Publications

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Søndergaard, D. & Pedersen, C. N. S. (2015). PATBox: A Toolbox for Classification and Analysis of P-Type ATPases. PLOS ONE, 10(9), Article e0139571. https://doi.org/10.1371/journal.pone.0139571

Agerbo, E., Sullivan, P. F., Vilhjálmsson, B. J., Pedersen, C. B., Mors, O., Børglum, A. D., Hougaard, D. M., Hollegaard, M. V., Meier, S., Mattheisen, M., Ripke, S., Wray, N. R. & Mortensen, P. B. (2015). Polygenic Risk Score, Parental Socioeconomic Status, Family History of Psychiatric Disorders, and the Risk for Schizophrenia: A Danish Population-Based Study and Meta-analysis. J A M A Psychiatry. https://doi.org/10.1001/jamapsychiatry.2015.0346

Qian, Y., Kehr, B. & Halldorsson, B. V. (2015). PopAlu: population-scale detection of Alu polymorphisms. PeerJ, 3, Article 1269. https://doi.org/10.7717/peerj.1269

Foldager, L., Munksgaard, L., Trénel, P. & Thomsen, P. T. (2015). Predicting daily eating activity of dairy cows from 3D accelerometer data and RFID signals by use of a random forests model. In C. H. Knight (Ed.), Proceedings of the Third DairyCare Conference 2015 (pp. 31-31)

Autzen, H. E., Siuda, I., Sonntag, Y., Nissen, P., Møller, J. V. & Thøgersen, L. (2015). Regulation of the Ca(2+)-ATPase by cholesterol: A specific or non-specific effect? Molecular Membrane Biology, 32(3), 75-87. https://doi.org/10.3109/09687688.2015.1073382

Nielsen, L. S., Villesen, P. & Lindholst, C. (2015). Stability of cocaine alkaloids and residual solvents applied in drug profiling.

Dutheil, J. Y., Munch, K., Nam, K., Mailund, T. & Schierup, M. H. (2015). Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence. P L o S Genetics, 11(8), e1005451. https://doi.org/10.1371/journal.pgen.1005451

Luo, X.-J., Mattheisen, M., Li, M., Huang, L., Rietschel, M., Børglum, A. D., Als, T. D., van den Oord, E. J., Aberg, K. A., Mors, O., Mortensen, P. B., Luo, Z., Degenhardt, F., Cichon, S., Schulze, T. G., Nöthen, M. M., Su, B., Zhao, Z., Gan, L. ... iPSYCH-GEMS SCZ working group (Jakob Grove, member) (2015). Systematic Integration of Brain eQTL and GWAS Identifies ZNF323 as a Novel Schizophrenia Risk Gene and Suggests Recent Positive Selection Based on Compensatory Advantage on Pulmonary Function. Schizophrenia Bulletin. https://doi.org/10.1093/schbul/sbv017

Nielsen, S. M., de Gier, C., Dimopoulou, C., Gupta, V., Hansen, L. H. & Nørskov-Lauritsen, N. (2015). The capsule biosynthesis locus of Haemophilus influenzae show conspicuous similarity to the corresponding locus in Haemophilus sputorum and may have been recruited from this species by horizontal gene transfer. Microbiology, 161(6), 1182-1188. https://doi.org/10.1099/mic.0.000081

Waltoft, B. L., Pedersen, C. B., Nyegaard, M. & Hobolth, A. (2015). The importance of distinguishing between the odds ratio and the incidence rate ratio in GWAS. B M C Medical Genetics, 16(1), 71. https://doi.org/10.1186/s12881-015-0210-1

Montes, M., Nielsen, M. M., Maglieri, G., Jacobsen, A., Hojfeldt, J., Agrawal-Singh, S., Hansen, K., Helin, K., de Werken, H. J. G. V., Pedersen, J. S. & Lund, A. H. (2015). The lncRNA MIR31HG regulates p16(^INK4A) expression to modulate senescence. Nature Communications, 6, Article 6967. https://doi.org/10.1038/ncomms7967

Wilton, P. R., Carmi, S. & Hobolth, A. (2015). The SMC' is a highly accurate approximation to the ancestral recombination graph. Genetics (Print), 200(1), 343-355. Article 1. http://intl.genetics.org/content/200/1/343.full

Møllegaard Friborg, R., Jon Ison, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael Jimenez, Nick Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Mičetić & Sebastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vařeková, Silvio C.E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen Parkinson, Peter Løngreen, Søren Brunak (2015). Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research, 44(D1), D38-D47. https://doi.org/10.1093/nar/gkv1116

Bailey, S., Hinz, A. & Kassen, R. (2014). Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population. Nature Communications, 5, Article 4076. https://doi.org/10.1038/ncomms5076

Gingold, H., Tehler, D., Christoffersen, N. R., Nielsen, M. M., Asmar, F., Kooistra, S. M., Christophersen, N. S., Christensen, L. L., Borre, M., Sørensen, K. D., Andersen, L. D., Andersen, C. L., Hulleman, E., Wurdinger, T., Ralfkiær, E., Helin, K., Grønbæk, K., Orntoft, T., Waszak, S. M. ... Pilpel, Y. (2014). A dual program for translation regulation in cellular proliferation and differentiation. Cell, 158(6), 1281-92. https://doi.org/10.1016/j.cell.2014.08.011

Munch, K., Mailund, T., Dutheil, J. Y. & Schierup, M. H. (2014). A fine-scale recombination map of the human-chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion. Genome Research. https://doi.org/10.1101/gr.158469.113

Sørensen, H. J., Foldager, L., Røge, R., Pristed, S. G., Andreasen, J. T. & Nielsen, J. (2014). An association between autumn birth and clozapine treatment in patients with schizophrenia: A population-based analysis. Nordic Journal of Psychiatry, 68(6), 428-432. https://doi.org/10.3109/08039488.2013.854408

Foldager, L. (2014). A statistical perspective on association studies of psychiatric disorders: Genetic effects of single-markers, haplotypes, gene-environment interactions and gene-gene interactions.

Foldager, L., Köhler, K. O., Steffensen, R. N., Thiel, S., Kristensen, A. S., Jensenius, J. C. & Mors, O. (2014). Bipolar and panic disorders may be associated with hereditary defects in the innate immune system. Journal of Affective Disorders, 164, 148-154. https://doi.org/10.1016/j.jad.2014.04.017

Ostenfeld, M. S., Jeppesen, D. K., Laurberg, J. R., Boysen, A. T., Bramsen, J. B., Primdal-Bengtson, B., Hendrix, A., Lamy, P., Dagnaes-Hansen, F., Rasmussen, M. H., Bui, K. H., Fristrup, N., Christensen, E. I., Nordentoft, I., Morth, J. P., Jensen, J. B., Pedersen, J. S., Beck, M., Theodorescu, D. ... Orntoft, T. F. (2014). Cellular Disposal of miR23b by RAB27-Dependent Exosome Release Is Linked to Acquisition of Metastatic Properties. Cancer Research, 74(20), 5758-5771. https://doi.org/10.1158/0008-5472.CAN-13-3512

Knudsen, M., Søndergaard, D. & Pedersen, C. N. S. (2014). Combinatorics of Non-Ribosomal Peptide Synthetases.

Foldager, L., Als, T. D. & Grove, J. (2014). Comparing methods for genome-wide gene-environment interaction analysis.

Tataru, P., Nirody, J. A. & Song, Y. S. (2014). diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals. Bioinformatics, 30(23), 3430-3431. https://doi.org/10.1093/bioinformatics/btu563

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. B M C 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. P L o S 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. P L o S 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

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Revised 21.08.2024

Palle Villesen