Publications

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Simonsen, M., Maetschke, S. R. & Ragan, M. A. (2012). Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling. Bioinformatics, 28(6), 851-857. https://doi.org/10.1093/bioinformatics/btr720

Simonsen, M., Christensen, M. H., Thomsen, R. & Pedersen, C. N. S. (2013). GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution. In S. tsutsui & P. Collet (Eds.), Massively Parallel Evolutionary Computation on GPGPUs Springer Publishing Company.

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

Sigurdsson, A. I., Louloudis, I., Banasik, K., Westergaard, D., Winther, O., Lund, O., Ostrowski, S. R., Erikstrup, C., Pedersen, O. B. V., Nyegaard, M., Brunak, S., Vilhjálmsson, B. J., Rasmussen, S. & DBDS Genomic Consortium (2023). Deep integrative models for large-scale human genomics. Nucleic Acids Research, 51(12), E67. Article e67. https://doi.org/10.1093/nar/gkad373

Sigurdsson, A. I., Gräf, J. F., Yang, Z., Ravn, K., Meisner, J., Thielemann, R., Webel, H., Smit, R. A. J., Niu, L., Mann, M., Vilhjalmsson, B., Neale, B. M., Holm, J.-C., Ganna, A., Hansen, T., Loos, R. J. F., Rasmussen, S. & FinnGen (2026). Complex genetic effects linked to plasma protein abundance in the UK Biobank. Nature Communications, 17(1), Article 533. Advance online publication. https://doi.org/10.1038/s41467-025-67235-0

Siegismund, H. & Christiansen, F. (1985). Selection component analysis of natural polymorphisms using population samples including mother-offspring combinations, III. Theoretical Population Biology, 27, 268–297.

Shuai, S., PCAWG Drivers and Functional Interpretation Working Group, Gallinger, S., Stein, L. & PCAWG Consortium (2020). Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nature Communications, 11(1), Article 734. https://doi.org/10.1038/s41467-019-13929-1

Shao, Y., Zhou, L., Li, F., Zhao, L., Zhang, B. L., Shao, F., Chen, J. W., Chen, C. Y., Bi, X., Zhuang, X. L., Zhu, H. L., Hu, J., Sun, Z., Li, X., Wang, D., Rivas-González, I., Wang, S., Wang, Y. M., Chen, W. ... Wu, D. D. (2023). Phylogenomic analyses provide insights into primate evolution. Science (New York, N.Y.), 380(6648), 913-924. https://doi.org/10.1126/science.abn6919

Shah, N., Hirakawa, H., Kusakabe, S., Sandal, N., Stougaard, J., Schierup, M. H., Sato, S. & Andersen, S. U. (2016). High-resolution genetic maps of Lotus japonicus and L. burttii based on re-sequencing of recombinant inbred lines. D N A Research, 23(5), 487-494. https://doi.org/10.1093/dnares/dsw033

Shah, N., Wakabayashi, T., Kawamura, Y., Skovbjerg, C. K., Wang, M.-Z., Mustamin, Y., Isomura, Y., Gupta, V., Jin, H., Mun, T., Sandal, N., Azuma, F., Fukai, E., Seren, Ü., Kusakabe, S., Kikuchi, Y., Nitanda, S., Kumaki, T., Hashiguchi, M. ... Andersen, S. U. (2020). Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan. Nature Communications, 11(1), Article 253. https://doi.org/10.1038/s41467-019-14213-y

Sengpiel, V., Elind, E., Bacelis, J., Nilsson, S., Grove, J., Myhre, R., Haugen, M., Margrete Meltzer, H., Alexander, J., Jacobsson, B. & Brantsæter, A.-L. (2013). Maternal caffeine intake during pregnancy is associated with birth weight but not with gestational length: results from a large prospective observational cohort study. B M C Medicine, 11(42). https://doi.org/10.1186/1741-7015-11-42

Sendrowski, J. & Bataillon, T. (2024). FastDFE: Fast and Flexible Inference of the Distribution of Fitness Effects. Molecular Biology and Evolution, 41(5), Article msae070. https://doi.org/10.1093/molbev/msae070

Sendrowski, J., Bataillon, T. & Ramstein, G. P. (2025). In silico prediction of variant effects: promises and limitations for precision plant breeding. Theoretical and Applied Genetics, 138(8), Article 193. https://doi.org/10.1007/s00122-025-04973-1

Sendrowski, J. & Hobolth, A. (2026). PhaseGen: exact solutions for time-inhomogeneous multivariate coalescent distributions under diverse demographies. Genetics, 232(1), Article iyaf135. https://doi.org/10.1093/genetics/iyaf135

Sendrowski, J. S.-O. (2026). Robust Inference Software in Population Genetics. [PhD dissertation, Aarhus University].

Schumer, M., Xu, C., Powell, D. L., Durvasula, A., Skov, L., Holland, C., Blazier, J. C., Sankararaman, S., Andolfatto, P., Rosenthal, G. G. & Przeworski, M. (2018). Natural selection interacts with recombination to shape the evolution of hybrid genomes. Science, 360(6389), 656-660. https://doi.org/10.1126/science.aar3684

Schultz, T. R., Solomon, S. A., Mueller, U. G., Villesen, P., Boomsma, JJ., Adams, R. M. M. & Norden, B. (2002). Cryptic speciation in the fungus-growing ant Cyphomyrmex longiscapus Weber and Cyphomyrmex muelleri Schultz and Solomon, new species (Formicidae, Attini). Insectes Sociaux, 49, 331-343.

Schrempf, D. & Hobolth, A. (2017). An alternative derivation of the stationary distribution of the multivariate neutral Wright–Fisher model for low mutation rates with a view to mutation rate estimation from site frequency data. Theoretical Population Biology, 114, 88-94. https://doi.org/10.1016/j.tpb.2016.12.001

Schoustra, S. E., Bataillon, T., Gifford, D. R. & Kassen, R. (2009). The properties of adaptive walks in evolving populations of fungus. PLOS Biology, 7(11), e1000250. https://doi.org/10.1371/journal.pbio.1000250

Schouby Bock, M., Nørgaard Van Achter, O., Dines, D., Simonsen Speed, M., Correll, C. U., Mors, O., Østergaard, S. D. & Kølbæk, P. (2020). Clinical validation of the self-reported Glasgow Antipsychotic Side-effect Scale using the clinician-rated UKU side-effect scale as gold standard reference. Journal of Psychopharmacology, 34(8), 820-828. https://doi.org/10.1177/0269881120916122

Schoen, D. J., David, J. L. & Bataillon, T. (1998). Deleterious mutation accumulation and the regeneration of genetic resources. Proceedings of the National Academy of Sciences (PNAS), 95(1), 394-9.

Schiøtt, B. & Lie, M. A. (2008). DFT Study of Solvation Effects on the Tautomeric Equlibrium and Catalytic Ylide Generation of Thiamin Models. Journal of Computational Chemistry, 29, 1037-1047.

Schild, S.-L. A., Foldager, L., Bonde, M., Andersen, H. M.-L. & Pedersen, L. J. (2019). Does hut climate matter for piglet survival in organic production? Animal, 13(4), 826-834. https://doi.org/10.1017/S175173111800201X

Schild, S.-L. A., Foldager, L., Bonde, M. K., Andersen, H. M.-L. & Pedersen, L. J. (2019). Hut climate impacts piglet survival. In Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science (Vol. 25, pp. 338). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-890-2

Schild, S. L. A., Foldager, L., Rangstrup-Christensen, L. & Pedersen, L. J. (2020). Characteristics of Piglets Born by Two Highly Prolific Sow Hybrids. Frontiers in Veterinary Science, 7, Article 355. https://doi.org/10.3389/fvets.2020.00355

Schierup, M. H. & Forsberg, R. (2003). Recombination and phylogenetic analysis of HIV-1. Paper presented at Atti dei Convegni Lincei - Tavola rotonda nell'ambito della Conferenza annuale della Ricerca, Roma 28-29 settember, 2001.

Schierup, M. H., Mable, B. K., Awadalla, P. & Charlesworth, D. (2001). Identification and Characterization of a Polymorphic Receptor Kinase Gene Linked to the Self-Incompatibility Locus of Arabidopsis lyrata. Genetics, 158(387-399), 12259-12254.

Schierup, M. H., nullA.M., M. & Hein, J. (2001). Recombination, Balancing Selection and Phylogenies in MHC and Self-Incompatibility Genes. Genetics, 159, 1833-1844.

Schierup, M. H., Bechsgaard, J. S., Nielsen, L. H. & Christiansen, F. B. (2006). Selection at work in self-incompatible Arabidopsis lyrata: Mating patterns in a natural population. Genetics, 172, 477-484.

Schierup, M. H., Jensen, T. M. & Wiuf, C. (2005). The effect of a single recombination event. Poster session presented at Genomic Studies and the HapMap, Oxford, United Kingdom.

Schierup, M. H., Mordhorst, CH., Müller, CP. & Christensen, LS. (2005). Evidence of recombination among early-vaccination era measles virus strains. BMC Evolutionary Biology, 5(52).

Schierup, M. H. (2006). Consanguinity, inbreeding, and genetic drift in Italy by LL Cavalli-Sforza, A Moroni and G Zei. Heredity, 96, 336-336.

Schierup, M. H. & Vekemans, X. (2008). Genomic consequences of selection on self-incompatibility genes. Current Opinion in Plant Biology, 116-122. https://doi.org/10.1016/j.pbi.2008.01.003

Schierup, M. H., Bechsgaard, J. S. & Christiansen, F. B. (2008). Selection at work in self-incompatible Arabidopsis lyrata. II. Spatial distribution of S haplotypes in Iceland. Genetics, 180(2), 1051-9. https://doi.org/10.1534/genetics.108.088799

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

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.

Schierup, M. H. (2020). The last pieces of a puzzling early meeting. Science (New York, N.Y.), 369(6511), 1565-1566. https://doi.org/10.1126/science.abe2766

Schick, A., Bailey, S. & Kassen, R. (2015). Evolution of fitness trade-offs in locally adapted populations of Pseudomonas fluorescens. American Naturalist, 186(S1), S48-S59. https://doi.org/10.1086/682932

Schepeler, T., Reinert, T., Ostenfeld, M. S., Christensen, L. L., Silahtaroglu, A. N., Dyrskjøt, L., Wiuf, C., Sørensen, F. J., Kruhøffer, M., Laurberg, S., Kauppinen, S., Ørntoft, T. F. & Andersen, C. L. (2008). Diagnostic and prognostic microRNAs in stage II colon cancer. Cancer Research, 68(15), 6416-24. https://doi.org/10.1158/0008-5472.CAN-07-6110

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

Schauser, L., Fredslund, J., Madsen, L. H., Sandal, N. N. & Stougaard, J. (2005). A computational pipeline towards the development of comparative anchor tagged sequence (CATS) markers. In M. O. Humphrey (Ed.), Proceedings of the International Grassland Congress (IGC) (pp. 73-81). Wageningen Academic Publishers.

Schauser, L., Subrahmanyam, S., Madsen, L. H., Sandal, N. N. & Stougaard, J. (2005). An in silico strategy towards the development of legume genome anchor markers using comparative sequence analysis. In In Márquez, A.J. ed. Lotus japonicus handbook (pp. 233-242). Springer.

Schauser, L., Wieloch, W. & Stougaard, J. (2005). Evolution of NIN-like proteins in Arabidopsis, rice and Lotus japonicus. Journal of Molecular Evolution, 60(2), 229-237. https://doi.org/10.1007/s00239-004-0144-2

Scally, A., Dutheil, J. Y., Hillier, L. W., Jordan, G. E., Goodhead, I., Herrero, J., Hobolth, A., Lappalainen, T., Mailund, T., Marques-Bonet, T., McCarthy, S., Montgomery, S. H., Schwalie, P. C., Tang, Y. A., Ward, M. C., Xue, Y., Yngvadottir, B., Alkan, C., Andersen, L. N. ... Durbin, R. (2012). Insights into hominid evolution from the gorilla genome sequence. Nature, 483(7388), 169-75. https://doi.org/10.1038/nature10842

Satterstrom, F. K., Walters, R. K., Singh, T., Wigdor, E. M., Lescai, F., Demontis, D., Kosmicki, J. A., Grove, J., Stevens, C., Bybjerg-Grauholm, J., Bækvad-Hansen, M., Palmer, D. S., Maller, J. B., iPSYCH-Broad Consortium, Nordentoft, M., Mors, O., Robinson, E. B., Hougaard, D. M., Werge, T. M. ... Daly, M. J. (2019). Autism spectrum disorder and attention deficit hyperactivity disorder have a similar burden of rare protein-truncating variants. Nature Neuroscience, 22(12), 1961-1965. https://doi.org/10.1038/s41593-019-0527-8

Satterstrom, F. K., Kosmicki, J. A., Wang, J., Breen, M. S., De Rubeis, S., An, J. Y., Peng, M., Collins, R., Grove, J., Klei, L., Stevens, C., Reichert, J., Mulhern, M. S., Artomov, M., Gerges, S., Sheppard, B., Xu, X., Bhaduri, A., Norman, U. ... Børglum, A. D. (2020). Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism. Cell, 180(3), 568-584.e23. https://doi.org/10.1016/j.cell.2019.12.036

Sanggaard, K. W., Bechsgaard, J. S., Fang, X., Duan, J., Dyrlund, T. F., Gupta, V., Jiang, X., Cheng, L., Fan, D., Feng, Y., Han, L., Huang, Z., Wu, Z., Liao, L., Settepani, V., Thøgersen, I. B., Vanthournout, B., Wang, T., Zhu, Y. ... Wang, J. (2014). Spider genomes provide insight into composition and evolution of venom and silk. Nature Communications, 5, Article 3765. https://doi.org/10.1038/ncomms4765

Sand, A., Brask, A. T., Pedersen, C. N. S., Mailund, T. & Brask, A. T. (2010). HMMlib: A C++ Library for General Hidden Markov Models Exploiting Modern CPUs. In 2010 Ninth International Workshop on Parallel and Distributed Methods in Verification and Second International Workshop on High Performance Computational Systems Biology (pp. 126 - 134 ). IEEE.

Sand, A., Pedersen, C. N. S., Mailund, T., Brodal, G. S. & Fagerberg, R. (2013). A practical O(n log² n) time algorithm for computing the triplet distance on binary trees. BMC Bioinformatics, 14(Suppl 2), S18. https://doi.org/10.1186/1471-2105-14-S2-S18

Sand, A., Holt, M. K., Johansen, J., Fagerberg, R., Pedersen, C. N. S., Brodal, G. S. & Mailund, T. (2013). Algorithms for Computing the Triplet and Quartet Distances for Binary and General Trees. Biology, 2(4), 1189-1209. https://doi.org/10.3390/biology2041189

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Revised 13.01.2026

Palle Villesen