Publications

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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.). BMC 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. PLoS 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

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

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. BMC 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 (PNAS). 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 (PNAS), 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

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. https://doi.org/10.1007/978-3-642-27440-4_1

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

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

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).

Saetre, P., Grove, J., Børglum, A., Mors, O., Werge, T. M., Andreassen, O. A., Vares, M., Agartz, I., Terenius, L. & Jönsson, E. G. (2012). Methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism and age at onset of schizophrenia: no consistent evidence for an association in the Nordic population. American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 159B(8).

Kraft, J. F., Vestergaard, M., Schiøtt, B. & Thøgersen, L. (2012). Modeling the Self-assembly and Stability of DHPC Micelles using Atomic Resolution and Coarse Grained MD Simulations. Journal of Chemical Theory and Computation, 8(5), 1556–1569. https://doi.org/10.1021/ct200921u

Siuda, I. A. (2012). Modelling Protein Dynamics on the Microsecond Time Scale: Problems and Solutions. Aarhus University, Faculty of Science and Technology.

Agerbo, E., Mortensen, P. B., Wiuf, C., Pedersen, M. S., McGrath, J., Hollegaard, M. V., Nørgaard-Pedersen, B., Hougaard, D. M., Mors, O. & Pedersen, C. B. (2012). Modelling the contribution of family history and variation in single nucleotide polymorphisms to risk of schizophrenia: A Danish national birth cohort-based study. Schizophrenia Research, 134(2-3), 246-52. https://doi.org/10.1016/j.schres.2011.10.025

Tuni, C., Goodacre, S., Bechsgaard, J. S. & Bilde, T. (2012). Moderate multiple parentage and low genetic variation reduces the potential for genetic incompatibility avoidance despite high risk of inbreeding. PLoS One, 7(1), e29636. https://doi.org/10.1371/journal.pone.0029636

Thomsen, P. F., Kielgast, J., Iversen, L. L., Wiuf, C. H., Rasmussen, M., Gilbert, M. T. P., Orlando, L. A. A. & Willerslev, E. (2012). Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology, 21(11), 2565-2573. https://doi.org/10.1111/j.1365-294X.2011.05418.x

Abdallah, M., Larsen, N., Mortensen, E. L., Atladóttir, H. Ó., Nørgaard-Pedersen, B., Bonefeld-Jørgensen, E. C., Grove, J. & Hougaard, D. M. (2012). Neonatal levels of cytokines and risk of autism spectrum disorders: An exploratory register-based historic birth cohort study utilizing the Danish Newborn Screening Biobank. Journal of Neuroimmunology, 252, 75-82. https://doi.org/10.1016/j.jneuroim.2012.07.013

Mattila, T., Bechsgaard, J. S., Hansen, T., Schierup, M. H. & Bilde, T. (2012). Ortholog genes identified by transcriptome sequencing in the spider genus Stegodyphus. BMC Genomics, 13(70). https://doi.org/10.1186/1471-2164-13-70

Miller, W., Schuster, S. C., Welch, A. J., Ratan, A., Bedoya-Reina, O. C., Zhao, F., Kim, H. L., Burhans, R. C., Drautz, D. I., Wittekindt, N. E., Tomsho, L. P., Ibarra-Laclette, E., Herrera-Estrella, L., Peacock, E., Farley, S., Sage, G. K., Rode, K., Obbard, M., Montiel, R. ... Lindqvist, C. (2012). Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proceedings of the National Academy of Sciences (PNAS). https://doi.org/10.1073/pnas.1210506109

Sükösd, Z., Knudsen, B., Kjems, J. & Pedersen, C. N. S. (2012). PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data. Bioinformatics, 28(20), 2691-2692. https://doi.org/10.1093/bioinformatics/bts488

Kjeldsen, K. U., Bataillon, T., Pinel, N., De Mita, S., Lund, M. B., Panitz, F., Bendixen, C., Stahl, D. A. & Schramm, A. (2012). Purifying selection and molecular adaptation in the genome of Verminephrobacter, the heritable symbiotic bacteria of earthworms. Genome Biology and Evolution, 4(3), 307-315. https://doi.org/10.1093/gbe/evs014

Kong, A., Frigge, M. L., Masson, G., Besenbacher, S., Sulem, P., Magnusson, G., Gudjonsson, S. A., Sigurdsson, A., Jonasdottir, A., Jonasdottir, A., Wong, W. S. W., Sigurdsson, G., Walters, G. B., Steinberg, S., Helgason, H., Thorleifsson, G., Gudbjartsson, D. F., Helgason, A., Magnusson, O. T. ... Stefansson, K. (2012). Rate of de novo mutations and the importance of father's age to disease risk. Nature, 488(7412), 471-5. https://doi.org/10.1038/nature11396

Feliu, E., Knudsen, M. & Wiuf, C. H. (2012). Signaling Cascades: Consequences of Varying Substrate and Phosphatase Levels. Advances in Experimental Medicine and Biology, 736, 81-94. https://doi.org/10.1007/978-1-4419-7210-1_4

Dai, N., Foldager, L., Gallego, J. A., Hack, L. M., Ji, Y., Lett, T. A. P., Liu, B., Loken, E. K., Mandelli, L., Mehta, D., Power, R. A., Sprooten, E., Stephens, S. H., Paska, A. V., Yan, J., Zai, C. C., Zai, G., Zhang-James, Y., O'Shea, A. & DeLisi, L. E. (2012). Summaries from the XIX World Congress of Psychiatric Genetics, Washington, DC, September 10-14 2011. American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 159B(1), 128-129. https://doi.org/10.1002/ajmg.b.32017

Prüfer, K., Munch, K., Hellmann, I., Akagi, K., Miller, J. R., Walenz, B., Koren, S., Sutton, G., Kodira, C., Winer, R., Knight, J. R., Mullikin, J. C., Meader, S. J., Ponting, C. P., Lunter, G., Higashino, S., Hobolth, A., Dutheil, J., Karakoç, E. ... Pääbo, S. (2012). The bonobo genome compared with the chimpanzee and human genomes. Nature, 486(7404), 527-31. https://doi.org/10.1038/nature11128

Jensen, K., Kristensen, L. M. & Mailund, T. (2012). The sweep-line state space exploration method. Theoretical Computer Science, 429, 169–179. https://doi.org/10.1016/j.tcs.2011.12.036

Musgaard, M., Thøgersen, L., Schiøtt, B. & Tajkhorshid, E. (2012). Tracing Cytoplasmic Ca²⁺ Ion and Water Access Points in the Ca²⁺-ATPase. Biophysical Journal, 102(2), 268-277. https://doi.org/10.1016/j.bpj.2011.12.009

Hilker, R., Sickinger, C., Pedersen, C. N. S. & Stoye, J. (2012). UniMoG - A unifying framework for genomic distance calculation and sorting based DCJ. Bioinformatics, 28(19), 2509-2511. https://doi.org/10.1093/bioinformatics/bts440

Mailund, T., Halager, A. E. & Westergaard, M. (2012). Using colored Petri nets to construct coalescent hidden markov models: Automatic translation from demographic specifications to efficient inference methods. Lecture Notes in Computer Science, 7347, 32-50. https://doi.org/10.1007/978-3-642-31131-4_3

Djernes, J. K., Gulmann, N. C., Foldager, L., Olesen, F. & Munk-Jørgensen, P. (2011). 13 year follow up of morbidity, mortality and use of health services among elderly depressed patients and general elderly populations. The Australian & New Zealand Journal of Psychiatry, 45(8), 654-662. https://doi.org/10.3109/00048674.2011.589368