Publications

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Anderson, J. W. J., Haas, P. A., Mathieson, L-A., Volynkin, V., Lyngsø, R., Tataru, P. & Hein, J. (2013). Oxfold: Kinetic Folding of RNA using Stochastic Context-Free Grammars and Evolutionary Information. Bioinformatics, 29(6), 704-710. https://doi.org/10.1093/bioinformatics/btt050

Dalby, R. B., Elfving, B., Poulsen, P. H. P., Foldager, L., Frandsen, J., Videbech, P. & Rosenberg, R. (2013). Plasma brain-derived neurotrophic factor and prefrontal white matter integrity in late-onset depression and normal aging. Acta Psychiatrica Scandinavica, 128(5), 387-396. https://doi.org/10.1111/acps.12085

Anderson, J. W., Novák, A., Sükösd, Z., Golden, M., Arunapuram, P., Edvardsson, I. & Hein, J. (2013). Quantifying variances in comparative RNA secondary structure prediction. B M C Bioinformatics, 14, [149]. https://doi.org/10.1186/1471-2105-14-149

Nexø, B. A., Hansen, B., Nissen, K. K., Gundestrup, L., Terkelsen, T., Villesen, P., Bahrami, S., Petersen, T., Pedersen, F. S. & Laska, M. J. (2013). Restriction genes for retroviruses influence the risk of multiple sclerosis. PLOS ONE, 8(9), e74063. https://doi.org/10.1371/journal.pone.0074063

Li, S., Li, R., Li, H., Lu, J., Li, Y., Bolund, L., Schierup, M. H. & Wang, J. (2013). SOAPindel: efficient identiﬁcation of indels from short paired reads. Genome Research, 23(1), 195-200. https://doi.org/10.1101/gr.132480.111

Møllegaard Friborg, R., Bjørndalen, J. M. & Vinter, B. (2013). Scaling PyCSP. Paper presented at Communicating Process Architectures 2013, Edinburgh, United Kingdom.

Paape, T., Bataillon, T., Zhou, P., J Y Kono, T., Briskine, R., Young, N. D. & Tiffin, P. (2013). Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula. Molecular Ecology, 22(13), 3525-3538. https://doi.org/10.1111/mec.12329

Holmstrup, M., Sørensen, J. G., Schmidt, I. K., Nielsen, P. L., Mason, S., Tietema, A., Smith, A. R., Bataillon, T., Beier, C. & Ehlers, B. K. (2013). Soil microarthropods are only weakly impacted after 13 years of repeated drought treatment in wet and dry heathland soils. Soil Biology & Biochemistry, 66, 110-118. https://doi.org/10.1016/j.soilbio.2013.06.023

Arunapuram, P., Edvardsson, I., Golden, M., Anderson, J. W. J., Novák, A., Sükösd, Z. & Hein, J. (2013). StatAlign 2.0: Combining statistical alignment with RNA secondary structure prediction. Bioinformatics, 29(5), 654-655. https://doi.org/10.1093/bioinformatics/btt025

Sand, A. & Steel, M. (2013). The standard lateral gene transfer model is statistically consistent for pectinate four-taxon trees. Journal of Theoretical Biology, 335, 295-298. https://doi.org/10.1016/j.jtbi.2013.07.002

Roug, A. S., Nederby, L., Kjeldsen, E., Villesen, P. & Nyvold, C. G. (2013). Two Hematological Pre-Malignancies In a Pair Of Homozygous Twins Revealing Differences In Their Pre-and Postnatal Development. Blood, 122(21), 5262-5262.

Aagaard, J., Nissen, F., Wernlund, A., Foldager, L. & Merinder, L. (2013). Valuable intervention against the excess mortality of psychiatric patients.

Castagnini, A. & Foldager, L. (2013). Variations in incidence rates and age of onset of acute and transient psychotic disorders. Social Psychiatry and Psychiatric Epidemiology, 48(12), 1917-1922. https://doi.org/10.1007/s00127-013-0726-7

Sükösd, Z. (2013). Viral RNA secondary structure prediction.

Nordentoft, I. K., Lamy, P., Birkenkamp-Demtröder, K., Vang, S., Reinert, T., Hedegaard, J., Thorsen, K., Fristrup, N., Borre, M., Andersen, L. D., Pedersen, J. S. & Ørntoft, T. F. (2013). Whole genome and transcriptome analysis reveals novel genomic alterations in bladder cancer. Poster session presented at American Association for Cancer Research, Washington, DC, United States.

Sand, A., Kristiansen, M., Pedersen, C. N. S. & Mailund, T. (2013). zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm. BMC Bioinformatics , 14(339), 339-348. https://doi.org/10.1186/1471-2105-14-339

Ehlers, B. K., Grøndahl, E., Ronfort, J. & Bataillon, T. (2012). "Ménage à trois": the presence/absence of thyme shapes the mutualistic interaction between the host plant Medicago truncatula (Fabaceae) and its symbiotic bacterium Sinorhizobium meliloti. Ecology and Evolution, 2(7), 1676-81. https://doi.org/10.1002/ece3.270

Gupta, V., Markmann, K., Pedersen, C. N. S., Stougaard, J. & Andersen, S. U. (2012). shortran: A pipeline for small RNA-seq data analysis. Bioinformatics, 28(20), 2698-2700. https://doi.org/10.1093/bioinformatics/bts496

Mailund, T., Halager, A. E., Westergaard, M., Dutheil, J. Y., Munch, K., Andersen, L. N., Lunter, G., Prüfer, K., Scally, A., Hobolth, A. & Schierup, M. H. (2012). A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species. P L o S Genetics, 8(12), e1003125. https://doi.org/10.1371/journal.pgen.1003125

Tidow, H., Poulsen, L. R., Andreeva, A., Knudsen, M., Hein, K. L., Wiuf, C., Palmgren, M. G. & Nissen, P. (2012). A bimodular mechanism of calcium control in eukaryotes. Nature, 491, 468-472. https://doi.org/10.1038/nature11539

Stukenbrock, E. H. & Bataillon, T. (2012). A population genomics perspective on the emergence and adaptation of new plant pathogens in agro-ecosystems. P L o S Pathogens, 8(9), e1002893. https://doi.org/10.1371/journal.ppat.1002893

Abdallah, M., Larsen, N., Grove, J., Nørgaard-Pedersen, B., Thorsen, P., Mortensen, E. L. & Hougaard, D. M. (2012). Amniotic Fluid Chemokines and Autism Spectrum Disorders: An Exploratory Study Utilizing a Danish Historic Birth Cohort. Brain, Behavior, and Immunity, 26(1), 170-176. https://doi.org/10.1016/j.bbi.2011.09.003

Abdallah, M., Pearce, B. D., Larsen, N., Greaves-Lord, K., Nørgaard-Pedersen, B., Hougaard, D. M., Mortensen, E. L. & Grove, J. (2012). Amniotic Fluid MMP-9 and Neurotrophins in Autism Spectrum Disorders: An Exploratory Study. Autism Research, 5(6), 428-33. https://doi.org/10.1002/aur.1254

Jin, X., He, M., Ferguson, B., Meng, Y., Ouyang, L., Ren, J., Mailund, T., Sun, F., Sun, L., Shen, J., Zhuo, M., Song, L., Wang, J., Ling, F., Zhu, Y., Hvilsom, C., Siegismund, H., Liu, X., Gong, Z. ... Wang, X. (2012). An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes. P L o S One, 7(7), e40637. https://doi.org/10.1371/journal.pone.0040637

Groenen, M. A. M., Archibald, A. L., Uenishi, H., Tuggle, C. K., Takeuchi, Y., Rothschild, M. F., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H-J., Li, S., Larkin, D. M., Kim, H., Frantz, L. A. F., Caccamo, M., Ahn, H., Aken, B. L., Anselmo, A., Anthon, C. ... Schook, L. B. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491(7424), 393-398. https://doi.org/10.1038/nature11622

Hobolth, A. (2012). Ancestral population genomics. In M. Anisimova (Ed.), Evolutionary Genomics: Statistical and Computational Methods (Vol. 856, pp. 293-313). Springer.

Li, J., Wang, K., Gao, F., Jensen, T. D., Li, S. T., Deangelis, P. M., Kølvraa, S., Proby, C., Forslund, O., Bolund, L. & Clausen, O. P. F. (2012). Array comparative genomic hybridization of keratoacanthomas and squamous cell carcinomas: different patterns of genetic aberrations suggest two distinct entities. Journal of Investigative Dermatology, 132(8), 2060-6. https://doi.org/10.1038/jid.2012.104

Rietschel, M., Mattheisen, M., Degenhardt, F., Kahn, R. S., Linszen, D. H., Os, J. V., Wiersma, D., Bruggeman, R., Cahn, W., de Haan, L., Krabbendam, L., Myin-Germeys, I., Mühleisen, T. W., Kirsch, P., Esslinger, C., Herms, S., Demontis, D., Steffens, M., Strohmaier, J. ... Cichon, S. (2012). Association between genetic variation in a region on chromosome 11 and schizophrenia in large samples from Europe. Molecular Psychiatry, 17(9), 906–917. https://doi.org/10.1038/mp.2011.80

Besenbacher, S., Mailund, T. & Schierup, M. H. (2012). Association mapping and disease: evolutionary perspectives. Methods in Molecular Biology, 856, 275-91. https://doi.org/10.1007/978-1-61779-585-5_11

Simonsen, M., Maetschke, S. R. & Ragan, M. A. (2012). Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling. Bioinformatics, 28(6), 851-857. https://doi.org/10.1093/bioinformatics/btr720

Simonsen, M., Maetschke, S. R. & Ragan, M. A. (2012). Automatic selection of reference taxa for protein–protein interaction prediction with phylogenetic profiling. Bioinformatics, 28(6), 851-857. https://doi.org/10.1093/bioinformatics/btr720

Ho-Huu, J., Ronfort, J., De Mita, S., Bataillon, T., Hochu, I., Weber, A. & Chantret, N. (2012). Contrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicago genus (L.). B M C Evolutionary Biology, 12, 195. https://doi.org/10.1186/1471-2148-12-195

Walker, R. S., Wichmann, S., Mailund, T. & Atkisson, C. J. (2012). Cultural phylogenetics of the tupi language family in lowland South america. P L o S One, 7(4), e35025. https://doi.org/10.1371/journal.pone.0035025

Bache, C., Christiansen, F. B., Løkke, A., Smith, N. & Sneppen, K. (2012). Danske Universiteter 2020: Forskningspolitisk årsmøde 2012. Det Kongelige Danske Videnskabernes Selskab. http://www.royalacademy.dk/Files/Filer/PDF/hvidboger/HVIDBOG.pdf

Elfving, B., Buttenschøn, H. N., Foldager, L., Poulsen, P. H. P., Andersen, J. H., Grynderup, M. B., Hansen, A. M., Kolstad, H. A., Kaerlev, L., Mikkelsen, S., Thomsen, J. F., Børglum, A. D., Wegener, G. & Mors, O. (2012). Depression, the Val66Met polymorphism, age, and gender influence the serum BDNF level. Journal of Psychiatric Research, 46(9), 1118-1125. https://doi.org/10.1016/j.jpsychires.2012.05.003

Feliu, E. & Wiuf, C. H. (2012). Enzyme-sharing as a cause of multi-stationarity in signalling systems. Journal of the Royal Society. Interface, 9(71), 1224-1232. https://doi.org/10.1098/rsif.2011.0664

Pedersen, C. N. S., Axelsen, K. B., Harper, J. F. & Palmgren, M. G. (2012). Evolution of plant P-type ATPases. Frontiers in Plant Science, 21. https://doi.org/10.3389/fpls.2012.00031

Anderson, J. WJ., Tataru, P. C., Stains, J., Hein, J. & Lyngsø, R. (2012). Evolving stochastic context-free grammars for RNA secondary structure prediction. B M C Bioinformatics, 13(78). https://doi.org/10.1186/1471-2105-13-78

Knudsen, M., Feliu, E. & Wiuf, C. H. (2012). Exact Analysis of Intrinsic Qualitative Features of Phosphorelays using Mathematical Models. Journal of Theoretical Biology, 300, 7-18. https://doi.org/10.1016/j.jtbi.2012.01.007

Hvilsom, C., Qian, Y., Bataillon, T., Li, Y., Mailund, T., Sallé, B., Carlsen, F., Li, R., Zheng, H., Jiang, T., Jiang, H., Jin, X., Munch, K., Hobolth, A., Siegismund, H. R., Wang, J. & Schierup, M. H. (2012). Extensive X-linked adaptive evolution in central chimpanzees. Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.1106877109

Thøgersen, L. & Nissen, P. (2012). Flexible P-type ATPases interacting with the membrane. Current Opinion in Structural Biology, 22(4), 491-499. https://doi.org/10.1016/j.sbi.2012.05.009

Stukenbrock, E. H., Christiansen, F. B., Hansen, T. T., Dutheil, J. & Schierup, M. H. (2012). Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species. Proceedings of the National Academy of Sciences of the United States of America, 107(27). https://doi.org/10.1073/pnas.1201403109

Swenson, M. S., Anderson, J., Ash, A., Gaurav, P., Sükösd, Z., Bader, D. A., Harvey, S. C. & Heitsch, C. E. (2012). GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops. BMC Research Notes, 5(341). https://doi.org/10.1186/1756-0500-5-341

Holmstrup, M., Sørensen, J. G., Maraldo, K., Schmidt, I., Tietema, A., Smith, A., Schmelz, R., Bataillon, T. & Ehlers, B. (2012). Increased frequency of drought depletes species richness of enchytraeid communities in both wet and dry heathland soils. Soil Biology & Biochemistry, 53, 43-49. https://doi.org/10.1016/j.soilbio.2012.05.001

Holmstrup, M., Sørensen, J. G., Maraldo, K., Schmidt, I. K., Mason, S., Tietema, A., Smith, A. R., Emmett, B., Schmelz, R., Bataillon, T., Beier, C. & Ehlers, B. K. (2012). Increased frequency of drought reduces species richness of enchytraeid communities in both wet and dry heathland soils. Soil Biology & Biochemistry, 53, 43-49. https://doi.org/10.1016/j.soilbio.2012.05.001

W. Abdallah, M., M. Hougaard, D., Nørgaard-Pedersen, B., Grove, J., Bonefeld-Jørgensen, E. C. & L. Mortensen, E. (2012). Infections during Pregnancy and after birth and risk of autism spectrum disorders: a register-based study utilizing a Danish historic birth cohort. Turk Psikiyatri Dergisi, 23(4). https://doi.org/10.5080/u6847

Scally, A., Dutheil, J. Y., Hillier, L. W., Jordan, G. E., Goodhead, I., Herrero, J., Hobolth, A., Lappalainen, T., Mailund, T., Marques-Bonet, T., McCarthy, S., Montgomery, S. H., Schwalie, P. C., Tang, Y. A., Ward, M. C., Xue, Y., Yngvadottir, B., Alkan, C., Andersen, L. N. ... Durbin, R. (2012). Insights into hominid evolution from the gorilla genome sequence. Nature, 483(7388), 169-75. https://doi.org/10.1038/nature10842

Foldager, L., Steffensen, R. N., Thiel, S., Als, T. D., Nielsen, H. J., Nordentoft, M., Mortensen, P. B., Mors, O. & Jensenius, J. C. (2012). MBL and MASP-2 concentrations in serum and MBL2 promoter polymorphisms are associated to schizophrenia. Acta Neuropsychiatrica, 24(4), 199-207. https://doi.org/10.1111/j.1601-5215.2011.00618.x

Asmussen, S. & Hobolth, A. (2012). Markov bridges, bisection and variance reduction. In L. Plaskota & H. Wozniakowski (Eds.), Monte Carlo and Quasi-Monte Carlo Methods 2010 (pp. 3-22). Springer. Springer Proceedings in Mathematics & Statistics Vol. 23 https://doi.org/10.1007/978-3-642-27440-4_1

Alsner, J., Toustrup, K., Sørensen, B. S., Wiuf, C. H., Nordsmark, M. & Overgaard, J. (2012). Method for determining clinically relevant hypoxia in cancer. (Patent No. WO/2012/146259).

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Palle Villesen