Publications

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Abascal, F., Corvelo, A., Cruz, F., Villanueva-Cañas, J. L., Vlasova, A., Marcet-Houben, M., Martínez-Cruz, B., Cheng, J. Y., Prieto, P., Quesada, V., Quilez, J., Li, G., García, F., Rubio-Camarillo, M., Frias, L., Ribeca, P., Capella-Gutiérrez, S., Rodríguez, J. M., Câmara, F. ... Godoy, J. A. (2016). Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Genome Biology (Online), 17(1), 251. Artikel 251. https://doi.org/10.1186/s13059-016-1090-1

Hanghøj, K., Seguin, A., Schubert, M., Madsen, T., Pedersen, J. S., Willerslev, E. & Orlando, L. (2016). Fast, accurate and automatic ancient nucleosome and methylation maps with epiPALEOMIX. Molecular Biology and Evolution, 33(12), 3284-3298. https://doi.org/10.1093/molbev/msw184

Hernandez-de Sosa, N., Athanasiadis, G., Malouf, J., Laiz, A., Muñoz-Marin, A. M., Herrera, S., Farrerons, J., Soria, J. M. & Casademont, J. (2016). Genetic Contribution of Femoral Neck Bone Geometry to the Risk of Developing Osteoporosis: A Family-Based Study. P L o S One, 11(5), Artikel 0154833. https://doi.org/10.1371/journal.pone.0154833

Jimenez Mena, B., Hospital, F. & Bataillon, T. (2016). Heterogeneity of effective population size and its implications in conservation genetics and animal breeding. Conservation Genetics Resources, 8(1), 35-41. https://doi.org/10.1007/s12686-015-0508-5

Shah, N., Hirakawa, H., Kusakabe, S., Sandal, N., Stougaard, J., Schierup, M. H., Sato, S. & Andersen, S. U. (2016). High-resolution genetic maps of Lotus japonicus and L. burttii based on re-sequencing of recombinant inbred lines. D N A Research, 23(5), 487-495. https://doi.org/10.1093/dnares/dsw033

Hobolth, A. (2016). Hvem er bedst? metoder til rangering i sport og videnskab. Aktuel Naturvidenskab, 5, 26-29.

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

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, Artikel 39447. https://doi.org/10.1038/srep39447

Nielsen, S., Simonsen, S. & Hobolth, A. (2016). Inferring Population Genetic Parameters: Particle Filtering, HMM, Ripley’s K-Function or Runs of Homozygosity? I M. Frith & C. Nørgaard Storm Pedersen (red.), Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings (Bind 9838, s. 234-245). Springer. http://link.springer.com/chapter/10.1007/978-3-319-43681-4_19/fulltext.html

Hancl, J. & Leppälä, K. (2016). IRRATIONALITY MEASURES FOR CONTINUED FRACTIONS WITH ASYMPTOTIC CONDITIONS. Kyushu journal of mathematics, 70(2), 205-216. https://doi.org/10.2206/kyushujm.70.205

Wiuf, C., Pallesen, J., Foldager, L. & Grove, J. (2016). LandScape: a simple method to aggregate p--Values and other stochastic variables without a priori grouping. Statistical Applications in Genetics and Molecular Biology, 15(4), 349-361. https://doi.org/10.1515/sagmb-2015-0085

Cheng, J. Y. (2016). Learning with Admixture: Modeling, Optimization, and Applications in Population Genetics. http://www.jade-cheng.com/au/tmp/thesis/thesis.pdf

Hartfield, M. & Glemin, S. (2016). Limits to Adaptation in Partially Selfing Species. Genetics, 203(2), 959-+. https://doi.org/10.1534/genetics.116.188821

Pebesma, E., Mailund, T. & Hiebert, J. (2016). Measurement units in R. The R Journal, 8(2), 486-494.

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

Athanasiadis, G., Cheng, J. Y., Vilhjálmsson, B. J., Jørgensen, F. G., Als, T. D., Le Hellard, S., Espeseth, T., Sullivan, P. F., Hultman, C. M., Kjærgaard, P. C., Schierup, M. H. & Mailund, T. (2016). Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity. Genetics, 204(2), 711-722. https://doi.org/10.1534/genetics.116.189241

Christiansen, F. B. (2016). Naturlig selektion. I K. Finster, T. Wang, F. Borchsenius & F. B. Christiansen (red.), Evolutionsbiologiske milepæle (s. 20-39). Aarhus Universitetsforlag.

Jimenez Mena, B., Tataru, P., Brøndum, R. F., Sahana, G., Guldbrandtsen, B. & Bataillon, T. (2016). One size fits all? Direct evidence for the heterogeneity of genetic drift throughout the genome. Biology Letters, 12(7), Artikel 20160426. https://doi.org/10.1098/rsbl.2016.0426

Hartfield, M. (2016). On the origin of asexual species by means of hybridization and drift. Molecular Ecology, 25(14), 3264-3265. https://doi.org/10.1111/mec.13713

Lamy, P., Nordentoft, I. K., Birkenkamp-Demtröder, K., Thomsen, M. B. H., Villesen, P., Vang, S., Hedegaard, J., Borre, M., Jensen, J. B., Ørntoft, T. F. & Andersen, L. D. (2016). Paired exome analysis reveals clonal evolution and potential therapeutic targets in urothelial carcinoma. Cancer Research, 76(19), 5894-5906. https://doi.org/10.1158/0008-5472.CAN-16-0436

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. P L o S One, 11(12), e0167437. Artikel e0167437. https://doi.org/10.1371/journal.pone.0167437

Jimenez Mena, B., Schad, K., Hanna, N. & Lacy, R. C. (2016). Pedigree analysis for the genetic management of group-living species. Ecology and Evolution, 6(10), 3067-3078. https://doi.org/10.1002/ece3.1831

Świtnicki, M. P., Rasmussen, M. J., Madsen, T., Sørensen, K. D. & Pedersen, J. S. (2016). PINCAGE: Probabilistic integration of cancer genomics data for perturbed gene identification and sample classification. Bioinformatics, 32(9), 1353-1365. https://doi.org/10.1093/bioinformatics/btv758

Höglund, J., Sørensen, M. T., Larsen, T., Foldager, L., Ferris, C., Bell, M., Carter, F., Santoro, A., Crowe, M. & Ingvartsen, K. L. (2016). Potential for novel metabolite measurements in milk as biomarker phenotypes for dairy traits. I Book of abstracts of the 67th Annual Meeting of the European Federation of Animal Science (s. 299). Wageningen Academic Publishers, The Netherlands. https://doi.org/10.3920/978-90-8686-830-8

Aschard, H., Vilhjálmsson, B. J., Joshi, A. D., Price, A. L. & Kraft, P. (2016). Response to Day et al. American Journal of Human Genetics, 98(2), 394-5. https://doi.org/10.1016/j.ajhg.2015.12.020

Hauberg, M. E., Holm-Nielsen, M. H., Mattheisen, M., Askou, A. L., Grove, J., Børglum, A. D. & Corydon, T. J. (2016). Schizophrenia risk variants affecting microRNA function and site-specific regulation of NT5C2 by miR-206. European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology, 26(9), 1522-6. https://doi.org/10.1016/j.euroneuro.2016.06.014

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

Athanasiadis, G., Jorgensen, F. G., Cheng, J. Y., Kjaergaard, P. C., Schierup, M. H. & Mailund, T. (2016). Spitting for Science: Danish High School Students Commit to a Large-Scale Self-Reported Genetic Study. P L o S One, 11(8), Artikel e0161822. https://doi.org/10.1371/journal.pone.0161822

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

Tataru, P., Simonsen, M., Bataillon, T. & Hobolth, A. (2016). Statistical Inference in the Wright–Fisher Model Using Allele Frequency Data. Systematic Biology, 66(1), e30-e46. https://doi.org/10.1093/sysbio/syw056

Malolepszy, A., Mun, T., Sandal, N., Gupta, V., Dubin, M., Urbanski, D. F., Shah, N., Bachmann, A., Fukai, E., Hirakawa, H., Tabata, S., Nadzieja, M., Markmann, K., Su, J., Umehara, Y., Soyano, T., Miyahara, A., Sato, S., Hayashi, M. ... Andersen, S. U. (2016). The LORE1 insertion mutant resource. The Plant Journal, 88(2), 306-317. https://doi.org/10.1111/tpj.13243

Hobolth, A. & Siren, J. (2016). The multivariate Wright–Fisher process with mutation: Moment-based analysis and inference using a hierarchical Beta model. Theoretical Population Biology, 108, 36-50. https://doi.org/10.1016/j.tpb.2015.11.001

Stevison, L. S., Woerner, A. E., Kidd, J. M., Kelley, J. L., Veeramah, K. R., McManus, K. F., Bustamante, C. D., Hammer, M. F., Wall, J. D., Great Ape Genome Project & Schierup, M. H. (2016). The Time Scale of Recombination Rate Evolution in Great Apes. Molecular Biology and Evolution, 33(4), 928-945. https://doi.org/10.1093/molbev/msv331

Rajkumar, A. P., Christensen, J. H., Mattheisen, M., Jacobsen, I., Bache, I., Pallesen, J., Grove, J., Qvist, P., Mcquillin, A., Gurling, H. M., Tümer, Z., Mors, O. & Børglum, A. D. (2015). Analysis of t(9;17)(q33.2;q25.3) chromosomal breakpoint regions and genetic association reveals novel candidate genes for bipolar disorder. Bipolar Disorders (English Edition, Online), 17(2), 205-211. https://doi.org/10.1111/bdi.12239

Cheng, J. Y. & Mailund, T. (2015). Ancestral population genomics using coalescence hidden Markov models and heuristic optimisation algorithms. Computational Biology and Chemistry, 57, 80-92. https://doi.org/10.1016/j.compbiolchem.2015.02.001

Vestergaard, M., Kraft, J. F., Vosegaard, T., Thøgersen, L. & Schiøtt, B. (2015). Bicelles and Other Membrane Mimics: Comparison of Structure, Properties, and Dynamics from MD Simulations. Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 119(52), 15831-15843. https://doi.org/10.1021/acs.jpcb.5b08463

Bailey, S. & Bataillon, T. (2015). Can the experimental evolution programme help us elucidate the genetic basis of adaptation in nature? Molecular Ecology. https://doi.org/10.1111/mec.13378

Andersen, H. M.-L., Jørgensen, E., Pedersen, L. J. & Foldager, L. (2015). Can use of online measurements in EVOP designs reduce the time to locate production optimum? I M. Guarino & D. Berckmans (red.), Precision Livestock Farmin '15: Papers presented at the 7th European Conference on Precision Livestock Farming (s. 269-275)

Loh, P.-R., Bhatia, G., Gusev, A., Finucane, H. K., Bulik-Sullivan, B. K., Pollack, S. J., Schizophrenia Working Group of the Psychiatric Genomics Consortium (Anders Børglum, Jakob Grove; members of -), O’Donovan, M. C., Neale, B. M., Patterson, N. & Price, A. L. (2015). Contrasting regional architectures of schizophrenia and other complex diseases using fast variance components analysis. Nature Genetics, 47, 1385–1392. https://doi.org/10.1038/ng.3431

Liu, S., Huang, S., Rao, J., Ye, W., Genome Denmark Consortium (Anders Børglum, member of -), Krogh, A. & Wang, J. (2015). Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale. GigaScience, 4, 64. https://doi.org/10.1186/s13742-015-0103-4

Kirkegaard, K. K., Fredsted, P. V., Jensen, J. M., Hindkjær, J. J., Kølvraa, S., Ingerslev, H. J. & Lykke-Hartmann, K. (2015). Distinct differences in global gene expression profiles in non-implanted blastocysts and blastocysts resulting in live birth. Gene, 571(2), 212-220. https://doi.org/10.1016/j.gene.2015.06.057

Schick, A., Bailey, S. & Kassen, R. (2015). Evolution of fitness trade-offs in locally adapted populations of Pseudomonas fluorescens. American Naturalist, 186(S1), S48-S59. https://doi.org/10.1086/682932

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

Hargreaves, A., Bailey, S. & Laird, R. (2015). Fitness declines towards range limits and local adaptation to climate affect dispersal evolution during climate‐induced range shifts. Journal of Evolutionary Biology, 28(8), 1489-1501. https://doi.org/10.1111/jeb.12669

Sukosd, Z., Andersen, E. S., Seemann, S. E., Jensen, M., Hansen, M. B., Gorodkin, J. & Kjems, J. (2015). Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain. Nucleic Acids Research, 43(21), 10168-10179. https://doi.org/10.1093/nar/gkv1039

Lassalle, F., Périan, S., Bataillon, T., Nesme, X., Duret, L. & Daubin, V. (2015). GC-Content evolution in bacterial genomes: the biased gene conversion hypothesis expands. P L o S Genetics, 11(2), e1004941. https://doi.org/10.1371/journal.pgen.1004941

Eickhardt, E. A., Als, T. D., Mattheisen, M., Hauberg, M. E., Grove, J., Børglum, A. & Lescai, F. (2015). Genome-Wide Landscape of Genetic Variation with a Functional Impact on Predicted Binding Activity of Transcription Factor Binding Sites. Poster session præsenteret på ESHG 2015, Glasgow, Storbritannien.

Qian, Y. (2015). Genome Wide Variation Analysis Using High Throughput Data.

Meier, S. M., Agerbo, E., Maier, R., Pedersen, C. B., Lang, M., Grove, J., Hollegaard, M. V., Demontis, D., Trabjerg, B. B., Hjorthøj, C., Ripke, S., Degenhardt, F., Nöthen, M. M., Rujescu, D., Maier, W., Werge, T., Mors, O., Hougaard, D. M., Børglum, A. D. ... MooDS SCZ Consortium (2015). High loading of polygenic risk in cases with chronic schizophrenia. Molecular Psychiatry, 1-6. https://doi.org/10.1038/mp.2015.130

Als, T. D., Lescai, F., Dahl, H., Demontis, D., Wang, A., Andorsdottir, G., Biskopstø, M., Johansen, O., Grove, J., Nyegaard, M., Bolund, L., Mors, O., Jun, W. & Børglum, A. (2015). Identifying Rare Variation in Cases of Schizophrenia in the Isolated Population of the Faroe Islands using Whole-genome Sequencing. Poster session præsenteret på XXIII World Congress of Psychiatric Genetics, Toronto, Canada.

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