Computational and RNA Biology

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  1. Published

    Allosteric regulation and communication between subunits in uracil phosphoribosyltransferase from Sulfolobus solfataricus

    Arent, S., Harris, P., Jensen, K. F. & Larsen, Sine, 2005, In: Biochemistry. 44, 3, p. 883-892

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

  2. Published

    Alterations in polyadenylation and its implications for endocrine disease

    Rehfeld, Anders Aagaard, Plass, M., Krogh, Anders & Friis-Hansen, Lennart Jan, 2013, In: Frontiers in Endocrinology. 4, 23 p., 53.

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

  3. Published

    Alternative Promoter Usage in Healthy and Inflamed Tissue

    Lilje, B., 2015, Department of Biology, Faculty of Science, University of Copenhagen.

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

  4. Published

    Alternative polyadenylation of tumor suppressor genes in small intestinal neuroendocrine tumors

    Rehfeld, Anders Aagaard, Plass, M., Døssing, K., Knigge, Ulrich, Kjær, Andreas, Krogh, Anders & Friis-Hansen, Lennart Jan, 2014, In: Frontiers in Endocrinology. 5, 10 p., 46.

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

  5. Published

    Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

    Huerta-Sanchez, E., Jin, X., Asan, Bianba, Z., Peter, B. M., Vinckenbosch, N., Liang, Y., Yi, X., He, M., Somel, M., Ni, P., Wang, B., Ou, X., Huasang, Luosang, J., Cuo, Z. X. P., Li, K., Gao, G., Yin, Y., Wang, W. & 7 others, Zhang, X., Xu, X., Yang, H., Li, Y., Wang, J., Wang, J. & Nielsen, Rasmus, 2014, In: Nature. 512, 7513, p. 194-197 4 p.

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

  6. Published

    Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq

    Jakobsen, J. S., Bagger, F. O., Hasemann, M. S., Schuster, Mikkel Bruhn, Frank, Anne-Katrine, Waage, J., Vitting-Seerup, K. & Porse, Bo Torben, 2015, In: BMC Genomics. 16, p. 46

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

  7. Published

    An LDLR missense variant poses high risk of familial hypercholesterolemia in 30% of Greenlanders and offers potential of early cardiovascular disease intervention

    Jørsboe, E., Andersen, M. K., Skotte, L., Stæger, F. F., Færgeman, N. J., Hanghøj, K., Santander, C. G., Senftleber, N. K., Diaz, L. J., Overvad, M., Waples, R. K., Geller, F., Bjerregaard, P., Melbye, M., Larsen, C. V. L., Feenstra, B., Anders Koch, K., Jørgensen, M. E., Grarup, N., Moltke, I. & 2 others, Albrechtsen, Anders & Hansen, Torben, 2022, In: Human Genetics and Genomics Advances. 3, 4, 10 p., 100118.

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

  8. Published

    An Aboriginal Australian genome reveals separate human dispersals into Asia

    Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K. E., Rasmussen, S., Albrechtsen, A., Skotte, L., Lindgreen, S., Metspalu, M., Jombart, T., Kivisild, T., Zhai, W., Eriksson, A., Manica, A., Orlando, L., De La Vega, F. M., Tridico, S., Metspalu, E., Nielsen, K., Avila Arcos, M. D. C. & 38 others, Moreno Mayar, J. Víctor, Muller, C., Dortch, J., Gilbert, M Thomas P, Lund, O., Wesolowska, A., Karmin, M., Weinert, L. A., Wang, B., Li, J., Tai, S., Xiao, F., Hanihara, T., van Driem, G., Jha, A. R., Ricaut, F., de Knijff, P., Migliano, A. B., Gallego Romero, I., Kristiansen, Karsten, Lambert, D. M., Brunak, Søren, Forster, P., Brinkmann, B., Nehlich, O., Bunce, M., Richards, M., Gupta, R., Bustamante, C. D., Krogh, Anders, Foley, R. A., Lahr, M. M., Balloux, F., Sicheritz-Pontén, T., Villems, R., Nielsen, Rasmus, Wang, J. & Willerslev, Eske, 2011, In: Science. 334, 6052, p. 94-98 5 p.

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

  9. 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

  10. Published

    An RNAi independent antiviral activity of the Arabidopsis thaliana DCL2

    Nielsen, C. P. S., 2020, Department of Biology, Faculty of Science, University of Copenhagen. 104 p.

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

  11. Published

    An atlas of active enhancers across human cell types and tissues

    Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Lange, J. B., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., Suzuki, T., Ntini, E., Arner, E., Valen, E., Li, K., Schwarzfischer, L., Glatz, D., Raithel, J., Lilje, B., Rapin, N., Bagger, F. O. & 30 others, Jørgensen, M., Andersen, P. R., Bertin, N., Rackham, O., Burroughs, A. M., Baillie, J. K., Ishizu, Y., Shimizu, Y., Furuhata, E., Maeda, S., Negishi, Y., Mungall, C. J., Meehan, T. F., Lassmann, T., Itoh, M., Kawaji, H., Kondo, N., Kawai, J., Lennartsson, A., Daub, C. O., Heutink, P., Hume, D. A., Jensen, T. H., Suzuki, H., Hayashizaki, Y., Mueller, F., Forrest, A. R. R., Carninci, P., Rehli, M. & Sandelin, Albin Gustav, 2014, In: Nature. 507, 7493, p. 455-461 7 p.

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

  12. Published

    An easy method for plant polysome profiling

    Lecampion, C., Floris, M. H. J., Fantino, J. R., Robaglia, C. & Laloi, C., 2016, In: Journal of Visualized Experiments. 2016, 114, e54231.

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

  13. 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

  14. 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

  15. Published

    An evolutionary method for learning HMM structure: prediction of protein secondary structure.

    Won, K., Hamelryck, Thomas Wim, Prügel-Bennett, A. & Krogh, Anders, 2007, In: BMC Bioinformatics. 8, p. 357

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

  16. Published

    An integrated expression atlas of miRNAs and their promoters in human and mouse

    de Rie, D., Abugessaisa, I., Alam, T., Arner, E., Arner, P., Ashoor, H., Åström, G., Babina, M., Bertin, N., Burroughs, A. M., Carlisle, A. J., Daub, C. O., Detmar, M., Deviatiiarov, R., Fort, A., Gebhard, C., Goldowitz, D., Guhl, S., Ha, T. J., Harshbarger, J. & 31 others, Hasegawa, A., Hashimoto, K., Herlyn, M., Heutink, P., Hitchens, K. J., Hon, C. C., Huang, E., Ishizu, Y., Kai, C., Kasukawa, T., Klinken, P., Lassmann, T., Lecellier, C., Lee, W., Lizio, M., Makeev, V., Mathelier, A., Medvedeva, Y. A., Mejhert, N., Mungall, C. J., Noma, S., Ohshima, M., Okada-Hatakeyama, M., Persson, H., Rizzu, P., Roudnicky, F., Sætrom, P., Sato, H., Vitting-Seerup, K., Sandelin, Albin Gustav & FANTOM Consortium, F. C., 21 Aug 2017, In: Nature Biotechnology. 35, 9, p. 872-878 7 p.

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

  17. Published

    An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants

    Xie, F., Jin, W., Si, H., Yuan, Y., Tao, Y., Liu, J., Wang, X., Yang, C., Li, Q., Yan, X., Lin, L., Jiang, Q., Zhang, L., Guo, C., Greening, C., Heller, R., Guan, L. L., Pope, P. B., Tan, Z., Zhu, W. & 4 others, Wang, M., Qiu, Q., Li, Z. & Mao, S., 2021, In: Microbiome. 9, 20 p., 137.

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

  18. Published

    An introduction to deep learning on biological sequence data: examples and solutions

    Jurtz, V. I., Johansen, A. R., Nielsen, M., Almagro Armenteros, J. J., Nielsen, H., Sønderby, C. K., Winther, Ole & Sønderby, S. K., 15 Nov 2017, In: Bioinformatics. 33, 22, p. 3685-3690 6 p.

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

  19. Published

    An investigation of the statistical power of neutrality tests based on comparative and population genetic data

    Zhai, W., Nielsen, Rasmus & Slatkin, M., 2009, In: Molecular Biology and Evolution. 26, 2, p. 273-83 10 p.

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

  20. Published

    An m6A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis

    Arribas Hernandez, Laura, Bressendorff, Simon, Hansen, M. H., Poulsen, C., Erdmann, S. & Brodersen, Peter, 2018, In: Plant Cell. 30, 5, p. 952-967 16 p.

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

  21. Published

    An update on principles of m6A targeting

    Bai, B., 2022, In: Trends in Plant Science. 27, 3, p. 224-226 3 p.

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

  22. Published

    An updated evolutionary classification of CRISPR-Cas systems

    Makarova, K. S., Wolf, Y. I., Alkhnbashi, O. S., Costa, F., Shah, S. A., Saunders, S. J., Barrangou, R., Brouns, S. J. J., Charpentier, E., Haft, D. H., Horvath, P., Moineau, S., Mojica, F. J. M., Terns, R. M., Terns, M. P., White, M. F., Yakunin, A. F., Garrett, R. A., van der Oost, J., Backofen, R. & 1 others, Koonin, E. V., 2015, In: Nature Reviews. Microbiology. 13, 11, p. 722-736 15 p.

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

  23. Published

    Analysing human genomes at different scales

    Liu, S., 2017, Department of Biology, Faculty of Science, University of Copenhagen.

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

  24. Published

    Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion

    Skov, L., Schierup, M. H., Danish Pan Genome Consortium, D. P. G. C., Sørensen, L. M., Petersen, Bent, Sibbesen, Jonas Andreas, Liu, S., Belling, K. G., Have, C. T., Bork-Jensen, J., Hansen, Torben, Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Rasmussen, Simon, Kristiansen, Karsten & Brunak, Søren, 2017, In: PLOS Genetics. 13, 8, p. e1006834

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

  25. Published

    Analysis of recent serotype O foot-and-mouth disease viruses from Livestock in Kenya: evidence of four independently evolving lineages

    Wekesa, S. N., Muwanika, V. B., Siegismund, Hans Redlef, Sangula, A. K., Namatovu, A., Dhikusooka, M. T., Tjørnehøj, K., Balinda, S. N., Wadsworth, J., Knowles, N. J. & Belsham, G. J., 2015, In: Transboundary and Emerging Diseases. 62, 3, p. 305-314 10 p.

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

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