg Winge, S., Almstrup, K., Hobolth, A., Bataillon, T. & Schierup, M. H. (2025). Estimating Gene Conversion Tract Length and Rate From PacBio HiFi Data. Molecular Biology and Evolution, 42(2), Article msaf019. https://doi.org/10.1093/molbev/msaf019

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

Nexø, B. A., Laska, M. J., Christensen, T., Møller-Larsen, A., Pedersen, F. S. & Villesen, P. (2010). Estimating disease risk of individual having/developing multiple sclerosis involves in genetic material sample from individual, assessing sequence polymorphism in specific genetic regions of human chromosome, obtaining and estimating step. (Patent No. WO2010112033).

Frydendahl, A., Rasmussen, M. H., Jensen, S. Ø., Henriksen, T. V., Demuth, C., Diekema, M., Ditzel, H. J., Wen, S. W. C., Pedersen, J. S., Dyrskjøt, L. & Andersen, C. L. (2024). Error-Corrected Deep Targeted Sequencing of Circulating Cell-Free DNA from Colorectal Cancer Patients for Sensitive Detection of Circulating Tumor DNA. International Journal of Molecular Sciences , 25(8), Article 4252. https://doi.org/10.3390/ijms25084252

Rheinbay, E., Nielsen, M. M., Abascal, F., Wala, J. A., Shapira, O., Tiao, G., Hornshøj, H., Hess, J. M., Juul, R. I., Lin, Z., Feuerbach, L., Sabarinathan, R., Madsen, T., Kim, J., Mularoni, L., Shuai, S., Lanzós, A., Herrmann, C., Maruvka, Y. E. ... PCAWG Drivers and Functional Interpretation Working Group (2023). Erratum: Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes (Nature (2020) 578 7793 (102-111)). Nature, 614(7948), E40. https://doi.org/10.1038/s41586-022-05599-9

Szalay, P. G., Thøgersen, L. S., Olsen, J., Kállay, M. & Gauss, J. (2004). Equilibrium Geometry of the Ethynyl (CCH) Radical. Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory, 108, 3030-3034.

Christiansen, F. (1988). Epistasis in the multiple locus symmetric viability model. Journal of Mathematical Biology, 26, 595-618.

Blanquart, F. & Bataillon, T. (2016). Epistasis and the Structure of Fitness Landscapes: Are Experimental Fitness Landscapes Compatible with Fisher's Geometric Model? Genetics, 203(2), 847-862. https://doi.org/10.1534/genetics.115.182691

Furrow, R. E., Christiansen, F. B. & Feldman, M. W. (2014). Epigenetic variation, phenotypic heritability, and evolution. In A. Naumova & C. Greenwood (Eds.), Epigenetics and Complex Traits (pp. 233-246). Springer. https://doi.org/10.1007/978-1-4614-8078-5_1

Rasmussen, M. Q., Tindbæk, G., Nielsen, M. M., Merrild, C., Steiniche, T., Pedersen, J. S., Moestrup, S. K., Degn, S. E. & Madsen, M. (2023). Epigenetic Silencing of LRP2 Is Associated with Dedifferentiation and Poor Survival in Multiple Solid Tumor Types. Cancers, 15(6), Article 1830. https://doi.org/10.3390/cancers15061830

Nielsen, M. M., Trolle, C., Vang, S., Hornshøj, H., Skakkebaek, A., Hedegaard, J., Nordentoft, I., Pedersen, J. S. & Gravholt, C. H. (2020). Epigenetic and transcriptomic consequences of excess X-chromosome material in 47,XXX syndrome-A comparison with Turner syndrome and 46,XX females. American Journal of Medical Genetics. Part C: Seminars in Medical Genetics, 184(2), 279-293. https://doi.org/10.1002/ajmg.c.31799

Castagnini, A. & Foldager, L. (2014). Epidemiology, course and outcome of acute polymorphic psychotic disorder: implications for ICD-11. Psychopathology, 47(3), 202-206. https://doi.org/10.1159/000357784

Christiansen, F. (2010). Epidemier: Truslen fra det ukendte. In M. A. Nielsen (Ed.), Det fremmede som historisk drivkraft: Danmark efter 1742 (pp. 68-76). Det Kongelige Danske Videnskabernes Selskab.

Feliu, E. & Wiuf, C. H. (2012). Enzyme-sharing as a cause of multi-stationarity in signalling systems. Journal of the Royal Society. Interface, 9(71), 1224-1232. https://doi.org/10.1098/rsif.2011.0664

Furrow, R., Christiansen, F. & Feldman, M. (2011). Environment-sensitive Epigenetics and the Heritability of Complex Diseases. Genetics, 189(4), 1377-1387. https://doi.org/10.1534/genetics.111.131912

Sand, A. (2014). Engineering of Algorithms for Hidden Markov models and Tree Distances. Department of Computer Science, Aarhus University.

Nielsen, J. (2011). Engineering Algorithms for Finding Patterns in Biological Data.

Lassen, J. K. & Villesen, P. (2025). End-To-End Deep Learning Explains Antimicrobial Resistance in Peak-Picking-Free MALDI-MS Data. Analytical Chemistry, 97(5), 2795-2800. https://doi.org/10.1021/acs.analchem.4c05113

Nissen, K. K., Laska, M. J., Hansen, B., Terkelsen, T., Villesen, P., Bahrami, S., Petersen, T., Pedersen, F. S. & Nexø, B. A. (2013). Endogenous retroviruses and multiple sclerosis-new pieces to the puzzle. B M C Neurology, 13(111), 1-5. https://doi.org/10.1186/1471-2377-13-111

Gupta, V., Markmann, K., Pedersen, C. N. S., Stougaard, J. & Andersen, S. U. (2012). shortran: A pipeline for small RNA-seq data analysis. Bioinformatics, 28(20), 2698-2700. https://doi.org/10.1093/bioinformatics/bts496

Fredslund, J. & Matarić, M. J. (2001). Robot Formations Using Only Local Sensing and Control. In Proceedings of the IEEE International Symposium on Computational Intelligence in Robotics and Automation (CIRA-01)

Hein, J., Schierup, M. H. & Wiuf, C. (2005). Gene Genealogies, Variation and Evolution.

Herbsleb, M., Andersen, T. T., Wiuf, C. & Ørntoft, T. F. (2006). Identification of New Transcriptional Correlations in Cancer Using Array Databases and Functional In Vitro Studies , presented at PhD Annual Day, Graduate School of Health, University of Aarhus.. Poster session presented at Identification of New Transcriptional Correlations in Cancer Using Array Databases and Functional In Vitro Studies , presented at PhD Annual Day, Graduate School of Health, University of Aarhus..

Riedel, C. S., Norager, N. H., Bertelsen, M., Mikkelsen, R., Juhler, M. & Hansen, T. S. (2024). Elevated systemic venous pressures as a possible pathology in prepubertal pediatric idiopathic intracranial hypertension. Child's Nervous System, 40(12), 4203-4209. https://doi.org/10.1007/s00381-024-06594-3

Hannon, E., Schendel, D., Ladd-Acosta, C., Grove, J., Hansen, C. S., Andrews, S. V., Hougaard, D. M., Bresnahan, M., Mors, O., Hollegaard, M. V., Bækvad-Hansen, M., Hornig, M., Mortensen, P. B., Børglum, A. D., Werge, T., Pedersen, M. G., Nordentoft, M., Buxbaum, J., Daniele Fallin, M. ... iPSYCH-Broad ASD Group (Mette Nyegaard, Per Qvist, Jane Hvarregaard Christensen - members of -) (2018). Elevated polygenic burden for autism is associated with differential DNA methylation at birth. Genome Medicine, 10(1), Article 19. https://doi.org/10.1186/s13073-018-0527-4

Østergaard, S. D., Speed, M. S., Kellner, C. H., Mueller, M., McClintock, S. M., Husain, M. M., Petrides, G., McCall, W. V., Lisanby, S. H. & for the CORE/PRIDE workgroup (2020). Electroconvulsive therapy (ECT) for moderate-severity major depression among the elderly: Data from the pride study. Journal of Affective Disorders, 274, 1134-1141. https://doi.org/10.1016/j.jad.2020.05.039

Zhou, Y., Zhan, X., Jin, J., Zhou, L., Bergman, J., Li, X., Rousselle, M. M. C., Belles, M. R., Zhao, L., Fang, M., Chen, J., Fang, Q., Kuderna, L., Marques-Bonet, T., Kitayama, H., Hayakawa, T., Yao, Y. G., Yang, H., Cooper, D. N. ... Zhang, G. (2023). Eighty million years of rapid evolution of the primate Y chromosome. Nature Ecology & Evolution, 7(7), 1114-1130. https://doi.org/10.1038/s41559-022-01974-x

Damsgaard, E. M., Frøland, A., Jørgensen, O. D. & Mogensen, C. E. (1992). Eight to nine year mortality in known non-insulin dependent diabetics and controls. Kidney International, 41(4), 731-5.

Ding, Z., Mailund, T. & Song, Y. (2008). Efficient Whole-Genome Association Mapping using Local Phylogenies for Unphased Genome Data. Bioinformatics, 2215-2221.

Kristensen, L. M. & Mailund (2003). Efficient Path Finding with the Sweep-Line Method using External Storage. In Proceedings of International Conference on Formal Engineering Methods (ICFEM 2003) (pp. 319-337)

Andersen, L. N., Mailund, T. & Hobolth, A. (2014). Efficient computation in the IM model. Journal of Mathematical Biology, 68(6), 1423-1451. https://doi.org/10.1007/s00285-013-0671-9

Qian, Y., Browning, B. L. & Browning, S. R. (2014). Efficient clustering of identity-by-descent between multiple individuals. Bioinformatics, 30(7), 915-922. https://doi.org/10.1093/bioinformatics/btt734

Simonsen, M. (2011). Efficient algorithms for tree reconstruction and prediction of molecular interactions. Department of Computer Science, Aarhus University.

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Palle Villesen