Publications

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Andersen, L. & Birkbak, N. J. (2025). Advancing circulating tumor DNA detection: Using whole-genome sequencing to power minimal residual disease monitoring in breast cancer. Annals of Oncology. Advance online publication. https://doi.org/10.1016/j.annonc.2025.03.008

Lassen, J. K. & Villesen, P. (2025). End-To-End Deep Learning Explains Antimicrobial Resistance in Peak-Picking-Free MALDI-MS Data. Analytical Chemistry, 97(5), 2795-2800. https://doi.org/10.1021/acs.analchem.4c05113

Charmouh, A. P., Porsborg, P. S., Hansen, L. T., Besenbacher, S., Boeg Winge, S., Almstrup, K., Hobolth, A., Bataillon, T. & Schierup, M. H. (2025). Estimating Gene Conversion Tract Length and Rate From PacBio HiFi Data. Molecular Biology and Evolution, 42(2), Article msaf019. https://doi.org/10.1093/molbev/msaf019

Foldager, L. (2025). FAIR data and Open Science: some insights from a work package in the PIGWEB project. In P. Linde (Ed.), Symposium i Anvendt Statistik 2025 (pp. 49-54). Økonomisk Institut og Klinisk Institut, Syddansk Universitet & Symposium i Anvendt Statistik. http://www.statistiksymposium.dk/Symposium%202025%20hele%20bogen%20(10%20MB).pdf

Cabrejas-Olalla, A., Jørgensen, F. G., Cheng, J. Y., Kjærgaard, P. C., Schierup, M. H., Mailund, T. & Athanasiadis, G. (2025). Genetic predictions of eye and hair colour in the Danish population. Forensic Science International: Genetics, 78, Article 103267. https://doi.org/10.1016/j.fsigen.2025.103267

PGC TS Working Group & 23andMe Research Team (2025). Genome-Wide Association Study Meta-Analysis of 9619 Cases With Tic Disorders. Biological Psychiatry, 97(7), 743-752. https://doi.org/10.1016/j.biopsych.2024.07.025

TRACERx Consortium & Genomics England Consortium (2025). ImmuneLENS characterizes systemic immune dysregulation in aging and cancer. Nature Genetics, 57(3), 694-705. Article 305. https://doi.org/10.1038/s41588-025-02086-5

Nielsen, S. B., Lyhne, N. M., Andersen, M., Plaschke, C. C., Gothelf, A. B., Johansen, J., Maare, C., Farhadi, M., Godballe, C., Primdahl, H., Holm, A. I. S., Alsner, J., Kjærgaard, T. & Overgaard, J. (2025). Management of head and neck cancer of unknown primary: A phase IV study by DAHANCA. European Journal of Cancer, 216, Article 115211. https://doi.org/10.1016/j.ejca.2024.115211

Rydder, P. M., Andreasen, L., Thomsen, S. H., Jensen, U. B., Becher, N., Dunø, M. & Vogel, I. (2025). Mosaic STS gene deletions in chorionic villus samples are often confined to the placenta, and they differ in size from STS gene deletions in patients with X-linked Ichthyosis. Placenta, 165, 16-22. https://doi.org/10.1016/j.placenta.2025.03.016

Subrahmaniam, H. J., Pico, X., Bataillon, T., Salomonsen, C. L., Glasius, M. & Ehlers, B. (2025). Natural variation in root exudate composition in the genetically structured Arabidopsis thaliana in the Iberian Peninsula. New Phytologist, 245(4), 1437-1449. https://doi.org/10.1111/nph.20314

Malham, M., Vestergaard, M. V., Bataillon, T., Villesen, P., Dempfle, A., Bang, C., Engsbro, A. L., Jakobsen, C., Franke, A., Wewer, V., Thingholm, L. B. & Petersen, A. M. (2025). The Composition of the Fecal and Mucosa-adherent Microbiota Varies Based on Age and Disease Activity in Ulcerative Colitis. Inflammatory Bowel Diseases, 31(2), 501-513. https://doi.org/10.1093/ibd/izae179

Ma, J., Bechsgaard, J. S., Lauridsen, A. A., Villesen, P., Bilde, T. & Schierup, M. H. (2025). The genomic consequences and persistence of sociality in spiders. Genome Research, 35(3), 499-511. https://doi.org/10.1101/gr.279503.124

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

TRACERx Consortium (2025). Ultrasensitive ctDNA detection for preoperative disease stratification in early-stage lung adenocarcinoma. Nature Medicine, 31(1), 70-76. https://doi.org/10.1038/s41591-024-03216-y

Duelund, N., Nisted, I., Jørgensen, M. E., Heegaard, S. & Jensen, H. (2025). Visual profiling and vision screening of preschool children in Greenland. International journal of circumpolar health, 84(1), Article 2489194. https://doi.org/10.1080/22423982.2025.2489194

Pedersen, E. M., Wimberley, T. & Vilhjálmsson, B. J. (2024). A cautionary tale for Alzheimer’s disease GWAS by proxy: Genetic epidemiology. Nature Genetics, 56(12), 2590-2591. Article 99. https://doi.org/10.1038/s41588-024-02023-y

Lashkari, S., Jensen, S. K., Foldager, L., Larsen, T. & Vestergaard, M. (2024). A high fat to vitamin E ratio in the feed protects and improves uptake of the natural form of vitamin E in postweaning calves. Journal of Animal Physiology and Animal Nutrition, 108(3), 724-734. https://doi.org/10.1111/jpn.13926

Rong, L., Kristensen, J. K., Jung, S., Zhang, G., Kobek-Kjeldager, C., Thodberg, K., Foldager, L. & Herskin, M. S. (2024). Air temperature measured by embedded sensors adopted by pig transporting vehicles in a scaled compartment model. In Book of Abstracts of the 75th Annual Meeting of the European Federation of Animal Science (pp. 783-783). Article Session 70, Poster 13 Wageningen Academic Publishers.

Montalbano, S., Krebs, M. D., Rosengren, A., Vaez, M., Hellberg, K. L. G., Mortensen, P. B., Børglum, A. D., Geschwind, D. H., Raznahan, A., Thompson, W. K., Helenius, D., Werge, T., Ingason, A. & iPSYCH Investigators (2024). Analysis of exonic deletions in a large population study provides novel insights into NRXN1 pathology. npj Genomic Medicine, 9(1), Article 67. https://doi.org/10.1038/s41525-024-00450-8

Mirarab, S., Rivas-González, I., Feng, S., Stiller, J., Fang, Q., Mai, U., Hickey, G., Chen, G., Brajuka, N., Fedrigo, O., Formenti, G., Wolf, J. B. W., Howe, K., Antunes, A., Schierup, M. H., Paten, B., Jarvis, E. D., Zhang, G. & Braun, E. L. (2024). A region of suppressed recombination misleads neoavian phylogenomics. Proceedings of the National Academy of Sciences (PNAS), 121(15), Article e2319506121. https://doi.org/10.1073/pnas.2319506121

Kofod Petersen, A., Forgie, A. H., Bindslev, D. A., Villesen, P. & Staun Larsen, L. (2024). Automatic removal of soft tissue from 3D dental photo scans; an important step in automating future forensic odontology identification. Scientific Reports, 14, Article 12421. https://doi.org/10.1038/s41598-024-63198-2

Kobek-Kjeldager, C., Jensen, L. D., Foldager, L., Gould, L. M., Thodberg, K., Schrøder-Petersen, D. L. & Herskin, M. S. (2024). Behaviour of cull sows during transport to slaughter – Effects of journey duration, a stationary period and temperature. Applied Animal Behaviour Science, 271, Article 106174. https://doi.org/10.1016/j.applanim.2024.106174

Loeschcke, V. & Schierup, M. H. (2024). Biographical sketch: Freddy Bugge Christiansen. Theoretical Population Biology, 156, 130. https://doi.org/10.1016/j.tpb.2024.02.006

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

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

Grelet, C., Millot, L., Wolf, V., Lidauer, M., Santschi, D., Hout, F., Naya, H., Meikle, A., Martin, B., Coppa, M., Leblois, J., Crowe, M., Bapst, B., Köck, A., Mensching, A., Gelé, M., GplusE Consortium & Dehareng, F. (2024). Constitution of an international dataset on blood biomarkers in dairy cows: a preliminary study to develop milk MIR models. In Book of Abstracts of the 75th Annual Meeting of the European Federation of Animal Science (pp. 674-674). Article Session 56; Theatre 12 Wageningen Academic Publishers.

Abdulkadir, M., Larsen, J. T., Clausen, L., Hübel, C., Albiñana, C., Thornton, L. M., Vilhjálmsson, B. J., Bulik, C. M., Yilmaz, Z. & Petersen, L. V. (2024). Descriptives and genetic correlates of eating disorder diagnostic transitions and presumed remission in the Danish registry. medRxiv : the preprint server for health sciences https://doi.org/10.1101/2024.09.05.24313142

Henriksen, B. I. F., Rousing, T., Foldager, L. & Møller, S. H. (2024). Development of qualitative behavioural assessment of mink: Why is it hard to achieve high inter- and intra-observer agreement in QBA-scoring of mink? In Book of Abstracts of the 9th International Conference on the Welfare Assessment of Animals at Farm Level (WAFL) (pp. 44-44). Article Session 4; Poster 10 EAAP.

Larsen, J. T., Yilmaz, Z., Bulik, C. M., Albiñana, C., Vilhjálmsson, B. J., Mortensen, P. B. & Petersen, L. V. (2024). Diagnosed eating disorders in Danish registers - incidence, prevalence, mortality, and polygenic risk. Psychiatry Research, 337, Article 115927. https://doi.org/10.1016/j.psychres.2024.115927

Palimaru Manhoobi, I., Tramm, T., Redsted, S., Bodilsen, A., Foldager, L. & Christiansen, P. (2024). Digital breast tomosynthesis versus X-ray of the breast specimen for intraoperative margin assessment: A randomized trial. The Breast, 73, Article 103616. https://doi.org/10.1016/j.breast.2023.103616

Schizophrenia Working Group of the Psychiatric Genomics Consortium (2024). Distinguishing different psychiatric disorders using DDx-PRS. https://doi.org/10.1101/2024.02.02.24302228

Ørnbjerg, L. M., Brahe, C. H., Linde, L., Jacobsson, L., Nissen, M. J., Kristianslund, E. K., Santos, M. J., Nordström, D., Rotar, Z., Gudbjornsson, B., Onen, F., Codreanu, C., Lindström, U., Möller, B., Kvien, T. K., Barcelos, A., Eklund, K. K., Tomšič, M., Love, T. J. ... Hetland, M. L. (2024). Drug effectiveness of 2nd and 3rd TNF inhibitors in psoriatic arthritis – relationship with the reason for withdrawal from the previous treatment. Joint Bone Spine, 91(4), Article 105729. https://doi.org/10.1016/j.jbspin.2024.105729

Foldager, L., Thodberg, K., Chen, G., Kristensen, J. K., Jensen, L. D., Kaiser, M., Kobek-Kjeldager, C., Rong, L. & Herskin, M. S. (2024). Effects of deck height during transport of weaners: in-vehicle conditions and clinical indicators. In Book of Abstracts of the 75th Annual Meeting of the European Federation of Animal Science (pp. 487-487). Article Session 38, Poster 12 Wageningen Academic Publishers.

Riedel, C. S., Norager, N. H., Bertelsen, M., Mikkelsen, R., Juhler, M. & Hansen, T. S. (2024). Elevated systemic venous pressures as a possible pathology in prepubertal pediatric idiopathic intracranial hypertension. Child's Nervous System, 40(12), 4203-4209. https://doi.org/10.1007/s00381-024-06594-3

Frydendahl, A., Rasmussen, M. H., Jensen, S. Ø., Henriksen, T. V., Demuth, C., Diekema, M., Ditzel, H. J., Wen, S. W. C., Pedersen, J. S., Dyrskjøt, L. & Andersen, C. L. (2024). Error-Corrected Deep Targeted Sequencing of Circulating Cell-Free DNA from Colorectal Cancer Patients for Sensitive Detection of Circulating Tumor DNA. International Journal of Molecular Sciences , 25(8), Article 4252. https://doi.org/10.3390/ijms25084252

Lin, Y., Rasmussen, M. H., Christensen, M. H., Frydendahl, A., Maretty, L., Andersen, C. L. & Besenbacher, S. (2024). Evaluating Bioinformatics Processing of Somatic Variant Detection in cfDNA Using Targeted Sequencing with UMIs. International Journal of Molecular Sciences , 25(21), Article 11439. https://doi.org/10.3390/ijms252111439

Chen, G., Kobek-Kjeldager, C., Jensen, L. D., Kristensen, J. K., Kaiser, M., Thodberg, K., Zhang, G., Rong, L., Herskin, M. S. & Foldager, L. (2024). Experimental study on temperature difference between the interior and exterior of the vehicle transporting weaner pigs. Biosystems Engineering, 247, 119-131. https://doi.org/10.1016/j.biosystemseng.2024.09.001

Andersen, L., Kisistók, J., Henriksen, T. V., Bramsen, J. B., Reinert, T., Øgaard, N., Mattesen, T. B., Birkbak, N. J. & Andersen, C. L. (2024). Exploring the biology of ctDNA release in colorectal cancer. European Journal of Cancer, 207, Article 114186. https://doi.org/10.1016/j.ejca.2024.114186

Breinbjerg, A., Jørgensen, C. S., Walters, G. B., Grove, J., Als, T. D., Kamperis, K., Stéfansdóttir, L., Thirstrup, J. P., Borg, B., Albiñana, C., Vilhjálmsson, B. J., Eðvarðsson, V. Ö., Stefánsson, H., Mortensen, P. B., Agerbo, E., Werge, T., Børglum, A., Demontis, D., Stefánsson, K. ... Christensen, J. H. (2024). Exploring the Genetic Risk of Childhood Daytime Urinary Incontinence: A Genome-Wide Association Study. The Journal of Urology, 212(6), 851-861. https://doi.org/10.1097/JU.0000000000004187

Ahrenfeldt, J., Carstensen, S., Eriksen, I. M. H. & Birkbak, N. J. (2024). Exploring the impact of body mass index on tumor biology and cancer development. Journal of Cancer Research and Clinical Oncology, 150(7), Article 372. https://doi.org/10.1007/s00432-024-05890-4

Andersen, L., Christensen, D. S., Kjær, A., Knudsen, M., Andersen, A. K., Laursen, M. B., Ahrenfeldt, J., Laursen, B. E. & Birkbak, N. J. (2024). Exploring the molecular landscape of cancer of unknown primary: A comparative analysis with other metastatic cancers. Molecular Oncology, 18(10), 2393-2406. https://doi.org/10.1002/1878-0261.13664

Weiss, S., Lamy, P., Rusan, M., Nørgaard, M., Ulhøi, B. P., Knudsen, M., Kassentoft, C. G., Farajzadeh, L., Jensen, J. B., Pedersen, J. S., Borre, M. & Sørensen, K. D. (2024). Exploring the tumor genomic landscape of aggressive prostate cancer by whole-genome sequencing of tissue or liquid biopsies. International Journal of Cancer, 155(2), 298-313. https://doi.org/10.1002/ijc.34949

McFarland, K. N., Tiwari, A., Hashem, V., Zhang, L., Zeng, D., Vincent, J., Arredondo, M. J., Johnson, K. L., Gan, S. R., Yabe, I., Skov, L., Rasmussen, A. & Ashizawa, T. (2024). Extended haplotype with rs41524547-G defines the ancestral origin of SCA10. Human Molecular Genetics, 33(18), 1567-1574. https://doi.org/10.1093/hmg/ddae092

Garcia-Erill, G., Wang, X., Rasmussen, MS., Quinn, L., Khan, A., Bertola, LD., Santander, CG., Balboa, RF., Ogutu, JO., Pečnerová, P., Hanghøj, K., Kuja, J., Nursyifa, C., Masembe, C., Muwanika, V., Bibi, F., Moltke, I., Siegismund, HR., Albrechtsen, A. & Heller, R. (2024). Extensive Population Structure Highlights an Apparent Paradox of Stasis in the Impala (Aepyceros melampus). Molecular Ecology, 33(22), Article e17539. https://doi.org/10.1111/mec.17539

Eskildsen, S. J., Hansen, C. A., Kallemose, T., Curtis, D. J., Wessel, I. & Poulsen, I. (2024). Factors Associated With Time to Decannulation in Patients With Tracheostomy Following Severe Traumatic Brain Injury. Respiratory Care, 69(5), 566-574. https://doi.org/10.4187/respcare.11376

Sendrowski, J. & Bataillon, T. (2024). FastDFE: Fast and Flexible Inference of the Distribution of Fitness Effects. Molecular Biology and Evolution, 41(5), Article msae070. https://doi.org/10.1093/molbev/msae070

Lashkari, S., Weisbjerg, M. R., Foldager, L. & Børsting, C. F. (2024). Fat supplement for dairy cows during early lactation – potentials, challenges, and risks – a meta-analysis. Journal of Applied Animal Research, 52(1), Article 2323625. https://doi.org/10.1080/09712119.2024.2323625

Giagnoni, G., Lassen, J., Lund, P., Foldager, L., Johansen, M. & Weisbjerg, M. R. (2024). Feed intake in housed dairy cows: validation of a three-dimensional camera−based feed intake measurement system. ANIMAL, 18(6), Article 101178. https://doi.org/10.1016/j.animal.2024.101178

Dybdahl Krebs, M., Georgii Hellberg, K. L., Lundberg, M., Appadurai, V., Ohlsson, H., Pedersen, E., Steinbach, J., Matthews, J., Border, R., LaBianca, S., Calle, X., Meijsen, J. J., Ingason, A., Buil, A., Vilhjálmsson, B. J., Flint, J., Bacanu, S. A., Cai, N., Dahl, A. ... iPSYCH Study Consortium (2024). Genetic liability estimated from large-scale family data improves genetic prediction, risk score profiling, and gene mapping for major depression. American Journal of Human Genetics, 111(11), 2494-2509. https://doi.org/10.1016/j.ajhg.2024.09.009

23andMe Research Team (2024). Genome-wide association study identifies 30 obsessive-compulsive disorder associated loci. https://doi.org/10.1101/2024.03.13.24304161

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Revised 21.08.2024

Palle Villesen