Computational and RNA Biology

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  1. 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

  2. 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

  3. Published

    African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival

    Balboa, R. F., Bertola, L. D., Brüniche-Olsen, A., Rasmussen, M. S., Liu, X., Besnard, G., Salmona, J., Santander, C. G., He, S., Zinner, D., Pedrono, M., Muwanika, V., Masembe, C., Schubert, M., Kuja, J., Quinn, L., Garcia-Erill, G., Stæger, F. F., Rakotoarivony, R., Henrique, M. & 14 others, Lin, Long, Wang, X., Heaton, M. P., Smith, T. P. L., Hanghøj, Kristian Ebbesen, Sinding, Mikkel Holger Strander, Atickem, A., Chikhi, L., Roos, C., Gaubert, P., Siegismund, Hans Redlef, Moltke, Ida, Albrechtsen, Anders & Heller, Rasmus, 2024, In: Nature Communications. 15, 1, 15 p., 172.

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

  4. 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

  5. Published

    Molecular characterization of SAT 2 foot-and-mouth disease virus from post-outbreak slaughtered animals: implications for disease control in Uganda

    Balinda, S., Belsham, G., Masembe, C., Sangula, A. K., Siegismund, Hans Redlef & Muwanika, V. B., 1 Aug 2010, In: Epidemiology and Infection. 138, 8, p. 1204-10 7 p.

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

  6. 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

  7. Published

    UPF2-dependent nonsense-mediated mRNA decay pathway is essential for spermatogenesis by selectively eliminating longer 3'UTR transcripts

    Bao, J., Vitting-Seerup, K., Waage, J. E., Tang, C., Ge, Y., Porse, Bo Torben & Yan, W., 2016, In: P L o S Genetics. 12, 5, 24 p., e1005863.

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

  8. 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

  9. Published

    Genome sequence and effectorome of Moniliophthora perniciosa and Moniliophthora roreri subpopulations

    Barbosa, C. S., Rodrigues da Fonseca, Rute Andreia, Batista, T. M., Barreto, M. A., Argolo, C. S., de Carvalho, M. R., Jordao do Amaral, D. O., de Andrade Silva, E. M., Arevalo-Gardini, E., Hidalgo, K. S., Franco, G. R., Pirovani, C. P., Micheli, F. & Gramacho, K. P., 3 Jul 2018, In: BMC Genomics. 19, 12 p., 509.

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

  10. Published

    Heat-shock protein 40 is the key farnesylation target in meristem size control, abscisic acid signaling, and drought resistance

    Barghetti, A., Sjögren, L. L. E., Floris, M. H. J., Botterweg Paredes, E., Wenkel, Stephan & Brodersen, Peter, 15 Nov 2017, In: Genes & Development. 31, 22, p. 2282-2295 14 p.

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

  11. Published

    Investigating membrane-bound Argonaute functions in Arabidopsis

    Barghetti, A., 2017, Department of Biology, Faculty of Science, University of Copenhagen.

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

  12. Published

    CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information

    Bartoli, L., Fariselli, P., Krogh, Anders & Casadio, R., 2009, In: Bioinformatics. 25, 21, p. 2757-63 6 p.

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

  13. Published

    Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing

    Bataillon, T., Duan, J., Hvilsom, C., Jin, X., Li, Y., Skov, L., Glemin, S., Munch, K., Jiang, T., Qian, Y., Hobolth, A., Wang, J., Mailund, T., Siegismund, Hans Redlef & Schierup, M. H., 2015, In: Genome Biology and Evolution. 7, 4, p. 1122-1132 11 p.

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

  14. Published

    Proteomic Profiling of Colorectal Adenomas Identifies a Predictive Risk Signature for Development of Metachronous Advanced Colorectal Neoplasia

    Bech, J. M., Terkelsen, Thilde Bagger, Bartels, Annette Snejbjerg, Coscia, F., Doll, S., Zhao, S., Zhang, Z., Brünner, N., Lindebjerg, J., Madsen, G. I., Fang, X., Mann, Matthias & Moreira, José, 2023, In: Gastroenterology. 165, 1, p. 121-132.e5

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

  15. Published

    Guidelines for evaluating the conservation value of African lion (Panthera leo) translocations

    Becker, M. S., Almeida, J., Begg, C., Bertola, L., Breitenmoser, C., Breitenmoser, U., Coals, P., Funston, P., Gaylard, A., Groom, R., Henschel, P., Ikanda, D., Jorge, A., Kruger, J., Lindsey, P., Maimbo, H., Mandisodza-Chikerema, R., Maude, G., Mbizah, M., Miller, S. M. & 17 others, Mudongo, E., Mwape, H., Mweetwa, T., Naude, V., Nyirenda, V. R., Parker, A., Parker, D., Reid, C., Robson, A., Sayer, E., Selier, S. J., Sichande, M., Simukonda, C., Uiseb, K., Williams, V. L., Zimba, D. & Hunter, L., 2022, In: Frontiers in Conservation Science. 3, 13 p., 963961.

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

  16. Published

    Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding

    Bendtsen, K. L., Xu, K., Luckmann, M., Winther, K. S., Shah, S. A., Pedersen, C. N. S. & Brodersen, D. E., 2017, In: Nucleic Acids Research. 45, 5, p. 2875-2886 12 p.

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

  17. Published

    Grey wolf genomic history reveals a dual ancestry of dogs

    Bergström, A., Stanton, D. W. G., Taron, U. H., Frantz, L., Sinding, M. H. S., Ersmark, E., Pfrengle, S., Cassatt-Johnstone, M., Lebrasseur, O., Girdland-Flink, L., Fernandes, D. M., Ollivier, M., Speidel, L., Gopalakrishnan, S., Westbury, M. V., Ramos-Madrigal, J., Feuerborn, T. R., Reiter, E., Gretzinger, J., Münzel, S. C. & 61 others, Swali, P., Conard, N. J., Carøe, C., Haile, James Seymour, Linderholm, A., Androsov, S., Barnes, I., Baumann, C., Benecke, N., Bocherens, H., Brace, S., Carden, R. F., Drucker, D. G., Fedorov, S., Gasparik, M., Germonpré, M., Grigoriev, S., Groves, P., Hertwig, S. T., Ivanova, V. V., Janssens, L., Jennings, R. P., Kasparov, A. K., Kirillova, I. V., Kurmaniyazov, I., Kuzmin, Y. V., Kosintsev, P. A., Lázničková-Galetová, M., Leduc, C., Nikolskiy, P., Nussbaumer, M., O’Drisceoil, C., Orlando, L., Outram, A., Pavlova, E. Y., Perri, A. R., Pilot, M., Pitulko, V. V., Plotnikov, V. V., Protopopov, A. V., Rehazek, A., Sablin, M., Seguin-Orlando, A., Storå, J., Verjux, C., Zaibert, V. F., Zazula, G., Crombé, P., Hansen, Anders Johannes, Willerslev, Eske, Leonard, J. A., Götherström, A., Pinhasi, R., Schuenemann, V. J., Hofreiter, M., Gilbert, M Thomas P, Shapiro, B., Larson, G., Krause, J., Dalén, L. & Skoglund, P., 2022, In: Nature. 607, 7918, p. 313-320

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

  18. Published

    Genetic guidelines for translocations: Maintaining intraspecific diversity in the lion (Panthera leo)

    Bertola, Laura, Miller, S. M., Williams, V. L., Naude, V. N., Coals, P., Dures, S. G., Henschel, P., Chege, M., Sogbohossou, E. A., Ndiaye, A., Kiki, M., Gaylard, A., Ikanda, D. K., Becker, M. S. & Lindsey, P., 2022, In: Evolutionary Applications. 15, 1, p. 22-39 18 p.

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

  19. Published

    A pragmatic approach for integrating molecular tools into biodiversity conservation

    Bertola, L. D., Brüniche-Olsen, A., Kershaw, F., Russo, I. R. M., MacDonald, A. J., Sunnucks, P., Bruford, M. W., Cadena, C. D., Ewart, K. M., de Bruyn, M., Eldridge, M. D. B., Frankham, R., Guayasamin, J. M., Grueber, C. E., Hoareau, T. B., Hoban, S., Hohenlohe, P. A., Hunter, M. E., Kotze, A., Kuja, J. & 21 others, Lacy, R. C., Laikre, L., Lo, N., Meek, M. H., Mergeay, J., Mittan-Moreau, C., Neaves, L. E., O'Brien, D., Ochieng, J. W., Ogden, R., Orozco-terWengel, P., Páez-Vacas, M., Pierson, J., Ralls, K., Shaw, R. E., Sogbohossou, E. A., Stow, A., Steeves, T., Vernesi, C., Watsa, M. & Segelbacher, G., 2024, In: Conservation Science and Practice. 6, 1, 15 p., e13053.

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

  20. Published

    Giraffe lineages are shaped by major ancient admixture events

    Bertola, L. D., Quinn, L., Hanghøj, K., Garcia-Erill, G., Rasmussen, M. S., Balboa, R. F., Meisner, J., Bøggild, T., Wang, X., Lin, L., Nursyifa, C., Liu, X., Li, Z., Chege, M., Moodley, Y., Brüniche-Olsen, A., Kuja, J., Schubert, M., Agaba, M., Santander, C. G. & 7 others, Sinding, Mikkel Holger Strander, Muwanika, V., Masembe, C., Siegismund, Hans Redlef, Moltke, Ida, Albrechtsen, Anders & Heller, Rasmus, 2024, In: Current Biology. 34, 7, p. 1576-1586.e5 11 p.

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

  21. Published

    Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios

    Besenbacher, S., Liu, S., Gonzalez-Izarzugaza, J. M., Grove, J., Belling, K. G., Bork-Jensen, J., Huang, S., Als, T. D., Li, S., Yadav, R., Rubio García, A., Lescai, F., Demontis, D., Rao, J., Ye, W., Mailund, T., Møllegaard Friborg, R., Pedersen, C. N. S., Xu, R., Sun, J. & 27 others, Liu, H., Wang, O., Cheng, X., Flores, D., Rydza, E. K., Rapacki, K., Sørensen, J. D., Chmura, P. J., Westergaard, D., Dworzynski, P., Sørensen, Thorkild I.A., Lund, O., Hansen, Torben, Xu, X., Li, N., Bolund, L., Pedersen, Oluf Borbye, Eiberg, Hans Rudolf Lytchoff, Krogh, Anders, Børglum, A. D., Brunak, Søren, Kristiansen, Karsten, Schierup, M. H., Wang, J., Gupta, R., Villesen, P. & Rasmussen, Simon, 2015, In: Nature Communications. 6, 9 p., 5969.

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

  22. Published

    A perspective on inverse design of battery interphases using multi-scale modelling, experiments and generative deep learning

    Bhowmik, A., Castelli, I. E., Garcia-Lastra, J. M., Bjørn-Jørgensen, P., Winther, Ole & Vegge, T., 2019, In: Energy Storage Materials. 21, p. 446-456

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

  23. Published

    Cardiovascular autonomic neuropathy and the impact on progression of diabetic kidney disease in type 1 diabetes

    Bjerre-Christensen, T., Winther, S. A., Tofte, N., Theilade, S., Ahluwalia, Tarun Veer Singh, Lajer, M., Hansen, T. W., Rossing, Peter & Hansen, C. S., 2021, In: B M J Open Diabetes Research & Care. 9, 1, 9 p., e002289.

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

  24. Published

    Rapid protein stability prediction using deep learning representations

    Blaabjerg, Lasse Møller, Kassem, M. M., Good, L. L., Jonsson, Nicolas, Cagiada, Matteo, Johansson, Kristoffer Enøe, Boomsma, Wouter, Stein, Amelie & Lindorff-Larsen, Kresten, 2023, In: eLife. 12, 19 p., e82593.

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

  25. Published

    The endangered White Sands pupfish (Cyprinodon tularosa) genome reveals low diversity and heterogenous patterns of differentiation

    Black, A. N., Willoughby, J. R., Brüniche-Olsen, Anna, Pierce, B. L. & DeWoody, J. A., 2021, In: Molecular Ecology Resources. 21, 7, p. 2520-2532 13 p.

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

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