Computational and RNA Biology

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  1. Published

    Disease-linked mutations cause exposure of a protein quality control degron

    Kampmeyer, Caroline, Larsen-Ledet, Sven, Wagnkilde, M. R., Michelsen, M., Iversen, Henriette Kring Mangor, Nielsen, S. V., Lindemose, Søren, Caregnato, A., Ravid, T., Stein, Amelie, Teilum, Kaare, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2022, In: Structure. 30, 9, p. 1245-1253.e5

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

  2. Published

    Disorder in a two-domain neuronal Ca2+-binding protein regulates domain stability and dynamics using ligand mimicry

    Staby, L., Kemplen, K. R., Stein, Amelie, Ploug, Michael, Clarke, J., Skriver, Karen, Heidarsson, P. O. & Kragelund, Birthe Brandt, 2021, In: Cellular and molecular life sciences : CMLS. 78, p. 2263-2278 16 p.

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

  3. Published

    Dispersal mediated coexistence of mud snails (Hydrobiidae) in an estuary

    Siegismund, Hans Redlef & Hylleberg, J., 1987, In: Marine Biology. 94, p. 395-402

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

  4. Published

    Dissecting the target specificity of RNase H recruiting oligonucleotides using massively parallel reporter analysis of short RNA motifs

    Rukov, J. L., Hagedorn, P. H., Høy, I. B., Feng, Y., Lindow, M. & Vinther, Jeppe, 2015, In: Nucleic Acids Research. 43, 17, p. 8476-8487 12 p.

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

  5. Published

    DivA: detection of non-homologous and very divergent regions in protein sequence alignments

    Zepeda Mendoza, M. L., Nygaard, S. & Rodrigues da Fonseca, Rute Andreia, 2014, In: BMC Research Notes. 7, 806, 6 p., 806.

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

  6. Published

    Diverse bacterial genomes encode an operon of two genes, one of which is a unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons

    Baranov, P., Vestergaard, Bente, Hamelryck, Thomas Wim, Gesteland, Nyborg, J. & Atking, J., 2006, In: Biology Direct. 13, p. 1-28 28 p.

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

  7. Published

    Diversity and transboundary mobility of serotype O foot-and-mouth disease virus in East Africa: implications for vaccination policies

    Balinda, S., Sangula, A. K., Heller, Rasmus, Muwanika, V. B., Belsham, G., Masembe, C. & Siegismund, Hans Redlef, 1 Oct 2010, In: Infection, Genetics and Evolution. 10, 7, p. 1058-65 8 p.

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

  8. Published

    Diversity of nature's assembly lines - recent discoveries in non-ribosomal peptide synthesis

    Payne, J. A. E., Schoppet, M., Hansen, M. H. & Cryle, M. J., 2017, In: Molecular BioSystems. 13, 1, p. 9-22 14 p.

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

  9. Published

    Dominance of a clonal green sulfur bacterial population in a stratified lake

    Gregersen, Lea Haarup, Habicht, K. S., Peduzzi, S., Tonolla, M., Canfield, D. E., Miller, M., Cox, R. P. & Frigaard, Niels-Ulrik, 2009, In: FEMS Microbiology Ecology. 70, 1, p. 30-41 12 p.

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

  10. Published

    Down-regulation of miR-129-5p and the let-7 family in neuroendocrine tumors and metastases leads to up-regulation of their targets Egr1, G3bp1, Hmga2 and Bach1

    Døssing, K. B. V., Binderup, Tina, Kaczkowski, B., Jacobsen, A. M. B., Rossing, M., Winther, O., Federspiel, B., Knigge, Ulrich, Kjær, Andreas & Friis-Hansen, L., 2015, In: Genes. 6, 1, p. 1-21 21 p.

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

  11. 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

  12. Published

    DoxoDB: A Database for the Expression Analysis of Doxorubicin-Induced lncRNA Genes

    Distefano, R., Ilieva, M., Madsen, J. H., Rennie, Sarah & Uchida, S., 2023, In: Non-coding RNA. 9, 4, 24 p., 39.

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

  13. Published

    Drosha regulates gene expression independently of RNA cleavage function

    Gromak, N., Dienstbier, M., Macias, S., Plass, M., Eyras, E., Cáceres, J. F. & Proudfoot, N. J., 2013, In: Cell Reports. 5, 6, p. 1499-510 12 p.

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

  14. 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

  15. Published

    ERG Controls B Cell Development by Promoting Igh V-to-DJ Recombination

    Søndergaard, E., Rauch, A., Michaut, Magali, Rapin, N., Rehn, M., Wilhelmson, Anna, Camponeschi, A., Hasemann, M. S., Bagger, F. O., Jendholm, J., Knudsen, K. J., Mandrup, S., Mårtensson, I. L. & Porse, Bo Torben, 26 Nov 2019, In: Cell Reports. 29, 9, p. 2756-2769.e6 21 p.

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

  16. Published

    ERG promotes the maintenance of hematopoietic stem cells by restricting their differentiation

    Knudsen, K. J., Rehn, M. C., Hasemann, M. S., Rapin, N. P. J., Bagger, F. O., Ohlsson, E. K., Willer, A., Frank, Anne-Katrine, Søndergaard, E., Jendholm, L. J., Thorén, L. A. M., Lee, J., Rak, J., Theilgaard-Mønch, Kim & Porse, Bo Torben, 2015, In: Genes & Development. 29, p. 1915-1929 15 p.

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

  17. Published

    EZH2 is a potential therapeutic target for H3K27M-mutant pediatric gliomas

    Mohammad, F., Weissmann, S., Leblanc, B. O., Pandey, D. P., Højfeldt, J. W., Comet, I., Zheng, C., Johansen, Jens Vilstrup, Rapin, N. P. J., Porse, Bo Torben, Tvardovskiy, A., Jensen, O. N., Olaciregui, N. G., Lavarino, C., Suñol, M., de Torres, C., Mora, J., Carcaboso, A. M. & Helin, K., Apr 2017, In: Nature Medicine. 23, 4, p. 483-492 10 p.

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

  18. Published

    EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance

    Larsen, T. S. & Krogh, Anders, 2003, In: BMC Bioinformatics. 4(1), p. 21

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

  19. Published

    Editorial: Long-read sequencing—Pitfalls, benefits and success stories

    Wohlers, I., Garg, S. & Hehir-Kwa, J. Y., 2023, In: Frontiers in Genetics. 13, 3 p., 1114542.

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

  20. Published

    Effect of alkaline treatment on bacteriochlorophyll a, quinones, and energy transfer in chlorosomes from Chlorobium tepidum and Chlorobium phaeobacteroides

    van Walree, C. A., Sakuragi, Y., Steensgaard, D. B., Bösinger, C. S., Frigaard, Niels-Ulrik, Cox, R. P., Holzwarth, A. R. & Miller, M., 1999, In: Photochemistry and Photobiology. 69, p. 322-328 7 p.

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

  21. Published

    Effect of chronic uremia on the transcriptional profile of the calcified aorta analyzed by RNA sequencing

    Rukov, J. L., Gravesen, Eva, Mace, M. L., Hofman-Bang, J., Vinther, Jeppe, Andersen, C. B., Lewin, E. & Ølgaard, Klaus, 2016, In: American Journal of Physiology: Renal Physiology. 310, 6, p. F477-F491 18 p.

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

  22. Published

    Effect of ecological and anthropogenic factors on grouping patterns in African lions across Kenya

    Chege, M., Bertola, Laura, De Snoo, G. R., Ngene, S., Otieno, T., Amoke, I., van 't Zelfde, M., Dolrenry, S., Broekhuis, F., Tamis, W., De Iongh, H. H. & Elliot, N. B., 2024, In: Ecology and Evolution. 14, 2, 14 p., e10982.

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

  23. Published

    Effect of energy metabolism on protein motility in the bacterial outer membrane

    Ryder, T. W., Xu, L., Berg-Sørensen, K., Brown, Stanley & Oddershede, L. B., 2009, In: Biophysical Journal. 97, 5, p. 1305-1312 8 p.

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

  24. Published

    Effect of supercoiling on the λ switch

    Norregaard, K., Andersson, M., Sneppen, Kim, Nielsen, Peter E., Brown, Stanley & Oddershede, L. B., 1 Jan 2014, In: Bacteriophage. 4, 2, p. 1-5 5 p., e27517.

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

  25. 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

  26. Published

    Efficient Generative Modelling of Protein Structure Fragments using a Deep Markov Model

    Thygesen, Christian Bahne, Al-Sibahi, A. S., Steenmanns, C. S., Sanz Moreta, Lys, Sørensen, A. B. & Hamelryck, Thomas Wim, 2021, International Conference on Machine Learning, 18-24 July 2021, Virtual. PMLR, p. 10258-10267 (Proceedings of Machine Learning Research, Vol. 139).

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

  27. Published

    Efficient approaches for large-scale GWAS with genotype uncertainty

    Jørsboe, E. & Albrechtsen, Anders, 2022, In: G3: Genes, Genomes, Genetics (Bethesda). 12, 1, 9 p., jkab385.

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

  28. Published

    Efficient statistical and computational methods for large scale sequencing data

    Li, Zilong, 2024, Department of Biology, Faculty of Science, University of Copenhagen. 149 p.

    Research output: Book/Report › Doctoral thesis › Research

  29. 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

  30. Published

    Eight millennia of matrilineal genetic continuity in the South Caucasus

    Margaryan, Ashot, Derenko, M., Hovhannisyan, H., Malyarchuk, B., Heller, Rasmus, Khachatryan, Z., Avetisyan, P., Badalyan, R., Bobokhyan, A., Melikyan, V., Sargsyan, G., Piliposyan, A., Simonyan, H., Mkrtchyan, R., Denisova, G., Yepiskoposyan, L., Willerslev, Eske & Allentoft, Morten Erik, 10 Jul 2017, In: Current Biology. 27, 13, p. 2023-2028 6 p.

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

  31. Published

    Electronic energy transfer involving carotenoid pigments in chlorosomes of two green bacteria: Chlorobium tepidum and Chloroflexus aurantiacus

    Melø, T. B., Frigaard, Niels-Ulrik, Matsuura, K. & Razi Naqvi, K., 2000, In: Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 56, 10, p. 2001-2010 10 p.

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

  32. Published

    Embryonic expression of Drosophila IMP in the developing CNS and PNS

    Adolph, S. K., Delotto, R., Nielsen, Finn Cilius & Christiansen, Jan, 2008, In: Gene Expression Patterns. 9, 3, p. 138-143 5 p.

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

  33. Published

    Emergence and radiation of distemper viruses in terrestrial and marine mammals

    Stokholm, Iben, Puryear, W., Sawatzki, K., Knudsen, Steen Wilhelm, Terkelsen, Thilde Bagger, Becher, P., Siebert, U. & Olsen, Morten Tange, 2021, In: Proceedings of the Royal Society B: Biological Sciences. 288, 1961, 9 p., 20211969.

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

  34. Published

    Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells

    Bakoulis, Stylianos, Krautz, Robert, Alcaraz, N., Salvatore, Marco & Andersson, Robin, 2022, In: Nucleic acids symposium series. 50, 4, p. 2111-2127 17 p., 088.

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

  35. Published

    Engineered iron oxide adhesion mutants of the lambda-receptor

    Brown, Stanley, 1992, In: Proceedings of the National Academy of Science of the United States of America. 89, p. 8651-8655

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

  36. Published

    Enhancer and Transcription Factor Dynamics during Myeloid Differentiation Reveal an Early Differentiation Block in Cebpa null Progenitors

    Pundhir, Sachin, Bratt Lauridsen, F. K., Schuster, Mikkel Bruhn, Jakobsen, J. S., Ge, Y., Schoof, E. M., Rapin, N. P. J., Waage, J., Hasemann, M. S. & Porse, Bo Torben, 2018, In: Cell Reports. 23, 9, p. 2744-2757 14 p.

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

  37. Published

    Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning

    Xiang, X., Corsi, G. I., Anthon, C., Qu, K., Pan, X., Liang, X., Han, P., Dong, Z., Liu, L., Zhong, J., Ma, T., Wang, J., Zhang, X., Jiang, H., Xu, F., Liu, X., Xu, X., Wang, J., Yang, H., Bolund, L. & 4 others, Church, G. M., Lin, L., Gorodkin, Jan & Luo, Y., 2021, In: Nature Communications. 12, 1, 9 p., 3238.

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

  38. Published

    Enterococcus faecalis infection causes inflammation, intracellular oxphos-independent ROS production, and DNA damage in human gastric cancer cells

    Strickertsson, J. A. B., Desler, Claus, Martin-Bertelsen, T., Machado, A. M. D., Wadstrøm, T., Winther, Ole, Rasmussen, Lene Juel & Friis-Hansen, Lennart Jan, 2013, In: PLOS ONE. 8, 4, p. 1-13 13 p., e63147.

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

  39. Published

    Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts

    Boomsma, Wouter, Tian, P., Frellsen, J., Ferkinghoff-Borg, J., Hamelryck, Thomas Wim, Lindorff-Larsen, Kresten & Vendruscolo, M., 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 38, p. 13852-13857 6 p.

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

  40. 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

  41. Published

    Escherichia coli phnN, encoding ribose 1,5-bisphosphokinase activity (phosphoribosyl diphosphate forming): dual role in phosphonate degradation and NAD biosynthesis pathways.

    Hove-Jensen, B., Rosenkrantz, T. J., Haldimann, A. & Wanner, B. L., 2003, In: Journal of Bacteriology. 185, 9, p. 2793-801 8 p.

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

  42. Published

    Estimating IBD tracts from low coverage NGS data

    Vieira, Filipe Garrett, Albrechtsen, Anders & Nielsen, Rasmus, 2016, In: Bioinformatics. 32, 14, p. 2096-2102 7 p.

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

  43. Published

    Estimating admixture pedigrees of recent hybrids without a contiguous reference genome

    Garcia Erill, Genís, Hanghøj, Kristian Ebbesen, Heller, Rasmus, Wiuf, Carsten & Albrechtsen, Anders, 2023, In: Molecular Ecology Resources. 23, 7, p. 1604-1619 16 p.

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

  44. Published

    Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation

    Vieira, Filipe Garrett, Fumagalli, M., Albrechtsen, Anders & Nielsen, Rasmus, 2013, In: Genome Research. 23, p. 1852-1861 10 p.

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

  45. Published

    Estimating individual admixture proportions from next generation sequencing data

    Skotte, L., Korneliussen, Thorfinn Sand & Albrechtsen, Anders, Nov 2013, In: Genetics. 195, 3, p. 693-702 10 p.

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

  46. Published

    Estimating narrow-sense heritability using family data from admixed populations

    Athanasiadis, G., Speed, D., Lepola, Mette Andersen, Appel, E. V. R., Grarup, Niels, Brandslund, I., Jørgensen, M. E., Larsen, C. V. L., Bjerregaard, P., Hansen, Torben & Albrechtsen, Anders, 2020, In: Heredity. 124, 6, p. 751-762 12 p.

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

  47. Published

    Estimating the timing of multiple admixture pulses during local ancestry inference

    Medina, P., Thornlow, B., Nielsen, Rasmus & Corbett-Detig, R., 2018, In: Genetics. 210, 3, p. 1089-1107 19 p.

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

  48. 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

  49. Published

    Estimation of site frequency spectra from low-coverage sequencing data using stochastic EM reduces overfitting, runtime, and memory usage

    Rasmussen, Malthe Sebro, Garcia Erill, Genís, Korneliussen, Thorfinn Sand, Wiuf, Carsten & Albrechtsen, Anders, 2022, In: Genetics. 222, 4, 15 p., iyac148.

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

  50. Published

    Estimation of the covariance structure from SNP allele frequencies

    van Waaij, J., Li, Z. & Wiuf, Carsten, 2022, In: Statistical Applications in Genetics and Molecular Biology. 21, 1, 20 p., 20220005.

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

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