Computational and RNA Biology

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  1. 2010
  2. Published

    Phylogenetic analyses of the polyprotein coding sequences of serotype O foot-and-mouth disease viruses in East Africa: evidence for interserotypic recombination

    Balinda, S. N., Siegismund, Hans Redlef, Muwanika, V. B., Sangula, A. K., Masembe, C., Ayebazibwe, C., Normann, P. & Belsham, G. J., 2010, In: Virology Journal. 7, p. 199

    Research output: Contribution to journal › Journal article › Research › peer-review

  3. Published

    Multivariate Hawkes process models of the occurrence of regulatory elements

    Carstensen, L., Sandelin, Albin Gustav, Winther, Ole & Hansen, Niels Richard, 2010, In: BMC Bioinformatics. 11, p. 456

    Research output: Contribution to journal › Journal article › Research › peer-review

  4. Published

    Identification of a novel locus for a USH3 like syndrome combined with congenital cataract

    Dad, S., Østergaard, Elsebet, Thykjær, T., Albrechtsen, Anders, Ravn, K. J. T., Rosenberg, T. & Møller, L. B., 2010, In: Clinical Genetics. 78, 4, p. 388-397 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  5. Published

    Differential expression of cellular microRNAs in HPV-11 transfected cells. An analysis by three different array platforms and qRT-PCR

    Dreher, A., Rossing, M., Kaczkowski, B., Nielsen, Finn Cilius & Norrild, B., 17 Dec 2010, In: Biochemical and Biophysical Research Communications. 403, 3-4, p. 357-62 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  6. Published

    Protein structure prediction using bee colony optimization metaheuristic

    Fonseca, R., Paluszewski, M. & Winter, Pawel, 2010, In: Journal of Mathematical Modelling and Algorithms. 9, 2, p. 181-194 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  7. Published

    MicroRNA-145 targets YES and STAT1 in colon cancer cells

    Gregersen, Lea Haarup, Jacobsen, A. B., Frankel, Lisa, Wen, J., Krogh, Anders & Lund, Anders H., 2010, In: PLoS ONE. 5, 1, p. e8836

    Research output: Contribution to journal › Journal article › Research › peer-review

  8. Published

    Potentials of mean force for protein structure prediction vindicated, formalized and generalized

    Hamelryck, Thomas Wim, Borg, M., Paluszewski, M., Paulsen, J., Frellsen, J., Andreetta, C., Boomsma, Wouter, Bottaro, S. & Ferkinghoff-Borg, J., 2010, In: PLoS ONE. 5, 11, 11 p., e13714.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. Published

    Beyond rotamers: a generative, probabilistic model of side chains in proteins

    Harder, T., Boomsma, Wouter, Paluszewski, M., Frellsen, J., Johansson, Kristoffer Enøe & Hamelryck, Thomas Wim, 1 Jan 2010, In: B M C Bioinformatics. 11, p. 306

    Research output: Contribution to journal › Journal article › Research › peer-review

  10. Published

    Can small wildlife conservancies maintain genetically stable populations of large mammals? Evidence for increased genetic drift in geographically restricted populations of Cape buffalo in East Africa

    Heller, Rasmus, Okello, J. B. A. & Siegismund, Hans Redlef, 2010, In: Molecular Ecology. 19, 7, p. 1324-34 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  11. Published

    Molecular signatures of thyroid follicular neoplasia

    Helweg-Larsen, R. B., Rossing, M., Henao Giraldo, R., Yamamoto, Y., Krogdahl, A., Godballe, C., Winther, Ole, Kiss, K., Christensen, L. H., Høgdall, Estrid Vilma Solyom, Bennedbæk, F. N. & Nielsen, Finn Cilius, 2010, In: Endocrine - Related Cancer. 17, 3, p. 691-708 18 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  12. Published

    Accumulation of intermediates of the carbon-phosphorus lyase pathway for phosphonate degradation in phn mutants of Escherichia coli

    Hove-Jensen, B., Rosenkrantz, T. J., Zechel, D. L. & Willemoës, Martin, 2010, In: Journal of Bacteriology. 192, 1, p. 370-374

    Research output: Contribution to journal › Journal article › Research › peer-review

  13. Published

    Signatures of RNA binding proteins globally coupled to effective microRNA target sites

    Jacobsen, A., Wen, J., Marks, D. S. & Krogh, Anders, 1 Aug 2010, In: Genome Research. 20, 8, p. 1010-9 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  14. Published

    miRMaid: a unified programming interface for microRNA data resources

    Jacobsen, A., Krogh, Anders, Kauppinen, S. & Lindow, M., 2010, In: BMC Bioinformatics. 11, Suppl 1, p. 29

    Research output: Contribution to journal › Journal article › Research › peer-review

  15. Published

    Design of association studies with pooled or un-pooled next-generation sequencing data

    Kim, S. Y., Li, Y., Guo, Y., Li, R., Holmkvist, J., Hansen, Torben, Pedersen, Oluf Borbye, Wang, J. & Nielsen, Rasmus, 2010, In: Genetic Epidemiology. 34, 5, p. 479-491 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  16. Published

    The sequence and de novo assembly of the giant panda genome

    Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., Zhang, Z., Zhang, Y., Wang, W., Li, J., Wei, F., Li, H., Jian, M., Li, J., Zhang, Z., Nielsen, R. & 103 others, Li, D., Gu, W., Yang, Z., Xuan, Z., Ryder, O. A., Leung, F. C., Zhou, Y., Cao, J., Sun, X., Fu, Y., Fang, X., Guo, X., Wang, B., Hou, R., Shen, F., Mu, B., Ni, P., Lin, R., Qian, W., Wang, G., Yu, C., Nie, W., Wang, J., Wu, Z., Liang, H., Min, J., Wu, Q., Cheng, S., Ruan, J., Wang, M., Shi, Z., Wen, M., Liu, B., Ren, X., Zheng, H., Dong, D., Cook, K., Shan, G., Zhang, H., Kosiol, C., Xie, X., Lu, Z., Zheng, H., Li, Y., Steiner, C. C., Lam, T. T., Lin, S., Zhang, Q., Li, G., Tian, J., Gong, T., Liu, H., Zhang, D., Fang, L., Ye, C., Zhang, J., Hu, W., Xu, A., Ren, Y., Zhang, G., Bruford, M. W., Li, Q., Ma, L., Guo, Y., An, N., Hu, Y., Zheng, Y., Shi, Y., Li, Z., Liu, Q., Chen, Y., Zhao, J., Qu, N., Zhao, S., Tian, F., Wang, X., Wang, H., Xu, L., Liu, X., Vinar, T., Wang, Y., Lam, T., Yiu, S., Liu, S., Zhang, H., Li, D., Huang, Y., Wang, X., Yang, G., Jiang, Z., Wang, J., Qin, N., Li, L., Li, J., Bolund, L., Kristiansen, Karsten, Wong, G. K., Olson, M., Zhang, X., Li, S., Yang, H., Wang, J. & Wang, J., 2010, In: Nature. 463, 7279, p. 311-317 7 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  17. Published

    Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants

    Li, Y., Vinckenbosch, N., Tian, G., Huerta-Sanchez, E., Jiang, T., Jiang, H., Albrechtsen, A., Andersen, G., Cao, H., Korneliussen, T. S., Grarup, N., Guo, Y., Hellman, I., Jin, X., Li, Q., Liu, J., Liu, X., Sparsø, T., Tang, M., Wu, H. & 18 others, Wu, R., Yu, C., Zheng, H., Astrup, A., Bolund, L., Holmkvist, J., Jørgensen, T., Kristiansen, Karsten, Schmitz, O., Schwartz, Thue W., Zhang, X., Li, R., Yang, H., Wang, J., Hansen, Torben, Pedersen, Oluf Borbye, Nielsen, Rasmus & Wang, J., 2010, In: Nature Genetics. 42, 11, p. 969-72 4 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  18. Published

    Bioinformatical approaches to RNA structure prediction & Sequencing of an ancient human genome

    Lindgreen, S., 2010, Biologisk Institut: Museum Tusculanum. 111 p.

    Research output: Book/Report › Ph.D. thesis › Research

  19. Published

    A long-standing Pleistocene refugium in southern Africa and a mosaic of refugia in East Africa: insights from mtDNA and the common eland antelope

    Lorenzen, Eline, Masembe, C., Arctander, P. & Siegismund, Hans Redlef, 2010, In: Journal of Biogeography. 37, 3, p. 571-581 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  20. Published

    A conceptual framework for the identification of candidate drugs and drug targets in acute promyelocytic leukemia

    Marstrand, T. T., Borup, R., Willer, A., Borregaard, N., Sandelin, Albin Gustav, Porse, Bo Torben & Theilgaard-Mønch, Kim, Jul 2010, In: Leukemia. 24, 7, p. 1265-75 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  21. Published

    Genetic diversity among ancient Nordic populations

    Melchior, L. C., Lynnerup, Niels, Siegismund, Hans Redlef, Kivisild, T. & Dissing, J., 2010, In: PLOS ONE. 5, 7, 9 p., e11898.

    Research output: Contribution to journal › Journal article › Research › peer-review

  22. Published

    Sequence reconstruction and improved non-coding RNA homology search

    Menzel, K. P., 2010, Department of Basic Animal and Veterinary Sciences, University of Copenhagen. 172 p.

    Research output: Book/Report › Ph.D. thesis › Research

  23. Published

    Gene expression analysis of the emergence of epileptiform activity after focal injection of kainic acid into mouse hippocampus

    Motti, D., Le Duigou, C., Eugène, E., Chemaly, N., Wittner, L., Lazarevic, D., Krmac, H., Marstrand, T., Valen, E., Sanges, R., Stupka, E., Sandelin, Albin Gustav, Cherubini, E., Gustincich, S. & Miles, R., 2010, In: European Journal of Neuroscience. 32, 8, p. 1364-79 15 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  24. Published

    Long- and short-term selective forces on malaria parasite genomes

    Nygaard, S., Braunstein, A., Malsen, G., Van Dongen, S., Gardner, P. P., Krogh, Anders, Otto, T. D., Pain, A., Berriman, M., McAuliffe, J., Dermitzakis, E. T. & Jeffares, D. C., 1 Sep 2010, In: P L o S Genetics. 6, 9

    Research output: Contribution to journal › Journal article › Research › peer-review

  25. Published

    Mocapy++ - a toolkit for inference and learning in dynamic Bayesian networks

    Paluszewski, M. & Hamelryck, Thomas Wim, 2010, In: BMC Bioinformatics. 11, Suppl 1, 6 p., 126.

    Research output: Contribution to journal › Journal article › Research › peer-review

  26. Published

    3-methylcholanthrene induces differential recruitment of aryl hydrocarbon receptor to human promoters

    Pansoy, A., Ahmed, S., Valen, E., Sandelin, Albin Gustav & Matthews, J., 2010, In: Toxicological Sciences. 117, 1, p. 90-100 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  27. Published

    Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system

    Rapin, N. P. J., Lund, O., Bernaschi, M. & Castiglione, F., 2010, In: PloS one. 5, 4, p. e9862

    Research output: Contribution to journal › Journal article › Research › peer-review

  28. Published

    Ancient human genome sequence of an extinct Palaeo-Eskimo

    Rasmussen, M., Li, Y., Lindgreen, S., Pedersen, J. S., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., Bertalan, M., Nielsen, K., Gilbert, T., Wang, Y., Raghavan, M., Campos, P., Kamp, H. L. M., Wilson, A. S., Gledhill, A., Tridico, S. & 32 others, Bunce, M., Lorenzen, Eline, Binladen, J. K. M. A., Guo, X., Zhao, J., Zhang, X., Zhang, H., Li, Z., Chen, M., Orlando, L. A. A., Kristiansen, Karsten, Bak, M., Tommerup, Niels, Bendixen, C., Pierre, T. L., Grønnow, B., Meldgaard, Morten, Andreasen, C., Fedorova, S. A., Osipova, L. P., Higham, T. F. G., Ramsey, C. B., Hansen, Thomas van Overeem, Nielsen, Finn Cilius, Crawford, M. H., Brunak, Søren, Sicheritz-Pontén, T., Villems, R., Nielsen, Rasmus, Krogh, Anders, Wang, J. & Willerslev, Eske, 11 Feb 2010, In: Nature. 463, 7282, p. 757-762 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  29. Published

    Positive selection on apoptosis related genes

    Rodrigues da Fonseca, Rute Andreia, Kosiol, C., Vinař, T., Siepel, A. & Nielsen, Rasmus, 2010, In: FEBS Letters. 584, 3, p. 469-476 8 p.

    Research output: Contribution to journal › Review › Research › peer-review

  30. Published

    A simple procedure for routine RNA extraction and miRNA array analyses from a single thyroid in vivo fine needle aspirate

    Rossing, M., Kaczkowski, B., Futoma-Kazmierczak, E., Glud, M., Klausen, M., Faber, Jens, Nygaard, Birte, Kiss, K., Sørensen, C. H., Nielsen, Finn Cilius, Bennedbæk, F. N. & Friis-Hansen, Lennart Jan, 2010, In: Scandinavian Journal of Clinical & Laboratory Investigation. 70, 8, p. 529-534 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  31. Published

    Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury

    Ryge, J., Winther, Ole, Wienecke, Jacob, Sandelin, Albin Gustav, Westerdahl, A., Hultborn, Hans & Kiehn, O., 2010, In: BMC Genomics. 11, 1, p. 365 22 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  32. Published

    Co-circulation of two extremely divergent serotype SAT 2 lineages in Kenya highlights challenges to foot-and-mouth disease control

    Sangula, A. K., Belsham, G. J., Muwanika, V. B., Heller, Rasmus, Balinda, S. N. & Siegismund, Hans Redlef, 2010, In: Archives of Virology. 155, 10, p. 1625-1630

    Research output: Contribution to journal › Journal article › Research › peer-review

  33. Published

    Evolutionary analysis of foot-and-mouth disease virus serotype SAT 1 isolates from East Africa suggests two independent introductions from southern Africa

    Sangula, A. K., Belsham, G., Muwanika, V. B., Heller, Rasmus, Balinda, S. N., Masembe, C. & Siegismund, Hans Redlef, 30 Nov 2010, In: BMC Evolutionary Biology. 10, 1, p. 371

    Research output: Contribution to journal › Journal article › Research › peer-review

  34. Published

    Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models

    Stovgaard, K., Andreetta, C., Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 1 Jan 2010, In: B M C Bioinformatics. 11, p. 429

    Research output: Contribution to journal › Journal article › Research › peer-review

  35. Published

    Genetic variation of inbreeding depression among floral and fitness traits in Silene nutans

    Thiele, J., Hansen, T. M., Siegismund, Hans Redlef & Hauser, T. P., 2010, In: Heredity. 104, 1, p. 52-60 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  36. Published

    Deciphering Transcriptional Regulation: Computational Approaches

    Valen, E., 2010, Museum Tusculanum. 97 p.

    Research output: Book/Report › Ph.D. thesis › Research

  37. Published

    Sequencing of 50 human exomes reveals adaptation to high altitude

    Yi, X., Liang, Y., Huerta-Sanchez, E., Jin, X., Cuo, Z. X. P., Pool, J. E., Xu, X., Jiang, H., Vinckenbosch, N., Korneliussen, T. S., Zheng, H., Liu, T., He, W., Li, K., Luo, R., Nie, X., Wu, H., Zhao, M., Cao, H., Zou, J. & 50 others, Shan, Y., Li, S., Yang, Q., Asan, G., Ni, P., Tian, G., Xu, J., Liu, X., Jiang, T., Wu, R., Zhou, G., Tang, M., Qin, J., Wang, T., Feng, S., Li, G., Huasang, G., Luosang, J., Wang, W., Chen, F., Wang, Y., Zheng, X., Li, Z., Bianba, Z., Yang, G., Wang, X., Tang, S., Gao, G., Yong, C., Luo, Z., Gusang, L., Cao, Z., Zhang, Q., Ouyang, W., Ren, X., Liang, H., Zheng, H., Huang, Y., Li, J., Bolund, L., Kristiansen, Karsten, Li, Y., Zhang, Y., Zhang, X., Li, R., Li, S., Yang, H., Nielsen, Rasmus, Wang, J. & Wang, J., 2 Jul 2010, In: Science. 329, 5987, p. 75-8 4 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  38. Published

    MicroRNAs and potential target interactions in psoriasis

    Zibert, J. R., Løvendorf, M. B., Litman, Thomas, Olsen, Jørgen, Kaczkowski, B. & Skov, Lone, 2010, In: Journal of Dermatological Science. 58, 3, p. 177-185 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  39. 2011
  40. Published

    Efficient, non-disruptive local moves for Monte Carlo sampling of proteins

    Bottaro, S., Boomsma, Wouter, Johansson, Kristoffer Enøe, Andreetta, C., Hamelryck, Thomas Wim & Ferkinghoff-Borg, J., 2011, Next Generation Statistics in Biosciences: Proceedings of the 30th Leeds Annual Statistical Research (LASR) Workshop. Mardia, K. V., Gusnanto, A., Riley, A. D. & Voss, J. (eds.). University of Leeds, p. 127 1 p.

    Research output: Chapter in Book/Report/Conference proceeding › Conference abstract in proceedings › Research

  41. Published

    miR-449 inhibits cell proliferation and is down-regulated in gastric cancer

    Bou Kheir, T., Futoma-Kazmierczak, E., Jacobsen, A., Krogh, Anders, Bardram, L., Hother, C., Grønbæk, Kirsten, Federspiel, B., Lund, Anders H. & Friis-Hansen, Lennart Jan, 2011, In: Molecular Cancer. 10, p. 1-12 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  42. Published

    The evolution of gene expression levels in mammalian organs

    Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csardi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., Albert, F. W., Zeller, U., Khaitovich, P., Gruetzner, F., Bergmann, S., Nielsen, Rasmus, Paeaebo, S. & Kaessmann, H., 20 Oct 2011, In: Nature. 478, 7369, p. 343-348 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  43. Published

    Particle-dissociating peptides

    Brown, Stanley & Mathiasen, Signe, 4 Jan 2011, In: Advanced Materials. 23, 1, p. 132-135 4 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  44. Published

    CTLs' repertoire shaping in the thymus: a Monte Carlo simulation

    Castiglione, F., Santoni, D. & Rapin, N. P. J., 2011, In: Autoimmunity. 44, 4, p. 261-270 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  45. Published

    Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data

    Chen, Y., Jørgensen, M., Kolde, R., Zhao, X., Parker, B., Valen, E., Wen, J. & Sandelin, Albin Gustav, 2011, In: BMC Genomics. 12, 1, 16 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  46. Published

    Differential expression of cellular microRNAs in HPV 11, -16, and -45 transfected cells

    Dreher, A., Rossing, M., Kaczkowski, B., Andersen, D. K., Larsen, T. J., Christophersen, M. K., Nielsen, Finn Cilius & Norrild, B., 2011, In: Biochemical and Biophysical Research Communications. 412, 1, p. 20-5 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  47. Published

    Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa

    Enroth, S., Rada-Iglesisas, A., Andersson, Robin, Wallerman, O., Wanders, A., Påhlman, L., Komorowski, J. & Wadelius, C., 2011, In: B M C Cancer. 11, 13 p., 450.

    Research output: Contribution to journal › Journal article › Research › peer-review

  48. Published

    microRNA-101 is a potent inhibitor of autophagy

    Frankel, Lisa, Wen, J., Lees, M., Høyer-Hansen, M., Farkas, T., Krogh, Anders, Jäättelä, M. & Lund, Anders H., 2011, In: E M B O Journal. 30, p. 4628-4641 14 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  49. Published

    Probabilistic methods in macromolecular structure prediction

    Frellsen, J., 2011, Københavns Universitet.

    Research output: Book/Report › Ph.D. thesis › Research

  50. Published

    Gene expression of the endolymphatic sac

    Friis, M., Martin-Bertelsen, T., Friis-Hansen, Lennart Jan, Winther, Ole, Henao Giraldo, R., Sørensen, Mads Sølvsten & Qvortrup, Klaus, 2011, In: Acta Oto-Laryngologica. 131, 12, p. 1257-63 7 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  51. Published

    Upregulation of alpha cell glucagon-like peptide 1 (GLP-1) in Psammomys obesus--an adaptive response to hyperglycaemia?

    Hansen, A. M. K., Bödvarsdottir, T. B., Nordestgaard, D. N. E., Heller, Rasmus, Gotfredsen, C. F., Maedler, K., Fels, J., Holst, Jens Juul & Karlsen, A., 2011, In: Diabetologia. 54, 6, p. 1379-87 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  52. Published

    Exploring the conformational space of proteins using probabilistic models

    Harder, T. P., 2011

    Research output: Book/Report › Ph.D. thesis › Research

  53. Published

    Are East African conservancies too small and isolated to maintain migratory bovid populations?

    Heller, Rasmus, Okello, J. B. A. & Siegismund, Hans Redlef, 2011, In: Gnusletter. 29, 2, p. 20-21

    Research output: Contribution to journal › Journal article › Research

  54. Published

    Isolation of RNP granules

    Jønson, L., Nielsen, Finn Cilius & Christiansen, Jan, 2011, RNA: methods and protocols. Nielsen, H. (ed.). Springer, Vol. 703. p. 265-273 9 p. (Methods in Molecular Biology).

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  55. Published

    Estimation of allele frequency and association mapping using next-generation sequencing data

    Kim, S. Y., Lohmueller, K. E., Albrechtsen, Anders, Li, Y., Korneliussen, Thorfinn Sand, Tian, G., Grarup, Niels, Jiang, T., Andersen, G., Witte, D., Jorgensen, T., Hansen, Torben, Pedersen, Oluf Borbye, Wang, J. & Nielsen, Rasmus, 2011, In: B M C Bioinformatics. 12, p. 231 16 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  56. Published

    A genome-wide scan in affected sib-pairs with idiopathic recurrent miscarriage suggests genetic linkage

    Kolte, A. M., Nielsen, Henriette Svarre, Moltke, Ida, Degn, B., Pedersen, B., Sunde, L., Nielsen, Finn Cilius & Christiansen, O. B., 2011, In: Molecular Human Reproduction. 17, 6, p. 379-385 7 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  57. Published

    Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

    Lin, M. F., Kheradpour, P., Washietl, S., Parker, B. J., Pedersen, Jakob Skou & Kellis, M., 2011, In: Genome Research. 21, 11, p. 1916-28 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  58. Published

    A high-resolution map of human evolutionary constraint using 29 mammals

    Lindblad-Toh, K., Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Jordan, G., Mauceli, E., Ward, L. D., Lowe, C. B., Holloway, A. K., Clamp, M., Gnerre, S., Moltke, Ida, Wen, J. & Pedersen, Jakob Skou, 27 Oct 2011, In: Nature. 478, 7370, p. 476-82 7 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  59. Published

    Natural selection affects multiple aspects of genetic variation at putatively peutral sites across the human genome

    Lohmueller, K. E., Albrechtsen, Anders, Li, Y., Kim, S. Y., Korneliussen, Thorfinn Sand, Vinckenbosch, N., Tian, G., Huerta-Sanchez, E., Feder, A. F., Grarup, Niels, Jørgensen, T., Jiang, T., Witte, D. R., Sandbæk, A., Hellmann, I., Lauritzen, T., Hansen, Torben, Pedersen, Oluf Borbye, Wang, J. & Nielsen, Rasmus, 2011, In: P L o S Genetics. 7, 10, 15 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  60. Published

    Species-specific responses of Late Quaternary megafauna to climate and humans

    Lorenzen, E., Nogues, D. B., Orlando, L. A. A., Weinstock Arenovitz, J., Binladen, J. K. M. A., Marske, K. A., Ugan, A., Borregaard, M. K., Gilbert, M. T. P., Nielsen, R., Ho, S. Y. W., Goebel, T., Graf, K. E., Byers, D., Stenderup, J., Rasmussen, M., Campos, P., Leonard, J. A., Koepfli, K-P., Froese, D. & 35 others, Zazula, G., Stafford jr., T., Aaris-Sørensen, Kim, Batra, P., Haywood, A. M., Singarayer, J. S., Valdes, P. J., Boeskorov, G., Burns, J. A., Davydov, S. P., Haile, James Seymour, Jenkins, D. L., Kosintsev, P., Kuznetsova, T., Lai, X., Martin, L. D., McDonald, H. G., Mol, D., Meldgaard, Morten, Munch, K., Stephan, E., Sablin, M., Sommer, R. S., Sipko, T., Scott, E., Suchard, M. A., Tikhonov, A., Willerslev, R., Wayne, R. K., Cooper, A., Hofreiter, M., Sher, A., Shapiro, B., Rahbek, Carsten & Willerslev, Eske, 2011, In: Nature. 479, 7373, p. 359-364 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  61. Published

    A statistical view on the reference ratio method

    Mardia, K., Frellsen, J., Borg, M., Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 2011. 6 p.

    Research output: Contribution to conference › Paper › Research

  62. Published

    maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences

    Menzel, K. P., Stadler, P. F. & Gorodkin, Jan, 2011, In: Bioinformatics. 27, 3, p. 317-325 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  63. Published

    A method for detecting IBD regions simultaneously in multiple individuals--with applications to disease genetics

    Moltke, Ida, Albrechtsen, Anders, Hansen, Thomas van Overeem, Nielsen, Finn Cilius & Nielsen, Rasmus, 2011, In: Genome Research. 21, 7, p. 1168-80 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  64. Published

    Statistical inference of Identity-By-Descent sharing in human genomes and its applications in evolutionary and medical genetics

    Moltke, Ida, 2011

    Research output: Book/Report › Ph.D. thesis › Research

  65. Published

    Genotype and SNP calling from next-generation sequencing data

    Nielsen, Rasmus, Paul, J. S., Albrechtsen, Anders & Song, Y. S., 2011, In: Nature Reviews. Genetics. 12, 6, p. 443-451 9 p.

    Research output: Contribution to journal › Review › Research › peer-review

  66. Published

    The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming

    Nygaard, S., Zhang, G., Schiøtt, M., Li, C., Wurm, Y., Hu, H., Zhou, J., Ji, L., Qiu, F., Rasmussen, M., Pan, H., Hauser, Frank, Krogh, Anders, Grimmelikhuijzen, Cornelis (Cok), Wang, J. & Boomsma, Jacobus J., 2011, In: Genome Research. 21, 8, p. 1339-1348 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  67. Published

    Generative probabilistic models extend the scope of inferential structure determination

    Olsson, S., Boomsma, Wouter, Frellsen, J., Bottaro, S., Harder, T. P., Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 2011, In: Journal of Magnetic Resonance. 213, 1, p. 182-186 5 p.

    Research output: Contribution to journal › Letter › Research › peer-review

  68. Published

    True single-molecule DNA sequencing of a pleistocene horse bone

    Orlando, L. A. A., Ginolhac, A., Raghavan, M., Mouatt, J. T. V., Rasmussen, M., Magnussen, K., Steinmann, K. E., Kapranov, P., Thompson, J. F., Zazula, G., Froese, D., Moltke, Ida, Shapiro, B., Hofreiter, M., Al-Rasheid, K. A. S., Gilbert, M Thomas P & Willerslev, Eske, 2011, In: Genome Research. 21, 10, p. 1705-1719 15 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  69. Published

    New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes.

    Parker, B. J., Moltke, Ida, Roth, A., Washietl, S., Wen, J., Kellis, M., Breaker, R. & Pedersen, Jakob Skou, 2011, In: Genome Research. 21, 11, p. 1929-1943 15 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  70. Published

    How the RNA isolation method can affect microRNA microarray results

    Podolska, A., Kaczkowski, B., Litman, Thomas, Fredholm, Merete & Cirera, Susanna, 2011, In: Acta Biochimica Polonica. 58, 4, p. 535-540 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  71. Published

    MicroRNA expression profiling of the porcine developing brain

    Podolska, A., Kaczkowski, B., Busk, P. K., Søkilde, R., Litman, T., Fredholm, Merete & Cirera, Susanna, 2011, In: P L o S One. 6, p. e14494 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  72. Published

    PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters

    Preker, P., Almvig, K., Christensen, M. S., Valen, E., Mapendano, C. K., Sandelin, Albin Gustav & Jensen, T. H., 19 May 2011, In: Nucleic Acids Research.

    Research output: Contribution to journal › Journal article › Research › peer-review

  73. Published

    Bistability in autoimmune diseases

    Rapin, N. P. J., Mosekilde, E. & Lund, O., 2011, In: Autoimmunity. 44, 4, p. 256-260 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  74. Published

    Immune system simulation online

    Rapin, N. P. J., Lund, O. & Castiglione, F., 2011, In: Bioinformatics. 27, 14, p. 2013-4 2 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  75. Published

    An Aboriginal Australian genome reveals separate human dispersals into Asia

    Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K. E., Rasmussen, S., Albrechtsen, A., Skotte, L., Lindgreen, S., Metspalu, M., Jombart, T., Kivisild, T., Zhai, W., Eriksson, A., Manica, A., Orlando, L., De La Vega, F. M., Tridico, S., Metspalu, E., Nielsen, K., Avila Arcos, M. D. C. & 38 others, Moreno Mayar, J. Víctor, Muller, C., Dortch, J., Gilbert, M Thomas P, Lund, O., Wesolowska, A., Karmin, M., Weinert, L. A., Wang, B., Li, J., Tai, S., Xiao, F., Hanihara, T., van Driem, G., Jha, A. R., Ricaut, F., de Knijff, P., Migliano, A. B., Gallego Romero, I., Kristiansen, Karsten, Lambert, D. M., Brunak, Søren, Forster, P., Brinkmann, B., Nehlich, O., Bunce, M., Richards, M., Gupta, R., Bustamante, C. D., Krogh, Anders, Foley, R. A., Lahr, M. M., Balloux, F., Sicheritz-Pontén, T., Villems, R., Nielsen, Rasmus, Wang, J. & Willerslev, Eske, 2011, In: Science. 334, 6052, p. 94-98 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  76. Published

    Aspects of RNA Regulation: Non-canonical microRNAs Biogenesis, microRNAs in Pharmacogenomics, and the Evolvability of Alternative Splicing

    Rukov, J. L., 2011, University of Copenhagen.

    Research output: Book/Report › Ph.D. thesis › Research

  77. Published

    MicroRNA pharmacogenomics: post-transcriptional regulation of drug response

    Rukov, J. L. & Shomron, N., 2011, In: Trends in Molecular Medicine. 17, 8, p. 412-23 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  78. Published

    Pharmacogenomics genes show varying perceptibility to microRNA regulation

    Rukov, J. L., Vinther, Jeppe & Shomron, N., 2011, In: Pharmacogenetics and Genomics. 21, 5, p. 251-62 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  79. Published

    The Value of Example Solutions in Pharmacy Education: The role of seniority and gender.

    Sandelin, Albin Gustav, Hansen, H. R., Baldursdóttir, S. G., Kristensen, Anders Skov, Bak, Lasse Kristoffer, Christiansen, Frederik Voetmann & Selhuber-Unkel, C. J. M., 2011, In: Pharmacy Education. 11, 1, p. 32-37 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  80. Published

    Low diversity of foot-and-mouth disease serotype C virus in Kenya: evidence for probable vaccine strain re-introductions in the field

    Sangula, A. K., Siegismund, Hans Redlef, Belsham, G. J., Balinda, S. N., Masembe, C. & Muwanika, V. B., 2011, In: Epidemiology and Infection. 139, 2, p. 189-196 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  81. Published

    Cross species comparison of C/EBPa and PPAR¿ profiles in mouse and human adipocytes reveals interdependent retention of binding sites

    Schmidt, S. F., Jørgensen, M., Chen, Y., Nielsen, R., Sandelin, Albin Gustav & Mandrup, S., 2011, In: BMC Genomics. 12, 16 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  82. Published

    The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

    Seemann, Ernst Stefan, Menzel, K. P., Backofen, R. & Gorodkin, Jan, 2011, In: Nucleic Acids Research. 39, Suppl. 2, p. W107-W111 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  83. Published

    Global microRNA analysis of the NCI-60 cancer cell panel

    Søkilde, R., Kaczkowski, B., Podolska, A., Cirera, Susanna, Gorodkin, Jan, Møller, S. & Litman, T., 2011, In: Molecular Cancer Therapeutics. 10, 3, p. 375-384 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  84. Published

    The post-transcriptional operon

    Tenenbaum, S. A., Christiansen, Jan & Nielsen, Henrik, 2011, RNA: methods and protocols. Nielsen, H. (ed.). Springer, p. 237-245 9 p. (Methods in Molecular Biology).

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  85. Published

    Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes

    Valen, E., Preker, P., Andersen, P. R., Zhao, X., Chen, Y., Ender, C., Dueck, A., Meister, G., Sandelin, Albin Gustav & Jensen, T. H., 2011, In: Nature Structural and Molecular Biology. 18, 9, p. 1075–1082 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  86. Published

    Genomic and chromatin signals underlying transcription start-site selection

    Valen, E. & Sandelin, Albin Gustav, 2011, In: Trends in Genetics. 27, 11, p. 475-485 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  87. Published

    Iterative ratio method: a formal justification for the potentials of mean force

    Valentin, J., Andreetta, C., Paluszewski, M., Borg, M., Frellsen, J., Paulsen, J., Boomsma, Wouter, Bottaro, S., Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 2011. 1 p.

    Research output: Contribution to conference › Poster › Research

  88. Published

    MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action

    Wen, J., Parker, B. J., Jacobsen, A. & Krogh, Anders, 2011, In: R N A. 17, 5, p. 820-34 15 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  89. Published

    Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

    Yan, G., Zhang, G., Fang, X., Zhang, Y., Li, C., Ling, F., Cooper, D. N., Li, Q., Li, Y., van Gool, A. J., Du, H., Chen, J., Chen, R., Zhang, P., Huang, Z., Thompson, J. R., Meng, Y., Bai, Y., Wang, J., Zhuo, M. & 26 others, Wang, T., Huang, Y., Wei, L., Li, J., Wang, Z., Hu, H., Yang, P., Le, L., Stenson, P. D., Li, B., Liu, X., Ball, E. V., An, N., Huang, Q., Zhang, Y., Fan, W., Zhang, X., Li, Y., Wang, W., Katze, M. G., Su, B., Nielsen, Rasmus, Yang, H., Wang, J., Wang, X. & Wang, J., 2011, In: Nature Biotechnology. 29, 11, p. 1019-1023 5 p.

    Research output: Contribution to journal › Letter › Research › peer-review

  90. Published

    Systematic clustering of transcription start site landscapes

    Zhao, X., Valen, E., Parker, B. J. & Sandelin, Albin Gustav, 2011, In: P L o S One. 6, 8, 16 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  91. 2012
  92. Published

    Fitness consequences of nest infiltration by the mutualist-exploiter Megalomyrmex adamsae

    Adams, R. M. M., Shah, K., Antonov, L. D. & Mueller, U. G., 2012, In: Ecological Entomology. 37, 6, p. 453-462 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  93. Published

    HemaExplorer: a Web server for easy and fast visualization of gene expression in normal and malignant hematopoiesis

    Bagger, F. O., Rapin, N. P. J., Theilgaard-Mønch, Kim, Kaczkowski, B., Jendholm, L. J., Winther, O. & Porse, Bo Torben, 2012, In: Blood. 119, 26, p. 6394-6395 2 p.

    Research output: Contribution to journal › Comment/debate › Research

  94. Published

    Probabilistic models of local biomolecular structure and their applications

    Boomsma, Wouter, Frellsen, J. & Hamelryck, Thomas Wim, 2012, Bayesian methods in structural bioinformatics. Hamelryck, T., Mardia, K. & Ferkinghoff-Borg, J. (eds.). Springer, p. 233-254 22 p. (Statistics for Biology and Health, Springer).

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  95. Published

    On the Physical Relevance and Statistical Interpretation of Knowledge-Based Potentials

    Borg, M., Hamelryck, Thomas Wim & Ferkinghoff-Borg, J., 2012, Bayesian Methods in Structural Bioinformatics. Hamelryck, T., Mardia, K. & Ferkinghoff-Borg, J. (eds.). Springer Publishing Company, p. 97-124 28 p. (Statistics for Biology and Health, Springer).

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  96. Published

    Subtle Monte Carlo updates in dense molecular systems

    Bottaro, S., Boomsma, Wouter, Johansson, Kristoffer Enøe, Andreetta, C., Hamelryck, Thomas Wim & Ferkinghoff-Borg, J., 2012, In: Journal of Chemical Theory and Computation. 8, 2, p. 695-702 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  97. Published

    microRNA-146a inhibits G protein-coupled receptor-mediated activation of NF-κB by targeting CARD10 and COPS8 in gastric cancer

    Crone, S. G., Jacobsen, A., Federspiel, B., Bardram, L., Krogh, Anders, Lund, Anders H. & Friis-Hansen, Lennart Jan, 2012, In: Molecular Cancer. 11, 71, p. 71 31 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  98. Published

    A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements.

    Enroth, S., Andersson, C., Andersson, Robin, Wadelius, C., Gustafsson, M. & Komorowski, J., 2012, In: Algorithms for Molecular Biology. 7, 1, p. 2 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  99. Published

    Towards a general probabilistic model of protein structure: the reference ratio method

    Frellsen, J., Mardia, K. V., Borg, M., Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 2012, Bayesian methods in structural bioinformatics. Hamelryck, T., Mardia, K. & Ferkinghoff-Borg, J. (eds.). Springer, p. 125-134 10 p. (Statistics for Biology and Health).

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  100. Published

    The rectal cancer microRNAome - microRNA expression in rectal cancer and matched normal mucosa

    Gaedcke, J., Grade, M., Camps, J., Søkilde, R., Kaczkowski, B., Schetter, A. J., Difilippantonio, M. J., Harris, C. C., Ghadimi, B. M., Møller, S., Beissbarth, T., Ried, T. & Litman, Thomas, 2012, In: Clinical Cancer Research. 18, 18, p. 4919-4930 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  101. Published

    microRNA-143 down-regulates Hexokinase 2 in colon cancer cells

    Gregersen, Lea Haarup, Jacobsen, A., Frankel, Lisa, Wen, J., Krogh, Anders & Lund, Anders H., 2012, In: B M C Cancer. 12, 232, 23 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  102. Published

    An Overview of Bayesian Inference and Graphical Models

    Hamelryck, Thomas Wim, 2012, Bayesian Methods in Structural Bioinformatics. Hamelryck, T., Mardia, K. & Ferkinghoff-Borg, J. (eds.). Springer, p. 3-48 46 p. (Statistics for Biology and Health, Springer).

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  103. Published

    Bayesian methods in structural bioinformatics

    Hamelryck, Thomas Wim (ed.), Mardia, K. (ed.) & Ferkinghoff-Borg, J. (ed.), 2012, Springer. 377 p. (Statistics for Biology and Health).

    Research output: Book/Report › Book › Research › peer-review

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