Computational and RNA Biology

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  1. Published

    Clinical diagnosis of genetic disorders at both single-nucleotide and chromosomal levels based on BGISEQ-500 platform

    Liu, Y., Mao, L., Huang, H., Li, W., Man, J., Zhang, W., Wang, L., Li, L., Sun, Y., Zhai, T., Guo, X., Du, L., Huang, J., Li, H., Wan, Y. & Wei, X., 2023, In: Human Genome Variation. 10, 1, 43 p., 15.

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

  2. Published

    ClockstaRX: testing molecular clock hypotheses with genomic data

    Duchene, David, Duchêne, S., Stiller, Josefin, Heller, Rasmus & Ho, S. Y. W., 2023, bioRxiv, 15 p.

    Research output: Working paper › Preprint › Research

  3. Published

    ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data

    Duchene, David, Duchêne, S., Stiller, Josefin, Heller, Rasmus & Ho, S. Y. W., 2024, In: Genome Biology and Evolution. 16, 4, 7 p., evae064.

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

  4. Published

    Co-Chaperones in Targeting and Delivery of Misfolded Proteins to the 26S Proteasome

    Abildgaard, A. B., Gersing, S. K., Larsen-Ledet, Sven, Nielsen, S. V., Stein, Amelie, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2020, In: Biomolecules. 10, 8, 24 p., 1141.

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

  5. Published

    Co-circulation of two extremely divergent serotype SAT 2 lineages in Kenya highlights challenges to foot-and-mouth disease control

    Sangula, A. K., Belsham, G. J., Muwanika, V. B., Heller, Rasmus, Balinda, S. N. & Siegismund, Hans Redlef, 2010, In: Archives of Virology. 155, 10, p. 1625-1630

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

  6. Published

    Coalescent inference using serially sampled, high-throughput sequencing data from intrahost HIV infection

    Dialdestoro, K., Sibbesen, Jonas Andreas, Sørensen, L. M., Raghwani, J., Gall, A., Kellam, P., Pybus, O. G., Hein, J. & Jenkins, P. A., 2016, In: Genetics (Print). 202, 4, p. 1449-1472 24 p.

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

  7. Published

    Codon usage determines translation rate in Escherichia coli

    Sørensen, Michael Askvad, Kurland, C. G. & Pedersen, Steen, 1989, In: Journal of Molecular Biology. 207, 2, p. 365-77 12 p.

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

  8. Published

    Cohort-wide deep whole genome sequencing and the allelic architecture of complex traits

    Gilly, A., Suyeges, D., Kuchenbaecker, K., Pollard, M., Southam, L., Hatzikotoulas, K., Farmaki, A-E., Bjornland, T., Waples, R., Appel, E. V. R., Casalone, E., Melloni, G., Kilian, B., Rayner, N. W., Ntalla, I., Kundu, K., Walter, K., Danesh, J., Butterworth, A., Barroso, I. & 5 others, Tsafantakis, E., Dedoussis, G., Zeggini, E., Moltke, Ida & Zeggini, E., 1 Dec 2018, In: Nature Communications. 9, p. 1-9 4674.

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

  9. Published

    Colonialism in South Africa leaves a lasting legacy of reduced genetic diversity in Cape buffalo

    Quinn, Liam James Elgaard, Garcia Erill, Genís, Santander, Cindy, Brüniche-Olsen, Anna, Liu, Xiaodong, Sinding, Mikkel Holger Strander, Heaton, M. P., Smith, T. P. L., Chrzanová Pecnerová, Patrícia, Bertola, Laura, Hanghøj, Kristian Ebbesen, Rasmussen, Malthe Sebro, De Jager, Deon, Siegismund, Hans Redlef, Albrechtsen, Anders, Heller, Rasmus & Moltke, Ida, 2023, In: Molecular Ecology. 32, 8, 15 p.

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

  10. Published

    Combined analysis of 19 common validated type 2 diabetes susceptibility gene variants shows moderate discriminative value and no evidence of gene-gene interaction

    Sparsø, T., Grarup, N., Andreasen, C., Albrechtsen, A., Holmkvist, J., Andersen, G., Jørgensen, T., Borch-Johnsen, K., Sandbaek, A., Lauritzen, T., Madsbad, S., Hansen, T., Pedersen, O., Sparsø, T., Grarup, N., Andreasen, C., Albrechtsen, A., Holmkvist, J., Andersen, G., Jørgensen, T. & 6 others, Borch-Johnsen, K., Sandbaek, A., Lauritzen, T., Madsbad, Sten, Hansen, T. & Pedersen, O., 2009, In: Diabetologia. 52, 7, p. 1308-14 6 p.

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

  11. Published

    Combined transcriptomic and proteomic analysis of the posterior salivary gland from the southern blue-ringed octopus and the southern sand octopus

    Whitelaw, B. L., Strugnell, J. M., Faou, P., Rodrigues da Fonseca, Rute Andreia, Hall, N. E., Norman, M., Finn, J. & Cooke, I. R., 2016, In: Journal of Proteome Research. 15, 9, p. 3284-3297 14 p.

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

  12. Published

    Combining Bayesian age models and genetics to investigate population dynamics and extinction of the last mammoths in northern Siberia

    Dehasque, M., Chrzanová Pecnerová, Patrícia, Muller, H., Tikhonov, A., Nikolskiy, P., Tsigankova, V. I., Danilov, G. K., Díez-del-Molino, D., Vartanyan, S., Dalén, L. & Lister, A. M., 2021, In: Quaternary Science Reviews. 259, 10 p., 106913.

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

  13. Published

    Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology

    de Flamingh, A., Ishida, Y., Chrzanová Pecnerová, Patrícia, Vilchis, S., Siegismund, Hans Redlef, van Aarde, R. J., Malhi, R. S. & Roca, A. L., 2023, In: Frontiers in Genetics. 13, 14 p., 1021004.

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

  14. Published

    Combining the multicanonical ensemble with generative probabilistic models of local biomolecular structure

    Frellsen, J., Hamelryck, Thomas Wim & Ferkinghoff-Borg, J., 2013, Proceedings of the 59th World Statistics Congress of the International Statistical Institute, 2013 . Hague, p. 139-144 6 p.

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

  15. Published

    Comment on “DpCoA tagSeq: Barcoding dpCoA-Capped RNA for Direct Nanopore Sequencing via Maleimide-Thiol Reaction”

    Vinther, Jeppe, 2024, In: Analytical Chemistry. 96, 1, p. 606-609 4 p.

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

  16. Published

    Community curation of bioinformatics software and data resources

    Ison, J., Ménager, H., Brancotte, B., Jaaniso, E., Salumets, A., Raček, T., Lamprecht, A. L., Palmblad, M., Kalaš, M., Chmura, Piotr Jaroslaw, Hancock, J. M., Schwämmle, V. & Ienasescu, H. I., 2020, In: Briefings in Bioinformatics. 21, 5, p. 1697-1705 9 p.

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

  17. Published

    Community genomics among stratified microbial assemblages in the ocean's interior

    DeLong, E. F., Preston, C. M., Mincer, T., Rich, V., Hallam, S. J., Frigaard, Niels-Ulrik, Martinez, A., Sullivan, M. B., Edwards, R., Brito, B. R., Chisholm, S. W. & Karl, D. M., 2006, In: Science. 311, 5760, p. 496-503 7 p.

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

  18. Published

    Comparative analysis of complete mitochondrial genomes suggests that relaxed purifying selection is driving high nonsynonymous evolutionary rate of the NADH2 gene in whitefish (Coregonus ssp.)

    Jacobsen, M. W., Rodrigues da Fonseca, Rute Andreia, Bernatchez, L. & Hansen, M. M., 2016, In: Molecular Phylogenetics and Evolution. 95, p. 161-170 10 p.

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

  19. Published

    Comparative metagenomics of eight geographically remote terrestrial hot springs

    Menzel, P., Islin, S. R., Rike, A. G., Lin, L., Zhang, Q., Contursi, P., Moracci, M., Kristjansson, J. K., Bolduc, B., Gavrilov, S., Ravin, N., Mardanov, A., Bonch-Osmolovskaya, E., Young, M., Krogh, Anders & Peng, Xu, 2015, In: Microbial Ecology. 70, 2, p. 411-424 14 p.

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

  20. Published

    Comparative phylogeography of African savannah ungulates

    Lorenzen, Eline, Heller, Rasmus & Siegismund, Hans Redlef, 2012, In: Molecular Ecology. 21, 15, p. 3656-3670 15 p.

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

  21. Published

    Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection

    Salgado-Albarrán, M., Navarro-Delgado, E. I., Del Moral-Morales, A., Alcaraz, N., Baumbach, J., González-Barrios, R. & Soto-Reyes, E., 2021, In: n p j Systems Biology and Applications. 7, 14 p., 21.

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

  22. Published

    Comparative transcriptomics of primary cells in vertebrates

    Alam, T., Agrawal, S., Severin, J., Young, R. S., Andersson, R., Arner, E., Hasegawa, A., Lizio, M., Ramilowski, J. A., Abugessaisa, I., Ishizu, Y., Noma, S., Tarui, H., Taylor, M. S., Lassmann, T., Itoh, M., Kasukawa, T., Kawaji, H., Marchionni, L., Sheng, G. & 5 others, Forrest, A. R. R., Khachigian, L. M., Hayashizaki, Y., Carninci, P. & de Hoon, M. J. L., 2020, In: Genome Research. 30, 7, p. 951-961 11 p.

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

  23. Published

    Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients

    Rapin, N. P. J., Bagger, F. O., Jendholm, L. J., Mora-Jensen, H., Krogh, Anders, Kohlmann, A., Thiede, C., Borregaard, N., Bullinger, L., Winther, Ole, Theilgaard-Mønch, Kim & Porse, Bo Torben, 6 Feb 2014, In: Blood (online). 123, 6, p. 894-904 11 p.

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

  24. Published

    Comparison of In-Frame Deletion, Homology-Directed Repair, and Prime Editing-Based Correction of Duchenne Muscular Dystrophy Mutations

    Zhao, X., Qu, Kunli, Curci, B., Yang, H., Bolund, L., Lin, L. & Luo, Y., 2023, In: Biomolecules. 13, 5, 15 p., 870.

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

  25. Published

    Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets

    Feuerborn, Tatiana Richtman, Palkopoulou, E., van der Valk, T., von Seth, J., Munters, A. R., Chrzanová Pecnerová, Patrícia, Dehasque, M., Ureña, I., Ersmark, E., Lagerholm, V. K., Krzewinska, M., Rodríguez-Varela, R., Götherström, A., Dalén, L. & Díez-del-Molino, D., 2020, In: BMC Genomics. 21, 10 p., 844.

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

  26. Published

    Complete Inactivation of Sebum-Producing Genes Parallels the Loss of Sebaceous Glands in Cetacea

    Lopes-Marques, M., Machado, A. M., Alves, L. Q., Fonseca, M. M., Barbosa, S., Sinding, M. S., Rasmussen, M. H., Iversen, M. R., Bertelsen, Mads Frost, Campos, P. F., Rodrigues da Fonseca, Rute Andreia, Ruivo, R. & Castro, L. F. C., 2019, In: MOLECULAR BIOLOGY AND EVOLUTION . 36, 6, p. 1270-1280

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

  27. Published

    Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx)

    Xia, Q., Guo, Y., Zhang, Z., Li, D., Xuan, Z., Li, Z., Dai, F., Li, Y., Cheng, D., Li, R., Cheng, T., Jiang, T., Becquet, C., Xu, X., Liu, C., Zha, X., Fan, W., Lin, Y., Shen, Y., Jiang, L. & 38 others, Jensen, J., Hellmann, I., Tang, S., Zhao, P., Xu, H., Yu, C., Zhang, G., Li, J., Cao, J., Liu, S., He, N., Zhou, Y., Liu, H., Zhao, J., Ye, C., Du, Z., Pan, G., Zhao, A., Shao, H., Zeng, W., Wu, P., Li, C., Pan, M., Li, J., Yin, X., Li, D., Wang, J., Zheng, H., Wang, W., Zhang, X., Li, S., Yang, H., Lu, C., Nielsen, Rasmus, Zhou, Z., Wang, J., Xiang, Z. & Wang, J., 2009, In: Science. 326, 5951, p. 433-6 3 p.

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

  28. Published

    Comprehensive profiling of the fission yeast transcription start site activity during stress and media response

    Thodberg, Malte, Thieffry, A., Lange, Jette Bornholdt, Boyd, M., Holmberg, Christian, Azad, A., Workman, C. T., Chen, Y., Ekwall, K., Nielsen, Olaf & Sandelin, Albin Gustav, 28 Feb 2019, In: Nucleic Acids Research. 47, 4, p. 1671-1691 21 p.

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

  29. Published

    Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families

    Shah, S. A., Alkhnbashi, O. S., Behler, J., Han, W., She, Q., Hess, W. R., Garrett, Roger Antony & Backofen, R., 2019, In: RNA Biology. 16, 4, p. 530-542 13 p.

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

  30. Published

    Computational Approaches to Understand Transcriptional Regulation and Alternative Promoter Usage in Mammals

    Jørgensen, M., 2014, Department of Biology, Faculty of Science, University of Copenhagen.

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

  31. Published

    Computational Investigations of Post-Transcriptional Regulation: The Intricate Dependency of MicroRNA Regulation on RNA-Binding Proteins

    Rasmussen, S. H., 2016, Department of Biology, Faculty of Science, University of Copenhagen.

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

  32. Published

    Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome

    Abildgaard, A. B., Stein, Amelie, Nielsen, S. V., Schultz-Knudsen, Katrine, Papaleo, E., Shrikhande, A., Hoffmann, Eva, Bernstein, I., Gerdes, Anne-Marie Axø, Takahashi, M., Ishioka, C., Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2019, In: eLife. 8, 28 p., e49138 .

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

  33. Published

    Computational cancer biology: from carcinogenesis to metastasis

    Kaczkowski, B., 2012, Department of Biology, Faculty of Science, University of Copenhagen. 125 p.

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

  34. Published

    Computational identification of signals predictive for nuclear RNA exosome degradation pathway targeting

    Wu, M., Schmid, M., Jensen, T. H. & Sandelin, Albin Gustav, 2022, In: NAR Genomics and Bioinformatics. 4, 3, 18 p., lqac071.

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

  35. Published

    Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system

    Rapin, N. P. J., Lund, O., Bernaschi, M. & Castiglione, F., 2010, In: PloS one. 5, 4, p. e9862

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

  36. Published

    Computational methods for chromosome-scale haplotype reconstruction

    Garg, S., 2021, In: Genome Biology. 22, 24 p., 101.

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

  37. Published

    Computational redesign of thioredoxin is hypersensitive towards minor conformational changes in the backbone template

    Johansson, Kristoffer Enøe, Johansen, Nicolai Tidemand, Christensen, S., Horowitz, S., Bardwell, J. C. A., Olsen, Johan Gotthardt, Willemoës, Martin, Lindorff-Larsen, Kresten, Ferkinghoff-Borg, J., Hamelryck, Thomas Wim & Winther, Jakob R., 2016, In: Journal of Molecular Biology. 428, 21, p. 4361-4377 17 p.

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

  38. 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

  39. Published

    Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle

    Rodrigues da Fonseca, Rute Andreia, Urena, I., Afonso, S., Pires, A. E., Jørsboe, E., Chikhi, L. & Ginja, C., 2019, In: BMC Genomics. 20, p. 1-13 334.

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

  40. Published

    Conservation genetic resources for effective species survival (ConGRESS): bridging the divide between conservation research and practice

    Hoban, S., Arntzen, J. W., Bertorelle, G., Bryja, J., Fernandes, M., Frith, K., Gaggiotti, O., Galbusera, P., Godoy, J. A., Hauffe, H. C., Hoelzel, A. R., Nichols, R. A., Perez-Espona, S., Primmer, C., Russo, I-R. M., Segelbacher, G., Siegismund, H. R., Sihvonen, M., Sjogren-Gulve, P., Vernesi, C. & 2 others, Vila, C. & Bruford, M. W., 2013, In: Journal for Nature Conservation. 21, 6, p. 433-437 5 p.

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

  41. Published

    Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing

    Hernández-Alonso, G., Ramos-Madrigal, J., Sun, X., Scharff-Olsen, C. H., Sinding, M. H. S., Martins, N. F., Ciucani, M. M., Mak, S. S. T., Lanigan, L. T., Clausen, C. G., Bhak, J., Jeon, S., Kim, C., Eo, K. Y., Cho, S. H., Boldgiv, B., Gantulga, G., Unudbayasgalan, Z., Kosintsev, P. A., Stenøien, H. K. & 2 others, Gilbert, M Thomas P & Gopalakrishnan, Shyam, 2023, In: Ecology and Evolution. 13, 8, 15 p., e10404.

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

  42. Published

    Context dependency of nucleotide probabilities and variants in human DNA

    Liang, Yuhu, Grønbæk, Christian, Fariselli, P. & Krogh, Anders, 2022, In: BMC Genomics. 23, 1, 15 p., 87.

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

  43. Published

    Context dependent prediction in DNA sequence using neural networks

    Grønbæk, Christian, Liang, Yuhu, Elliott, Desmond & Krogh, Anders, 2022, In: PeerJ. 10, 22 p., e13666.

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

  44. Published

    Contrasting demographic histories of the neighboring bonobo and chimpanzee

    Hvilsom, C., Carlsen, F., Heller, Rasmus, Jaffré, N. & Siegismund, Hans Redlef, 2014, In: Primates. 55, 1, p. 101-112 12 p.

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

  45. Published

    Contrastive learning enables rapid mapping to multimodal single-cell atlas of multimillion scale

    YANG, Meng, Yang, Y., Xie, C., Ni, M., Liu, J., Yang, H., Mu, F. & Wang, J., 2022, In: Nature Machine Intelligence. 4, 8, p. 696-709 14 p.

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

  46. Published

    Convergent molecular evolution of thermogenesis and circadian rhythm in Arctic ruminants

    Li, M., Li, X., Wu, Z., Zhang, G., Wang, N., Dou, M., Liu, S., Yang, C., Meng, G., Sun, H., Hvilsom, C., Xie, G., Li, Y., Li, Z. H., Wang, W., Jiang, Y., Heller, Rasmus & Wang, Y., 2023, In: Proceedings of the Royal Society B: Biological Sciences. 290, 1999, 10 p., 20230538.

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

  47. Published

    Convolutional LSTM networks for subcellular localization of proteins

    Sønderby, S. K., Sønderby, C. K., Nielsen, H. & Winther, Ole, 2015, Algorithms for Computational Biology. Dediu, A-H., Hernández-Quiroz, F., Martín-Vide, C. & Rosenblueth, D. A. (eds.). Springer, p. 68-80 13 p. (Lecture notes in computer science, Vol. 9199).

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

  48. Published

    Correcting estimators of theta and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process

    Ramírez-Soriano, A. & Nielsen, Rasmus, 2009, In: Genetics. 181, 2, p. 701-10 9 p.

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

  49. 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

  50. Published

    Cross species comparison of C/EBPa and PPAR¿ profiles in mouse and human adipocytes reveals interdependent retention of binding sites

    Schmidt, S. F., Jørgensen, M., Chen, Y., Nielsen, R., Sandelin, Albin Gustav & Mandrup, S., 2011, In: BMC Genomics. 12, 16 p.

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

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