Publications

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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

Laurila, K., Øster, B., Andersen, C. L., Lamy, P., Orntoft, T., Yli-Harja, O. & Wiuf, C. (2011). A Beta-Mixture Model for Dimensionality Reduction, Sample Classification and Analysis. BMC Bioinformatics, 12(1), 215. https://doi.org/10.1186/1471-2105-12-215

Nielsen, J. (2011). A Coarse-to-Fine Approach to Computing the k-best Viterbi Paths. Lecture Notes in Computer Science, 6661, 376-387. https://doi.org/10.1007/978-3-642-21458-5_32

Nielsen, J. & Sand, A. (2011). Algorithms for a parallel implementation of Hidden Markov Models with a small state space. In 2011 IEEE IPDPS Workshops & PhD Forum (pp. 447-454). IEEE Computer Society Press. https://doi.org/10.1109/IPDPS.2011.181

Abdallah, M., Larsen, N., Grove, J., Nørgaard-Pedersen, B., Hougaard, D. M. & Mortensen, E. L. (2011). Amniotic Fluid Chemokines Levels and Autism Spectrum Disorders, a study utilizing a Danish historic birth cohort. Abstract from World Congress of Epidemiology, Edinburgh, United Kingdom.

Feliu, E., Knudsen, M., Andersen, L. N. & Wiuf, C. H. (2011). An Algebraic Approach to Signaling Cascades with n Layers. Bulletin of Mathematical Biology, 74(1), 45-72. https://doi.org/10.1007/s11538-011-9658-0

Penner, R., Knudsen, M., Wiuf, C. H. & Andersen, J. E. (2011). An Algebro-Topological Description of Protein Domain Structure. PLoS One. https://doi.org/10.1371/journal.pone.0019670

Lamy, P., Grove, J. & Wiuf, C. (2011). A review of software for microarray genotyping. Human Genomics (Online), 5(4), 304-9.

Demontis, D., Nyegaard, M., Buttenschøn, H. N., Hedemand, A., Pedersen, C. B., Grove, J., Flint, T. J., Nordentoft, M., Werge, T., Hougaard, D. M., Sørensen, K. M., Yolken, R. H., Mors, O., Børglum, A. D. & Mortensen, P. B. (2011). Association of GRIN1 and GRIN2A-D With schizophrenia and genetic interaction with maternal herpes simplex virus-2 infection affecting disease risk. American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 156(8), 913-922. https://doi.org/10.1002/ajmg.b.31234

Nielsen, J., Kristensen, A. K., Mailund, T. & Pedersen, C. N. S. (2011). A sub-cubic time algorithm for computing the quartet distance between two general trees. Algorithms for Molecular Biology, 6(15). https://doi.org/10.1186/1748-7188-6-15

Abdallah, M., Grove, J. & David M. Hougaard, Bent Nørgaard-Pedersen, Fuad Ibrahimov, Erik L. Mortensen (2011). Autism spectrum disorders and maternal serum alpha-fetoprotein levels during pregnancy. Poster session presented at 10th World Congress of Biological Psychiatry, Prague, Czech Republic.

Abdallah, M., Grove, J., Hougaard, D. M., Nørgaard-Pedersen, B., Ibrahimov, F. & Mortensen, E. L. (2011). Autism Spectrum Disorders and Maternal Serum α-Fetoprotein Levels During Pregnancy. The Canadian Journal of Psychiatry, 56(12).

Steinberg, S., de Jong, S., Andreassen, O. A., Werge, T., Børglum, A. D., Mors, O., Mortensen, P. B., Gustafsson, O., Costas, J., Pietiläinen, O. P. H., Demontis, D., Papiol, S., Huttenlocher, J., Mattheisen, M., Breuer, R., Vassos, E., Giegling, I., Fraser, G., Walker, N. ... Irish Schizophrenia Genomics Consortium (2011). Common Variants at VRK2 and TCF4 Conferring Risk of Schizophrenia. Human Molecular Genetics, 20(20), 4076-81. https://doi.org/10.1093/hmg/ddr325

Locke, D. P., Hillier, L. W., Warren, W. C., Yang, S.-P., Wang, Z., Chinwalla, A. T., Minx, P., Mitreva, M., Cook, L., Delehaunty, K. D., Fronick, C., Schmidt, H., Fulton, L. A., Fulton, R. S., Nelson, J. O., Magrini, V., Pohl, C., Graves, T. A., Markovic, C. ... de Jong, P. J. (2011). Comparative and demographic analysis of orang-utan genomes. Nature, 469, 529-533. https://doi.org/10.1038/nature09687

Fei, G., Luo, Y., Li, S., Li, J., Lin, L., Nielsen, A. L., Sørensen, C. B., Vajta, G., Wang, J., Zhang, X., Du, Y., Yang, H. & Bolund, L. (2011). Comparison of gene expression and genome-wide DNA methylation profiling between phenotypically normal cloned pigs and conventionally bred controls. PLoS One, 6(10), e25901. https://doi.org/10.1371/journal.pone.0025901

Tataru, P. C. & Hobolth, A. (2011). Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains. BMC Bioinformatics, 12(1), 465. https://doi.org/10.1186/1471-2105-12-465

Reinert, T., Modin, C., Mansilla Castano, F., Lamy, P., Wojdacz, T. K., Hansen, L. L., Wiuf, C., Borre, M., Andersen, L. D. & Ørntoft, T. F. (2011). Comprehensive genome methylation analysis in bladder cancer;identification and validation of novel methylated genes and application of these as urinary tumor markers. Clinical Cancer Research. https://doi.org/10.1158/1078-0432.CCR-10-2659

Dalby, R. B., Elfving, B., Plougmann, P. H., Foldager, L., Rosenberg, R. & Videbech, P. (2011). Correlations between brain-derived neurotrophic factor (BDNF), vascular endothelial growth factor (VEGF), and vascular risk factors in late-onset major depression. Poster session presented at IBRO 8th World Congress of Neuroscience, Firenze, Italy.

Bataillon, T., Zhang, T. & Kassen, R. (2011). Cost of Adaptation and Fitness Effects of Beneficial Mutations in Pseudomonas fluorescens. Genetics, 189(3), 939-949. https://doi.org/10.1534/genetics.111.130468

Abdallah, M., Larsen, N., Grove, J., Nørgaard-Pedersen, B., Mortensen, E. L. & Hougaard, D. M. (2011). Cytokine Levels In Amniotic Fluid: a Marker of Maternal Immune Activation. Abstract from International Meeting for Autism Research (IMFAR 2011), San Diego, CA, United States.

Mapendano, C. K., Preker, P., Villesen, P., Prokop, A., Piatkowski, J., Schierup, M. H. & Jensen, T. H. (2011). Depletion of the RNA exosome triggers hypermethylation of human promoters.. Abstract from Third EMBO meeting on 'Chromatin and Epigenetics, Heidelberg, Germany.

Buttenschøn, H. N., Elfving, B., Foldager, L., Plougmann, P. H., Andersen, J. H., Bonde, J. P., Grynderup, M., Hansen, A. M., Kolstad, H., Kærgaard, A., Kærlev, L., Mikkelsen, S., Thomsen, J. F., Børglum, A., Wegener, G. & Mors, O. (2011). Depression og Val66Met polymorfien påvirker serum BDNF niveauet. Poster session presented at Psykiatriens 6. Forskningsdag, Risskov, Denmark.

Gao, F., Li, S., Lin, L., Li, J., Luo, Y., Zhang, X., Nielsen, A. L. & Bolund, L. (2011). DNA methylation in peripheral blood cells of pigs cloned by somatic cell nuclear transfer. Cellular Reprogramming, 13(4), 307-14. https://doi.org/10.1089/cell.2010.0099, https://doi.org/10.1089/cell.2010.0099

Simonsen, M. (2011). Efficient algorithms for tree reconstruction and prediction of molecular interactions. Department of Computer Science, Aarhus University.

Nielsen, J. (2011). Engineering Algorithms for Finding Patterns in Biological Data.

Furrow, R., Christiansen, F. & Feldman, M. (2011). Environment-sensitive Epigenetics and the Heritability of Complex Diseases. Genetics, 189(4), 1377-1387. https://doi.org/10.1534/genetics.111.131912

Mailund, T., Dutheil, J., Hobolth, A., Lunter, G. & Schierup, M. H. (2011). Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model. PLoS Genetics, 7(3). https://doi.org/10.1371/journal.pgen.1001319

Rafnar, T., Vermeulen, S. H., Sulem, P., Thorleifsson, G., Aben, K. K., Witjes, J. A., Grotenhuis, A. J., Verhaegh, G. W., Hulsbergen-van de Kaa, C. A., Besenbacher, S., Gudbjartsson, D., Stacey, S. N., Gudmundsson, J., Johannsdottir, H., Bjarnason, H., Zanon, C., Helgadottir, H., Jonasson, J. G., Tryggvadottir, L. ... Kiemeney, L. A. (2011). European genome-wide association study identifies SLC14A1 as a new urinary bladder cancer susceptibility gene. Human Molecular Genetics, 20(21), 4268-4281. https://doi.org/10.1093/hmg/ddr303

Maetschke, S. R., Simonsen, M., Davis, M. J. & Mark, A. (2011). Gene Ontology-driven inference of protein-protein interactions using inducers. Bioinformatics, 28(1), 69-75. https://doi.org/10.1093/bioinformatics/btr610

Li, Q., Li, N., Hu, X., Li, J., Du, Z., Chen, L., Yin, G., Duan, J., Zhang, H., Zhao, Y., Wang, J. & Li, N. (2011). Genome-wide mapping of DNA methylation in chicken. PLoS One, 6(5), e19428. https://doi.org/10.1371/journal.pone.0019428

Grove, J., Demontis, D., Hollegaard, M. V., Pedersen, C. B., Ørntoft, T. F., Yolken, R., Didriksen, M., Hougaard, D., Wiuf, C. H., Mors, O., Mortensen, P. B. & Børglum, A. (2011). Genome-Wide Significant Interaction by Cytomegalovirus with Respect to Risk of Schizophrenia. Poster session presented at XIX World Congress on Psychiatric Genetics, Washington DC, United States.

Slotte, T., Bataillon, T., Hansen, T. T., St Onge, K., Wright, S. I. & Schierup, M. H. (2011). Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biology and Evolution, 3, 1210-1219. https://doi.org/10.1093/gbe/evr094

Simonsen, M., Thomsen, R., Christensen, M. H. & Pedersen, C. N. S. (2011). GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution. In GECCO'11 Proceedings of the 13th annual conference on Genetic and evolutionary computation (pp. 1803-1810). Association for Computing Machinery. https://doi.org/10.1145/2001576.2001818

Luo, Y., Li, J., Liu, Y., Lin, L., Du, Y., Li, S., Yang, H., Vajta, G., Callesen, H., Bolund, L. & Sørensen, C. B. (2011). High efficiency of BRCA1 knockout using rAAV-mediated gene targeting: developing a pig model for breast cancer. Transgenic Research, 20, 975-988. https://doi.org/10.1007/s11248-010-9472-8

Wiechec, E., Wiuf, C., Overgaard, J. & Hansen, L. L. (2011). High-resolution melting analysis for mutation screening of RGSL1, RGS16, and RGS8 in breast cancer. Cancer Epidemiology, Biomarkers & Prevention, 20(2), 397-407. https://doi.org/10.1158/1055-9965.EPI-10-0514

Jensen, T. D., Li, J., Wang, K., Lindebjerg, J., Kølvraa, S., Bolund, L., Jakobsen, A., Bruun-Petersen, G., Li, S. & Crüger, D. G. (2011). Identification of chromosome aberrations in sporadic microsatellite stable and unstable colorectal cancers using array comparative genomic hybridization. Cancer Genetics and Cytogenetics, 204(2), 84-95. https://doi.org/10.1016/j.cancergencyto.2010.08.019

Martins, H. & Villesen, P. (2011). Improved integration time estimation of endogenous retroviruses with phylogenetic data. PLoS One, 6(3), e14745. https://doi.org/10.1371/journal.pone.0014745

Hobolth, A., Dutheil, J., Hawks, J., Schierup, M. H. & Mailund, T. (2011). Incomplete lineage sorting patterns among human, chimpanzee and orangutan suggest recent orangutan speciation and widespread selection. Genome Research, 21(3), 349-356. https://doi.org/10.1101/gr.114751.110

Simonsen, M., Mailund, T. & Pedersen, C. N. S. (2011). Inference of Large Phylogenies Using Neighbour-Joining. Biomedical Engineering Systems and Technologies, 127(5), 334-344. https://doi.org/10.1007/978-3-642-18472-7_26

Andersen, L. N. (2011). Inferring Population Histories In The IM-model Using Site Pattern Analysis. Poster session presented at SMBE 2011, Kyoto, Japan.

Villesen, P., Gosmer, K. & Lindholst, C. (2011). Kemiske fingeraftryk fælder narkoforbryderne. Aktuel Naturvidenskab, (3).

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Palle Villesen