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Section for Bioinformatics and Computational Biology

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Debost, J.-C., Petersen, L., Grove, J., Khashan, A., Henriksen, T., Mors, O., Hollegaard, M., Hougaard, D., Nyegaard, M., Børglum, A. & Mortensen, P. B. (2015). Investigating interactions between early life stress and two single nucleotide polymorphisms in HSD11B2 on the risk of schizophrenia. Psychoneuroendocrinology, 60, 18-27. https://doi.org/10.1016/j.psyneuen.2015.05.013

Fredsted, T., Wincentz, T. & Villesen, P. (2006). Introgression of mountain hare (Lepus timidus) mitochondrial DNA into wild brown hares (Lepus europaeus) in Denmark. BMC Ecology, 6(17).

Christiansen, F. (1988). Intraspecific competition and evolution: Contributions to Theoretical Ecology. Paper presented at Intraspecific competition and evolution, Julich, Germany.

Christiansen, F. & Loeschcke, V. (1980). Intraspecific competition and evolution. In C. Barigozzi (Ed.), Vito Volterra Symposium on Mathematical Models in Biology (pp. 151-170). Springer.

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.

Thomsen, A. H., Leth, P. M., Hougen, H. P. & Villesen, P. (2023). Intimate partner homicides in Denmark 1992-2016. Forensic Science International: Synergy, 6, Article 100337. https://doi.org/10.1016/j.fsisyn.2023.100337

Pearce, B. D., Grove, J., Bonney, E. A., Bliwise, N., Dudley, D. J., Schendel, D. & Thorsen, P. (2010). Interrelationship of cytokines, hypothalamic-pituitary-adrenal axis hormones, and psychosocial variables in the prediction of preterm birth. Gynecologic and Obstetric Investigation, 70(1), 40-46. https://doi.org/10.1159/000284949

Papini, N. M., Presseller, E., Bulik, C. M., Holde, K., Larsen, J. T., Thornton, L. M., Albiñana, C., Vilhjálmsson, B. J., Mortensen, P. B., Yilmaz, Z. & Petersen, L. V. (2024). Interplay of polygenic liability with birth-related, somatic, and psychosocial factors in anorexia nervosa risk: a nationwide study. Psychological Medicine, 54(9), 2073-2086. https://doi.org/10.1017/S0033291724000175

Brikell, I., Wimberley, T., Albiñana, C., Vilhjálmsson, B. J., Agerbo, E., Børglum, A. D., Demontis, D., Schork, A. J., LaBianca, S., Werge, T., Hougaard, D. M., Nordentoft, M., Mors, O., Mortensen, P. B., Petersen, L. V. & Dalsgaard, S. (2023). Interplay of ADHD Polygenic Liability With Birth-Related, Somatic, and Psychosocial Factors in ADHD: A Nationwide Study. The American Journal of Psychiatry (Spanish Edition), 180(1), 73-88. https://doi.org/10.1176/appi.ajp.21111105

Grove, J., Foldager, L., Demontis, D., Hollegaard, M. V., Pedersen, C. B., Yolken, R. H., Hougaard, D. M., Mors, O., Mortensen, P. B., The Psychiatric Genomics Consortium – Schizophrenia & Børglum, A. (2013). Interaction between polygenic scores for schizophrenia and infection by herpes simples virus 1 and 2. Poster session presented at XXIst World Congress of Psychiatric Genetics, Boston, United States.

Foldager, L., Thorup, V. M., Pastell, M., Frandsen, M., Jensen, B. B. & Krogh, M. A. (2024). IntelliRAS - some results from a project on precision fish farming in recirculation aquaculture systems. In Book of Abstracts of the 75th Annual Meeting of the European Federation of Animal Science (pp. 284-284). Article Session 14; Theatre 11 Wageningen Academic Publishers.

Paczkowska, M., Barenboim, J., Sintupisut, N., Fox, N. S., Zhu, H., Abd-Rabbo, D., Mee, M. W., Boutros, P. C., PCAWG Drivers and Functional Interpretation Working Group, Reimand, J. & PCAWG Consortium (2020). Integrative pathway enrichment analysis of multivariate omics data. Nature Communications, 11(1), Article 735. https://doi.org/10.1038/s41467-019-13983-9

Winge, S. B., Soraggi, S., Schierup, M. H., Rajpert-De Meyts, E. & Almstrup, K. (2020). Integration and reanalysis of transcriptomics and methylomics data derived from blood and testis tissue of men with 47,XXY Klinefelter syndrome indicates the primary involvement of Sertoli cells in the testicular pathogenesis. American Journal of Medical Genetics. Part C: Seminars in Medical Genetics, 184(2), 239-255. https://doi.org/10.1002/ajmg.c.31793

GROUP Investigators & iPSYCH-GEMS SCZ (Jakob Grove, member of -) (2014). Integrated Pathway-Based Approach Identifies Association between Genomic Regions at CTCF and CACNB2 and Schizophrenia. PLoS Genetics, 10(6), e1004345. https://doi.org/10.1371/journal.pgen.1004345

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

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

Lan, T., Leppälä, K., Tomlin, C., Talbot, S. L., Sage, G. K., Farley, S. D., Shideler, R. T., Bachmann, L., Wiig, Ø., Albert, V. A., Salojärvi, J., Mailund, T., Drautz-Moses, D. I., Schuster, S. C., Herrera-Estrella, L. & Lindqvist, C. (2022). Insights into bear evolution from a Pleistocene polar bear genome. Proceedings of the National Academy of Sciences (PNAS), 119(24), Article e2200016119. https://doi.org/10.1073/pnas.2200016119

Sjödin, P., Bataillon, T. & Schierup, M. H. (2010). Insertion and deletion processes in recent human history. PLoS One, 5(1), e8650. https://doi.org/10.1371/journal.pone.0008650

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)

Boni, M. F., Gog, J. R., Andreasen, V. & Christiansen, F. B. (2004). Influenza drift and epidemic size: the race between generating and escaping immunity. Theoretical Population Biology, 65, 179-191.

Ravn, P., Forsberg, R. & Christiansen, F. (2007). Influenza: - menneskets uforudsigelige følgesvend. Aktuel Naturvidenskab, 2007(2), 16-20.

Cheng, Z., Little, M. W., Ferris, C., Takeda, H., Ingvartsen, K. L., Crowe, M. A., Wathes, D. C. & GplusE Consortium (2023). Influence of the concentrate inclusion level in a grass silage-based diet on hepatic transcriptomic profiles in Holstein-Friesian dairy cows in early lactation. Journal of Dairy Science, 106(8), 5805-5824. https://doi.org/10.3168/jds.2022-22860

Winters, J. F. M., Foldager, L., Krogh, U., Nørskov, N. & Sørensen, M. T. (2022). Influence of glyphosate residues in sow diets on piglet diarrhoea, kinky tails and stillbirth. In Book of Abstracts of the 73rd Annual Meeting of the European Federation of Animal Science (pp. 284-284). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-937-4

Sørensen, M. T., Dalgaard, T. S., Kjærup, R. B., Mandrioli, D. & Foldager, L. (2026). Influence of glyphosate in feed on egg hatchability and health of chicks and breeder hens. British Poultry Science. Advance online publication. https://doi.org/10.1080/00071668.2026.2615732

Sørensen, M. T., Krogh, U., Højberg, O., Nørskov, N. P. & Foldager, L. (2026). Influence of diet glyphosate residues on performance and mineral status in group-housed weaning pigs. Livestock Science, 311, 1-7. Article 106001. Advance online publication. https://doi.org/10.1016/j.livsci.2026.106001

Mailund, T., Munch, K. & Schierup, M. H. (2014). Inferring the Process of Human–Chimpanzee Speciation. In Encyclopedia of Life Sciences Wiley. https://doi.org/10.1002/9780470015902.a0020833.pub2

Charmouh, A. P., Bocedi, G. & Hartfield, M. (2023). Inferring the distributions of fitness effects and proportions of strongly deleterious mutations. G3: Genes, Genomes, Genetics, 13(9), Article jkad140. https://doi.org/10.1093/g3journal/jkad140

Madsen, T., Nielsen, M. M., Pedersen, J. S., PCAWG Evolution and Heterogeneity Working Group & PCAWG Consortium (2020). Inferring structural variant cancer cell fraction. Nature Communications, 11(1), Article 730. https://doi.org/10.1038/s41467-020-14351-8

Wiuf, C. (2003). Inferring population history from geneaological trees. Journal of Mathematical Biology, 46, 241-264. https://doi.org/10.1007/s00285-002-0180-8

Andersen, L. N. (2011). Inferring Population Histories In The IM-model Using Site Pattern Analysis. Poster session presented at SMBE 2011, Kyoto, Japan.

Nielsen, S., Simonsen, S. & Hobolth, A. (2016). Inferring Population Genetic Parameters: Particle Filtering, HMM, Ripley’s K-Function or Runs of Homozygosity? In M. Frith & C. Nørgaard Storm Pedersen (Eds.), Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings (Vol. 9838, pp. 234-245). Springer. https://doi.org/10.1007/978-3-319-43681-4_19

Privé, F., Albiñana, C., Arbel, J., Pasaniuc, B. & Vilhjálmsson, B. J. (2023). Inferring disease architecture and predictive ability with LDpred2-auto. American Journal of Human Genetics, 110(12), 2042-2055. https://doi.org/10.1016/j.ajhg.2023.10.010

Tataru, P., Bataillon, T. & Hobolth, A. (2015). Inference Under a Wright-Fisher Model Using an Accurate Beta Approximation. Genetics, 201(3), 1133-1141.

Wiuf, C. (2004). Inference on recombination and block structure using unphased data. Genetics, 166, 537-545.

Mollion, M. (2018). Inference on adaptation from population genomics data.

Bataillon, T., Duan, J., Hvilsom, C., Jin, X., Li, Y., Skov, L., Glemin, S., Munch, K., Jiang, T., Qian, Y., Hobolth, A., Wang, J., Mailund, T., Siegismund, H. R. & Schierup, M. H. (2015). Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing. Genome Biology and Evolution, 7(4), 1122-32. https://doi.org/10.1093/gbe/evv058

Tataru, P. (2015). Inference of population history and patterns from molecular data. Department of Computer Science, Aarhus University.

Simonsen, M., Mailund, T. & Pedersen, C. N. S. (2011). Inference of Large Phylogenies Using Neighbour-Joining. Biomedical Engineering Systems and Technologies, 127(5), 334-344. https://doi.org/10.1007/978-3-642-18472-7_26

Tataru, P., Mollion, M., Glémin, S. & Bataillon, T. (2017). Inference of distribution of fitness effects and proportion of adaptive substitutions from polymorphism data. Genetics, 207(3), 1103-1119. https://doi.org/10.1534/genetics.117.300323

W. Abdallah, M., M. Hougaard, D., Nørgaard-Pedersen, B., Grove, J., Bonefeld-Jørgensen, E. C. & L. Mortensen, E. (2012). Infections during Pregnancy and after birth and risk of autism spectrum disorders: a register-based study utilizing a Danish historic birth cohort. Turk Psikiyatri Dergisi, 23(4). https://doi.org/10.5080/u6847

Dam, M., Centanni, M., Friberg, L. E., Centanni, D., Karlsson, M. O., Stensig Lynggaard, L., Johannsdottir, I. M., Wik, H. S., Malmros, J., Vaitkeviciene, G. E., Griskevicius, L., Hallböök, H., Jónsson, Ó. G., Overgaard, U., Schmiegelow, K., Hansen, S. N., Heyman, M. & Albertsen, B. K. (2024). Increase in peg-asparaginase clearance as a predictor for inactivation in patients with acute lymphoblastic leukemia. Leukemia, 38(4), 712-719. https://doi.org/10.1038/s41375-024-02153-6

Nielsen, J., Foldager, L. & Meyer, J. M. (2009). Increased use of antibiotics in patients treated with clozapine. European Neuropsychopharmacology, 19(7), 483-486.

Pedersen, J. G., Sokac, M., Sørensen, B. S., Luczak, A. A., Aggerholm-Pedersen, N., Birkbak, N. J., Øllegaard, T. H. & Jakobsen, M. R. (2022). Increased Soluble PD-1 Predicts Response to Nivolumab plus Ipilimumab in Melanoma. Cancers, 14(14), Article 3342. https://doi.org/10.3390/cancers14143342

Jørgensen, F. G. & Schierup, M. H. (2009). Increased rate of human mutations where DNA and RNA polymerases collide. Trends in Genetics, 25(12), 523-527. https://doi.org/10.1016/j.tig.2009.10.002

Holmstrup, M., Sørensen, J. G., Maraldo, K., Schmidt, I. K., Mason, S., Tietema, A., Smith, A. R., Emmett, B., Schmelz, R., Bataillon, T., Beier, C. & Ehlers, B. K. (2012). Increased frequency of drought reduces species richness of enchytraeid communities in both wet and dry heathland soils. Soil Biology & Biochemistry, 53, 43-49. https://doi.org/10.1016/j.soilbio.2012.05.001

Holmstrup, M., Sørensen, J. G., Maraldo, K., Schmidt, I., Tietema, A., Smith, A., Schmelz, R., Bataillon, T. & Ehlers, B. (2012). Increased frequency of drought depletes species richness of enchytraeid communities in both wet and dry heathland soils. Soil Biology & Biochemistry, 53, 43-49. https://doi.org/10.1016/j.soilbio.2012.05.001

Herbsleb, M., Birkenkamp-Demtröder, K., Andersen, T. T., Wiuf, C., Hein, A.-M. K., Ørntoft, T. F. & Andersen, L. D. (2008). Increased cell motility and invasion upon knockdown of lipolysis stimulated lipoprotein receptor (LSR) in SW780 bladder cancer cells. BMC Medical Genomics, 1. https://doi.org/10.1186/1755-8794-1-31

Herbsleb, M., Birkenkamp-Demtroder, K., Thykjaer, T., Wiuf, C., Hein, A.-M. K., Orntoft, T. F. & Andersen, L. D. (2008). Increased cell motility and invasion upon knockdown of lipolysis stimulated lipoprotein receptor (LSR) in SW780 bladder cancer cells. BMC Medical Genomics, 1, 31. https://doi.org/10.1186/1755-8794-1-31

Dittmer, J., Thøgersen, L., Underhaug, J., Bertelsen, K., Vosegaard, T., Pedersen, J. M., Schiøtt, H. B., Tajkhorshid, E., Skrydstrup, T. & Nielsen, N. C. (2009). Incorporation of Antimicrobial Peptides into Membranes: A Combined Liquid-State NMR and Molecular Dynamics Study of Alamethicin in DMPC/DHPC Bicelles. Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 113(19), 6928-6937. https://doi.org/10.1021/jp811494p

Ehlers, B. & Bataillon, T. (2007). ‘Inconstant males' and the maintenance of labilesex expression in subdioecious plants. New Phytologist. https://doi.org/10.1111/j.1469-8137.2007.01975.x

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