Publications

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Leppälä, K., Nielsen, S. & Mailund, T. (2017). admixturegraph: an R package for admixture graph manipulation and fitting. Bioinformatics (Online), 33(11), 1738-1740. https://doi.org/10.1093/bioinformatics/btx048

Mailund, T. (2017). Advanced Object-Oriented Programming in R: Statistical Programming for Data Science, Analysis, and Finance . Apress.

Prüfer, K., de Filippo, C., Grote, S., Mafessoni, F., Korlević, P., Hajdinjak, M., Vernot, B., Skov, L., Hsieh, P., Peyrégne, S., Reher, D., Hopfe, C., Nagel, S., Maricic, T., Fu, Q., Theunert, C., Theunert, C., Rogers, R., Skoglund, P. ... Pääbo, S. (2017). A high-coverage Neandertal genome from Vindija Cave in Croatia. Science, 358(6363), 655-658. https://doi.org/10.1126/science.aao1887

Schrempf, D. & Hobolth, A. (2017). An alternative derivation of the stationary distribution of the multivariate neutral Wright–Fisher model for low mutation rates with a view to mutation rate estimation from site frequency data. Theoretical Population Biology, 114, 88-94. https://doi.org/10.1016/j.tpb.2016.12.001

Skov, L., Schierup, M. H. & Danish Pan Genome Consortium (2017). Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion. PLoS Genetics, 13(8), Article e1006834. https://doi.org/10.1371/journal.pgen.1006834

Palmgren, M., Engström, K., Hallström, B. M., Wahlberg, K., Søndergaard, D. A., Säll, T., Vahter, M. & Broberg, K. (2017). AS3MT-mediated tolerance to arsenic evolved by multiple independent horizontal gene transfers from bacteria to eukaryotes. PLoS One, 12(4), e0175422. Article e0175422. https://doi.org/10.1371/journal.pone.0175422

St Pourcain, B., Robinson, E. B., Anttila, V., Sullivan, B. B., Maller, J., Golding, J., Skuse, D., Ring, S., Evans, D. M., Zammit, S., Fisher, S. E., Neale, B. M., Anney, R. J. L., Ripke, S., Hollegaard, M. V., Werge, T., Ronald, A., Grove, J., Hougaard, D. M. ... iPSYCH-SSI-Broad Autism Group (2017). ASD and schizophrenia show distinct developmental profiles in common genetic overlap with population-based social communication difficulties. Molecular Psychiatry, 23, 263-270. https://doi.org/10.1038/mp.2016.198

Bertl, J., Guo, Q., Rasmussen, M. J., Besenbacher, S., Nielsen, M. M., Hornshøj, H., Pedersen, J. S. & Hobolth, A. (2017). A Site Specific Model And Analysis Of The Neutral Somatic Mutation Rate In Whole-Genome Cancer Data. https://doi.org/10.1101/122879

Jensen, J. M., Villesen, P., Friborg, R. M., Mailund, T., Besenbacher, S., Schierup, M. H. & Danish Pan-Genome Consortium (Jakob Grove, member of -) (2017). Assembly and analysis of 100 full MHC haplotypes from the Danish population. Genome Research, 27(9), 1597-1607. https://doi.org/10.1101/gr.218891.116

Álvarez-Álvarez, M. M., Zanetti, D., Carreras-Torres, R., Moral, P. & Athanasiadis, G. (2017). A survey of sub-Saharan gene flow into the Mediterranean at risk loci for coronary artery disease. European Journal of Human Genetics, 25(4), 472-476. https://doi.org/10.1038/ejhg.2016.200

Mailund, T. (2017). Beginning Data Science in R: Data Analysis, Visualization, and Modelling for the Data Scientist. Apress.

Duan, J. (2017). Biological insights from next-generation sequencing data analysis.

Okholm, T. L. H., Nielsen, M. M., Hamilton, M., Christensen, L.-L., Vang, S., Hedegaard, J., Hansen, T. B., Kjems, J., Dyrskjøt, L. & Pedersen, J. S. (2017). Circular RNA expression is abundant and correlated to aggressiveness in early-stage bladder cancer. npj Genomic Medicine, 2(1), Article 36. https://doi.org/10.1038/s41525-017-0038-z

Debost, J.-C., Debost, M., Grove, J., Mors, O., Hougaard, D. M., Børglum, A. D., Mortensen, P. B. & Petersen, L. (2017). COMT Val158Met and MTHFR C677T moderate risk of schizophrenia in response to childhood adversity. Acta Psychiatrica Scandinavica, 136(1), 85-95. https://doi.org/10.1111/acps.12761

Aschard, H., Guillemot, V., Vilhjalmsson, B., Patel, C. J., Skurnik, D., Ye, C. J., Wolpin, B., Kraft, P. & Zaitlen, N. (2017). Covariate selection for association screening in multiphenotype genetic studies. Nature Genetics, 49(12), 1789-1795. https://doi.org/10.1038/ng.3975

Foldager, L., Gildbjerg, L. B., Voss, H., Trénel, P., Munksgaard, L. & Thomsen, P. T. (2017). Daily eating activity of dairy cows from 3D accelerometer data and RFID signals: prediction by random forests and detection of sick cows. In P. Linde (Ed.), Symposium i Anvendt Statistik (pp. 109-122)

Jónsson, H., Sulem, P., Kehr, B., Kristmundsdottir, S., Zink, F., Hjartarson, E., Hardarson, M. T., Hjorleifsson, K. E., Eggertsson, H. P., Gudjonsson, S. A., Ward, L. D., Arnadottir, G. A., Helgason, E. A., Helgason, H., Gylfason, A., Jonasdottir, A., Jonasdottir, A., Rafnar, T., Besenbacher, S. ... Stefansson, K. (2017). Data Descriptor: Whole genome characterization of sequence diversity of 15,220 Icelanders. Scientific Data, 4, Article 170115. https://doi.org/10.1038/sdata.2017.115

Midzi, N., Mduluza, T., Mudenge, B., Foldager, L. & Leutscher, P. D. C. (2017). Decrease in Seminal HIV-1 RNA Load After Praziquantel Treatment of Urogenital Schistosomiasis Coinfection in HIV-Positive Men—An Observational Study. Open Forum Infectious Diseases, 4(4), Article ofx199. https://doi.org/10.1093/ofid/ofx199

Boel, M. & Foldager, L. (2017). Development of a predictive algorithm for a pig farming decision support system. In P. Linde (Ed.), Symposium i Anvendt Statistik (pp. 123-123)

Brodersen, D. E., Bendtsen, K. L., Xu, K., Luckmann, M., Winther, K., Shah, S. A. & Pedersen, C. N. S. (2017). Discrete Structural Dynamics of Pseudo-Palindromic Motifs Control DNA Binding of Bacterial Toxin-Antitoxin Complexes. The FASEB Journal, 31(No. 1 supplement), Article 777.2. http://www.fasebj.org/doi/abs/10.1096/fasebj.31.1_supplement.777.2

James, J., Esteve, D. C. & Eyre-Walker, A. (2017). DNA sequence diversity and the efficiency of natural selection in animal mitochondrial DNA. Heredity, 118(1), 88-95. https://doi.org/10.1038/hdy.2016.108

Ernst, E. H., Grøndahl, M. L., Grund, S., Hardy, K., Heuck, A., Sunde, L., Franks, S., Andersen, C. Y., Villesen, P. & Lykke-Hartmann, K. (2017). Dormancy and activation of human oocytes from primordial and primary follicles: molecular clues to oocyte regulation. Human Reproduction, 32(8), 1684-1700. https://doi.org/10.1093/humrep/dex238

Bechsgaard, J., Jorgensen, T. H. & Schierup, M. H. (2017). Evidence for Adaptive Introgression of Disease Resistance Genes Among Closely Related Arabidopsis Species. G3: Genes, Genomes, Genetics (Bethesda), 7(8), 2677-2683. https://doi.org/10.1534/g3.117.043984

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

Salavati, M. & GplusE Consortium (2017). Exploratory classification of multiparous dairy cows based on fertility related phenotypes. In Book of Abstracts of the 68th Annual Meeting of the European Federation of Animal Science (pp. 402-402). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-859-9

Cheng, J. Y., Mailund, T. & Nielsen, R. (2017). Fast admixture analysis and population tree estimation for SNP and NGS data. Bioinformatics (Online), 33(14), 2148–2155. https://doi.org/10.1093/bioinformatics/btx098

Mailund, T. (2017). Functional data structures in R: advanced statistical programming in R. Apress. https://doi.org/10.1007/978-1-4842-3144-9

Mailund, T. (2017). Functional Programming in R: Advanced Statistical Programming for Data Science, Analysis and Finance . Apress.

Hammami, H., Colinet, F. G., Bastin, C., Grelet, C., Vanlierde, A., Dehareng, F., Gengler, N. & GplusE Consortium (2017). Genetic analysis of milk MIR predicted blood and milk biomarkers linked to the physiological status. In Book of Abstracts of the 68th Annual Meeting of the European Federation of Animal Science (pp. 403-403). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-859-9

Tataru, P., Mollion, M., Glémin, S. & Bataillon, T. (2017). Inference of distribution of fitness effects and proportion of adaptive substitutions from polymorphism data. Genetics, 207(3), 1103-1119. https://doi.org/10.1534/genetics.117.300323

Salavati, M. & GplusE Consortium (2017). Investigating metabolic phenotypes in multiparous dairy cows by component analysis and clustering. In Book of Abstracts of the 68th Annual Meeting of the European Federation of Animal Science (pp. 404-404). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-859-9

Birkenkamp-Demtröder, K., Christensen, E., Nordentoft, I. K., Knudsen, M., Taber, A., Høyer, S., Lamy, P., Agerbæk, M., Jensen, J. B. & Dyrskjøt, L. (2017). Liquid Biopsies for monitoring treatment response and metastatic relapse in bladder cancer patients. Poster session presented at 1st Annual Research Meeting at the Department of Clinical Medicine, Aarhus, Denmark.

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

Mailund, T. (2017). Metaprogramming in R: Advanced Statistical Programming for Data Science, Analysis and Finance . Apress.

Skov, L. (2017). Methods for analyzing genetic variation in modern and archaic humans.

Starnawski, P., Bataillon, T., Ettema, T. J. G., Jochum, L. M., Schreiber, L., Chen, X., Lever, M. A., Polz, M. F., Jørgensen, B. B., Schramm, A. & Kjeldsen, K. U. (2017). Microbial community assembly and evolution in subseafloor sediment. Proceedings of the National Academy of Sciences (PNAS), 114(11), 2940-2945. https://doi.org/10.1073/pnas.1614190114

Rasmussen, M. J., Bertl, J., Guo, Q., Nielsen, M. M., Świtnicki, M., Hornshøj, H., Madsen, T., Hobolth, A. & Pedersen, J. S. (2017). Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate. eLife, 6, Article e21778. https://doi.org/10.7554/eLife.21778

Weiner, D. J., Wigdor, E. M., Ripke, S., Walters, R. K., Kosmicki, J. A., Grove, J., Samocha, K. E., Goldstein, J. I., Okbay, A., Bybjerg-Grauholm, J., Werge, T., Hougaard, D. M., Taylor, J., Skuse, D., Devlin, B., Anney, R., Sanders, S. J., Bishop, S., Mortensen, P. B. ... iPSYCH-Broad Autism Group (2017). Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders. Nature Genetics, 49(7), 978-985. https://doi.org/10.1038/ng.3863

Grelet, C., Vanlierde, A., Dehareng, F., Froidmont, E. & GplusE Consortium (2017). Prediction of energy status of dairy cows using MIR milk spectra. In Book of Abstracts of the 68th Annual Meeting of the European Federation of Animal Science (Vol. 23, pp. 403-403). Wageningen Academic Publishers.

Grelet, C., Vanlierde, A., Salavati, M., Hostens, M., Foldager, L., Dehareng, F. & GplusE Consortium (2017). Prediction of energy status of dairy cows using MIR milk spectra. Abstract from ICAR 2017, United Kingdom. http://www.icar.org/wp-content/uploads/2017/06/1.-Clement-Grelet.pdf

Søndergaard, D., Nielsen, S., Pedersen, C. N. S. & Besenbacher, S. (2017). Prediction of Primary Tumors in Cancers of Unknown Primary. Journal of Integrative Bioinformatics, 14(2). https://doi.org/10.1515/jib-2017-0013

Villesen, P. & Stride Nielsen, L. (2017). Profiling of cocaine using ratios of GC-MS peaks. Scientific Reports, 7(1), 11646. Article 11646. https://doi.org/10.1038/s41598-017-12042-x

Foldager, L. & GplusE Consortium (2017). Random forests prediction of blood metabolic clusters by milk metabolites and enzymes in dairy cows. In Book of Abstracts of the 68th Annual Meeting of the European Federation of Animal Science (pp. 402-402). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-859-9

Leppälä, K., Matala-aho, T. & Törmä, T. (2017). Rational approximations of the exponential function at rational points. Journal of Number Theory, 179, 220-239. https://doi.org/10.1016/j.jnt.2017.03.014

Athanasiadis, G. (2017). Recent migration and sample representativeness in a Danish genetic study. Annals of Human Biology, 44(5), 484-486. https://doi.org/10.1080/03014460.2017.1336253

Jensen, J. M. (2017). Reference free phasing and representation of complex variation.

Madsen, T. (2017). Robust statistical methods for significance evaluation and applications in cancer driver detection and biomarker discovery.

Bolvig, A. K., Nørskov, N., van Vliet, S., Foldager, L., Curtasu, M. V., Hedemann, M. S., Sørensen, J. F., Lærke, H. N. & Knudsen, K. E. B. (2017). Rye bran modified with cell wall-degrading enzymes influences the kinetics of plant lignans but not of enterolignans in multicatheterized pigs. Journal of Nutrition, 147(12), 2220-2227 . https://doi.org/10.3945/jn.117.258483

Maretty, L., Jensen, J. M., Petersen, B., Sibbesen, J. A., Liu, S., Villesen, P., Skov, L., Belling, K. C., Theil Have, C., Izarzugaza, J. M. G., Grosjean, M., Bork-Jensen, J., Grove, J., Als, T. D., Huang, S., Chang, Y., Xu, R., Ye, W., Rao, J. ... Schierup, M. H. (2017). Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nature, 548(7665), 87-91. https://doi.org/10.1038/nature23264

Madsen, T., Hobolth, A., Jensen, J. L. & Pedersen, J. S. (2017). Significance evaluation in factor graphs. BMC Bioinformatics , 18(1), 199. Article 199. https://doi.org/10.1186/s12859-017-1614-z

Displaying results 551 to 600 out of 1406

Revised 13.01.2026

Palle Villesen