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

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. Advance online publication. 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

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, 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

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. Advance online publication. 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.

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. Advance online publication. 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.

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

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.

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

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

Mailund, T., Halager, A. E. & Westergaard, M. (2012). Using colored Petri nets to construct coalescent hidden markov models: Automatic translation from demographic specifications to efficient inference methods. Lecture Notes in Computer Science, 7347, 32-50. https://doi.org/10.1007/978-3-642-31131-4_3

Emily, M., Mailund, T., Hein, J., Schauser, L. & Schierup, M. H. (2009). Using biological networks to search for interacting loci in genomewide association studies. European Journal of Human Genetics. https://doi.org/10.1038/ejhg.2009.15

Mansilla, F., Lamy, P., Ørntoft, T. F. & Birkenkamp-Demtröder, K. (2008). Upregulation of genes involved in rRNA processing in colon cancer. Poster session presented at EACR Annual Meeting of the European Association of Cancer Research, Lyon, France.

Krogh, M. A., Enemark, P. S. & Foldager, L. (2019). Unsupervised outlier detection in questionnaire data. Poster session presented at Annunal Conference of the Society for Veterinary Epidemiology and Preventive Medicine (SVEPM), Utrecht, Netherlands.

Renaud, G., Nørgaard, M., Lindberg, J., Grönberg, H., De Laere, B., Jensen, J. B., Borre, M., Andersen, C. L., Sørensen, K. D., Maretty, L. & Besenbacher, S. (2022). Unsupervised detection of fragment length signatures of circulating tumor DNA using non-negative matrix factorization. eLife, 11, Article e71569. https://doi.org/10.7554/ELIFE.71569

Munch, K., Schierup, M. H. & Mailund, T. (2014). Unraveling recombination rate evolution using ancestral recombination maps. BioEssays, 36(9), 892-900. https://doi.org/10.1002/bies.201400047

Hilker, R., Sickinger, C., Pedersen, C. N. S. & Stoye, J. (2012). UniMoG - A unifying framework for genomic distance calculation and sorting based DCJ. Bioinformatics, 28(19), 2509-2511. https://doi.org/10.1093/bioinformatics/bts440

Bechsgaard, J., Bataillon, T. & Schierup, M. H. (2004). Uneven segregation of sporophytic self-incompatibility alleles in Arabidopsis lyrata. J. Evol. Biol., 17, 554-561.

Bechsgaard, J., Bataillon, T. & Schierup, M. H. (2004). Uneven segregation of sporophytic self-incompatibility alleles in arabidopsis lyrata. Journal of Evolutionary Biology, 17(3), 554-561.

Villesen, P., Madsen, B. E. & Wiuf, C. H. (2008). Ultra short tandem repeats: A target for disease mutations. Poster session presented at 9th International Conference on Systems Biology, Gothenburg, Sweden.

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Revised 17.04.2023

Palle Villesen