Publications

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Christiansen, F. (1987). Pleiotropy in dynamical parameters of models on the evolution of simple phenotypes. In V. Loeschcke (Ed.), Genetic Constraints on Adaptive Evolution (pp. 107-124). Springer.

Dalby, R. B., Elfving, B., Poulsen, P. H. P., Foldager, L., Frandsen, J., Videbech, P. & Rosenberg, R. (2013). Plasma brain-derived neurotrophic factor and prefrontal white matter integrity in late-onset depression and normal aging. Acta Psychiatrica Scandinavica, 128(5), 387-396. https://doi.org/10.1111/acps.12085

Wernersson, R., Schierup, M. H., Jørgensen, F. G., Gorodkin, J., Panitz, F., Staerfeldt, HH., Christensen, O. F., Mailund, T., Hornshøj, H., Klein, A., Jun, W., Liu, B., Hu, S., Dong, W., Li, W., Wong, GK-S., Yu, J., Wang, J., Bendixen, C. ... Bolund, L. (2005). Pigs in Sequence Space: A 0.66X Coverage Pig Genome Survey based on Shotgun Sequencing. B M C Genomics, 6(70). http://www.biomedcentral.com/1471-2164/6/70

Swine Genome Sequencing Consortium (2012). Pig genomes provide insight into porcine demography, domestication and evolution. Nature, 491, 393-398. https://doi.org/10.1038/nature11622

Mikalsen, S-O., Tausen, M. & Kongsstovu, S. I. (2020). Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies. BMC Genomics, 21(1), [223]. https://doi.org/10.1186/s12864-020-6620-2

Zheng, J., Richardson, T. G., Millard, L. A. C., Hemani, G., Elsworth, B. L., Raistrick, C. A., Vilhjalmsson, B., Neale, B. M., Haycock, P. C., Smith, G. D. & Gaunt, T. R. (2018). PhenoSpD: an integrated toolkit for phenotypic correlation estimation and multiple testing correction using GWAS summary statistics. GigaScience, 7(8), 1-10. https://doi.org/10.1093/gigascience/giy090

Watkins, T. B. K., Lim, E. L., Petkovic, M., Elizalde, S., Birkbak, N. J., Wilson, G. A., Moore, D. A., Grönroos, E., Rowan, A., Dewhurst, S. M., Demeulemeester, J., Dentro, S. C., Horswell, S., Au, L., Haase, K., Escudero, M., Rosenthal, R., Bakir, M. A., Xu, H. ... Swanton, C. (2020). Pervasive chromosomal instability and karyotype order in tumour evolution. Nature, 587, 126-132. https://doi.org/10.1038/s41586-020-2698-6

Andreasen, V. & Christiansen, F. (1989). Persistence of an infectious disease in a subdivided population. Mathematical Biosciences, 96, 239-253.

Krogh, U., Højberg, O., Foldager, L., Rani, S., Nørskov, N. P. & Sørensen, M. T. (2021). Performance and mineral status of weaning pigs fed diets with different levels of glyphosate and tryptophan. Livestock Science, 252, [104681]. https://doi.org/10.1016/j.livsci.2021.104681

Thøgersen, L., Schiøtt, B., Vosegaard, T., Nielsen, N. C. & Tajkhorshid, E. (2008). Peptide Aggregation and Pore Formation in a Lipid Bilayer: A Combined Coarse-Grained and All Atom Molecular Dynamics Study. Biophysical Journal, 95(9), 4337-4347. https://doi.org/10.1529/biophysj.108.133330

Jimenez Mena, B., Schad, K., Hanna, N. & Lacy, R. C. (2016). Pedigree analysis for the genetic management of group-living species. Ecology and Evolution, 6(10), 3067-3078. https://doi.org/10.1002/ece3.1831

Villesen, P. & Boomsma, JJ. (2003). Patterns of male parentage in the fungus-growing ants. Behavioral Ecology and Sociobiology, 53(4), 246-253.

Glémin, S., Ronfort, J. & Bataillon, T. (2003). Patterns of inbreeding depression and architecture of the load in subdivided populations. Genetics, 165(4), 2193-212.

Mollion, M., Ehlers, B., Figuet, E., Santoni, S., Lenormand, T., Maurice, S., Galtier, N. & Bataillon, T. (2018). Patterns of genome-wide nucleotide diversity in the gynodioecious plant Thymus vulgaris are compatible with recent sweeps of cytoplasmic genes. Genome Biology and Evolution, 10(1), 239-248. https://doi.org/10.1093/gbe/evx272

Reyna, M. A., Haan, D., Paczkowska, M., Verbeke, L. P. C., Vazquez, M., Kahraman, A., Pulido-Tamayo, S., Barenboim, J., Wadi, L., Dhingra, P., Shrestha, R., Getz, G., Lawrence, M. S., Pedersen, J. S., Rubin, M. A., Wheeler, D. A., Brunak, S., Izarzugaza, J. M. G., Khurana, E. ... PCAWG Consortium (2020). Pathway and network analysis of more than 2500 whole cancer genomes. Nature Communications, 11(1), [729]. https://doi.org/10.1038/s41467-020-14367-0

Nielsen, A. L-L., Olsen, L. C., Saetrom, P., Drabløs, F., Besenbacher, S., Steenberg, L. R., Johansen, C. & Iversen, L. (2016). Pathway Analysis of Skin from Psoriasis Patients after Adalimumab Treatment Reveals New Early Events in the Anti-Inflammatory Mechanism of Anti-TNF-α. P L o S One, 11(12), e0167437. https://doi.org/10.1371/journal.pone.0167437

Kumar, S., Warrell, J., Li, S., McGillivray, P. D., Meyerson, W., Salichos, L., Harmanci, A., Martinez-Fundichely, A., Chan, C. W. Y., Nielsen, M. M., Lochovsky, L., Zhang, Y., Li, X., Lou, S., Pedersen, J. S., Herrmann, C., Getz, G., Khurana, E. & Gerstein, M. B. (2020). Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences. Cell, 180(5), 915-927.e16. https://doi.org/10.1016/j.cell.2020.01.032

Gusev, A., Lee, S. H., Trynka, G., Finucane, H., Vilhjálmsson, B. J., Xu, H., Zang, C., Ripke, S., Bulik-Sullivan, B., Stahl, E., Kähler, A. K., Hultman, C. M., Purcell, S. M., McCarroll, S. A., Daly, M., Pasaniuc, B., Sullivan, P. F., Neale, B. M., Wray, N. R. ... Schizophrenia Working Group of the Psychiatric Genomics Consortium (Manuel Mattheisen and Jakob Grove, members) (2014). Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases. American Journal of Human Genetics, 95(5), 535-52. https://doi.org/10.1016/j.ajhg.2014.10.004

Mailund (1999). Parameterised coloured Petri nets. In Prorceedings of the second workshop on practical use of coloured Petri nets and Design/CPN (pp. 133-151)

Andersen, L. N. & Asmussen, S. (2008). Parallel computing, failure recovery and extreme values. Journal of Statistical Theory and Practice, 2(2), 279-292.

Hornshøj, H., Nielsen, M. M., Sinnott-Armstrong, N. A., Świtnicki, M. P., Juul, M., Madsen, T., Sallari, R., Kellis, M., Ørntoft, T., Hobolth, A. & Pedersen, J. S. (2018). Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival. npj Genomic Medicine, 3, 1. https://doi.org/10.1038/s41525-017-0040-5

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020). Pan-cancer analysis of whole genomes. Nature, 578(7793), 82-93. https://doi.org/10.1038/s41586-020-1969-6

Lamy, P., Nordentoft, I. K., Birkenkamp-Demtröder, K., Thomsen, M. B. H., Villesen, P., Vang, S., Hedegaard, J., Borre, M., Jensen, J. B., Ørntoft, T. F. & Andersen, L. D. (2016). Paired exome analysis reveals clonal evolution and potential therapeutic targets in urothelial carcinoma. Cancer Research, 5894-5906. https://doi.org/10.1158/0008-5472.CAN-16-0436

Cavassim, M. I. A., Baker, Z., Hoge, C., Schierup, M. H., Schumer, M. & Przeworski, M. (2022). PRDM9 losses in vertebrates are coupled to those of paralogs ZCWPW1 and ZCWPW2. PNAS (Proceedings of the National Academy of Sciences of the United States of America), 119(9), [e2114401119]. https://doi.org/10.1073/pnas.2114401119

Sükösd, Z., Knudsen, B., Kjems, J. & Pedersen, C. N. S. (2012). PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data. Bioinformatics, 28(20), 2691-2692. https://doi.org/10.1093/bioinformatics/bts488

Świtnicki, M. P., Rasmussen, M. J., Madsen, T., Sørensen, K. D. & Pedersen, J. S. (2016). PINCAGE: Probabilistic integration of cancer genomics data for perturbed gene identification and sample classification. Bioinformatics, 32(9), 1353-1365. https://doi.org/10.1093/bioinformatics/btv758

Fredslund, J. (2006). PHY∙FI: fast and easy online creation and manipulation of phylogeny color figures. B M C Bioinformatics, 7(315). https://doi.org/10.1186/1471-2105-7-315

Søndergaard, D. & Pedersen, C. N. S. (2015). PATBox: A Toolbox for Classification and Analysis of P-Type ATPases. PLOS ONE, 10(9), [e0139571]. https://doi.org/10.1371/journal.pone.0139571

Anderson, J. W. J., Haas, P. A., Mathieson, L-A., Volynkin, V., Lyngsø, R., Tataru, P. & Hein, J. (2013). Oxfold: Kinetic Folding of RNA using Stochastic Context-Free Grammars and Evolutionary Information. Bioinformatics, 29(6), 704-710. https://doi.org/10.1093/bioinformatics/btt050

Rousselle, M., Mollion, M., Nabholz, B., Bataillon, T. & Galtier, N. (2018). Overestimation of the adaptive substitution rate in fluctuating populations. Biology Letters, 14(5), [20180055]. https://doi.org/10.1098/rsbl.2018.0055

Mattila, T., Bechsgaard, J. S., Hansen, T., Schierup, M. H. & Bilde, T. (2012). Ortholog genes identified by transcriptome sequencing in the spider genus Stegodyphus. B M C Genomics, 13(70). https://doi.org/10.1186/1471-2164-13-70

Malmkvist, J., Coutant, M. P., Foldager, L., Kaiser, M. Ø. & Herskin, M. S. (2022). Optimering af procedure for lokalbedøvelse af pattegrise forud for kastration. Aarhus Universitet - DCA - Nationalt Center for Fødevarer og Jordbrug. Rådgivningsrapport fra DCA - Nationalt Center for Fødevarer og Jordbrug

Kristensen, T. G. & Pedersen, C. S. (2009). Optimal Overlay of Ligands with Flexible Bonds Using Differential Evolution. In J. Zhang, G-Z. Li & J. Y. Yang (Eds.), Proceedings of the 2009 International Joint conferences on Bioinformatics, System biology and Intelligent Computing (IJCBS2009) (pp. 331-334). IEEE Computer Society Press. https://doi.org/10.1109/IJCBS.2009.36

Pedersen, C. S. & Kristensen, T. G. (2009). Optimal Overlay of Ligands with Flexible Bonds Using Differential Evolution. Poster session presented at 17th Annual International Conference on Intelligent Systems for Molecular Bioligy (ISMB) & 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden. http://www.iscb.org/ismbeccb2009/poster_list.php?cat=C

Aagaard, J., Skadhede, S. C., Andersen, M. B., Kølbæk, P., Hastrup, L. H., Foldager, L. & Nielsen, J. A. (2014). Opsøgende Psykoseteams i Region Nordjylland: En monitoreringsundersøgelse med to års opfølgning af de Opsøgende Psykoseteams i Region Nordjylland og en registerbaseret undersøgelse af udviklingen i voksenpsykiatrien i Region Nordjylland. Aalborg Universitetsforlag.

Fredsted, T. & Villesen, P. (2006). Operation "Red Aben". Jyllands-Posten, 8-8.

Fredsted, T. & Villesen, P. (2006). Operation "Red aben". Jyllands-Posten.

Østergaard, S., Krogh, M. A., Oliveira, V. H. S. D., Larsen, T., GplusE Consortium & Otten, N. D. (2020). Only few benefits from propylene glycol drench in early lactation for cows identified as physiologically imbalanced based on milk spectra analyses. Journal of Dairy Science, 103(2), 1831-1842. https://doi.org/10.3168/jds.2019-17205

Ehlers, B., Bataillon, T. & Damgaard, C. (2021). Ongoing decline in insect-pollinated plants across Danish grasslands. Biology Letters, 17, [0210493]. https://doi.org/0.1098/rsbl.2021.0493

Jimenez Mena, B., Tataru, P., Brøndum, R. F., Sahana, G., Guldbrandtsen, B. & Bataillon, T. (2016). One size fits all? Direct evidence for the heterogeneity of genetic drift throughout the genome. Biology Letters, 12(7). https://doi.org/10.1098/rsbl.2016.0426

Hartfield, M. (2016). On the origin of asexual species by means of hybridization and drift. Molecular Ecology, 25(14), 3264-3265. https://doi.org/10.1111/mec.13713

Wiuf, C. (2002). On the minimum number of topologies explaining a sample of DNA sequences. Theor Pop Biol, 62, 357-363.

Wiuf, C. (2000). On the genealogy of a sample of neutral rare alleles. Theor Pop Biol, 58(1), 61-75. https://doi.org/10.1006/tpbi.2000.1469

Goldringer, I. & Bataillon, T. (2004). On the distribution of temporal variations in allele frequency: consequences for the estimation of effective population size and the detection of loci undergoing selection. Genetics, 168(1), 563-8. https://doi.org/10.1534/genetics.103.025908

Dinér, P., Laursen, A. K. K., Lie, M. A. & Jørgensen, K. A. (2007). On the Origin of the Stereoselectivity in Organocatalysed Reactions with Trimethylsilyl-Protected Diarylprolinol. Chemistry: A European Journal, 14(1), 122-127.

Feldman, M. W., Christiansen, F. & Liberman, U. (1983). On some models of fertility selection. Genetics, 105, 1003-1010.

Hobolth, A., Andersen, L. N. & Mailund, T. (2011). On computing the coalescence time density in an isolation-with-migration model with few samples. Genetics, 187, 1242-1243. https://doi.org/10.1534/genetics.110.124164

Davies, J., Simancik, F., Lyngsø, R., Mailund, T. & Hein, J. (2007). On Recombination-Induced Multiple and Simultaneous Coalescent Events. Genetics, 177, 2151-2160.

Li, J., Gromov, P., Gromova, I., Moreira, J. M., Timmermans-Wielenga, V., Rank, F., Wang, K., Li, S., Li, H., Wiuf, C., Yang, H., Zhang, X., Bolund, L. & Celis, J. E. (2008). Omics-based profiling of carcinoma of the breast and matched regional lymph node metastasis. Proteomics, 8(23-24), 5038-52. https://doi.org/10.1002/pmic.200800303

Lund, H. H., Arendt, J. A., Fredslund, J. & Pagliarini, L. (1999). Ola: What Goes Up, Must Fall Down. In Proceedings of Artificial Life and Robotics 1999 (AROB'99) (pp. I-9 - I-15)

Displaying results 351 to 400 out of 1109

Revised 05.04.2022 -

Palle Villesen