Publications

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Bulik, C. M., Thornton, L. M., Parker, R., Kennedy, H., Baker, J. H., MacDermod, C., Guintivano, J., Cleland, L., Miller, A. L., Harper, L., Larsen, J. T., Yilmaz, Z., Grove, J., Sullivan, P. F., Petersen, L. V., Jordan, J., Kennedy, M. A. & Martin, N. G. (2021). The Eating Disorders Genetics Initiative (EDGI): study protocol. BMC Psychiatry, 21(1), Article 234. https://doi.org/10.1186/s12888-021-03212-3

Bergeron, L. A., Besenbacher, S., Bakker, J., Zheng, J., Li, P., Pacheco, G., Sinding, M. H. S., Kamilari, M., Gilbert, M. T. P., Schierup, M. H. & Zhang, G. (2021). The germline mutational process in rhesus macaque and its implications for phylogenetic dating. GigaScience, 10(5), Article giab029. https://doi.org/10.1093/gigascience/giab029

Juul, R. I., Nielsen, M. M., Juul, M., Feuerbach, L. & Pedersen, J. S. (2021). The landscape and driver potential of site-specific hotspots across cancer genomes. npj Genomic Medicine, 6(1), Article 33. https://doi.org/10.1038/s41525-021-00197-6

Pathi, A., Wright, M., Smed, M. K., Nelson, J. L., Olsen, J., Hetland, M. L., Zoffmann, V. & Jawaheer, D. (2021). The rheumatoid arthritis gene expression signature among women who improve or worsen during pregnancy: A pilot study. Journal of Rheumatology, 48(7), 985-991. https://doi.org/10.3899/jrheum.201128

Miles, A. E., Dos Santos, F. C., Byrne, E. M., Renteria, M. E., McIntosh, A. M., Adams, M. J., Pistis, G., Castelao, E., Preisig, M., Baune, B. T., Schubert, K. O., Lewis, C. M., Jones, L. A., Jones, I., Uher, R., Smoller, J. W., Perlis, R. H., Levinson, D. F., Potash, J. B. ... Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium (2021). Transcriptome-based polygenic score links depression-related corticolimbic gene expression changes to sex-specific brain morphology and depression risk. Neuropsychopharmacology, 46(13), 2304-2311. https://doi.org/10.1038/s41386-021-01189-x

Breddam Mosegaard, S., Rytter, S., Madsen, F., Odgaard, A., Søballe, K. & Stilling, M. (2021). Two-year fixation and ten-year clinical outcomes of total knee arthroplasty inserted with normal-curing bone cement and slow-curing bone cement: a randomized controlled trial in 54 patients. Knee, 33, 110-124. https://doi.org/10.1016/j.knee.2021.08.027

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

Tedde, A., Grelet, C., Ho, P. N., Pryce, J. E., Hailemariam, D., Wang, Z., Plastow, G., Gengler, N., Brostaux, Y., Froidmont, E., Dehareng, F., Bertozzi, C., Crowe, M. A., Dufrasne, I., GplusE Consortium & Soyeurt, H. (2021). Validation of dairy cow bodyweight prediction using traits easily recorded by dairy herd improvement organizations and its potential improvement using feature selection algorithms. Animals, 11(5), Article 1288. https://doi.org/10.3390/ani11051288

Atashi, H., Salavati, M., De Koster, J., Crowe, M., Opsomer, G., Hostens, M. & GplusE Consortium (2020). A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach. Animals, 10(3), 1-13. Article 500. https://doi.org/10.3390/ani10030500

Rheinbay, E., Nielsen, M. M., Abascal, F., Wala, J. A., Shapira, O., Tiao, G., Hornshøj, H., Hess, J. M., Juul, R. I., Lin, Z., Feuerbach, L., Sabarinathan, R., Madsen, T., Kim, J., Mularoni, L., Shuai, S., Lanzós, A., Herrmann, C., Maruvka, Y. E. ... PCAWG Consortium (2020). Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature, 578(7793), 102-111. https://doi.org/10.1038/s41586-020-1965-x

Cheng, J. Y. & Mailund, T. (2020). Ancestral population genomics with Jocx, a coalescent hidden markov model. In J. Y. Dutheil (Ed.), Statistical population genomics (pp. 167-189). Humana Press. https://doi.org/10.1007/978-1-0716-0199-0_8

Hobolth, A., Guo, Q., Kousholt, A. & Jensen, J. L. (2020). A Unifying Framework and Comparison of Algorithms for Non-negative Matrix Factorisation. International Statistical Review, 88(1), 29-53. https://doi.org/10.1111/insr.12331

Krogh, M. A., Hostens, M., Salavati, M., Grelet, C., Sørensen, M. T., Wathers, D. C., Ferris, C. P., Marchitelli, C., Signorelli, F., Napolitano, F., Becker, F., Larsen, T., Matthews, E., Carter, F., Vanlierde, A., Opsomer, G., Gengler, N., Dehareng, F., Crowe, M. A. ... Foldager, L. (2020). Between- and within-herd variation in blood and milk biomarkers in Holstein cows in early lactation. Animal, 14(5), 1067-1075. Article 1751731119002659. https://doi.org/10.1017/S1751731119002659

Birkbak, N. J. & McGranahan, N. (2020). Cancer Genome Evolutionary Trajectories in Metastasis. Cancer Cell, 37(1), 8-19. https://doi.org/10.1016/j.ccell.2019.12.004

Carlevaro-Fita, J., Lanzós, A., Feuerbach, L., Hong, C., Mas-Ponte, D., Pedersen, J. S., PCAWG Drivers and Functional Interpretation Group, Johnson, R. & PCAWG Consortium (2020). Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Communications Biology, 3(1), Article 56. https://doi.org/10.1038/s42003-019-0741-7

Schild, S. L. A., Foldager, L., Rangstrup-Christensen, L. & Pedersen, L. J. (2020). Characteristics of Piglets Born by Two Highly Prolific Sow Hybrids. Frontiers in Veterinary Science, 7, Article 355. https://doi.org/10.3389/fvets.2020.00355

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

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

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

Kongsted, H., Foldager, L. & Sørensen, J. T. (2020). Data from routine meat inspection is a poor indicator of the prevalence of tail lesions in undocked pigs. Porcine Health Management, 6(1), Article 10. https://doi.org/10.1186/s40813-020-00149-z

Duan, H., Mansour, S., Reed, R., Gillis, M. K., Parent, B., Liu, B., Sztupinszki, Z., Birkbak, N., Szallasi, Z., Elia, A. E. H., Garber, J. E. & Pathania, S. (2020). E3 ligase RFWD3 is a novel modulator of stalled fork stability in BRCA2-deficient cells. The Journal of Cell Biology, 219(6), Article e201908192. https://doi.org/10.1083/jcb.201908192

Ettema, J., Krogh, M. A., Østergaard, S. & GplusE Consortium (2020). Economic value of information from an alert system on physiological imbalance in fresh cows. Preventive Veterinary Medicine, 181, Article 105039. https://doi.org/10.1016/j.prevetmed.2020.105039

Østergaard, S. D., Speed, M. S., Kellner, C. H., Mueller, M., McClintock, S. M., Husain, M. M., Petrides, G., McCall, W. V., Lisanby, S. H. & for the CORE/PRIDE workgroup (2020). Electroconvulsive therapy (ECT) for moderate-severity major depression among the elderly: Data from the pride study. Journal of Affective Disorders, 274, 1134-1141. https://doi.org/10.1016/j.jad.2020.05.039

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

Athanasiadis, G., Speed, D., Andersen, M. K., Appel, E. V. R., Grarup, N., Brandslund, I., Jørgensen, M. E., Larsen, C. V. L., Bjerregaard, P., Hansen, T. & Albrechtsen, A. (2020). Estimating narrow-sense heritability using family data from admixed populations. Heredity, 124(6), 751-762. https://doi.org/10.1038/s41437-020-0311-2

Speed, D., Holmes, J. & Balding, D. J. (2020). Evaluating and improving heritability models using summary statistics. Nature Genetics, 52(4), 458-462. https://doi.org/10.1038/s41588-020-0600-y

Waldvogel, A. M., Feldmeyer, B., Rolshausen, G., Exposito-Alonso, M., Rellstab, C., Kofler, R., Mock, T., Schmid, K., Schmitt, I., Bataillon, T., Savolainen, O., Bergland, A., Flatt, T., Guillaume, F. & Pfenninger, M. (2020). Evolutionary genomics can improve prediction of species’ responses to climate change. Evolution Letters, 4(1), 4-18. https://doi.org/10.1002/evl3.154

Rousing, T., Rothmann Holm, J., Krogh, M. A., Østergaard, S. & GplusE Consortium (2020). Expert-based development of a generic HACCP-based risk management system to prevent critical negative energy balance in dairy herds. Preventive Veterinary Medicine, 175, Article 104849. https://doi.org/10.1016/j.prevetmed.2019.104849

Shah, N., Wakabayashi, T., Kawamura, Y., Skovbjerg, C. K., Wang, M.-Z., Mustamin, Y., Isomura, Y., Gupta, V., Jin, H., Mun, T., Sandal, N., Azuma, F., Fukai, E., Seren, Ü., Kusakabe, S., Kikuchi, Y., Nitanda, S., Kumaki, T., Hashiguchi, M. ... Andersen, S. U. (2020). Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan. Nature Communications, 11(1), Article 253. https://doi.org/10.1038/s41467-019-14213-y

Lee, Y. L., Takada, H., Moreira, G. C. M., Karim, L., GplusE Consortium, Bosse, M., Bouwman, A., Mullaart, E., Coppieters, W., Georges, M., Druet, T. & Charlier, C. (2020). Fine resolution CNV catalogue from deeply sequenced cattle genomes. In Book of Abstracts of the 71st Annual Meeting of the European Federation of Animal Science (Vol. 26, pp. 188). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-900-8

Adams, M. J., Howard, D. M., Luciano, M., Clarke, T.-K., Davies, G., Hill, W. D., Smith, D., Deary, I. J., Porteous, D. J., McIntosh, A. M., 23andMe Research Team & Major Depressive Disorder Working Group of the Psychiatric Genomic Consortium (2020). Genetic stratification of depression by neuroticism: revisiting a diagnostic tradition. Psychological Medicine, 50(15), 2526–2535. https://doi.org/10.1017/S0033291719002629

Atashi, H., Salavati, M., De Koster, J., Crowe, M., Opsomer, G., GplusE Consortium & Hostens, M. (2020). Genome-wide association for metabolic clusters in early-lactation Holstein dairy cows. Journal of Dairy Science, 103(7), 6392-6406. https://doi.org/10.3168/jds.2019-17369

Atashi, H., Salavati, M., De Koster, J., Ehrlich, J., Crowe, M., Opsomer, G., GplusE Consortium & Hostens, M. (2020). Genome‐wide association for milk production and lactation curve parameters in Holstein dairy cows. Journal of Animal Breeding and Genetics, 137(3), 292-304. https://doi.org/10.1111/jbg.12442

Coleman, J. R. I., Peyrot, W. J., Purves, K. L., Davis, K. A. S., Rayner, C., Choi, S. W., Hubel, C., Gaspar, H. A., Kan, C., Van der Auwera, S., Adams, M. J., Lyall, D. M., Choi, K. W., Psychiat Genomics Consortium, Dunn, E. C., Vassos, E., Danese, A., Maughan, B., Grabe, H. J. ... Breen, G. (2020). Genome-wide gene-environment analyses of major depressive disorder and reported lifetime traumatic experiences in UK Biobank. Molecular Psychiatry, 25(7), 1430-1446. https://doi.org/10.1038/s41380-019-0546-6

Fan, R., Gu, Z., Guang, X., Marín, J. C., Varas, V., González, B. A., Wheeler, J. C., Hu, Y., Li, E., Sun, X., Yang, X., Zhang, C., Gao, W., He, J., Munch, K., Corbett-Detig, R., Barbato, M., Pan, S., Zhan, X. ... Dong, C. (2020). Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca. Genome Biology, 21(1), Article 159. https://doi.org/10.1186/s13059-020-02080-6

Tausen, M., Clausen, M. M., Moeskjær, S., Shihavuddin, ASM., Dahl, A. B., Janss, L. & Andersen, S. U. (2020). Greenotyper: Image-based plant phenotyping using distributed computing and deep learning. Frontiers in Plant Science, 11, Article 1181. https://doi.org/10.3389/fpls.2020.01181

Thomsen, P. T., Capion, N. & Foldager, L. (2020). Higher odds of abortion in dairy cows hoof trimmed late in gestation. Research in Veterinary Science, 133, 1-3. https://doi.org/10.1016/j.rvsc.2020.08.016

Galtier, N. & Rousselle, M. (2020). How much does Ne vary among species? Genetics, 216(2), 559-572. https://doi.org/10.1534/genetics.120.303622

Thomsen, A. H., Villesen, P., Brink, O., Leth, P. M. & Hougen, H. P. (2020). Improved medical treatment could explain a decrease in homicides with a single stab wound. Forensic Science, Medicine, and Pathology, 16(3), 415-422. https://doi.org/10.1007/s12024-020-00246-z

Zhang, Q., Cai, Z., Lhomme, M., Sahana, G., Lesnik, P., Guerin, M., Fredholm, M. & Karlskov-Mortensen, P. (2020). Inclusion of endophenotypes in a standard GWAS facilitate a detailed mechanistic understanding of genetic elements that control blood lipid levels. Scientific Reports, 10(1), Article 18434. https://doi.org/10.1038/s41598-020-75612-6

Madsen, T., Nielsen, M. M., Pedersen, J. S., PCAWG Evolution and Heterogeneity Working Group & PCAWG Consortium (2020). Inferring structural variant cancer cell fraction. Nature Communications, 11(1), Article 730. https://doi.org/10.1038/s41467-020-14351-8

Winge, S. B., Soraggi, S., Schierup, M. H., Rajpert-De Meyts, E. & Almstrup, K. (2020). Integration and reanalysis of transcriptomics and methylomics data derived from blood and testis tissue of men with 47,XXY Klinefelter syndrome indicates the primary involvement of Sertoli cells in the testicular pathogenesis. American Journal of Medical Genetics. Part C: Seminars in Medical Genetics, 184(2), 239-255. https://doi.org/10.1002/ajmg.c.31793

Paczkowska, M., Barenboim, J., Sintupisut, N., Fox, N. S., Zhu, H., Abd-Rabbo, D., Mee, M. W., Boutros, P. C., PCAWG Drivers and Functional Interpretation Working Group, Reimand, J. & PCAWG Consortium (2020). Integrative pathway enrichment analysis of multivariate omics data. Nature Communications, 11(1), Article 735. https://doi.org/10.1038/s41467-019-13983-9

Kongsted, H., Foldager, L. & Sørensen, J. T. (2020). Kødkontrollen fanger ikke forekomst af halebid på hele haler. Dansk Veterinærtidsskrift, 2020(7), 18-19. https://dvt.ddd.dk/bladarkiv/2020/nr-07/koedkontrollen-fanger-ikke-forekomst-af-halebid-paa-hele-haler/

Satterstrom, F. K., Kosmicki, J. A., Wang, J., Breen, M. S., De Rubeis, S., An, J. Y., Peng, M., Collins, R., Grove, J., Klei, L., Stevens, C., Reichert, J., Mulhern, M. S., Artomov, M., Gerges, S., Sheppard, B., Xu, X., Bhaduri, A., Norman, U. ... Børglum, A. D. (2020). Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism. Cell, 180(3), 568-584.e23. https://doi.org/10.1016/j.cell.2019.12.036

Privé, F., Arbel, J. & Vilhjálmsson, B. J. (2020). LDpred2: better, faster, stronger. Bioinformatics, 36(22-23), 5424-5431. https://doi.org/10.1093/bioinformatics/btaa1029

Omland, L. H., Holm-Hansen, C., Lebech, A. M., Dessau, R. B., Bodilsen, J., Andersen, N. S., Roed, C., Christiansen, C. B., Ellermann-Eriksen, S., Midgley, S., Nielsen, L., Benfield, T., Hansen, A. B. E., Andersen, C., Rothman, K. J., Sørensen, H. T., Fischer, T. K. & Obel, N. (2020). Long-Term Survival, Health, Social Functioning, and Education in Patients With an Enterovirus Central Nervous System Infection, Denmark, 1997-2016. The Journal of Infectious Diseases, 222(4), 619-627. https://doi.org/10.1093/infdis/jiaa151

Buchholtz, P. E., Ashkanian, M., Hjerrild, S., Hauptmann, L. K., Devantier, T. A., Jensen, P., Wissing, S., Thorgaard, M., Bjerager, L., Saugberg, J. L., Alrø, A., Speed, M., Brund, R. B. K. & Videbech, P. (2020). Low frequency rTMS inhibits the anti-depressive effect of ECT: A pilot study. Acta Neuropsychiatrica, 32(6), 328-338. https://doi.org/10.1017/neu.2020.28

Buggiotti, L., Cheng, Z., Wathes, D. C., GplusE Consortium & Ingvartsen, K. L. (2020). Mining the unmapped reads in bovine RNA-Seq data reveals the prevalence of bovine herpes virus-6 in European dairy cows and the associated changes in their phenotype and leucocyte transcriptome. Viruses, 12(12), Article 1451. https://doi.org/10.3390/v12121451

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

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