Publications

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Nielsen, J. & Sand, A. (2011). Algorithms for a parallel implementation of Hidden Markov Models with a small state space. In 2011 IEEE IPDPS Workshops & PhD Forum (pp. 447-454). IEEE Computer Society Press. https://doi.org/10.1109/IPDPS.2011.181

Nielsen, J., Kristensen, A. K., Mailund, T. & Pedersen, C. N. S. (2011). A sub-cubic time algorithm for computing the quartet distance between two general trees. Algorithms for Molecular Biology, 6(15). https://doi.org/10.1186/1748-7188-6-15

Nielsen, J. (2011). A Coarse-to-Fine Approach to Computing the k-best Viterbi Paths. Lecture Notes in Computer Science, 6661, 376-387. https://doi.org/10.1007/978-3-642-21458-5_32

Nielsen, M. M., Tataru, P., Madsen, T., Hobolth, A. & Pedersen, J. S. (2016). Motif discovery in ranked lists of sequences. (pp. 1-4). http://biorxiv.org/content/biorxiv/suppl/2016/01/11/035956.DC2/035956-1.pdf

Nielsen, S. M., de Gier, C., Dimopoulou, C., Gupta, V., Hansen, L. H. & Nørskov-Lauritsen, N. (2015). The capsule biosynthesis locus of Haemophilus influenzae show conspicuous similarity to the corresponding locus in Haemophilus sputorum and may have been recruited from this species by horizontal gene transfer. Microbiology, 161(6), 1182-1188. https://doi.org/10.1099/mic.0.000081

Nielsen, L. S., Villesen, P. & Lindholst, C. (2015). Stability of cocaine alkaloids and residual solvents applied in drug profiling.

Nielsen, L. S., Villesen, P. & Lindholst, C. (2016). Stability of cocaine impurity profiles during 12 months of storage. Forensic Science International, 264, 56-62. https://doi.org/10.1016/j.forsciint.2016.03.012

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. PLoS One, 11(12), e0167437. Article e0167437. https://doi.org/10.1371/journal.pone.0167437

Nielsen, L. S., Lindholst, C. & Villesen, P. (2016). Illegal drugs and bioinformatics - Classification and stability of amphetamine impurities applied in criminal investigations.

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

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

Nielsen, L. S., Villesen, P. & Lindholst, C. (2018). Stability of amphetamine impurity profiles during 12 months of storage. Forensic Science International, 290, 129-136. https://doi.org/10.1016/j.forsciint.2018.06.039

Nielsen, M. M., Tataru, P., Madsen, T., Hobolth, A. & Pedersen, J. S. (2018). Regmex: A statistical tool for exploring motifs in ranked sequence lists from genomics experiments. Algorithms for Molecular Biology, 13(1), Article 17. https://doi.org/10.1186/s13015-018-0135-2

Nielsen, K. L., Villesen, P. & Johannsen, M. (2018). Aging of Biological Traces - A Forensic Application. Poster session presented at 1st Aarhus Metabolomics Symposium, Aarhus, Denmark.

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

Nielsen, M. M., Trolle, C., Vang, S., Hornshøj, H., Skakkebaek, A., Hedegaard, J., Nordentoft, I., Pedersen, J. S. & Gravholt, C. H. (2020). Epigenetic and transcriptomic consequences of excess X-chromosome material in 47,XXX syndrome-A comparison with Turner syndrome and 46,XX females. American Journal of Medical Genetics. Part C: Seminars in Medical Genetics, 184(2), 279-293. https://doi.org/10.1002/ajmg.c.31799

Nielsen, M. M. & Pedersen, J. S. (2021). miRNA activity inferred from single cell mRNA expression. Scientific Reports, 11(1), Article 9170. https://doi.org/10.1038/s41598-021-88480-5

Nielsen, S. V., Vaughn, A. H., Leppälä, K., Landis, M. J., Mailund, T. & Nielsen, R. (2023). Bayesian inference of admixture graphs on Native American and Arctic populations. PLoS Genetics, 19(2), Article e1010410. https://doi.org/10.1371/journal.pgen.1010410

Nielsen, S. B., Larsen, M. H. H., Channir, H. I., Kiss, K., Ulhøi, B. P., Godballe, C., Eriksen, J. G., Rubek, N., Kjaergaard, T. & von Buchwald, C. (2025). Tongue base mucosectomy: A case for precision. Oral Oncology, 161, 107166. Article 107166. https://doi.org/10.1016/j.oraloncology.2024.107166

Nielsen, J. (2011). Engineering Algorithms for Finding Patterns in Biological Data.

Ng, K. W., Boumelha, J., Enfield, K. S. S., Almagro, J., Cha, H., Pich, O., Karasaki, T., Moore, D. A., Salgado, R., Sivakumar, M., Young, G., Molina-Arcas, M., de Carné Trécesson, S., Anastasiou, P., Fendler, A., Au, L., Shepherd, S. T. C., Martínez-Ruiz, C., Puttick, C. ... CAPTURE Consortium (2023). Antibodies against endogenous retroviruses promote lung cancer immunotherapy. Nature, 616(7957), 563-573. https://doi.org/10.1038/s41586-023-05771-9

Nexø, B. A., Nissen, K. K., Hansen, B., Laska, M. J., Villesen, P., Christensen, T., Oturai, A. B., Møller-Larsen, A., Petersen, T. & Pedersen, F. S. (2010). Involvement of the endogenous HERV-F(c)1 retroviral locus on the human X chromosome in the etiology of multiple sclerosis. Journal of NeuroVirology, (S1), 61.

Nexø, B. A., Hansen, B., Nissen, K. K., Gundestrup, L., Terkelsen, T., Villesen, P., Bahrami, S., Petersen, T., Pedersen, F. S. & Laska, M. J. (2013). Restriction genes for retroviruses influence the risk of multiple sclerosis. PLoS One, 8(9), e74063. https://doi.org/10.1371/journal.pone.0074063

Nexø, B. A., Laska, M. J., Christensen, T., Møller-Larsen, A., Pedersen, F. S. & Villesen, P. (2010). Estimating disease risk of individual having/developing multiple sclerosis involves in genetic material sample from individual, assessing sequence polymorphism in specific genetic regions of human chromosome, obtaining and estimating step. (Patent No. WO2010112033).

Nexø, B. A., Villesen, P., Nissen, K. K., Lindegaard, H. M., Rossing, P., Petersen, T., Tarnow, L., Hansen, B., Lorenzen, T., Hørslev-Petersen, K., Bisgaard Jensen, S., Bahrami, S., Lajer, M., Schmidt, K. L. M., Parving, H.-H., Junker, P. & Laska, M. J. (2016). Are human endogenous retroviruses triggers of autoimmune diseases? Unveiling associations of three diseases and viral loci. Immunologic Research, 64(1), 55-63. https://doi.org/10.1007/s12026-015-8671-z

Nathan, N. O., Mørch, L. S., Wu, C. S., Olsen, J., Hetland, M. L., Li, J. & Rom, A. L. (2020). Rheumatoid arthritis and risk of spontaneous abortion: a Danish nationwide cohort study. Rheumatology (Oxford, England), 59(8), 1984-1991. https://doi.org/10.1093/rheumatology/kez565

Nam, K., Munch, K., Hobolth, A., Dutheil, J. Y., Veeramah, K. R., Woerner, A. E., Hammer, M. F., Mailund, T., Schierup, M. H. & Great Ape Genome Diversity Project (2015). Extreme selective sweeps independently targeted the X chromosomes of the great apes. Proceedings of the National Academy of Sciences (PNAS), 112(20). https://doi.org/10.1073/pnas.1419306112

Nam, K., Munch, K., Mailund, T., Nater, A., Greminger, M. P., Krützen, M., Marquès-Bonet, T. & Schierup, M. H. (2017). Evidence that the rate of strong selective sweeps increases with population size in the great apes. Proceedings of the National Academy of Sciences (PNAS), 114(7), 1613-1618. https://doi.org/10.1073/pnas.1605660114

Nam, K., Munch, K., Hobolth, A., Y. Dutheil, J., Veeramah, K., Woerner, A., F. Hammer, M., Ape Genome Diversity Project, G., Mailund, T. & H. Schierup, M. (2014). Strong selective sweeps associated with ampliconic regions in great ape X chromosomes. ArXiv.

Muyle, A., Martin, H., Zemp, N., Mollion, M., Gallina, S., Tavares, R., Silva, A., Bataillon, T., Widmer, A., Glémin, S., Touzet, P. & Marais, G. A. B. (2021). Dioecy Is Associated with High Genetic Diversity and Adaptation Rates in the Plant Genus Silene. Molecular Biology and Evolution, 38(3), 805-818. https://doi.org/10.1093/molbev/msaa229

Musliner, K. L., Andersen, K. K., Agerbo, E., Albiñana, C., Vilhjalmsson, B. J., Rajagopal, V. M., Bybjerg-Grauholm, J., Bækved-Hansen, M., Pedersen, C. B., Pedersen, M. G., Munk-Olsen, T., Benros, M. E., Als, T. D., Grove, J., Werge, T., Børglum, A. D., Hougaard, D. M., Mors, O., Nordentoft, M. ... Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium (2023). Polygenic liability, stressful life events and risk for secondary-treated depression in early life: a nationwide register-based case-cohort study. Psychological Medicine, 53(1), 217-226. https://doi.org/10.1017/S0033291721001410

Musgaard, M., Thøgersen, L. & Schiøtt, H. B. (2008). Molecular Dynamics Simulations of the E2 Form of the Ca²⁺-ATPase: Preliminary Results. Poster session presented at 12^th International ATPase Conference. Na,K-ATPase and Related Transport ATPases of P-type: Structures, Mechanisms, and Roles in Health and Disease, Aarhus, Denmark.

Musgaard, M., Thøgersen, L. & Schiøtt, B. (2011). Protonation States of Important Acidic Residues in the Central Ca²⁺ Ion Binding Sites of the Ca²⁺-ATPase: A Molecular Modeling Study. Biochemistry, 50(51), 11109-11120. https://doi.org/10.1021/bi201164b

Musgaard, M., Thøgersen, L., Schiøtt, B. & Tajkhorshid, E. (2012). Tracing Cytoplasmic Ca²⁺ Ion and Water Access Points in the Ca²⁺-ATPase. Biophysical Journal, 102(2), 268-277. https://doi.org/10.1016/j.bpj.2011.12.009

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

Murat, F., Mbengue, N., Winge, S. B., Trefzer, T., Leushkin, E., Sepp, M., Cardoso-Moreira, M., Schmidt, J., Schneider, C., Mößinger, K., Brüning, T., Lamanna, F., Riera Belles, M., Conrad, C., Kondova, I., Bontrop, R., Behr, R., Khaitovich, P., Pääbo, S. ... Kaessmann, H. (2023). The molecular evolution of spermatogenesis across mammals. Nature, 613(7943), 308-316. https://doi.org/10.1038/s41586-022-05547-7

Munn-Chernoff, M. A., Johnson, E. C., Chou, Y.-L., Coleman, J. R. I., Thornton, L. M., Walters, R. K., Yilmaz, Z., Baker, J. H., Hübel, C., Gordon, S., Medland, S. E., Watson, H. J., Gaspar, H. A., Bryois, J., Hinney, A., Leppä, V. M., Mattheisen, M., Ripke, S., Yao, S. ... Agrawal, A. (2021). Shared genetic risk between eating disorder- and substance-use-related phenotypes: Evidence from genome-wide association studies. Addiction Biology, 26(1), Article e12880. https://doi.org/10.1111/adb.12880

Munkacsi, A. B., Pan, J. J., Villesen, P., Mueller, U. G., Blackwell, M. & McLaughlin, D. J. (2004). Convergent coevolution in the domestication of coral mushrooms by fungus-growing ants. Proceedings of the Royal Society B: Biological Sciences, 271(1550), 1777-1782.

Mundy, J., Hall, A. S. M., Steinbach, J., Albinaña, C., Agerbo, E., Als, T. D., Thapar, A., McGrath, J. J., Vilhjálmsson, B. J., Nordentoft, M., Werge, T., Børglum, A., Mortensen, P. B. & Musliner, K. L. (2024). Polygenic liabilities and treatment trajectories in early-onset depression: a Danish register-based study. Psychological Medicine, 54(14), 3828-3837. https://doi.org/10.1017/S0033291724002186

Munch, K., Mailund, T., Dutheil, J. Y. & Schierup, M. H. (2014). A fine-scale recombination map of the human-chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion. Genome Research. https://doi.org/10.1101/gr.158469.113

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

Munch, K., Nam, K., Schierup, M. H. & Mailund, T. (2016). Selective sweeps across twenty millions years of primate evolution. Molecular Biology and Evolution, 33(12), 3065-3074. https://doi.org/10.1093/molbev/msw199

Munch, D., Gupta, V., Bachmann, A., Busch, W., Kelly, S., Mun, T. & Andersen, S. U. (2018). The Brassicaceae family displays divergent, shoot-skewed NLR resistance gene expression. Plant Physiology, 176(2), 1598-1609. https://doi.org/10.1104/pp.17.01606

Munch, T. N., Hedley, P. L., Hagen, C. M., Bækvad-Hansen, M., Bybjerg-Grauholm, J., Grove, J., Nordentoft, M., Børglum, A. D., Mortensen, P. B., Werge, T. M., Melbye, M., Hougaard, D. M. & Christiansen, M. (2021). Co-occurring hydrocephalus in autism spectrum disorder: a Danish population-based cohort study. Journal of Neurodevelopmental Disorders, 13(1), 19. Article 19. https://doi.org/10.1186/s11689-021-09367-0

Mun, T., Bachmann, A., Gupta, V., Stougaard, J. & Andersen, S. U. (2016). Lotus Base: An integrated information portal for the model legume Lotus japonicus. Scientific Reports, 6, Article 39447. https://doi.org/10.1038/srep39447

Mullins, N., Forstner, A. J., O'Connell, K. S., Coombes, B., Coleman, J. R. I., Qiao, Z., Als, T. D., Bigdeli, T. B., Børte, S., Bryois, J., Charney, A. W., Drange, O. K., Gandal, M. J., Hagenaars, S. P., Ikeda, M., Kamitaki, N., Kim, M., Krebs, K., Panagiotaropoulou, G. ... HUNT All-In Psychiatry (2021). Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology. Nature Genetics, 53(6), 817-829. https://doi.org/10.1038/s41588-021-00857-4

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

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

Mørup, N., Stakaitis, R., Golubickaite, I., Riera, M., Dalgaard, M. D., Schierup, M. H., Jørgensen, N., Daugaard, G., Juul, A. & Almstrup, K. (2021). Small RNAs in Seminal Plasma as Novel Biomarkers for Germ Cell Tumors. Cancers, 13(10), Article 2346. https://doi.org/10.3390/cancers13102346

Mortensen, L. M., Lundbye-Christensen, S., Schmidt, E. B., Calder, P. C., Schierup, M. H., Tjønneland, A., Parner, E. T. & Overvad, K. (2017). Long-chain n-3 and n-6 polyunsaturated fatty acids and risk of atrial fibrillation: Results from a Danish cohort study. PLoS One, 12(12), e0190262. Article e0190262. https://doi.org/10.1371/journal.pone.0190262

Displaying results 451 to 500 out of 1384

Revised 13.01.2026

Palle Villesen