Computational and RNA Biology

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  1. Published

    Pigments and proteins in green bacterial chlorosomes studied by matrix-assisted laser desorption ionization mass spectrometry

    Persson, S., Sönksen, C. P., Frigaard, Niels-Ulrik, Cox, R. P., Roepstorff, P. & Miller, M., 2000, In: European Journal of Biochemistry. 267, 2, p. 450-456 7 p.

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

  2. Published

    Physiological responses of narwhals to anthropogenic noise: A case study with seismic airguns and vessel traffic in the Arctic

    Williams, T. M., Blackwell, S. B., Tervo, O., Garde, E., Sinding, Mikkel Holger Strander, Richter, B. & Heide-Jørgensen, M. P., 2022, In: Functional Ecology. 36, 9, p. 2251-2266 16 p.

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

  3. Published

    Physiological and Genetic Adaptations to Diving in Sea Nomads

    Ilardo, M. A., Moltke, Ida, Korneliussen, Thorfinn Sand, Cheng, J., Stern, A. J., Racimo, Fernando, Damgaard, P. D. B., Sikora, Martin, Seguin-Orlando, A., Rasmussen, Simon, van den Munckhof, I. C. L., ter Horst, R., Joosten, L. A. B., Netea, M. G., Salingkat, S., Nielsen, Rasmus & Willerslev, Eske, 2018, In: Cell. 173, 3, p. 569-580 12 p., e15.

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

  4. Published

    Physical activity attenuates postprandial hyperglycaemia in homozygous TBC1D4 loss-of-function mutation carriers

    Schnurr, T. M., Jørsboe, E., Chadt, A., Dahl-Petersen, I. K., Kristensen, Jonas Møller, Wojtaszewski, Jørgen F P, Springer, C., Bjerregaard, P., Brage, S., Pedersen, Oluf Borbye, Moltke, Ida, Grarup, Niels, Al-Hasani, H., Albrechtsen, Anders, Jørgensen, M. E. & Hansen, Torben, 2021, In: Diabetologia. 64, p. 1795-1804

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

  5. 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

  6. Published

    Phylogenetic ANOVA: the expression variance and evolution model for quantitative trait evolution

    Rohlfs, R. V. & Nielsen, Rasmus, 2015, In: Systematic Biology. 64, 5, p. 695-708 14 p.

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

  7. Published

    Pheophytinization of bacteriochlorophyll c and energy transfer in cells of Chlorobium tepidum

    Tokita, S., Hirota, M., Frigaard, Niels-Ulrik, Shimada, K. & Matsuura, K., 1999, In: Archives of Microbiology. 172, 1, p. 40-44 5 p.

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

  8. Published

    Pharmacology and optimization of thiopurines and methotrexate in inflammatory bowel disease

    Coskun, M., Steenholdt, Casper, de Boer, N. K. & Nielsen, Ole Haagen, 2016, In: Clinical Pharmacokinetics. 55, 3, p. 257-274 18 p.

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

  9. 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

  10. Published

    Pharmaco-miR: linking microRNAs and drug effects

    Rukov, J. L., Wilentzik, R., Jaffe, I., Vinther, Jeppe & Shomron, N., 2014, In: Briefings in Bioinformatics. 15, 4, p. 648-659 12 p.

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

  11. Published

    Phaistos user manual

    Boomsma, Wouter, Bottaro, S., Hamelryck, Thomas Wim, Frellsen, J., Andreetta, C., Borg, M., Harder, T., Johansson, Kristoffer Enøe, Stovgaard, K. & Tian, P., 2013, 90 p.

    Research output: Book/Report › Book › Education

  12. Published

    Personalized B cell response to the Lactobacillus rhamnosus GG probiotic in healthy human subjects: a randomized trial

    Lange, Jette Bornholdt, Chen, Y., Rago, Alfredo, Sloth, S., Hendel, J., Melsæther, C., Müller, C. V., Juul Nielsen, M., Strickertsson, J., Engelholm, Lars Henning, Vitting-Seerup, K., Jensen, Kim Bak, Baker, A. & Sandelin, Albin Gustav, 9 Nov 2020, In: Gut Microbes. 12, 1, p. 1-14 14 p.

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

  13. Published

    Persistent Topology of Protein Space

    Hamilton, W., Borgert, J. E., Hamelryck, Thomas Wim & Marron, J. S., 2022, Research in Computational Topology 2. Springer, p. 223-244 (Association for Women in Mathematics Series, Vol. 30).

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

  14. Published

    Performance characterization of PCR-free whole genome sequencing for clinical diagnosis

    Zhou, G., Zhou, M., Zeng, F., Zhang, N., Sun, Y., Qiao, Z., Guo, X., Zhou, S., Yun, G., Xie, J., Wang, X., Liu, F., Fan, C., Wang, Y., Fang, Z., Tian, Z., Dai, W., Sun, J., Peng, Z. & Song, L., 2022, In: Medicine. 101, 10, 8 p., e28972.

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

  15. Published

    Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality

    Pundhir, Sachin, Bagger, F. O., Lauridsen, F. K. B., Rapin, N. P. J. & Porse, Bo Torben, 2016, In: Nucleic Acids Research. 44, 9, p. 4037-4051 15 p.

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

  16. Published

    Patterns, risk factors and characteristics of reported and perceived foot-and-mouth disease (FMD) in Uganda

    Ayebazibwe, C., Tjørnehøj, K., Mwiine, F. N., Muwanika, V. B., Ademun Okurut, A. R., Siegismund, Hans Redlef & Alexandersen, S., 2010, In: Tropical Animal Health and Production. 42, 7, p. 1547-59 12 p.

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

  17. Published

    Pasteurella multocida toxin induces IL-6, but not IL-1 alpha or TNF alpha in fibroblasts.

    Rosendal, S., Frandsen, P. L., Nielsen, Jens Peter & Gallily, R., Apr 1995, In: Canadian journal of veterinary research = Revue canadienne de recherche vétérinaire. 59, 2, p. 154-156 3 p.

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

  18. 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

  19. Published

    Partial self-incompatibility in the polyploid endemic species Scalesia affinis (Asteraceae) from the Galápagos: remnants of a self-incompatibility system?

    Nielsen, Lene Rostgaard, Siegismund, Hans Redlef & PHILIPP, M., 1 May 2003, In: Botanical Journal of the Linnean Society. 142, 1, p. 93-101 9 p.

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

  20. Published

    Partial USH2A deletions contribute to Usher syndrome in Denmark

    Dad, S., Rendtorff, N. D., Kann, E., Albrechtsen, Anders, M. Mehrjouy, M., Bak, M., Tommerup, Niels, Tranebjærg, Lisbeth, Rosenberg, T., Jensen, H. & Møller, L. B., 2015, In: European Journal of Human Genetics. 23, p. 1646-1651 6 p.

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

  21. Published

    Parallel GPGPU Evaluation of Small Angle X-ray Scattering Profiles in a Markov Chain Monte Carlo Framework

    Antonov, L. D., Andreetta, C. & Hamelryck, Thomas Wim, 2013, Biomedical Engineering Systems and Technologies. Gabriel, J., Schier, J. & Huffel, S. V. (eds.). Springer Science+Business Media, Vol. 357. p. 222-235 14 p. (Communications in Computer and Information Science).

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

  22. Published

    Pan-African Genetic Structure in the African Buffalo (Syncerus caffer): Investigating Intraspecific Divergence

    Smitz, N., Berthouly, C., Cornélis, D., Heller, Rasmus, Hooft, P. V., Chardonnet, P., Caron, A., Prins, H., Vuuren, B. J. V., Iongh, H. D. & Michaux, J., 2013, In: P L o S One. 8, 2, p. 1-17 17 p., e56235.

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

  23. Published

    Palaeoproteomics identifies beaver fur in Danish high-status Viking Age burials - direct evidence of fur trade

    Brandt, Luise Ørsted, Taurozzi, Alberto John, Mackie, Meaghan, Sinding, Mikkel Holger Strander, Vieira, Filipe Garrett, Schmidt, A. L., Rimstad, C., Collins, Matthew James & Mannering, U., 2022, In: PLoS ONE. 17, 7, 14 p., e0270040.

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

  24. 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

  25. Published

    PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells

    Agrawal-Singh, S., Lerdrup, Mads, Gomes, A. R., van de Werken, H. J. G., Johansen, Jens Vilstrup, Andersson, Robin, Sandelin, Albin Gustav, Helin, K. & Hansen, K., 2019, In: eLife. 8, p. 1-32 32 p., e40364.

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

  26. Published

    PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure

    Boomsma, Wouter, Frellsen, J., Harder, T. P., Bottaro, S., Johansson, Kristoffer Enøe, Tian, P., Stovgaard, K., Andreetta, C., Olsson, S., Valentin, J., Antonov, L. D., Christensen, A. S., Borg, M., Jensen, Jan Halborg, Lindorff-Larsen, Kresten, Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 2013, In: Journal of Computational Chemistry. 34, 19, p. 1697-1705 9 p.

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

  27. Published

    PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave

    Thieffry, A., López Márquez, Diego, Lange, Jette Bornholdt, Gholami Malekroudi, M., Bressendorff, Simon, Barghetti, A., Sandelin, Albin Gustav & Brodersen, Peter, 2022, In: The Plant Cell. 34, 7, 23 p.

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

  28. Published

    Oxygen uncouples light absorption by the chlorosome antenna and photosynthetic electron transfer in the green sulfur bacterium Chlorobium tepidum

    Frigaard, Niels-Ulrik & Matsuura, K., 1999, In: BBA General Subjects. 1412, 2, p. 108-117 10 p.

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

  29. Published

    Overexpression of ATG8/LC3 enhances wound-induced somatic reprogramming in Physcomitrium patens

    Kanne, J. V., Ishikawa, M., Bressendorff, Simon, Ansbøl, Jeppe, Hasebe, M., Rodriguez, Eleazar & Petersen, Morten, 2022, In: Autophagy. 18, 6, p. 1463-1466 4 p.

    Research output: Contribution to journal › Comment/debate › Research › peer-review

  30. Published

    Orthologous proteins of experimental de- and remyelination are differentially regulated in the CSF proteome of multiple sclerosis subtypes

    Martin, N. A., Nawrocki, A., Molnar, V., Elkjaer, M. L., Thygesen, E. K., Palkovits, M., Acs, P., Sejbaek, T., Nielsen, H. H., Hegedus, Z., Sellebjerg, Finn Thorup, Molnar, T., Barbosa, E. G. V., Alcaraz, N., Gallyas, F. J., Svenningsen, A. F., Baumbach, J., Lassmann, H., Larsen, M. R. & Illes, Z., 2018, In: PLOS ONE. 13, 8, p. 1-26 e0202530.

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

  31. Published

    Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds

    Ji, Y., Feng, S., Wu, L., Fang, Q., Brüniche-Olsen, Anna, DeWoody, J. A., Cheng, Y., Zhang, D., Hao, Y., Song, G., Qu, Y., Suh, A., KU, thw266, Hackett, S. J. & Lei, F., 2022, In: Science Advances. 8, 35, 11 p., eabo0099.

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

  32. Published

    Origin and expansion of the world’s most widespread pinniped: Range-wide population genomics of the harbour seal (Phoca vitulina)

    Liu, X., Schjøtt, S. R., Granquist, S. M., Rosing-Asvid, A., Dietz, R., Teilmann, J., Galatius, A., Cammen, K., O’Corry-Crowe, G., Harding, K., Härkönen, T., Hall, A., Carroll, E. L., Kobayashi, Y., Hammill, M., Stenson, G., Kirstine Frie, A., Lydersen, C., Kovacs, K. M., Andersen, L. W. & 6 others, Hoffman, J. I., Goodman, S. J., Vieira, Filipe Garrett, Heller, Rasmus, Moltke, Ida & Olsen, Morten Tange, 2022, In: Molecular Ecology. 31, 6, p. 1682-1699

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

  33. Published

    Organismal benefits of transcription speed control at gene boundaries

    Leng, Xueyuan, Ivanov, M., Kindgren, P., Malik, I., Thieffry, A., Brodersen, Peter, Sandelin, Albin Gustav, Kaplan, C. D. & Marquardt, Sebastian, 2020, In: EMBO Reports. 21, 4, 16 p., e49315.

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

  34. Published

    Organism- and disease-specific atlases of transcription start sites using Cap Analysis of Gene Expression (CAGE)

    Thodberg, Malte, 2018, Department of Biology, Faculty of Science, University of Copenhagen.

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

  35. Published

    Oral health status in historic population: Macroscopic and metagenomic evidence

    Willmann, C., Mata, X., Hanghøj, Kristian Ebbesen, Tonasso, L., Tisseyre, L., Jeziorski, C., Cabot, E., Chevet, P., Crubézy, E., Orlando, L., Esclassan, R., Thèves, C. & Caramelli, D., 2018, In: PLOS ONE. 13, 5, 18 p., e0196482.

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

  36. Published

    Optimal Variance Control of the Score-Function Gradient Estimator for Importance Weighted Bounds

    Liévin, V., Dittadi, A., Christensen, Anders & Winther, Ole, 2020, In: Advances in Neural Information Processing Systems. 2020-December, 12 p.

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

  37. Published

    Opportunities and challenges of macrogenetic studies

    Leigh, D. M., van Rees, C. B., Millette, K. L., Breed, M. F., Schmidt, C., Bertola, Laura, Hand, B. K., Hunter, M. E., Jensen, E. L., Kershaw, F., Liggins, L., Luikart, G., Manel, S., Mergeay, J., Miller, J. M., Segelbacher, G., Hoban, S. & Paz-Vinas, I., 2021, In: Nature Reviews Genetics. 22, 12, p. 791-807 17 p.

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

  38. Published

    Oncogenic p95HER2 regulates Na+-HCO3- cotransporter NBCn1 mRNA stability in breast cancer cells via 3'UTR-dependent processes

    Gorbatenko, A., Olesen, C. W., Loebl, N., Sigurdsson, H. H., Bianchi, C., Pedraz Cuesta, E., Christiansen, Jan & Pedersen, Stine Helene Falsig, 2016, In: Biochemical Journal. 473, 21, p. 4027-4044 18 p.

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

  39. Published

    Oncogenic fusion proteins expressed in immature hematopoietic cells fail to recapitulate the transcriptional changes observed in human AML

    Rapin, N. & Porse, Bo Torben, 2014, In: Oncogenesis. 3, p. 1-5 5 p., e106.

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

  40. Published

    On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase

    Ienasescu, H., Li, K., Andersson, Robin, Vitezic, M., Rennie, Sarah, Chen, Y., Vitting-Seerup, K., Lagoni, E., Boyd, M., Lange, Jette Bornholdt, de Hoon, M. J. L., Kawaji, H., Lassmann, T., FANTOM Consortium, F. C., Hayashizaki, Y., Forrest, A. R. R., Carninci, P. & Sandelin, Albin Gustav, 2016, In: Database: The Journal of Biological Databases and Curation. 2016, 0, 10 p., baw144.

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

  41. Published

    On the total number of genes and their length distribution in complete microbial genomes

    Skovgaard, M., Jensen, Lars Juhl, Brunak, Søren, Ussery, D. & Krogh, Anders, 2001, In: Trends in Genetics. 17, 8, p. 425-8 4 p.

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

  42. Published

    On the origin of regulatory elements: Computational analyses of transposable elements in pluripotency and development

    Bakoulis, Stylianos, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 135 p.

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

  43. Published

    On the accuracy of short read mapping

    Menzel, K. P., Frellsen, J., Plass, M., Rasmussen, S. H. & Krogh, Anders, 2013, Deep Sequencing Data Analysis. Shomron, N. (ed.). Springer Science+Business Media, p. 39-59 21 p. (Methods in Molecular Biology, Vol. 1038).

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

  44. 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

  45. 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

  46. Published

    On detecting incomplete soft or hard selective sweeps using haplotype structure

    Ferrer-Admetlla, A., Liang, M., Korneliussen, Thorfinn Sand & Nielsen, Rasmus, 2014, In: Molecular Biology and Evolution. 31, 5, p. 1275-1291 17 p.

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

  47. Published

    Omega-3 fatty acids and risk of cardiovascular disease in Inuit: First prospective cohort study

    Senftleber, N. K., Albrechtsen, Anders, Lauritzen, Lotte, Larsen, C. L., Bjerregaard, P., Diaz, L. J., Rønn, P. F. & Jørgensen, M. E., 2020, In: Atherosclerosis. 312, p. 28-34 7 p.

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

  48. Published

    Om kvalitet i forskningen.

    Willemoës, Martin, 1999, In: Biozoom. 3

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

  49. Published

    Occurrence and Functions of m6A and Other Covalent Modifications in Plant mRNA

    Arribas Hernandez, Laura & Brodersen, Peter, 2020, In: Plant Physiology. 182, 1, p. 79-96 18 p.

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

  50. Published

    Når enzymer tøver - CTP - biosyntesen i mælkesyrebakterier

    Martinussen, J., Willemoës, Martin, Kilstrup, M., Jensen, P. R. & Hammer, K., 2005, In: Dansk Kemi. 86, 8, p. 20-22

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

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