Computational and RNA Biology

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  1. 2011
  2. 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

  3. Published

    Exploring the conformational space of proteins using probabilistic models

    Harder, T. P., 2011

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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. Published

    Probabilistic methods in macromolecular structure prediction

    Frellsen, J., 2011, Københavns Universitet.

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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 2012
  41. 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

  42. Published

    AdapterRemoval: easy cleaning of next generation sequencing reads

    Lindgreen, S., 2012, In: BMC Research Notes. 5, 337, 7 p., 337.

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

  43. 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

  44. Published

    An efficient null model for conformational fluctuations in proteins

    Harder, T. P., Bottaro, S., Boomsma, Wouter, Olsson, S., Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 2012, In: Structure. 20, 6, p. 1028-1039 12 p.

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

  45. Published

    An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes

    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. R., Liu, X., Gong, Z., Ji, F. & 15 others, Wang, X., Liu, B., Zhang, Y., Hou, J., Wang, J., Zhao, H., Wang, Y., Fang, X., Zhang, G., Wang, J., Zhang, X., Schierup, M. H., Du, H., Wang, J. & Wang, X., 2012, In: P L o S One. 7, 7, 13 p.

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

  46. Published

    Association testing for next-generation sequencing data using score statistics

    Skotte, L., Korneliussen, Thorfinn Sand & Albrechtsen, Anders, 2012, In: Genetic Epidemiology. 36, 5, p. 430-437 8 p.

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

  47. 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

  48. Published

    Biological systems on a small scale

    Pedersen, L., 2012, Center for Ice & Climate: Faculty of Science, University of Copenhagen. 184 p.

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

  49. Published

    Cape buffalo mitogenomics reveals a holocene shift in the African human-megafauna dynamics

    Heller, Rasmus, Brüniche-Olsen, A. & Siegismund, Hans Redlef, 2012, In: Molecular Ecology. 21, 16, p. 3947-3959 13 p.

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

  50. Published

    Comparative phylogeography of African savannah ungulates

    Lorenzen, Eline, Heller, Rasmus & Siegismund, Hans Redlef, 2012, In: Molecular Ecology. 21, 15, p. 3656-3670 15 p.

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

  51. Published

    Computational cancer biology: from carcinogenesis to metastasis

    Kaczkowski, B., 2012, Department of Biology, Faculty of Science, University of Copenhagen. 125 p.

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

  52. Published

    Cross-species ChIP-seq studies provide insights into regulatory strategies of PPAR¿ in adipocytes

    Schmidt, S. F., Jørgensen, M., Sandelin, Albin Gustav & Mandrup, S., 2012, In: Transcription. 3, 1, p. 19-24 6 p.

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

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