Publications

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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

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

Foldager, L., Kaiser, M. Ø., Chen, G., Jensen, L. D., Kristensen, J. K., Kobek-Kjeldager, C., Thodberg, K., Rong, L. & Herskin, M. S. (2022). Deck height during transport of weaners – piglet height and microclimatic conditions inside trucks. 129-142. Abstract from Symposium i Anvendt Statistik 2022, København, Denmark.

Foldager, L., Kaiser, M., Chen, G., Jensen, L. D., Kristensen, J. K., Kobek-Kjeldager, C., Thodberg, K., Rong, L. & Herskin, M. S. (2022). Deck height during transport of weaners – piglet height and microclimatic conditions inside trucks. In Book of Abstracts of the 73rd Annual Meeting of the European Federation of Animal Science (pp. 181-181). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-937-4

Foldager, L., Kaiser, M. Ø., Chen, G., Jensen, L. D., Kristensen, J. K., Kobek-Kjeldager, C., Thodberg, K., Rong, L. & Herskin, M. S. (2022). Deck height during transport of weaners – piglet height and microclimatic conditions inside trucks. In P. Linde (Ed.), Symposium i anvendt statistik (pp. 129-142). SEGES Innovation. http://www.statistiksymposium.dk/Symposium%202022_Web.pdf

Kobek-Kjeldager, C., Jensen, L. D., Foldager, L., Kaiser, M., Thodberg, K. & Herskin, M. S. (2025). Deck height did not affect behavioural measures of ‘natural movements’ and ‘adequate ventilation’ during 8 h and 23 h transport of weaner pigs. Applied Animal Behaviour Science, 290, Article 106714. https://doi.org/10.1016/j.applanim.2025.106714

Fredslund, J. (2008). DATFAP: A Database of Primers and Homology Alignments for Transcription Factors from 13 Plant Species. BMC Genomics.

Kristensen, T. G. & Pedersen, C. N. S. (2010). Data Structures for Accelerating Tanimoto Queries on Real Valued Vectors. In V. Moulton & M. Singh (Eds.), Algorithms in Bioinformatics: 10th International Workshop (WABI 2010) (Vol. 6293, pp. 28-39). Springer.

Kongsted, H., Foldager, L. & Sørensen, J. T. (2020). Data from routine meat inspection is a poor indicator of the prevalence of tail lesions in undocked pigs. Porcine Health Management, 6(1), Article 10. https://doi.org/10.1186/s40813-020-00149-z

Jónsson, H., Sulem, P., Kehr, B., Kristmundsdottir, S., Zink, F., Hjartarson, E., Hardarson, M. T., Hjorleifsson, K. E., Eggertsson, H. P., Gudjonsson, S. A., Ward, L. D., Arnadottir, G. A., Helgason, E. A., Helgason, H., Gylfason, A., Jonasdottir, A., Jonasdottir, A., Rafnar, T., Besenbacher, S. ... Stefansson, K. (2017). Data Descriptor: Whole genome characterization of sequence diversity of 15,220 Icelanders. Scientific Data, 4, Article 170115. https://doi.org/10.1038/sdata.2017.115

Bache, C., Christiansen, F. B., Løkke, A., Smith, N. & Sneppen, K. (2012). Danske Universiteter 2020: Forskningspolitisk årsmøde 2012. Det Kongelige Danske Videnskabernes Selskab. http://www.royalacademy.dk/Files/Filer/PDF/hvidboger/HVIDBOG.pdf

Kongsted, H., Krogh, M. A., Nielsen, C. L., Henriksen, B. I. F., Foldager, L. & Sørensen, J. T. (2022). Danish welfare-label pig production systems: Usage of antibiotics and occurrence of disease. 83-91. Paper presented at 20th Congress of the International Society for Animal Hygiene , Berlin, Germany.

Foldager, L., Gildbjerg, L. B., Voss, H., Trénel, P., Munksgaard, L. & Thomsen, P. T. (2017). Daily eating activity of dairy cows from 3D accelerometer data and RFID signals: prediction by random forests and detection of sick cows. In P. Linde (Ed.), Symposium i Anvendt Statistik (pp. 109-122)

Abdallah, M., Larsen, N., Grove, J., Nørgaard-Pedersen, B., Mortensen, E. L. & Hougaard, D. M. (2011). Cytokine Levels In Amniotic Fluid: a Marker of Maternal Immune Activation. Abstract from International Meeting for Autism Research (IMFAR 2011), San Diego, CA, United States.

Walker, R. S., Wichmann, S., Mailund, T. & Atkisson, C. J. (2012). Cultural phylogenetics of the tupi language family in lowland South america. PLoS One, 7(4), e35025. https://doi.org/10.1371/journal.pone.0035025

Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G., Reshetnikova, L., Clark, B. F. & Nyborg, J. (1995). Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science, 270(5241), 1464-72.

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.

Hansen, AJ., Mitchell, D., Wiuf, C., Paniker, L., Brand, TB., Binladen, J., Gilichinsky, DA., Rønn, R. & Willerslev, E. (2006). Crosslinks rather than Strand Breaks Determine Access to Ancient DNA Sequences from Frozen Sediments. Genetics, 173, 1175-1179. https://doi.org/10.1534/genetics.106.057349

Aschard, H., Guillemot, V., Vilhjalmsson, B., Patel, C. J., Skurnik, D., Ye, C. J., Wolpin, B., Kraft, P. & Zaitlen, N. (2017). Covariate selection for association screening in multiphenotype genetic studies. Nature Genetics, 49(12), 1789-1795. https://doi.org/10.1038/ng.3975

Bataillon, T., Zhang, T. & Kassen, R. (2011). Cost of Adaptation and Fitness Effects of Beneficial Mutations in Pseudomonas fluorescens. Genetics, 189(3), 939-949. https://doi.org/10.1534/genetics.111.130468

Krogh, M. A., Ettema, J., Østergaard, S. & GplusE Consortium (2018). Cost/benefit analyses on indicator-based intervention on physiological imbalance in dairy cows. 471-471. Poster session presented at The 15th International Symposium of Veterinary Epidemiology and Economic. , Chiang Mai, Thailand.

Wathes, D. C., Cheng, Z., Salavati, M., Buggiotti, L., Takeda, H., Tang, L., Becker, F., Ferris, C. P., Hostens, M., Crowe, M. A. & GplusE Consortium (2021). Corrigendum to "Relationships between metabolic profiles and gene expression in liver and leukocytes of dairy cows in early lactation" (J. Dairy Sci. 104: 3596-3616). Journal of Dairy Science, 104(5), 6327. https://doi.org/10.3168/jds.2021-104-5-6327

Kobek-Kjeldager, C., Jensen, L. D., Foldager, L., Kaiser, M., Thodberg, K. & Herskin, M. S. (2025). Corrigendum to:“Deck height did not affect behavioural measures of ‘natural movements’ and ‘adequate ventilation’ during 8 h and 23 h transport of weaner pigs” (Applied Animal Behaviour Science, (2025), 290, C, (106714), (S0168159125002126), 10.1016/j.applanim.2025.106714). Applied Animal Behaviour Science, 292, Article 106793. https://doi.org/10.1016/j.applanim.2025.106793

Dalby, R. B., Elfving, B., Plougmann, P. H., Foldager, L., Rosenberg, R. & Videbech, P. (2011). Correlations between brain-derived neurotrophic factor (BDNF), vascular endothelial growth factor (VEGF), and vascular risk factors in late-onset major depression. Poster session presented at IBRO 8th World Congress of Neuroscience, Firenze, Italy.

Johnson, S. S., Hebsgaard, M. B., Christensen, T. R., Mastepanov, M., Nielsen, R., Munch, K., Brand, T., Gilbert, M. T. P., Zuber, M. T., Bunce, M., Rønn, R., Gilichinsky, D., Froese, D. & Willerslev, E. (2008). Correction for Johnson et al., Ancient bacteria show evidence of DNA repair. Proceedings of the National Academy of Sciences (PNAS), 105(30). https://doi.org/10.1073/pnas.0804198105

Munch, T. N., Hedley, P. L., Hagen, C. M., Bækvad-Hansen, M., Bybjerg-Grauholm, J., Grove, J., Nordentoft, M., Børglum, A. D., Mortensen, P. B., Werge, T. M., Melbye, M., Hougaard, D. M. & Christiansen, M. (2021). Co-occurring hydrocephalus in autism spectrum disorder: a Danish population-based cohort study. Journal of Neurodevelopmental Disorders, 13(1), 19. Article 19. https://doi.org/10.1186/s11689-021-09367-0

Lee, H., Ko, K., Kim, S., Lee, G., Kim, S., Lee, J., Song, D. Y., Bong, G., Han, J. H., Lee, J., Kim, Y. R., Lee, Y., Kim, E., Børglum, A. D., Grove, J., Kim, S. H., Sun, W., Yoo, H. J. & An, J. Y. (2026). Co-occurrence of rare variants implicates gene pairs in cytoskeletal pathways and is associated with increased severity in autism spectrum disorder. Genome Biology, 27(1), Article 147. https://doi.org/10.1186/s13059-026-04041-x

Horsdal, H. T., Albiñana, C., Zhu, Z., Boelt, S. G., Borbye-Lorenzen, N., Cohen, A. S., Skogstrand, K., Melgaard, L., MacSween, N. J., Thorbek, M. J., Plana-Ripoll, O., Petersen, L. V., Bulik, C. M., Børglum, A. D., Mors, O., Nordentoft, M., Werge, T., Moen, G.-H., D'Urso, S. ... McGrath, J. J. (2025). Convergent evidence linking neonatal vitamin D status and risk of neurodevelopmental disorders: a Danish case-cohort study. The Lancet Psychiatry, 12(6), 410-420. https://doi.org/10.1016/S2215-0366(25)00099-9

Munkacsi, A. B., Pan, J. J., Villesen, P., Mueller, U. G., Blackwell, M. & McLaughlin, D. J. (2004). Convergent coevolution in the domestication of coral mushrooms by fungus-growing ants. Proceedings of the Royal Society B: Biological Sciences, 271(1550), 1777-1782.

Hagberg, O. & Wiuf, C. (2006). Convergence properties of the degree distribution of some network models. Bull Math Biol, 68, 1275-1291. https://doi.org/10.1007/s11538-006-9085-9

Loh, P.-R., Bhatia, G., Gusev, A., Finucane, H. K., Bulik-Sullivan, B. K., Pollack, S. J., Schizophrenia Working Group of the Psychiatric Genomics Consortium (Anders Børglum, Jakob Grove; members of -), O’Donovan, M. C., Neale, B. M., Patterson, N. & Price, A. L. (2015). Contrasting regional architectures of schizophrenia and other complex diseases using fast variance components analysis. Nature Genetics, 47, 1385–1392. https://doi.org/10.1038/ng.3431

Ho-Huu, J., Ronfort, J., De Mita, S., Bataillon, T., Hochu, I., Weber, A. & Chantret, N. (2012). Contrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicago genus (L.). BMC Evolutionary Biology, 12, 195. https://doi.org/10.1186/1471-2148-12-195

Grelet, C., Millot, L., Wolf, V., Lidauer, M., Santschi, D., Hout, F., Naya, H., Meikle, A., Martin, B., Coppa, M., Leblois, J., Crowe, M., Bapst, B., Köck, A., Mensching, A., Gelé, M., GplusE Consortium & Dehareng, F. (2024). Constitution of an international dataset on blood biomarkers in dairy cows: a preliminary study to develop milk MIR models. In Book of Abstracts of the 75th Annual Meeting of the European Federation of Animal Science (pp. 674-674). Article Session 56; Theatre 12 Wageningen Academic Publishers.

Wiuf, C. (2006). Consistency of estimators of population scaled parameters using composite likelihood. Journal of Mathematical Biology, 53, 821-841. https://doi.org/10.1007/s00285-006-0031-0

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

Streja, E., Wu, C., Uldall, P. V., Grove, J., Arah, O. & Olsen, J. (2013). Congenital cerebral palsy, child sex and parent cardiovascular risk. PLoS One, 8(11), e79071. https://doi.org/10.1371/journal.pone.0079071

Siuda, I. & Thøgersen, L. (2013). Conformational flexibility of the leucine binding protein examined by protein domain coarse-grained molecular dynamics. Journal of Molecular Modeling, 19(11), 4931-4945. https://doi.org/10.1007/s00894-013-1991-9

Hansen, L. L., Madsen, B. E., Pedersen, K. & Wiuf, C. (2007). Conflicting results in SNP genotype assessment. BioTechniques, (43), 756-762.

Wiuf, C. & Donelly, P. (1999). Conditional Genealogies and the Age of a Neutral Mutant. Theoretical Population Biology, 56(2), 183-201. https://doi.org/10.1006/tpbi.1998.1411

Christensen, S., Kristensen, L. M. & Mailund (2001). Condensed State Spaces for Timed Petri Nets. In Proceedings of International Conference on Application and Theory of Petri Nets (ICATPN 2001) (pp. 101-120)

Debost, J.-C., Debost, M., Grove, J., Mors, O., Hougaard, D. M., Børglum, A. D., Mortensen, P. B. & Petersen, L. (2017). COMT Val158Met and MTHFR C677T moderate risk of schizophrenia in response to childhood adversity. Acta Psychiatrica Scandinavica, 136(1), 85-95. https://doi.org/10.1111/acps.12761

Christiansen, C., Mailund , Pedersen, C. N. S. & Randers, M. (2005). Computing the Quartet Distance between Trees of Arbitrary Degree. In Proceedings of the 5th International Workshop on Algorithms in Bioinformatics (WABI) (pp. 77-88)

Stissing, M., Pedersen, C. N. S., Mailund, T. & Brodal, G. S. (2007). Computing the Quartet Distance between Evolutionary Trees of Bounded Degree. In Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC) (pp. 101-110)

Brodal, G. S., Fagerberg, R. & Pedersen, C. N. S. (2003). Computing the Quartet Distance Between Evolutionary Trees in Time O(n log n). Algorithmica, 38(2), 377-395. https://doi.org/10.1007/s00453-003-1065-y

Stissing, M., Mailund, T., Pedersen, C. N. S., Brodal, G. S. & Fagerberg, R. (2007). Computing the All-Pairs Quartet Distance on a Set of Evolutionary Trees. In Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC) (pp. 91-100)

Stissing, M., Mailund, T., Pedersen, C. S., Brodal, G. S. & Fagerberg, R. (2008). Computing the all-pairs quartet distance on a set of evolutionary trees. Journal of Bioinformatics and Computational Biology, 6(1), 37-50.

Knudsen, M., Søndergaard, D. A., Tofting-Olesen, C., Hansen, F. T., Brodersen, D. E. & Pedersen, C. S. (2016). Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases. Bioinformatics, 32(3), 325-329. https://doi.org/10.1093/bioinformatics/btv600

Søndergaard, D. A., Knudsen, M. & Pedersen, C. S. (2016). Computational Classification of P-Type ATPases. Methods in Molecular Biology, 1377, 493-502. https://doi.org/10.1007/978-1-4939-3179-8

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Palle Villesen