Computational and RNA Biology

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  1. Published

    CTCF-KDM4A complex correlates with histone modifications that negatively regulate CHD5 gene expression in cancer cell lines

    Guerra-Calderas, L., González-Barrios, R., Patiño, C. C., Alcaraz, N., Salgado-Albarrán, M., de León, D. C., Hernández, C. C., Sánchez-Pérez, Y., Maldonado-Martínez, H. A., De la Rosa-Velazquez, I. A., Vargas-Romero, F., Herrera, L. A., García-Carrancá, A. & Soto-Reyes, E., 2018, In: OncoTarget. 9, 24, p. 17028-17042 15 p.

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

  2. Published

    Population size and social structure of lions in a west African protected area

    Gueye, M., Pellaton, R., Van Cauteren, D., Mengual, L., Van Dongen, S., Leirs, H., Bertola, Laura, Faye, P. M., Diop, B., Diop, M. M., Kanté, A. & de Iongh, H., 2024, In: African Journal of Ecology. 62, 1, 11 p., e13226.

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

  3. Published

    Conflicts between large carnivores and local pastoralists around Niokolo Koba National Park, Senegal

    Gueye, M., Van Cauteren, D., Mengual, L., Pellaton, R., Leirs, H., Bertola, Laura & de Iongh, H., 2022, In: European Journal of Wildlife Research. 68, 1, 11 p., 9.

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

  4. Published

    Identifying the genetic causes of phenotypically diagnosed Pakistani mucopolysaccharidoses patients by whole genome sequencing

    Gul, Rutaba, Firasat, S., Schubert, Mikkel, Ullah, A., Peña, E., Thuesen, Anne Cathrine Baun, Hussain, M., Stæger, Frederik Filip Vinggaard, Gjesing, A. P., Albrechtsen, Anders & Hansen, Torben, 2023, In: Frontiers in Genetics. 14, 13 p., 1128850.

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

  5. Published

    Requirement of a deeply conserved ARGONAUTE phospho-cluster for target- mediated microRNA degradation in plants

    Guo, F., 2022, Department of Biology, Faculty of Science, University of Copenhagen. 118 p.

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

  6. Published

    YeastFab: The design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae

    Guo, Y., Dong, J., Zhou, T., Auxillos, Jamie Yam, Li, T., Zhang, W., Wang, L., Shen, Y., Luo, Y., Zheng, Y., Lin, J., Chen, G. Q., Wu, Q., Cai, Y. & Dai, J., 27 Apr 2015, In: Nucleic Acids Research. 43, 13, p. e88

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

  7. Published

    BloodSpot 3.0: a database of gene and protein expression data in normal and malignant haematopoiesis

    Gíslason, M. H., Demircan, G. S., Prachar, Marek, Furtwängler, Benjamin, Schwaller, J., Schoof, E., Porse, Bo Torben, Rapin, N. & Bagger, F., 2024, In: Nucleic acids symposium series. 52, D1, p. D1138–D1142 5 p.

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

  8. 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

  9. Published

    Interactions between Barley a-Amylases, Substrates, Inhibitors and Regulatory Proteins

    Hachem, M. A., Bozonnet, S., Willemoës, Martin, Bønsager, B. C., Nielsen, M. M., Fukuda, K., Kramhøft, B., Maeda, K., Sigurskjold, B. W., Hägglund, P., Finnie, C., Mori, H., Robert, X., Jensen, M. H., Tranier, S., Aghajari, N., Haser, R. & Svensson, B., 2006, In: Journal of Applied Glycoscience. 53, 2, p. 163-169

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

  10. Published

    FoxA1 in synergy with IFNβ controls PDL1 expression in anti-inflammatory T cells via binding to a 60-nucleotide region in the Pdl1 promoter

    Hadi, M., Rasmussen, L. M., Kosicki, M., Carlsson, R. & Issazadeh-Navikas, Shohreh, Oct 2018, p. 596-597.

    Research output: Contribution to conference › Conference abstract for conference › Research

  11. Published

    Ancient DNA reveals late survival of mammoth and horse in interior Alaska

    Haile, James Seymour, Froese, D. G., Macphee, R. D. E., Roberts, R. G., Arnold, L. J., Reyes, A. V., Rasmussen, M., Nielsen, Rasmus, Brook, B. W., Robinson, S., Demuro, M., Gilbert, M Thomas P, Munch, K., Austin, J. J., Cooper, A., Barnes, I., Möller, P. & Willerslev, Eske, 2009, In: Proceedings of the National Academy of Science of the United States of America. 106, 52, p. 22352-7 5 p.

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

  12. 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

  13. Published

    Probabilistic models and machine learning in structural bioinformatics

    Hamelryck, Thomas Wim, 2009, In: Statistical Methods in Medical Research. 18, 5, p. 505-26 21 p.

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

  14. 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

  15. Published

    Proteins, physics and probability kinematics: a Bayesian formulation of the protein folding problem

    Hamelryck, Thomas Wim, Boomsma, Wouter, Ferkinghoff-Borg, J., Foldager, J. I., Frellsen, J., Haslett, J. & Theobald, D., 2015, Geometry driven statistics. Dryden, I. L. & Kent, J. T. (eds.). Wiley, p. 356-376 21 p.

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

  16. 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

  17. 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

  18. Published

    Expression of IGF-II mRNA-binding proteins (IMPs) in gonads and testicular cancer

    Hammer, N. A., Hansen, Thomas van Overeem, Byskov, A. G., Rajpert-De Meyts, E., Grøndahl, M. L., Bredkjaer, H. E., Wewer, Ulla M., Christiansen, Jan & Nielsen, Finn Cilius, 2005, In: Reproduction. 130, 2, p. 203-12 10 p.

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

  19. Published

    Investigating the possible function of DCL2 as a viral RNA sensor in Arabidopsis

    Han, L., 2019, Department of Biology, Faculty of Science, University of Copenhagen.

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

  20. Published

    DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage

    Hanghøj, Kristian Ebbesen, Renaud, Gabriel, Albrechtsen, Anders & Orlando, L., 2019, In: GigaScience. 8, 4, 6 p., giz025.

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

  21. Published

    Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding

    Hanghøj, Kristian Ebbesen, Moltke, Ida, Andersen, P. A., Manica, A. & Korneliussen, Thorfinn Sand, May 2019, In: GigaScience. 8, 5, 9 p., giz034.

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

  22. Published

    Genomic investigations of horse domestication using ancient DNA and a novel statistical method for epigenomic inference from ancient DNA sequencing data

    Hanghøj, Kristian Ebbesen, 2018, Department of Biology, Faculty of Science, University of Copenhagen.

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

  23. 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

  24. Published

    H3K9 dimethylation safeguards cancer cells against activation of the interferon pathway

    Hansen, A. M., Ge, Y., Schuster, Mikkel Bruhn, Pundhir, Sachin, Jakobsen, J. S., Kalvisa, A., Tapia, Marta Cecylia, Gordon, Sandra, Ambri, F., Bagger, F. O., Pandey, D., Helin, K. & Porse, Bo Torben, 2022, In: Science Advances. 8, 11, eabf8627.

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

  25. Published

    The Muskox Lost a Substantial Part of Its Genetic Diversity on Its Long Road to Greenland

    Hansen, C. C. R., Hvilsom, C., Schmidt, N. M., Aastrup, P., de Groot, P. J. V. C., Siegismund, Hans Redlef & Heller, Rasmus, 2018, In: Current Biology. 28, 24, p. 4022-4028, e1-e5

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

  26. Published

    Genomic diversity and differentiation between island and mainland populations of white-tailed eagles (Haliaeetus albicilla)

    Hansen, C. C. R., Láruson, Á. J., Rasmussen, Jacob Agerbo, Ballesteros, J. A. C., Sinding, Mikkel Holger Strander, Hallgrimsson, G. T., von Schmalensee, M., Stefansson, R. A., Skarphédinsson, K. H., Labansen, A. L., Leivits, M., Sonne, C., Dietz, R., Skelmose, K., Boertmann, D., Eulaers, I., Martin, M. D., Helgason, A. S., Gilbert, M Thomas P & Pálsson, S., 2023, In: Molecular Ecology. 32, 8, p. 1925-1942 18 p.

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

  27. Published

    Cardiovascular Autonomic Neuropathy in Type 1 Diabetes Is Associated With Disturbances in TCA, Lipid, and Glucose Metabolism

    Hansen, C. S., Suvitaival, T., Theilade, Karen Simone, Mattila, I., Lajer, M., Trošt, K., Ahonen, L., Hansen, T. W., Legido-Quigley, C., Rossing, Peter & Ahluwalia, Tarun Veer Singh, 2022, In: Frontiers in Endocrinology. 13, 831793.

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

  28. Published

    Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation

    Hansen, H. T., Rasmussen, S. H., Adolph, S. K., Plass, M., Krogh, Anders, Sanford, J., Nielsen, Finn Cilius & Christiansen, Jan, 2015, In: Genome Biology (Online Edition). 16, 16 p., 123.

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

  29. 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

  30. Published

    Effects of Four Different Regulatory Mechanisms on the Dynamics of Gene Regulatory Cascades

    Hansen, S., Krishna, S., Semsey, S. & Svenningsen, Sine Lo, 17 Jul 2015, In: Scientific Reports. 5, 12186.

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

  31. 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

  32. Published

    Between inflammation, homeostasis and adaptation: Systemic and tissue-specific responses to maternal immune activation

    Hansen, Signe Schmidt Kjølner, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 177 p.

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

  33. Published

    A common Greenlandic Inuit BRCA1 RING domain founder mutation

    Hansen, T. V. O., Ejlertsen, Bent Laursen, Albrechtsen, Anders, Bergsten, E., Bjerregaard, P., Hansen, T., Myrhoj, T., Nielsen, P. B., Timmermans-Wielenga, V., Andersen, M. K., Jonson, L. & Nielsen, F. C., 2009, In: Breast Cancer Research and Treatment. 115, 1, p. 69-76 7 p.

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

  34. Published

    Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting.

    Hansen, T. M., Reihani, S. N. S., Oddershede, L. B. & Sørensen, Michael Askvad, 2007, In: Proceedings of the National Academy of Science of the United States of America. 104, 14, p. 5830-5 5 p.

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

  35. Published

    Dwarfism and impaired gut development in insulin-like growth factor II mRNA-binding protein 1-deficient mice

    Hansen, Thomas van Overeem, Hammer, N. A., Nielsen, J., Madsen, Mette, Dalbaeck, C., Wewer, Ulla M., Christiansen, Jan & Nielsen, Finn Cilius, 2004, In: Molecular and Cellular Biology. 24, 10, p. 4448-64 17 p.

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

  36. Published

    Large BRCA1 and BRCA2 genomic rearrangements in Danish high risk breast-ovarian cancer families

    Hansen, Thomas van Overeem, Jønson, L., Albrechtsen, Anders, Andersen, M. K., Ejlertsen, Bent Laursen & Nielsen, Finn Cilius, May 2009, In: Breast Cancer Research and Treatment. 115, 2, p. 315-323 9 p.

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

  37. E-pub ahead of print

    High N6-methyladenosine-activated TCEAL8 mRNA is a novel pancreatic cancer marker

    Hara, T., Meng, S., Sato, H., Tatekawa, S., Sasaki, K., Takeda, Y., Tsuji, Y., Arao, Y., Ofusa, K., Kitagawa, T., Yamada, D., Takahashi, H., Kobayashi, S., Motooka, D., Suzuki, Y., Rennie, S., Uchida, S., Mori, M., Ogawa, K., Doki, Y. & 2 others, Eguchi, H. & Ishii, H., 2024, (E-pub ahead of print) In: Cancer Science.

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

  38. 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

  39. 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

  40. Published

    Exploring the conformational space of proteins using probabilistic models

    Harder, T. P., 2011

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

  41. 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

  42. Published

    Inferring demographic history from a spectrum of shared haplotype lengths

    Harris, K. & Nielsen, Rasmus, 2013, In: P L o S Genetics. 9, 6, 20 p., e1003521.

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

  43. Published

    Error-prone polymerase activity causes multinucleotide mutations in humans

    Harris, K. & Nielsen, Rasmus, 1 Sep 2014, In: Genome Research. 24, 9, p. 1445-1454 10 p.

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

  44. Published

    C/EBPα Is Required for Long-Term Self-Renewal and Lineage Priming of Hematopoietic Stem Cells and for the Maintenance of Epigenetic Configurations in Multipotent Progenitors

    Hasemann, M. S., Lauridsen, F. K. B., Waage, J., Jakobsen, J. S., Frank, Anne-Katrine, Schuster, Mikkel Bruhn, Rapin, N. P. J., Bagger, F. O., Hoppe, P. S., Schroeder, T. & Porse, Bo Torben, Jan 2014, In: P L o S Genetics (Online). 10, 1, p. 1-10 10 p., e1004079.

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

  45. Published

    Inbreeding and outbreeding effects on pollen fitness and zygote survival in Silene nutans (Caryophyllaceae)

    Hauser, T. P. & Siegismund, Hans Redlef, 2000, In: Journal of Evolutionary Biology. 13, p. 446-454 9 p.

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

  46. Published

    A fluorescent substrate for carbon-phosphorus lyase: towards the pathway for organophosphonate metabolism in bacteria

    He, S., Lou, Y., Hove-Jensen, B. & Zechel, D. L., 2009, In: Bioorganic & Medicinal Chemistry Letters. 19, 20, p. 5954-5957

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

  47. Published

    Quantitative Evaluation of Stem-like Markers of Human Glioblastoma Using Single-Cell RNA Sequencing Datasets

    He, Yue, Døssing, Kristina Benedikte V, Sloth, Ane Beth, He, Xuening, Rossing, M. & Kjær, Andreas, 2023, In: Cancers. 15, 5, 16 p., 1557.

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

  48. 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

  49. 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

  50. 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

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