Publications

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Sørensen, F. J., Andersen, C. L. & Wiuf, C. (2007). SNPTools: A software tool for visualization and analysis of microarray data. Bioinformatics, 23(12), 1550-52. https://doi.org/10.1093/bioinformatics/btm122

Wiuf, C. & Hein, J. (1997). On the number of ancestors to a DNA sequence. Genetics, 147, 1459-1468.

De Mita, S., Santoni, S., Hochu, I., Ronfort, J. & Bataillon, T. (2006). Molecular evolution and positive selection of the symbiotic gene NORK in Medicago truncatula. Journal of Molecular Evolution, 62(2), 234-244.

Glemin, S., Ronfort, J., Vimond, L., Bataillon, T. & Mignot, A. (2006). Marker-based investigation of inbreeding depression in the endangered species Brassica insularis. Iden, 97(4), 304-311.

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

Lamy, P., Andersen, C. L., Andersen, L. D., Tørring, N., Ørntoft, T. F. & Wiuf, C. (2006). Are microRNAs located in cancer specific regions in the genome? British Journal of Cancer, 95(10), 1415-8. https://doi.org/10.1038/sj.bjc.6603381

Sand, A., Kristiansen, M., Pedersen, C. N. S. & Mailund, T. (2013). zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm. BMC Bioinformatics , 14(339), 339-348. https://doi.org/10.1186/1471-2105-14-339

Bergman, J., Pedersen, R., Lundgren, E. J., Lemoine, R. T., Monsarrat, S., Pearce, E. A., Schierup, M. H. & Svenning, J. C. (2023). Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change. Nature Communications, 14(1), Article 7679. https://doi.org/10.1038/s41467-023-43426-5

Murra, M., Lützen, L., Barut, A., Zbinden, R., Lund, M., Villesen, P. & Nørskov-Lauritsen, N. (2018). Whole-genome sequencing of aggregatibacter species isolated from human clinical specimens and description of Aggregatibacter kilianii sp. Nov. Journal of Clinical Microbiology, 56(7), Article UNSP e00053-18. https://doi.org/10.1128/JCM.00053-18

Bai, H., Guo, X., Narisu, N., Lan, T., Wu, Q., Xing, Y., Zhang, Y., Bond, S. R., Pei, Z., Zhang, Y., Zhang, D., Jirimutu, J., Zhang, D., Yang, X., Morigenbatu, M., Zhang, L., Ding, B., Guan, B., Cao, J. ... Yin, Y. (2018). Whole-genome sequencing of 175 Mongolians uncovers population-specific genetic architecture and gene flow throughout North and East Asia. Nature Genetics, 50(12), 1696–1704. https://doi.org/10.1038/s41588-018-0250-5

Kim, S. W., Lee, H., Song, D. Y., Lee, G. H., Ji, J., Park, J. W., Han, J. H., Lee, J. W., Byun, H. J., Son, J. H., Kim, Y. R., Lee, Y., Kim, J., Jung, A., Lee, J., Kim, E., Kim, S. H., Lee, J. H., Satterstrom, F. K. ... An, J. Y. (2024). Whole genome sequencing analysis identifies sex differences of familial pattern contributing to phenotypic diversity in autism. Genome Medicine, 16(1), 114. Article 114. https://doi.org/10.1186/s13073-024-01385-6

Branca, A., Paape, T. D., Zhou, P., Briskine, R., Farmer, A. D., Mudge, J., Bharti, A. K., Woodward, J. E., May, G. D., Gentzbittel, L., Ben, C., Denny, R., Sadowsky, M. J., Ronfort, J., Bataillon, T., Young, N. D. & Tiffin, P. (2011). Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proceedings of the National Academy of Sciences (PNAS), 108(42), 864-870. https://doi.org/10.1073/pnas.1104032108

Mailund, T., Besenbacher, S. & Schierup, M. H. (2006). Whole genome association mapping by incompatibilities and local perfect phylogenies. B M C Bioinformatics, 7(454). https://doi.org/10.1186/1471-2105-7-454

Nordentoft, I. K., Lamy, P., Birkenkamp-Demtröder, K., Vang, S., Reinert, T., Hedegaard, J., Thorsen, K., Fristrup, N., Borre, M., Andersen, L. D., Pedersen, J. S. & Ørntoft, T. F. (2013). Whole genome and transcriptome analysis reveals novel genomic alterations in bladder cancer. Poster session presented at American Association for Cancer Research, Washington, DC, United States.

Stukenbrock, E., Jørgensen, F., Zala, M., Hansen, T. T., McDonald, B. A. & Schierup, M. H. (2010). Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola. P L o S Genetics, 23(6).

Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., Suh, A., Weber, C. C., da Fonseca, R. R., Li, J., Zhang, F., Li, H., Zhou, L., Narula, N., Liu, L. ... Zhang, G. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320-31. https://doi.org/10.1126/science.1253451

Heinz, J. L., Swagemakers, S. M. A., von Hofsten, J., Helleberg, M., Thomsen, M. M., De Keukeleere, K., de Boer, J. H., Ilginis, T., Verjans, G. M. G. M., van Hagen, P. M., van der Spek, P. J. & Mogensen, T. H. (2023). Whole exome sequencing of patients with varicella-zoster virus and herpes simplex virus induced acute retinal necrosis reveals rare disease-associated genetic variants. Frontiers in Molecular Neuroscience, 16, Article 1253040. https://doi.org/10.3389/fnmol.2023.1253040

Lescai, F., Als, T. D., Li, Q., Nyegaard, M., Andorsdottir, G., Biskopstø, M., Hedemand, A., Fiorentino, A., O'Brien, N. L., Jarram, A., Liang, T. J., Grove, J., Pallesen, J., Eickhardt, E., Mattheisen, M., Bolund, L., Demontis, D., Wang, A. G., McQuillin, A. ... Børglum, A. D. (2017). Whole-exome sequencing of individuals from an isolated population implicates rare risk variants in bipolar disorder. Translational Psychiatry, 7(2), e1034. Article 3. https://doi.org/10.1038/tp.2017.3

Lavigne, F., Martin, G., Anciaux, Y., Papaix, J. & Roques, L. (2020). When sinks become sources: Adaptive colonization in asexuals. Evolution, 74(1), 29-42. https://doi.org/10.1111/evo.13848

Ehlers, B. & Schierup, M. H. (2008). When gametophytic self-incompatibility meets gynodioecy. Genetics Research, 90(1), 27-35. https://doi.org/10.1017/S0016672307009007

Bailey, S. F., Blanquart, F., Bataillon, T. & Kassen, R. (2017). What drives parallel evolution? How population size and mutational variation contribute to repeated evolution. BioEssays, 39(1), 1-9. https://doi.org/10.1002/bies.201600176

Chen, J., Bataillon, T., Glémin, S. & Lascoux, M. (2022). What does the distribution of fitness effects of new mutations reflect? Insights from plants. New Phytologist, 233(4), 1613-1619. https://doi.org/10.1111/nph.17826

Ye, J., Fang, L., Zheng, H., Zhang, Y., Chen, J., Zhang, Z., Wang, J., Li, S., Li, R., Bolund, L. & Wang, J. (2006). WEGO: a web tool for plotting GO annotations. Nucleic Acids Research, 34(Web Server issue), W293-7. https://doi.org/10.1093/nar/gkl031

Winters, J. F. M., Schönherz, A. A., Canibe, N., Foldager, L. & Pedersen, L. J. (2022). Weaning intact litters in farrowing pens for loose housed sows: diarrhoea and microbiota composition . In Book of Abstracts of the 73rd Annual Meeting of the European Federation of Animal Science (pp. 348-348). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-937-4

Nilsson, J., Sengupta, J., Gursky, R., Kjeldgaard, M., Nissen, P. & Frank, J. (2008). Visualization of the eEF2-80S ribosome transition-state complex by cryo-electron microscopy. Journal of Molecular Biology, 382(1), 179-187.

Kristensen, T. G. (2011). Virtual screening algorithms. Department of Computer Science, Aarhus University.

Sükösd, Z. (2013). Viral RNA secondary structure prediction.

Lauterbur, M. E., Munch, K. & Enard, D. (2023). Versatile Detection of Diverse Selective Sweeps with Flex-Sweep. Molecular Biology and Evolution, 40(6), Article msad139. https://doi.org/10.1093/molbev/msad139

Castagnini, A. & Foldager, L. (2013). Variations in incidence rates and age of onset of acute and transient psychotic disorders. Social Psychiatry and Psychiatric Epidemiology, 48(12), 1917-1922. https://doi.org/10.1007/s00127-013-0726-7

Moutinho, A. F., Bataillon, T. & Dutheil, J. Y. (2020). Variation of the adaptive substitution rate between species and within genomes. Evolutionary Ecology, 34(3), 315-338. https://doi.org/10.1007/s10682-019-10026-z

Stride Nielsen, L., Villesen, P. & Lindholst, C. (2017). Variation in chemical profiles within large seizures of cocaine bricks. Forensic Science International, 280, 194-199. https://doi.org/10.1016/j.forsciint.2017.10.007

Li, S., Besenbacher, S., Li, Y., Kristiansen, K., Grarup, N., Albrechtsen, A., Sparsø, T. H., Korneliussen, T. S., Hansen, T., Wang, J., Nielsen, R., Pedersen, O., Bolund, L. & Schierup, M. H. (2014). Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population. European Journal of Human Genetics. https://doi.org/10.1038/ejhg.2013.282

Hannon, E., Schendel, D., Ladd-Acosta, C., Grove, J., Hansen, C. S., 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. D., Fallin, M. D., Bybjerg-Grauholm, J. ... Mill, J. (2019). Variable DNA methylation in neonates mediates the association between prenatal smoking and birth weight. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1770), Article 20180120. https://doi.org/10.1098/rstb.2018.0120

Aagaard, J., Nissen, F., Wernlund, A., Foldager, L. & Merinder, L. (2013). Valuable intervention against the excess mortality of psychiatric patients.

Aagaard, J., Nissen, F., Wernlund, A., Foldager, L. & Merinder, L. (2014). Valuable intervention against the excess mortality of psychiatric patients. Poster session presented at Annual Conference of the International Society for Bipolar Disorder, Seoul, Korea, Republic of. https://doi.org/10.1111/bdi.12189

Riber, A. B., Foldager, L. & Tahamtani, F., (2019). Validitet og pålidelighed af Øko-metoden anvendt til fjerdragtsbedømmelse hos æglæggere, No. 2019-760-001051, 5 p., Sept 16, 2019.

Soyeurt, H., Froidmont, E., Dufrasne, I., Wang, Z., Gengler, N., Dehareng, F., GplusE Consortium & Grelet, C. (2019). Validation of the prediction of body weight from dairy cow characteristics and milk MIR spectra. In Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science (Vol. 25, pp. 606). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-890-2

Tedde, A., Grelet, C., Ho, P. N., Pryce, J. E., Hailemariam, D., Wang, Z., Plastow, G., Gengler, N., Brostaux, Y., Froidmont, E., Dehareng, F., Bertozzi, C., Crowe, M. A., Dufrasne, I., GplusE Consortium & Soyeurt, H. (2021). Validation of dairy cow bodyweight prediction using traits easily recorded by dairy herd improvement organizations and its potential improvement using feature selection algorithms. Animals, 11(5), Article 1288. https://doi.org/10.3390/ani11051288

Kobek-Kjeldager, C., Jensen, L. D., Foldager, L., Kaiser, M., Thodberg, K. & Herskin, M. S. (2024). Validation of behavioural sampling techniques for 20-25 kg pigs during transport. Livestock Science, 280, Article 105411. https://doi.org/10.1016/j.livsci.2024.105411

Kobek-Kjeldager, C., Jensen, L. D., Foldager, L., Kaiser, M., Thodberg, K. & Herskin, M. S. (2022). Validation of behavioural sampling techniques for 20-25 kg pigs during 23-hour transport. In M. Kjosevski, S. Waiblinger & V. Ilieski (Eds.), Proceedings of the 55th Congress of the ISAE: Animal Behaviour and Beyond (pp. 167-167). https://www.applied-ethology.org/res/ISAE_2022_PROCEEDINGS_e-version.pdf

Chen, Y., Atashi, H., Mota, R. R., Grelet, C., Vanderick, S., Hu, H., GplusE Consortium & Gengler, N. (2023). Validating genomic prediction for nitrogen efficiency index and its composition traits of Holstein cows in early lactation. Journal of Animal Breeding and Genetics (Online), 140(6), 695-706. https://doi.org/10.1111/jbg.12819

Andersen, F. F., Villesen, P., Knudsen, B., Wiuf, C. H., Desideri, A. & Knudsen, B. R. (2011). Utilization of Computer Science for Construction and Characterization of DNA nano-Structures. In DNA Microarrays, Synthesis and Synthetic DNA Nova Science Publishers.

Simonsen, M., Sand, A., Mailund, T. & Pedersen, C. N. S. (2010). Using the Power of Modern Processors in Bioformatics. Poster session presented at Conference on IT research at AU, Århus, Denmark.

Kazemi Naeini, M., Akbarzadeh, M., Kazemi, I., Speed, D. & Hosseini, S. M. (2024). Using the Bayesian variational spike and slab model in a genome-wide association study for finding associated loci with bipolar disorder. Annals of Human Genetics, 88(3), 212-246. https://doi.org/10.1111/ahg.12538

Hartfield, M., Poulsen, N. A., Guldbrandtsen, B. & Bataillon, T. (2021). Using singleton densities to detect recent selection in Bos taurus. Evolution Letters, 5(6), 595-606. https://doi.org/10.1002/evl3.263

Hammami, H., Mota, R. R., Vanderick, S., Naderi, S., Bastin, C., Gengler, N. & GplusE Consortium (2019). Using milk MIR spectra to identify candidate genes associated with climate--smart traits in cattle. In Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science (Vol. 25, pp. 607). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-890-2

Foldager, L. (2010). Using logic regression to identify SNP interactions based on individually time-matched case-control data. Abstract from PhD Day 2010, Århus, Denmark.

Ratmann, O., Jørgensen, O., Hinkley, T., Stumpf, M., Richardson, S. & Wiuf, C. (2007). Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum. PLoS Comp Biol, 3(e320). https://doi.org/10.1371/journal.pcbi.0030230.eor

Kristensen, T. G., Nielsen, J. & Pedersen, C. N. S. (2011). Using Inverted Indices for Accelerating LINGO Calculations. Journal of Chemical Information and Modeling, 51(3), 597-600. https://doi.org/10.1021/ci100437e

Gaspar, H. A., Gerring, Z., Hübel, C., Middeldorp, C. M., Derks, E. M., Breen, G. & Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium (2019). Using genetic drug-target networks to develop new drug hypotheses for major depressive disorder. Translational Psychiatry, 9(1), Article 117. https://doi.org/10.1038/s41398-019-0451-4

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Revised 21.08.2024

Palle Villesen