Publications

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Gaspar, H. A., Gerring, Z., Hübel, C., Middeldorp, C. M., Derks, E. M., Breen, G. & Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium (2019). Using genetic drug-target networks to develop new drug hypotheses for major depressive disorder. Translational Psychiatry, 9(1), Article 117. https://doi.org/10.1038/s41398-019-0451-4

Hammami, H., Mota, R. R., Vanderick, S., Naderi, S., Bastin, C., Gengler, N. & GplusE Consortium (2019). Using milk MIR spectra to identify candidate genes associated with climate--smart traits 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

Soyeurt, H., Froidmont, E., Dufrasne, I., Wang, Z., Gengler, N., Dehareng, F., GplusE Consortium & Grelet, C. (2019). Validation of the prediction of body weight from dairy cow characteristics and milk MIR spectra. In Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science (Vol. 25, pp. 606). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-890-2

Riber, A. B., Foldager, L. & Tahamtani, F., (2019). Validitet og pålidelighed af Øko-metoden anvendt til fjerdragtsbedømmelse hos æglæggere, No. 2019-760-001051, 5 p., Sept 16, 2019.

Hannon, E., Schendel, D., Ladd-Acosta, C., Grove, J., Hansen, C. S., Hougaard, D. M., Bresnahan, M., Mors, O., Hollegaard, M. V., Bækvad-Hansen, M., Hornig, M., Mortensen, P. B., Børglum, A. D., Werge, T., Pedersen, M. G., Nordentoft, M., Buxbaum, J. D., Fallin, M. D., Bybjerg-Grauholm, J. ... Mill, J. (2019). Variable DNA methylation in neonates mediates the association between prenatal smoking and birth weight. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1770), Article 20180120. https://doi.org/10.1098/rstb.2018.0120

Palkopoulou, E., Lipson, M., Mallick, S., Nielsen, S., Rohland, N., Baleka, S., Karpinski, E., Ivancevic, A. M., To, T.-H., Kortschak, R. D., Raison, J. M., Qu, Z., Chin, T.-J., Alt, K. W., Claesson, S., Dalén, L., MacPhee, R. D. E., Meller, H., Roca, A. L. ... Reich, D. (2018). A comprehensive genomic history of extinct and living elephants. Proceedings of the National Academy of Sciences (PNAS), 115(11), E2566-E2574. https://doi.org/10.1073/pnas.1720554115

Jordan, V. E., Walker, J. A., Beckstrom, T. O., Steely, C. J., McDaniel, C. L., St Romain, C. P., The Baboon Genome Analysis Consortium, Worley, K. C., Phillips-Conroy, J., Jolly, C. J., Rogers, J., Konkel, M. K. & Batzer, M. A. (2018). A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms. Mobile DNA, 9(1), Article 13. https://doi.org/10.1186/s13100-018-0118-3

Castagnini, A., Foldager, L. & Berrios, G. E. (2018). Acute polymorphic psychotic disorder: concepts, empirical findings and challenges for ICD-11. Journal of Nervous and Mental Disease, 206(11), 887-895. https://doi.org/10.1097/NMD.0000000000000882

Grelet, C., Froidmont, E., Hostens, M., Vanlierde, A., Foldager, L., Salavati, M., Ingvartsen, K. L., Sørensen, M. T., Crowe, M., Ferris, C. P., Marchitelli, C., Becker, F., GplusE Consortium & Dehareng, F. (2018). A first approach to predict nitrogen efficiency of dairy cows through milk FT-MIR spectra. In EAAP 2018 Book of abstracts (pp. 477-477)

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 Baboon Genome Analysis Consortium (2018). Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis. Mobile DNA, 9(1), Article 10. https://doi.org/10.1186/s13100-018-0115-6

Bertl, J., Guo, Q., Juul, M., Besenbacher, S., Nielsen, M. M., Hornshøj, H., Pedersen, J. S. & Hobolth, A. (2018). A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data. BMC Bioinformatics , 19(147), Article 147. https://doi.org/10.1186/s12859-018-2141-2

Greve, A. N., Jepsen, J. R. M., Mortensen, E. L., Uher, R., Mackenzie, L., Foldager, L., Gantriis, D. L. L., Burton, B. K., Ellersgaard, D. V., Christiani, C. J., Spang, K. S., Hemager, N., Henriksen, M. T., Zahle, K. K., Stadsgaard, H. B., Thorup, A. A. E., Nordentoft, M., Plessen, K., Mors, O. & Bliksted, V. F. (2018). Associations between intelligence, verbal working memory and processing speed in parents with schizophrenia or bipolar disorder and their 7-year old offspring. Schizophrenia Bulletin, 44(Suppl_1), S252-S252.

Matey-Hernandez, M. L., Brunak, S., Izarzugaza, J. M. G. & Danish Pan-Genome Consortium (Jakob Grove, member of -) (2018). Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios. BMC Bioinformatics, 19(1), Article 239. https://doi.org/10.1186/s12859-018-2239-6

Gao, S., Hu, X., Xu, F., Gao, C., Xiong, K., Zhao, X., Chen, H., Zhao, S., Wang, M., Fu, D., Zhao, X., Bai, J., Mao, L., Li, B., Wu, S., Wang, J., Li, S., Yang, H., Bolund, L. & Pedersen, C. N. S. (2018). BS-virus-finder: virus integration calling using bisulfite sequencing data. GigaScience, 7(1), 1-7. https://doi.org/10.1093/gigascience/gix123

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

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

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

Krogh, M. A., Ettema, J., Østergaard, S. & GplusE Consortium (2018). Cost/benefit analyses on indicator-based intervention on physiological imbalance in dairy cows. 471-471. Poster session presented at The 15th International Symposium of Veterinary Epidemiology and Economic. , Chiang Mai, Thailand.

Mineur, A., Mota, R., Gengler, N., Vanderick, S., Hammami, H. & GplusE Consortium (2018). Defining and using novel milk composition based heat stress resilience traits in the context of genomic selection for more robust dairy cows in Wallonia. In J. Bryant, M. Burke, R. Cook, B. Harris, C. Mosconi & B. Wickham (Eds.), Proceedings of the ICAR Conference (Vol. 23, pp. 229-234) https://www.icar.org/wp-content/uploads/2018/07/ICAR-Technical-Series-23-Auckland-2018-Proceedings.pdf

Skov, L., Hui, R., Shchur, V., Hobolth, A., Scally, A., Schierup, M. H. & Durbin, R. (2018). Detecting archaic introgression using an unadmixed outgroup. PLoS Genetics, 14(9), Article e1007641. https://doi.org/10.1371/journal.pgen.1007641

Hartfield, M. (2018). Digest: Effects of spatially-spreading adaptive mutations on genome-wide diversity. Evolution, 72(4), 1015-1016. https://doi.org/10.1111/evo.13462

Skakkebæk, A., Nielsen, M. M., Trolle, C., Vang, S., Hornshøj, H., Hedegaard, J., Wallentin, M., Bojesen, A., Hertz, J. M., Fedder, J., Østergaard, J. R., Pedersen, J. S. & Gravholt, C. H. (2018). DNA hypermethylation and differential gene expression associated with Klinefelter syndrome. Scientific Reports, 8(1), Article 13740. https://doi.org/10.1038/s41598-018-31780-0

Mailund, T. (2018). Domain-Specific Languages in R: Advanced Statistical Programming. Apress.

Lucotte, E. A., Skov, L., Jensen, J. M., Coll Macià, M., Munch, K. & Schierup, M. H. (2018). Dynamic Copy Number Evolution of X- and Y-Linked Ampliconic Genes in Human Populations. Genetics, 209(3), 907-920. https://doi.org/10.1534/genetics.118.300826

Hannon, E., Schendel, D., Ladd-Acosta, C., Grove, J., Hansen, C. S., Andrews, S. V., Hougaard, D. M., Bresnahan, M., Mors, O., Hollegaard, M. V., Bækvad-Hansen, M., Hornig, M., Mortensen, P. B., Børglum, A. D., Werge, T., Pedersen, M. G., Nordentoft, M., Buxbaum, J., Daniele Fallin, M. ... iPSYCH-Broad ASD Group (Mette Nyegaard, Per Qvist, Jane Hvarregaard Christensen - members of -) (2018). Elevated polygenic burden for autism is associated with differential DNA methylation at birth. Genome Medicine, 10(1), Article 19. https://doi.org/10.1186/s13073-018-0527-4

the iPSYCH-Broad autism group & the 23andMe Research Team (2018). Genome-wide analyses of self-reported empathy: Correlations with autism, schizophrenia, and anorexia nervosa. Translational Psychiatry, 8(1), Article 35. https://doi.org/10.1038/s41398-017-0082-6

Generation Scotland & Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium (2018). Genome-wide interaction study of a proxy for stress-sensitivity and its prediction of major depressive disorder. PLoS One, 13(12), Article e0209160. https://doi.org/10.1371/journal.pone.0209160

Ernst, E. H., Franks, S., Hardy, K., Villesen, P. & Lykke-Hartmann, K. (2018). Granulosa cells from human primordial and primary follicles show differential global gene expression profiles. Human Reproduction, 33(4), 666-679. https://doi.org/10.1093/humrep/dey011

Finucane, H. K., Reshef, Y. A., Anttila, V., Slowikowski, K., Gusev, A., Byrnes, A., Gazal, S., Loh, P.-R., Lareau, C., Shoresh, N., Genovese, G., Saunders, A., Macosko, E., Pollack, S., Brainstorm Consortium, Perry, J. R. B., Buenrostro, J. D., Bernstein, B. E., Raychaudhuri, S. ... Price, A. L. (2018). Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nature Genetics, 50(4), 621-629. https://doi.org/10.1038/s41588-018-0081-4

Kongsted, H., Foldager, L. & Sørensen, J. T., (2018). Identifikation af mulighederne for at minimere forekomsten af læsioner hos økologiske svin og frilandssvin (del 2), No. 2018-760-000666, 28 p., Jun 04, 2018.

Bailey, S. F., Guo, Q. & Bataillon, T. (2018). Identifying Drivers of Parallel Evolution: A Regression Model Approach. Genome Biology and Evolution, 10(10), 2801-2812. https://doi.org/10.1093/gbe/evy210

Feyera, T., Pedersen, T. F., Larsen, U. K., Foldager, L. & Theil, P. K. (2018). Impact of sow energy status during farrowing on farrowing kinetics, frequency of stillborn piglets, and farrowing assistance: Sow energy status and farrowing kinetics. Journal of Animal Science, 96(6), 2320–2331. Article 96. https://doi.org/10.1093/jas/sky141

Maier, R. M., Zhu, Z., Lee, S. H., Trzaskowski, M., Ruderfer, D. M., Stahl, E. A., Ripke, S., Wray, N. R., Yang, J., Visscher, P. M., Robinson, M. R., Forstner, A. J., Mcquillin, A., Trubetskoy, V., Wang, W., Wang, Y., Coleman, J. R. I., Gaspar, H. A., De Leeuw, C. A. ... Zammit, S. (2018). Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications, 9(1), Article 989. https://doi.org/10.1038/s41467-017-02769-6

Mollion, M. (2018). Inference on adaptation from population genomics data.

Foldager, L., Liu, Y., Pedersen, H. S., Larsen, K. E., Kristensen, K., Callesen, H. & Sørensen, M. T. (2018). In-vitro fertilization and in-vitro embryo culture in mouse as a reprotoxicity model for xenobiotics: some considerations on how to analyse data and present results. In P. Linde (Ed.), Symposium i anvendt statistik 2018 (pp. 188-199)

Ehlers, B., Holmstrup, M., Schmidt, I. K., Sørensen, J. G. & Bataillon, T. (2018). Joint impact of competition, summer precipitation, and maternal effects on survival and reproduction in the perennial Hieracium umbellatum. Evolutionary Ecology, 32(5), 529-545. https://doi.org/10.1007/s10682-018-9953-4

Dahl-Pedersen, K., Foldager, L., Herskin, M. S., Houe, H. & Thomsen, P. T. (2018). Lameness scoring and assessment of fitness for transport in dairy cows: Agreement among and between farmers, veterinarians and livestock drivers. Research in Veterinary Science, 119, 162-166. https://doi.org/10.1016/j.rvsc.2018.06.017

Bjerg, J. T., Boschker, H. T. S., Larsen, S., Berry, D., Schmid, M., Millo, D., Tataru, P., Meysman, F. J. R., Wagner, M., Nielsen, L. P. & Schramm, A. (2018). Long-distance electron transport in individual, living cable bacteria. Proceedings of the National Academy of Sciences (PNAS), 115(22), 5786-5791. https://doi.org/10.1073/pnas.1800367115

Salvador-Martínez, I., Coronado-Zamora, M., Castellano, D., Barbadilla, A. & Salazar-Ciudad, I. (2018). Mapping selection within Drosophila melanogaster embryo's anatomy. Molecular Biology and Evolution, 35(1), 66-79. https://doi.org/10.1093/molbev/msx266

Gengler, N., Mineur, A., Vanderick, S., Hammami, H. & GplusE Consortium (2018). Milk mid-infrared spectra based biomarkers contributing to genetic improvement for udder health, fertility and longevity. In J. Bryant, M. Burke, R. Cook, B. Harris, C. Mosconi & B. Wickham (Eds.), Proceedings of the ICAR Conference (Vol. 23, pp. 221-227) https://www.icar.org/wp-content/uploads/2018/07/ICAR-Technical-Series-23-Auckland-2018-Proceedings.pdf

Birkenkamp-Demtröder, K., Christensen, E., Nordentoft, I. K., Knudsen, M., Taber, A., Høyer, S., Lamy, P., Agerbæk, M., Jensen, J. B. & Dyrskjøt, L. (2018). Monitoring treatment response and metastatic relapse in advanced bladder cancer by liquid biopsy analysis. European Urology, 73(4), 535-540. https://doi.org/10.1016/j.eururo.2017.09.011

Schumer, M., Xu, C., Powell, D. L., Durvasula, A., Skov, L., Holland, C., Blazier, J. C., Sankararaman, S., Andolfatto, P., Rosenthal, G. G. & Przeworski, M. (2018). Natural selection interacts with recombination to shape the evolution of hybrid genomes. Science, 360(6389), 656-660. https://doi.org/10.1126/science.aar3684

Castellano, D., James, J. & Eyre-Walker, A. (2018). Nearly Neutral Evolution across the Drosophila melanogaster Genome. Molecular Biology and Evolution, 35(11), 2685-2694. https://doi.org/10.1093/molbev/msy164

Waltoft, B. L. & Hobolth, A. (2018). Non-parametric estimation of population size changes from the site frequency spectrum. Statistical Applications in Genetics and Molecular Biology, 17(3), Article 20170061. https://doi.org/10.1515/sagmb-2017-0061

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

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), 1. Article 40. https://doi.org/10.1038/s41525-017-0040-5

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

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

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Palle Villesen