Publications

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Bataillon, T. & Bailey, S. F. (2014). Effects of new mutations on fitness: insights from models and data. New York Academy of Sciences. Annals, 1320(1), 76-92. https://doi.org/10.1111/nyas.12460

Qian, Y., Browning, B. L. & Browning, S. R. (2014). Efficient clustering of identity-by-descent between multiple individuals. Bioinformatics, 30(7), 915-922. https://doi.org/10.1093/bioinformatics/btt734

Andersen, L. N., Mailund, T. & Hobolth, A. (2014). Efficient computation in the IM model. Journal of Mathematical Biology, 68(6), 1423-1451. https://doi.org/10.1007/s00285-013-0671-9

Sand, A. (2014). Engineering of Algorithms for Hidden Markov models and Tree Distances. Department of Computer Science, Aarhus University.

Castagnini, A. & Foldager, L. (2014). Epidemiology, course and outcome of acute polymorphic psychotic disorder: implications for ICD-11. Psychopathology, 47(3), 202-206. https://doi.org/10.1159/000357784

Furrow, R. E., Christiansen, F. B. & Feldman, M. W. (2014). Epigenetic variation, phenotypic heritability, and evolution. In A. Naumova & C. Greenwood (Eds.), Epigenetics and Complex Traits (pp. 233-246). Springer. https://doi.org/10.1007/978-1-4614-8078-5_1

Jimenez Mena, B., Verrier, E. & Hospital, F. (2014). Facing the estimation of effective population size based on molecular markers: comparison of estimators.. Abstract from World Congress on Genetics Applied to Livestock Production, Vancouvers, Canada. https://asas.org/docs/default-source/wcgalp-posters/440_paper_9030_manuscript_372_0.pdf?sfvrsn=2

Sørensen, J. L., Knudsen, M., Hansen, F. T., Olesen, C., Romans Fuertes, P., Lee, T. V., Søndergaard, T. E., Pedersen, C. N. S., Brodersen, D. E. & Giese, H. (2014). Fungal NRPS-dependent siderophores: From function to prediction. In J.-F. Martin, C. Garcia-Estrada & S. Zeilinger (Eds.), Biosynthesis and Molecular Genetics of Fungal Secondary Metabolites (pp. 317-339). Springer. https://doi.org/10.1007/978-1-4939-1191-2_15

Nordentoft, I. K., Birkenkamp-Demtröder, K., Lamy, P., Reinert, T., Vang, S., Hedegaard, J., Thorsen, K., Dyrskjøt, L., Pedersen, J. S. & Ørntoft, T. F. (2014). Genome and RNA sequencing identifies fusion transcripts in bladder cancer. Abstract from AACR Annual Meeting 2014, San Diego, California, United States.

Pujolar, J. M., Jacobsen, L. M. W., Als, T. D., Frydenberg, J., Munch, K., Jonsson, B., Jian, J. B., Cheng, L., Maes, G. E., Bernatchez, L. & Hansen, M. M. (2014). Genome-wide single generation signatures of local selection in the panmictic European eel. Molecular Ecology, 23, 2514-2528. https://doi.org/10.1111/mec.12753

Børglum, A. D., Demontis, D., Grove, J., Pallesen, J., Hollegaard, M. V., Pedersen, C. B., Hedemand, A., Mattheisen, M., Uitterlinden, A., Nyegaard, M., Orntoft, T., Wiuf, C., Didriksen, M., Nordentoft, M., Nöthen, M. M., Rietschel, M., Ophoff, R. A., Cichon, S., Yolken, R. H. ... GROUP Investigators (2014). Genome-wide study of association and interaction with maternal cytomegalovirus infection suggests new schizophrenia loci. Molecular Psychiatry, Mar;19(3), 325-33. https://doi.org/10.1038/mp.2013.2

Jacobsen, L. M. W., Pujolar, J. M., Bernatchez, L., Munch, K., Jian, J., Niu, Y. & Hansen, M. M. (2014). Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. Rostrata). Molecular Ecology, 23(19), 4785-4798. https://doi.org/10.1111/mec.12896

Grove, J., Børglum, A. & Pearce, B. D. (2014). GWAS, Cytomegalovirus Infection, and Schizophrenia. Current Behavioral Neuroscience Reports, 1(4), 215-223. https://doi.org/10.1007/s40473-014-0022-1

Qian, Y., Besenbacher, S., Mailund, T. & Schierup, M. H. (2014). Identifying disease associated genes by network propagation. BMC Systems Biology, 8(Suppl 1), S6. https://doi.org/10.1186/1752-0509-8-S1-S6

Mailund, T., Munch, K. & Schierup, M. H. (2014). Inferring the Process of Human–Chimpanzee Speciation. In Encyclopedia of Life Sciences Wiley. https://doi.org/10.1002/9780470015902.a0020833.pub2

GROUP Investigators & iPSYCH-GEMS SCZ (Jakob Grove, member of -) (2014). Integrated Pathway-Based Approach Identifies Association between Genomic Regions at CTCF and CACNB2 and Schizophrenia. PLoS Genetics, 10(6), e1004345. https://doi.org/10.1371/journal.pgen.1004345

Pedersen, B. P., Ifrim, G., Liboriussen, P., Axelsen, K. B., Palmgren, M. G., Nissen, P., Wiuf, C. H. & Pedersen, C. N. S. (2014). Large Scale Identification and Categorization of Protein Sequences Using Structured Logistic Regression. PLoS One, 9(1), Article e85139. https://doi.org/10.1371/journal.pone.0085139

Mailund, T., Munch, K. & Schierup, M. H. (2014). Lineage sorting in apes. Annual Review of Genetics, 48, 519-535. https://doi.org/10.1146/annurev-genet-120213-092532

Hansen, S. K., Vestergaard, M., Thøgersen, L., Schiøtt, B., Nielsen, N. C. & Vosegaard, T. (2014). Lipid Dynamics Studied by Calculation of 31P Solid-State NMR Spectra Using Ensembles from Molecular Dynamics Simulations. Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 118(19), 5119-5129. https://doi.org/10.1021/jp5000304

Søndergaard, D., Knudsen, M. & Pedersen, C. N. S. (2014). Machine learning approaches to functional prediction of P-Type ATPases.

Hobolth, A. & Jensen, J. L. (2014). Markovian approximation to the finite loci coalescent with recombination along multiple sequences. Theoretical Population Biology, 98, 48-58. https://doi.org/10.1016/j.tpb.2014.01.002

Nordentoft, I. K., Lamy, P., Birkenkamp-Demtröder, K., Shumansky, K., Vang, S., Hornshøj, H., Juul, M., Villesen, P., Hedegaard, J., Roth, A., Thorsen, K., Høyer, S., Borre, M., Reinert, T., Fristrup, N., Dyrskjøt, L., Shah, S., Pedersen, J. S. & Ørntoft, T. F. (2014). Mutational context and diverse clonal development in early and late bladder cancer: Genomic changes in bladder cancer. Cell Reports, 7(5), 1649–1663. https://doi.org/10.1016/j.celrep.2014.04.038

Buttenschøn, H. N., Foldager, L., Elfving, B., Poulsen, P. H. P., Uher, R. & Mors, O. (2014). Neurotrophic factors in depression in response to treatment.

Hedegaard, J., Thorsen, K., Lund, M. K., Hein, A.-M. K., Hamilton-Dutoit, S. J., Vang, S., Nordentoft, I., Birkenkamp-Demtröder, K., Kruhøffer, M., Hager, H., Knudsen, B., Andersen, C. L., Sørensen, K. D., Pedersen, J. S., Orntoft, T. F. & Dyrskjøt, L. (2014). Next-generation sequencing of RNA and DNA isolated from paired fresh-frozen and formalin-fixed paraffin-embedded samples of human cancer and normal tissue. PLoS One, 9(5), e98187. https://doi.org/10.1371/journal.pone.0098187

Aagaard, J., Skadhede, S. C., Andersen, M. B., Kølbæk, P., Hastrup, L. H., Foldager, L. & Nielsen, J. A. (2014). Opsøgende Psykoseteams i Region Nordjylland: En monitoreringsundersøgelse med to års opfølgning af de Opsøgende Psykoseteams i Region Nordjylland og en registerbaseret undersøgelse af udviklingen i voksenpsykiatrien i Region Nordjylland. Aalborg Universitetsforlag.

Ehlers, B. & Bataillon, T. (2014). På forkant med selektionen. Evolution2. Weekendavisen.

Gusev, A., Lee, S. H., Trynka, G., Finucane, H., Vilhjálmsson, B. J., Xu, H., Zang, C., Ripke, S., Bulik-Sullivan, B., Stahl, E., Kähler, A. K., Hultman, C. M., Purcell, S. M., McCarroll, S. A., Daly, M., Pasaniuc, B., Sullivan, P. F., Neale, B. M., Wray, N. R. ... Schizophrenia Working Group of the Psychiatric Genomics Consortium (Manuel Mattheisen and Jakob Grove, members) (2014). Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases. American Journal of Human Genetics, 95(5), 535-52. https://doi.org/10.1016/j.ajhg.2014.10.004

Als, T. D., Lescai, F., Dahl, H. A., Grove, J., Demontis, D., Wang, A. G., Andorsdottir, G., Biskopstø, M., Johansen, O., Nyegaard, M., Bolund, L., Mors, O., Wang, J. & Børglum, A. (2014). Population Structure & Cryptic Relatedness of the isolated Population of the Faroe Islands. Poster session presented at XXII World Congress of Psychiatric Genetics, København, Denmark.

Blanquart, F., Achaz, G., Bataillon, T. & Tenaillon, O. (2014). Properties of selected mutations and genotypic landscapes under Fisher's geometric model. Evolution, 68(12), 3537-54. https://doi.org/10.1111/evo.12545

Dam, S., Dyrlund, T. F., Ussatjuk, A., Jochimsen, B., Nielsen, K., Goffard, N., Ventosa, M. A. L., Lorentzen, A. M., Gupta, V., Andersen, S. U., Enghild, J. J., Ronson, C. W., Roepstorff, P. & Stougaard, J. (2014). Proteome reference maps of the Lotus japonicus nodule and root. Proteomics, 14(2-3), 230-240. https://doi.org/10.1002/pmic.201300353

Perfeito, L., Sousa, A., Bataillon, T. & Gordo, I. (2014). Rates of fitness decline and rebound suggest pervasive epistasis. Evolution, 68(1), 150-162. https://doi.org/10.1111/evo.12234

Hobolth, A. & Jeff, T. (2014). Sampling and summary statistics of endpoint-conditioned paths in DNA sequence evolution. In M.-H. Chen, L. Kuo & P. O. Lewis (Eds.), Bayesian Phylogenetics: Methods, Algorithms, and Applications (1 ed., Vol. 1). CRC Press.

Sükösd, Z., Andersen, E. S. & Lyngsø, R. (2014). SCFGs in RNA secondary structure prediction: a hands-on approach. Methods in Molecular Biology, 1097, 143-62. https://doi.org/10.1007/978-1-62703-709-9__8, https://doi.org/10.1007/978-1-62703-709-9_8

Lindgreen, S., Krogh, A. & Pedersen, J. S. (2014). SNPest: a probabilistic graphical model for estimating genotypes. BMC Research Notes, 7, 698. https://doi.org/10.1186/1756-0500-7-698

Sanggaard, K. W., Bechsgaard, J. S., Fang, X., Duan, J., Dyrlund, T. F., Gupta, V., Jiang, X., Cheng, L., Fan, D., Feng, Y., Han, L., Huang, Z., Wu, Z., Liao, L., Settepani, V., Thøgersen, I. B., Vanthournout, B., Wang, T., Zhu, Y. ... Wang, J. (2014). Spider genomes provide insight into composition and evolution of venom and silk. Nature Communications, 5, Article 3765. https://doi.org/10.1038/ncomms4765

Nam, K., Munch, K., Hobolth, A., Y. Dutheil, J., Veeramah, K., Woerner, A., F. Hammer, M., Ape Genome Diversity Project, G., Mailund, T. & H. Schierup, M. (2014). Strong selective sweeps associated with ampliconic regions in great ape X chromosomes. ArXiv.

Bay-Richter, C., Buttenschøn, H. N., Foldager, L., Kolstad, H. A., Kaerlev, L., Mors, O. & Wegener, G. (2014). Toxoplasma gondii seropositivity is positively associated with anxiety and burnout-syndrome. Abstract from CINP World Congress, Vancouver, Canada. https://doi.org/10.1017/S1461145714000741

Sand, A., Holt, M. K., Johansen, J., Brodal, G. S., Mailund, T. & Pedersen, C. N. S. (2014). tqDist: A Library for Computing the Quartet and Triplet Distances Between Binary and General Trees. Bioinformatics, 30(4), 2079-2080. https://doi.org/10.1093/bioinformatics/btu157

Munch, K., Schierup, M. H. & Mailund, T. (2014). Unraveling recombination rate evolution using ancestral recombination maps. BioEssays, 36(9), 892-900. https://doi.org/10.1002/bies.201400047

Aagaard, J., Nissen, F., Wernlund, A., Foldager, L. & Merinder, L. (2014). Valuable intervention against the excess mortality of psychiatric patients. Poster session presented at Annual Conference of the International Society for Bipolar Disorder, Seoul, Korea, Republic of. https://doi.org/10.1111/bdi.12189

Li, S., Besenbacher, S., Li, Y., Kristiansen, K., Grarup, N., Albrechtsen, A., Sparsø, T. H., Korneliussen, T. S., Hansen, T., Wang, J., Nielsen, R., Pedersen, O., Bolund, L. & Schierup, M. H. (2014). Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population. European Journal of Human Genetics. https://doi.org/10.1038/ejhg.2013.282

Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., Suh, A., Weber, C. C., da Fonseca, R. R., Li, J., Zhang, F., Li, H., Zhou, L., Narula, N., Liu, L. ... Zhang, G. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320-31. https://doi.org/10.1126/science.1253451

Thorgeirsson, T. E., Gudbjartsson, D. F., Sulem, P., Besenbacher, S., Styrkarsdottir, U., Thorleifsson, G., Walters, G. B., Furberg, H., Sullivan, P. F., Marchini, J., McCarthy, M. I., Steinthorsdottir, V., Thorsteinsdottir, U., Stefansson, K. & TAG Consortium (2013). A common biological basis of obesity and nicotine addiction. Translational Psychiatry, 3, e308. https://doi.org/10.1038/tp.2013.81

Sand, A., Holt, M. K., Johansen, J., Fagerberg, R., Pedersen, C. N. S., Brodal, G. S. & Mailund, T. (2013). Algorithms for Computing the Triplet and Quartet Distances for Binary and General Trees. Biology, 2(4), 1189-1209. https://doi.org/10.3390/biology2041189

Tataru, P., Sand, A., Hobolth, A., Mailund, T. & Pedersen, C. N. S. (2013). Algorithms for Hidden Markov Models Restricted to Occurrences of Regular Expressions. Biology, 2(4), 1282-1295. https://doi.org/10.3390/biology2041282

Abdallah, M., Larsen, N., Grove, J., Nørgaard-Pedersen, B., Thorsen, P., Mortensen, E. L. & Hougaard, D. M. (2013). Amniotic Fluid Inflammatory Cytokines: Potential Markers of Immunologic Dysfunction in Autism Spectrum Disorders. World Journal of Biological Psychiatry, 14(7), 528-538. https://doi.org/10.3109/15622975.2011.639803

Buttenschøn, H. N., Flint, T. J., Foldager, L., Qin, P., Christoffersen, S., Hansen, N. F., Kristensen, I. B., Mortensen, P. B., Børglum, A. D. & Mors, O. (2013). An association study of suicide and candidate genes in the serotonergic system. Journal of Affective Disorders, 148(2-3), 291-8. https://doi.org/10.1016/j.jad.2012.12.011

Sand, A., Pedersen, C. N. S., Mailund, T., Brodal, G. S. & Fagerberg, R. (2013). A practical O(n log² n) time algorithm for computing the triplet distance on binary trees. BMC Bioinformatics, 14(Suppl 2), S18. https://doi.org/10.1186/1471-2105-14-S2-S18

Hollegaard, M. V., Grauholm, J., Nielsen, R., Grove, J., Mandrup, S. & Hougaard, D. M. (2013). Archived neonatal dried blood spot samples can be used for accurate whole genome and exome-targeted next-generation sequencing. Molecular Genetics and Metabolism, 110(1-2), 65-72. https://doi.org/10.1016/j.ymgme.2013.06.004

Bataillon, T., Joyce, P. & Sniegowski, P. (2013). As it happens: current directions in experimental evolution. Biology Letters, 9(1), Article 20120945. https://doi.org/10.1098/rsbl.2012.0945

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Palle Villesen