Publications

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Ahrenfeldt, J., Christensen, D. S., Sokač, M., Kisistók, J., McGranahan, N. & Birkbak, N. J. (2022). Computational Analysis Reveals the Temporal Acquisition of Pathway Alterations during the Evolution of Cancer. Cancers, 14(23), Article 5817. https://doi.org/10.3390/cancers14235817

Reinert, T., Modin, C., Mansilla Castano, F., Lamy, P., Wojdacz, T. K., Hansen, L. L., Wiuf, C., Borre, M., Andersen, L. D. & Ørntoft, T. F. (2011). Comprehensive genome methylation analysis in bladder cancer;identification and validation of novel methylated genes and application of these as urinary tumor markers. Clinical Cancer Research. https://doi.org/10.1158/1078-0432.CCR-10-2659

Nielsen, R. & Wiuf, C. (2005). Composite likelihood estimation applied to Single Nucleotide Polymorphism (SNP) data. ISI Conference Proceedings 2005.. Paper presented at Composite likelihood estimation applied to Single Nucleotide Polymorphism (SNP) data. ISI Conference Proceedings 2005..

Stiller, J., Feng, S., Chowdhury, A.-A., Rivas-González, I., Duchêne, D. A., Fang, Q., Deng, Y., Kozlov, A., Stamatakis, A., Claramunt, S., Nguyen, J. M. T., Ho, S. Y. W., Faircloth, B. C., Haag, J., Houde, P., Cracraft, J., Balaban, M., Mai, U., Chen, G. ... Zhang, G. (2024). Complexity of avian evolution revealed by family-level genomes. Nature, 629(8013), 851-860. https://doi.org/10.1038/s41586-024-07323-1

Sigurdsson, A. I., Gräf, J. F., Yang, Z., Ravn, K., Meisner, J., Thielemann, R., Webel, H., Smit, R. A. J., Niu, L., Mann, M., Vilhjalmsson, B., Neale, B. M., Holm, J.-C., Ganna, A., Hansen, T., Loos, R. J. F., Rasmussen, S. & FinnGen (2026). Complex genetic effects linked to plasma protein abundance in the UK Biobank. Nature Communications, 17(1), Article 533. https://doi.org/10.1038/s41467-025-67235-0

Guillemet, M., Chabas, H., Nicot, A., Gatchich, F., Ortega-Abboud, E., Buus, C., Hindhede, L., Rousseau, G. M., Bataillon, T., Moineau, S. & Gandon, S. (2022). Competition and coevolution drive the evolution and the diversification of CRISPR immunity. Nature Ecology & Evolution, 6(10), 1480-1488. https://doi.org/10.1038/s41559-022-01841-9

Buggiotti, L., Cheng, Z., Salavati, M., Wathes, D. C. & GplusE Consortium (2021). Comparison of the transcriptome in circulating leukocytes in early lactation between primiparous and multiparous cows provides evidence for age-related changes. BMC Genomics, 22(1), 1-17. Article 693. https://doi.org/10.1186/s12864-021-07977-5

Castellano, D., Macià, M. C., Tataru, P., Bataillon, T. & Munch, K. (2019). Comparison of the Full Distribution of Fitness Effects of New Amino Acid Mutations Across Great Apes. Genetics, 213(3), 953-966. https://doi.org/10.1534/genetics.119.302494

Gündel, S., Munksgaard, L., Looft, C. & Foldager, L. (2022). Comparison of the feeding behaviour of primiparous and multiparous Jersey and Holstein cows kept under equal conditions throughout lactation. Journal of Dairy Research, 89(1), 37-43. https://doi.org/10.1017/S0022029922000061

Foldager, L., Als, T. D. & Grove, J. (2013). Comparison of methods for genome-wide gene-environment interaction analysis. Poster session presented at XXIst World Congress of Psychiatric Genetics, Boston, United States.

Tataru, P. C. & Hobolth, A. (2011). Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains. BMC Bioinformatics, 12(1), 465. https://doi.org/10.1186/1471-2105-12-465

Fei, G., Luo, Y., Li, S., Li, J., Lin, L., Nielsen, A. L., Sørensen, C. B., Vajta, G., Wang, J., Zhang, X., Du, Y., Yang, H. & Bolund, L. (2011). Comparison of gene expression and genome-wide DNA methylation profiling between phenotypically normal cloned pigs and conventionally bred controls. PLoS One, 6(10), e25901. https://doi.org/10.1371/journal.pone.0025901

Foldager, L., Als, T. D. & Grove, J. (2014). Comparing methods for genome-wide gene-environment interaction analysis.

Pedersen, J. S., Meyer, I. M., Forsberg, R., Simmonds, P. & nullJA, H. (2004). Comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res Sep 24, 32(16), 4925-4936.

Zhang, B. L., Chen, W., Wang, Z., Pang, W., Luo, M. T., Wang, S., Shao, Y., He, W. Q., Deng, Y., Zhou, L., Chen, J., Yang, M. M., Wu, Y., Wang, L., Fernández-Bellon, H., Molloy, S., Meunier, H., Wanert, F., Kuderna, L. ... Wu, D. D. (2023). Comparative genomics reveals the hybrid origin of a macaque group. Science Advances, 9(22), Article eadd3580. https://doi.org/10.1126/sciadv.add3580

de Groot, S., Mailund, T. & Hein, J. (2007). Comparative Annotation of Viral Genomes with Non-Conserved Gene Structure. Bioinformatics, 23(9), 1080-1089. https://doi.org/10.1093/bioinformatics/btm078

Locke, D. P., Hillier, L. W., Warren, W. C., Yang, S.-P., Wang, Z., Chinwalla, A. T., Minx, P., Mitreva, M., Cook, L., Delehaunty, K. D., Fronick, C., Schmidt, H., Fulton, L. A., Fulton, R. S., Nelson, J. O., Magrini, V., Pohl, C., Graves, T. A., Markovic, C. ... de Jong, P. J. (2011). Comparative and demographic analysis of orang-utan genomes. Nature, 469, 529-533. https://doi.org/10.1038/nature09687

Jørgensen, F. G., Hobolth, A., Hornshøj, H., Bendixen, C., Fredholm, M. & Schierup, M. H. (2005). Comparative analysis of protein coding sequences from Human, Mouse and the domesticated Pig. BMC Biology, 3(2). https://doi.org/10.1186/1741-7007-3-2

Steinberg, S., de Jong, S., Andreassen, O. A., Werge, T., Børglum, A. D., Mors, O., Mortensen, P. B., Gustafsson, O., Costas, J., Pietiläinen, O. P. H., Demontis, D., Papiol, S., Huttenlocher, J., Mattheisen, M., Breuer, R., Vassos, E., Giegling, I., Fraser, G., Walker, N. ... Irish Schizophrenia Genomics Consortium (2011). Common Variants at VRK2 and TCF4 Conferring Risk of Schizophrenia. Human Molecular Genetics, 20(20), 4076-81. https://doi.org/10.1093/hmg/ddr325

GERAD1 Consortium: (2018). Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection. Nature Genetics, 50(3), 381-389. https://doi.org/10.1038/s41588-018-0059-2

Wurtz, K. E., Thodberg, K., Berenjian, A., Foldager, L., Tahamtani, F. M. & Riber, A. B. (2022). Commercial layer hybrids kept under organic conditions: a comparison of range use, welfare, and egg production in two layer strains. Poultry Science, 101(9), Article 102005. https://doi.org/10.1016/j.psj.2022.102005

Liu, Y., Pedersen, H. S., Larsen, K. E., Kristensen, K., Foldager, L., Callesen, H. & Sørensen, M. T. (2019). Combined in vitro fertilization and culture (IVF/IVC) in mouse for reprotoxicity assessment of xenobiotic exposure. Reproductive Toxicology, 89(October), 115-123. https://doi.org/10.1016/j.reprotox.2019.07.006

Shuai, S., PCAWG Drivers and Functional Interpretation Working Group, Gallinger, S., Stein, L. & PCAWG Consortium (2020). Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nature Communications, 11(1), Article 734. https://doi.org/10.1038/s41467-019-13929-1

Knudsen, M., Søndergaard, D. & Pedersen, C. N. S. (2014). Combinatorics of Non-Ribosomal Peptide Synthetases.

Brameier, M. & Wiuf, C. (2007). Co-clustering and visualization of gene expression data and gene ontology terms for Saccharomyces cerevisiae using self-organizing maps. J Biomed Inform, 40, 160-173. https://doi.org/10.1016/j.jbi.2006.05.001

Nielsen, L. S., Lindholst, C. & Villesen, P. (2016). Cocaine classification using alkaloid and residual solvent profiling. Forensic Science International, 269, 42-49. https://doi.org/10.1016/j.forsciint.2016.11.007

Mailund, T. (2006). CoaSim Guile Manual — Using the Guile-based CoaSim Simulator.

Mailund , Schierup, M. H., Pedersen, C. N. S., Mechlenborg, P., Madsen, J. N. & Schauser, L. (2005). CoaSim: A Flexible Environment for Simulating Genetic Data under Coalescent Models. BMC Bioinformatics, 6(252). http://www.biomedcentral.com/1471-2105/6/252

Hartfield, M., Wright, S. I. & Agrawal, A. F. (2016). Coalescent times and patterns of genetic diversity in species with facultative sex: Effects of gene conversion, population structure, and heterogeneity. Genetics, 202(1), 297-312. https://doi.org/10.1534/genetics.115.178004

Agrawal, A. F. & Hartfield, M. (2016). Coalescence with background and balancing selection in systems with Bi- and uniparental reproduction: Contrasting partial asexuality and selfing. Genetics, 202(1), 313-326. https://doi.org/10.1534/genetics.115.181024

Hartfield, M., Wright, S. I. & Agrawal, A. F. (2018). Coalescence and linkage disequilibrium in facultatively sexual diploids. Genetics, 210(2), 683-701. https://doi.org/10.1534/genetics.118.301244

van der Zalm, Y. C., Foldager, L., Termorshuizen, F., Sommer, I. E., Nielsen, J. & Selten, J.-P. (2021). Clozapine and mortality: A comparison with other antipsychotics in a nationwide Danish cohort study. Acta Psychiatrica Scandinavica, 143(3), 216-226. https://doi.org/10.1111/acps.13267

d'Amore, F., Chan, E., Iqbal, J., Geng, H., Young, K., Xiao, L., Hess, M. M., Sanger, W. G., Smith, L., Wiuf, C., Hagberg, O., Fu, K., Chan, W. C. & Dave, B. J. (2008). Clonal evolution in t(14;18)-positive follicular lymphoma, evidence for multiple common pathways, and frequent parallel clonal evolution. Clinical Cancer Research, 14(22), 7180-7. https://doi.org/10.1158/1078-0432.CCR-08-0752

Schouby Bock, M., Nørgaard Van Achter, O., Dines, D., Simonsen Speed, M., Correll, C. U., Mors, O., Østergaard, S. D. & Kølbæk, P. (2020). Clinical validation of the self-reported Glasgow Antipsychotic Side-effect Scale using the clinician-rated UKU side-effect scale as gold standard reference. Journal of Psychopharmacology, 34(8), 820-828. https://doi.org/10.1177/0269881120916122

Thomsen, T. H., Jørgensen, L. B., Kjær, T. W., Haahr, A., Vogel, A., Larsen, I. U. & Winge, K. (2022). Clinical Markers of 6 Pre-dominant Coping Behaviors in Living With Parkinson Disease: A Convergent Mixed Methods Study. Inquiry, 59. https://doi.org/10.1177/00469580221129929

Aagaard, J., Buus, N., Wernlund, A. G., Foldager, L. & Merinder, L. (2016). Clinically useful predictors for premature mortality among psychiatric patients visiting a psychiatric emergency room. International Journal of Social Psychiatry, 62(5), 462-470. https://doi.org/10.1177/0020764016642490

Thodberg, K., Foldager, L., Schrøder-Petersen, D. L., Kobek-Kjeldager, C., Gould, L. M. & Herskin, M. S. (2024). Clinical condition of cull sows before and after transport to slaughter – Effects of journey duration and a stationary period. Research in Veterinary Science, 168, Article 105124. https://doi.org/10.1016/j.rvsc.2023.105124

Faber, A. H., Bataillon, T. & Ehlers, B. K. (2026). Climate-Driven Convergence of Chemical Ecotypes in Mediterranean Lamiaceae. Journal of Biogeography, 53(5), Article e70247. https://doi.org/10.1111/jbi.70247

Sokac, M., Ahrenfeldt, J., Litchfield, K., Watkins, T. B. K., Knudsen, M., Dyrskjøt, L., Jakobsen, M. R. & Birkbak, N. J. (2022). Classifying cGAS-STING Activity Links Chromosomal Instability with Immunotherapy Response in Metastatic Bladder Cancer. Cancer Research Communications, 2(8), 762-771. https://doi.org/10.1158/2767-9764.CRC-22-0047, https://doi.org/10.1158/2767-9764.CRC-22-0047

Søndergaard, D. A. (2018). Classification and analysis of biological data.

Rivas, S., Rougon-Cardoso, A., Smoker, M., Schauser, L., Yoshioka, H. & Jones, J. D. G. (2004). CITRX thioredoxin interacts with the tomato Cf-9 resistance protein and negatively regulates defence. EMBO Journal, 23, 2156-2165.

Hollensen, A. K., Thomsen, H. S., Lloret-Llinares, M., Kamstrup, A. B., Jensen, J. M., Luckmann, M., Birkmose, N., Palmfeldt, J., Jensen, T. H., Hansen, T. B. & Damgaard, C. K. (2020). circZNF827 nucleates a transcription inhibitory complex to balance neuronal differentiation. eLife, 9, 1-29. Article e58478. https://doi.org/10.7554/eLife.58478

Rasmussen, A. M., Okholm, T. L. H., Knudsen, M., Vang, S., Dyrskjøt, L., Hansen, T. B. & Pedersen, J. S. (2023). Circular stable intronic RNAs possess distinct biological features and are deregulated in bladder cancer. NAR Cancer, 5(3), Article zcad041. https://doi.org/10.1093/narcan/zcad041

Okholm, T. L. H., Nielsen, M. M., Hamilton, M., Christensen, L.-L., Vang, S., Hedegaard, J., Hansen, T. B., Kjems, J., Dyrskjøt, L. & Pedersen, J. S. (2017). Circular RNA expression is abundant and correlated to aggressiveness in early-stage bladder cancer. npj Genomic Medicine, 2(1), Article 36. https://doi.org/10.1038/s41525-017-0038-z

Mota, R. R., Hammami, H., Vanderick, S., Naderi, S., Gengler, N. & GplusE Consortium (2019). Chromosome regions affecting MIR spectra indirect predictors of cheese--making properties 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

Zieger, K., Wiuf, C. H., Jensen, K. M.-E., Ørntoft, T. F. & Andersen, L. D. (2009). Chromosomal imbalance in the progression of high-risk non-muscle invasive bladder cancer. B M C Cancer, 9, 149.

Zieger, K., Wiuf, C., Jensen, K. M.-E., Ørntoft, T. F. & Andersen, L. D. (2009). Chromosomal imbalance in the progression of high-risk non-muscle invasive bladder cancer. B M C Cancer, 9, 149. https://doi.org/10.1186/1471-2407-9-149

Lucotte, E. A., Guðmundsdóttir, V. B., Jensen, J. M., Skov, L., Macià, M. C., Almstrup, K., Schierup, M. H., Helgason, A. & Stefansson, K. (2023). Characterizing the evolution and phenotypic impact of ampliconic Y chromosome regions. Nature Communications, 14(1), Article 3990. https://doi.org/10.1038/s41467-023-39644-6

Eskildsen, S., Justesen, J., Schierup, M. H. & Hartmann, R. (2003). Characterization of the 2′-5′-oligoadenylate synthetase ubiquitin-like family. Nucl. Acids Res., 31, 3166-3173.

Eskildsen, S., Justesen, J., Schierup, M. H. & Hartmann, R. (2003). Characterization of the 2'-5'-oligoadenylate synthetase ubiquitin-like family. Nucleic Acids Research, 31(12), 3166-3173.

Displaying results 1151 to 1200 out of 1417

Revised 13.01.2026

Palle Villesen