Computational and RNA Biology

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  1. 2012
  2. Published

    DGCR8 HITS-CLIP reveals novel functions for the microprocessor

    Macias, S., Plass, M., Stajuda, A., Michlewski, G., Eyras, E. & Cáceres, J. F., 2012, In: Nature Structural and Molecular Biology. 19, 8

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

  3. Published

    Down-regulation of microRNAs controlling tumourigenic factors in follicular thyroid carcinoma

    Rossing, M., Helweg-Larsen, R. B., Henao Giraldo, R., Winther, Ole, Vikeså, J., Niazi, O., Godballe, C., Krogdahl, A., Glud, M., Sørensen, C. H., Kiss, K., Bennedbæk, F. N. & Nielsen, Finn Cilius, 2012, In: Journal of Molecular Endocrinology. 48, 1, p. 11-23 13 p.

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

  4. Published

    Extensive X-linked adaptive evolution in central chimpanzees

    Hvilsom, C., Qian, Y., Bataillon, T., Li, Y., Mailund, T., Sallé, B., Carlsen, F., Li, R., Zheng, H., Jiang, T., Jiang, H., Jin, X., Terkelsen, K. M., Hobolth, A., Siegismund, Hans Redlef, Wang, J. & Schierup, M. H., 2012, In: Proceedings of the National Academy of Sciences USA (PNAS). 109, 6, p. 2054-2059 6 p.

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

  5. Published

    Fast large-scale clustering of protein structures using Gauss integrals

    Harder, T. P., Borg, M., Boomsma, Wouter, Røgen, P. & Hamelryck, Thomas Wim, 2012, In: Bioinformatics. 28, 4, p. 510-515 6 p.

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

  6. 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

  7. Published

    GMD: measuring the distance between histograms with applications on high-throughput sequencing reads

    Zhao, X. & Sandelin, Albin Gustav, 2012, In: Bioinformatics. 28, 8, p. 1164-1165 2 p.

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

  8. Published

    Genetic diversity in the desert warthog (Phacochoerus aethiopicus delameri) population of eastern Africa

    Muwanika, V. B., Kock, R., Masembe, C. & Siegismund, Hans Redlef, 2012, In: South African Journal of Wildlife Research. 42, 1, p. 54-59 6 p.

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

  9. 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

  10. Published

    Improving ancient DNA read mapping against modern reference genomes

    Schubert, Mikkel, Ginolhac, A., Lindgreen, S., Thompson, J. F., Al-Rasheid, K. A. S., Willerslev, Eske, Krogh, Anders & Orlando, L. A. A., 2012, In: BMC Genomics. 13, 15 p., 178.

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

  11. Published

    Integrative analyses reveal novel strategies in HPV11,-16 and -45 early infection

    Kaczkowski, B., Rossing, M., Andersen, D. K., Dreher, A., Morevati, M., Visser, M. A., Winther, Ole, Nielsen, Finn Cilius & Norrild, B., 2012, In: Scientific Reports. 2, p. 515

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

  12. Published

    Interaction of antidepressants with the serotonin and norepinephrine transporters: mutational studies of the S1 substrate binding pocket

    Sørensen, L., Andersen, J., Thomsen, M., Hansen, S. M. R., Zhao, X., Sandelin, Albin Gustav, Strømgaard, Kristian & Kristensen, Anders Skov, 2012, In: The Journal of Biological Chemistry. 287, 52, p. 43694-43707 14 p.

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

  13. Published

    Interaction of antidepressants with the serotonin and norepinephrine transporters: mutational studies of the S1 substrate binding pocket

    Sørensen, L., Andersen, J., Thomsen, M., Hansen, S. M. R., Zhao, X., Sandelin, Albin Gustav, Strømgaard, Kristian & Kristensen, Anders Skov, 2012, In: Journal of Biological Chemistry. 287, p. 43694-43707 14 p.

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

  14. Published

    Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns

    Weischenfeldt, Joachim Lütken, Waage, J. E., Tian, G., Zhao, J., Damgaard, I., Jakobsen, J. S., Kristiansen, Karsten, Krogh, Anders, Wang, J. & Porse, Bo Torben, 2012, In: Genome Biology (Online Edition). 13, 5, 19 p.

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

  15. Published

    Mediator regulates non-coding RNA transcription at fission yeast centromeres

    Thorsen, M., Hansen, H., Venturi, M., Holmberg, Steen & Thon, Genevieve, 2012, In: Epigenetics & Chromatin. 5, p. 1-10 10 p.

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

  16. Published

    Metazoan promoters: emerging characteristics and insights into transcriptional regulation

    Lenhard, B., Sandelin, Albin Gustav & Carninci, P., 2012, In: Nature Reviews. Genetics. 13, 4, p. 233-245 13 p.

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

  17. Published

    MicroRNAs and Their Antagonists as Novel Therapeutics

    Vinther, Jeppe, Rukov, J. & Shomron, N., 2012, From Nucleic Acids Sequences to Molecular Medicine. Erdmann, V. A. & Barciszewski, J. (eds.). Springer Publishing Company, p. 503-523 21 p. (RNA Technologies).

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

  18. Published

    Mixtures of concentrated multivariate sine distributions with applications to bioinformatics

    Mardia, K. V., Kent, J. T., Zhang, Z., Taylor, C. C. & Hamelryck, Thomas Wim, 2012, In: Journal of Applied Statistics. 39, 11, p. 2475-2492 18 p.

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

  19. Published

    On gene regulation in eukaryotes: computational approaches to decipher transcriptional regulation at genetic and epigenetic level

    Zhao, X., 2012, Department of Biology, Faculty of Science, University of Copenhagen. 170 p.

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

  20. 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

  21. Published

    Predictive active set selection methods for Gaussian processes

    Henao, R. & Winther, Ole, 2012, In: Neurocomputing. 80, p. 10-18 9 p.

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

  22. Published

    Prey diversity is affected by climate and differs between age classes in the Red-backed Shrike (Lanius collurio)

    Pedersen, L., Geertsma, M. & Tøttrup, Anders P., 2012, In: Ornis Fennica. 89, 2, p. 99-108 10 p.

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

  23. 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

  24. Published

    RILogo: visualising RNA-RNA interactions

    Menzel, K. P., Seemann, Ernst Stefan & Gorodkin, Jan, 2012, In: Bioinformatics. 28, 19, p. 2523-2526 4 p.

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

  25. Published

    Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

    Xu, X., Liu, X., Ge, S., Jensen, J. D., Hu, F., Li, X., Dong, Y., Gutenkunst, R. N., Fang, L., Huang, L., Li, J., He, W., Zhang, G., Zheng, X., Zhang, F., Li, Y., Yu, C., Kristiansen, K., Zhang, X., Wang, J. & 5 others, Wright, M., McCouch, S., Nielsen, Rasmus, Wang, J. & Wang, W., 2012, In: Nature Biotechnology. 30, 1, p. 105-111 7 p.

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

  26. Published

    SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data

    Nielsen, Rasmus, Korneliussen, Thorfinn Sand, Albrechtsen, Anders, Li, Y. & Wang, J., 2012, In: PLoS ONE. 7, 7, 11 p., e37558.

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

  27. Published

    Serotype identification and VP1 coding sequence analysis of foot-and-mouth disease viruses from outbreaks in Eastern and Northern Uganda in 2008/9

    Kasambula, L., Belsham, G., Siegismund, Hans Redlef, Muwanika, V. B., Ademun-Okurut, A. R. & Masembe, C., 2012, In: Transboundary and Emerging Diseases. 59, 4, p. 323-330 8 p.

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

  28. Published

    Significance of calcium binding, tyrosine phosphorylation, and lysine trimethylation for the essential function of calmodulin in vertebrate cells analyzed in a novel gene replacement system

    Panina, S., Stephan, A., la Cour, J. M., Jacobsen, K., Kallerup, L. K., Bumbuleviciute, R., Knudsen, K. V. K., Sanchez-Gonzalez, P., Villalobo, A., Olesen, U. H. & Berchtold, Martin Werner, 2012, In: Journal of Biological Chemistry. 287, 22, p. 18173-18181 9 p.

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

  29. Published

    Statistics of bivariate von mises distributions

    Mardia, K. V. & Frellsen, J., 2012, Bayesian methods in structural bioinformatics. Hamelryck, T., Mardia, K. & Ferkinghoff-Borg, J. (eds.). Springer, p. 159-178 20 p. (Statistics for Biology and Health).

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

  30. 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

  31. Published

    Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

    Pauli, A., Valen, E., Lin, M. F., Garber, M., Vastenhouw, N. L., Levin, J. Z., Fan, L., Sandelin, Albin Gustav, Rinn, J. L., Regev, A. & Schier, A. F., 2012, In: Genome Research. 22, p. 577-591 15 p.

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

  32. 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

  33. Published

    The role of miRNAs in human papilloma virus (HPV)-associated cancers: bridging between HPV-related head and neck cancer and cervical cancer

    Lajer, C. B., Garnæs, E., Friis-Hansen, Lennart Jan, Norrild, B., Therkildsen, M. H., Glud, M., Rossing, M., Lajer, H., Svane, D., Skotte, L., Specht, Lena, von Buchwald, Christian & Nielsen, Finn Cilius, 2012, In: B J C. 106, p. 1526-1534 9 p.

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

  34. 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

  35. Published

    mRNA pseudoknot structures can act as ribosomal roadblocks

    Hansen, J. T., Oddershede, L. B. & Sørensen, Michael Askvad, 2012, In: Nucleic Acids Research. 40, 1, p. 303-313 11 p.

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

  36. 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

  37. 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

  38. Published

    Current and emerging approaches to define intestinal epithelium-specific transcriptional networks

    Olsen, A. K., Boyd, M., Danielsen, E. T. & Troelsen, J. T., Feb 2012, In: American Journal of Physiology: Gastrointestinal and Liver Physiology. 302, 3, p. G277-86

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

  39. 2013
  40. Published

    SigniSite: identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments

    Jessen, L. E., Hoof, I., Lund, O. & Nielsen, M., 2013, In: Nucleic Acids Research. 41, W1, p. W286-W291 6 p.

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

  41. Published

    A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies: [plus] Erratum

    Cao, H., Wang, Y., Zhang, W., Chai, X., Zhang, X., Chen, S., Yang, F., Zhang, C., Guo, Y., Liu, Y., Tang, Z., Chen, C., Xue, Y., Zhen, H., Xu, Y., Rao, B., Liu, T., Zhao, M., Zhang, W., Li, Y. & 6 others, Zhang, X., Tellier, L. C. A. M., Krogh, Anders, Kristiansen, Karsten, Wang, J. & Li, J., 2013, In: Human Mutation. 34, 12, p. 1715-1720 6 p.

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

  42. Published

    A simple probabilistic model of multibody interactions in proteins

    Johansson, Kristoffer Enøe & Hamelryck, Thomas Wim, 2013, In: Proteins: Structure, Function, and Bioinformatics. 81, 8, p. 1340-1350 11 p.

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

  43. Published

    A study of bacterial gene regulatory mechanisms: Dynamic features of gene regulatory mechanisms in EscherichEia coli and small RNA post-transcriptional regulation in Vibrio cholerae

    Hansen, S., 2013, Department of Biology, Faculty of Science, University of Copenhagen. 134 p.

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

  44. Published

    Acute Genome-wide effects of Rosiglitazone on PPARγ transcriptional networks in Adipocytes

    Haakonsson, A. K., Madsen, M. S., Nielsen, R., Sandelin, Albin Gustav & Mandrup, S., 2013, In: Molecular Endocrinology. 27, 9, p. 1536-1549 14 p.

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

  45. Published

    Alterations in polyadenylation and its implications for endocrine disease

    Rehfeld, Anders Aagaard, Plass, M., Krogh, Anders & Friis-Hansen, Lennart Jan, 2013, In: Frontiers in Endocrinology. 4, 23 p., 53.

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

  46. Published

    BlockLogo: visualization of peptide and sequence motif conservation

    Olsen, L. R., Kudahl, U. J., Simon, C., Sun, J., Schönbach, C., Reinherz, E. L., Zhang, G. L. & Brusic, V., 2013, In: Journal of Immunological Methods. 400-401, p. 37-44 8 p.

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

  47. Published

    Body fluid identification of blood, saliva and semen using second generation sequencing of micro-RNA

    Petersen, C. H., Hjort, B. B., Tvedebrink, T., Kielpinski, L. J., Vinther, Jeppe & Morling, Niels, 2013, In: Forensic Science International: Genetics Supplement Series. 4, 1, p. e204-5 2 p.

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

  48. Published

    Bringing genetic diversity to the forefront of conservation policy and management

    Hoban, S. M., Hauffe, H. C., Pérez-Espona, S., Arntzen, J. W., Bertorelle, G., Bryja, J., Frith, K., Gaggiotti, O. E., Galbusera, P., Godoy, J. A., Hoelzel, A. R., Nichols, R. A., Primmer, C. R., Russo, I., Segelbacher, G., Siegismund, Hans Redlef, Sihvonen, M., Vernesi, C., Vilà, C. & Bruford, M. W., 2013, In: Conservation Genetics Resources. 5, 2, p. 593-598 6 p.

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

  49. Published

    Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data

    Korneliussen, Thorfinn Sand, Moltke, Ida, Albrechtsen, Anders & Nielsen, Rasmus, 2013, In: B M C Bioinformatics. 14, 14 p., 289.

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

  50. Published

    Combining the multicanonical ensemble with generative probabilistic models of local biomolecular structure

    Frellsen, J., Hamelryck, Thomas Wim & Ferkinghoff-Borg, J., 2013, Proceedings of the 59th World Statistics Congress of the International Statistical Institute, 2013 . Hague, p. 139-144 6 p.

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

  51. Published

    Conservation genetic resources for effective species survival (ConGRESS): bridging the divide between conservation research and practice

    Hoban, S., Arntzen, J. W., Bertorelle, G., Bryja, J., Fernandes, M., Frith, K., Gaggiotti, O., Galbusera, P., Godoy, J. A., Hauffe, H. C., Hoelzel, A. R., Nichols, R. A., Perez-Espona, S., Primmer, C., Russo, I-R. M., Segelbacher, G., Siegismund, H. R., Sihvonen, M., Sjogren-Gulve, P., Vernesi, C. & 2 others, Vila, C. & Bruford, M. W., 2013, In: Journal for Nature Conservation. 21, 6, p. 433-437 5 p.

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

  52. Published

    Detection of Active Matriptase using a Biotinylated Chloromethyl Ketone Peptide

    Godiksen, S., Soendergaard, C., Friis, S., Jensen, J. K., Lange, Jette Bornholdt, Sales, K. U., Huang, M., Bugge, T. H. & Vogel, Lotte, 2013, In: P L o S One. 8, 10, 10 p., e77146.

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

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