Computational and RNA Biology

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  1. 2023
  2. Published

    Towards routine chromosome-scale haplotype-resolved reconstruction in cancer genomics

    Garg, S., 2023, In: Nature Communications. 14, 1, 11 p., 1358.

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

  3. Published

    Transcription factor expression is the main determinant of variability in gene co-activity

    van Duin, Lucas, Krautz, Robert, Rennie, Sarah & Andersson, Robin, 2023, In: Molecular Systems Biology. 19, 7, 17 p., e11392.

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

  4. Published

    Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation

    Pikkupeura, Laura Maarit, Bardini Bressan, Raul, Guiu, J., Chen, Y., Maimets, Martti, Mayer, Daniela, Schweiger, P. J., Hansen, Stine Lind, Maciag, Grzegorz Jerzy, Larsen, Hjalte List, Lõhmussaar, Kadi, Pedersen, M. T., Teves, Joji Marie Yap, Lange, Jette Bornholdt, Benes, V., Sandelin, Albin Gustav & Jensen, Kim Bak, 2023, In: Science Advances. 9, 28, 16 p., eadf9460.

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

  5. Published

    Transfer learning identifies sequence determinants of cell-type specific regulatory element accessibility

    Salvatore, Marco, Horlacher, M., Marsico, A., Winther, Ole & Andersson, Robin, 2023, In: NAR Genomics and Bioinformatics. 5, 2, 10 p., 026.

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

  6. Published

    Two Novel α-Thalassemia Mutations CD 39 -C [Thr > Pro] and CD 109 ACC > CCC [Thr > Pro] Identified in Two Chinese Families: A Case Report

    Zhang, W., Han, X., Deng, J., Zhou, R., Du, X., Wu, C. & Li, M., 2023, In: Hemoglobin. 47, 4, 8 p.

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

  7. Published

    Uncertainty-aware and explainable machine learning for early prediction of battery degradation trajectory

    Rieger, L. H., Flores, E., Nielsen, K. F., Norby, P., Ayerbe, E., Winther, Ole, Vegge, T. & Bhowmik, A., 2023, In: Digital Discovery. 2, 1, p. 112-122 11 p.

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

  8. Published

    Unraveling the genetic basis of neurological diseases and thalassemia: the clinical utility of high throughput sequencing

    ZHANG, W., 2023, Department of Biology, Faculty of Science, University of Copenhagen. 117 p.

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

  9. Published

    Variational Open-Domain Question Answering

    Liévin, V., Motzfeldt, A. G., Jensen, I. R. & Winther, Ole, 2023, In: Proceedings of Machine Learning Research. 202, p. 20950-20977 28 p.

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

  10. Published

    Genetic architecture of spatial electrical biomarkers for cardiac arrhythmia and relationship with cardiovascular disease

    Young, W. J., Haessler, J., Benjamins, J-W., Repetto, L., Yao, J., Isaacs, A., Harper, A. R., Ramirez, J., Garnier, S., van Duijvenboden, S., Baldassari, A. R., Concas, M. P., Duong, T., Foco, L., Isaksen, J. L., Mei, H., Noordam, R., Nursyifa, C., Richmond, A., Santolalla, M. L. & 74 others, Sitlani, C. M., Soroush, N., Thériault, S., Trompet, S., Aeschbacher, S., Ahmadizar, F., Alonso, A., Brody, J. A., Campbell, A., Correa, A., Darbar, D., De Luca, A., Deleuze, J., Ellervik, Christina, Fuchsberger, C., Goel, A., Grace, C., Guo, X., Hansen, Torben, Heckbert, S. R., Jackson, R. D., Kors, J. A., Lima-Costa, M. F., Linneberg, Allan René, Macfarlane, P. W., Morrison, A. C., Navarro, P., Porteous, D. J., Pramstaller, P. P., Reiner, A. P., Risch, L., Schotten, U., Shen, X., Sinagra, G., Soliman, E. Z., Stoll, M., Tarazona-Santos, E., Tinker, A., Trajanoska, K., Villard, E., Warren, H. R., Whitsel, E. A., Wiggins, K. L., Arking, D. E., Avery, C. L., Conen, D., Girotto, G., Grarup, Niels, Hayward, C., Jukema, J. W., Mook-Kanamori, D. O., Olesen, Morten Steen Salling, Padmanabhan, S., Psaty, B. M., Pattaro, C., Ribeiro, A. L. P., Rotter, J. I., Stricker, B. H., van der Harst, P., van Duijn, C. M., Verweij, N., Wilson, J. G., Orini, M., Charron, P., Watkins, H., Kooperberg, C., Lin, H. J., Wilson, J. F., Kanters, Jørgen K., Sotoodehnia, N., Mifsud, B., Lambiase, P. D., Tereshchenko, L. G. & Munroe, P. B., 14 Mar 2023, In: Nature Communications. 14, 1, 16 p., 1411.

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

  11. Published

    A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species

    Dai, X., Bian, P., Hu, D., Luo, F., Huang, Y., Jiao, S., Wang, X., Gong, M., Li, R., Cai, Y., Wen, J., Yang, Q., Deng, W., Nanaei, H. A., Wang, Y., Wang, F., Zhang, Z., Rosen, B. D., Heller, Rasmus & Jiang, Y., Aug 2023, In: Genome Research. 33, 8, p. 1284-1298 15 p.

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

  12. 2024
  13. 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

  14. Published

    AI Implementation and Capability Development in Manufacturing: An Action Research Case

    Eklöf, Jon, Snis, U. L., Hamelryck, Thomas Wim, Grima, A. & Rønning, Ola, 2024, Proceedings of the 57th Hawaii International Conference on System Sciences - HICSS 2024. Hawaii International Conference on System Sciences, 10 p.

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

  15. 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

  16. 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

  17. Published

    Can large language models reason about medical questions?

    Liévin, V., Hother, C. E., Motzfeldt, A. G. & Winther, Ole, 2024, In: Patterns. 5, 3, 12 p., 100943.

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

  18. Published

    Characterizing glucokinase variant mechanisms using a multiplexed abundance assay

    Gersing, S., Schulze, Thea Klarsø, Cagiada, Matteo, Stein, Amelie, Roth, F. P., Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2024, In: Genome Biology. 25, 1, 22 p., 98.

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

  19. Published

    Chromatin image-driven modelling

    Kadlof, M., Banecki, K., Chilinski, Mateusz & Plewczynski, D., 2024, In: Methods. 226, p. 54-60 7 p.

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

  20. 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

  21. 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

  22. Published

    DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning

    Wang, Jun, Horlacher, M., Cheng, L. & Winther, Ole, 2024, In: Bioinformatics. 40, 2, 10 p., btae065.

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

  23. Published

    DiscoTope-3.0: improved B-cell epitope prediction using inverse folding latent representations

    Høie, M. H., Gade, F. S., Johansen, J., Würtzen, C., Winther, Ole, Nielsen, M. & Marcatili, P., 2024, In: Frontiers in Immunology. 15, 12 p., 1322712.

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

  24. 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

  25. 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

  26. Published

    GWAS of lipids in Greenlanders finds association signals shared with Europeans and reveals an independent PCSK9 association signal

    Senftleber, N. K., Andersen, M. K., Jørsboe, E., Stæger, Frederik Filip Vinggaard, Nøhr, A. K., Garcia Erill, Genís, Meisner, Jonas, Santander, Cindy, Balboa, Renzo Fidel Ferdinando, Gilly, A., Bjerregaard, P., Larsen, C. V. L., Grarup, Niels, Jørgensen, M. E., Zeggini, E., Moltke, Ida, Hansen, Torben & Albrechtsen, Anders, 2024, In: European Journal of Human Genetics. 32, p. 215–223 9 p.

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

  27. Published

    Genetic diversity of lion populations in Kenya: Evaluating past management practices and recommendations for future conservation actions

    Chege, M., Sewalt, B., Lesilau, F., de Snoo, G., Patterson, B. D., Kariuki, L., Otiende, M., Omondi, P., de Iongh, H., Vrieling, K. & Bertola, Laura, 2024, In: Evolutionary Applications. 17, 3, 14 p., e13676.

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

  28. 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

  29. 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

  30. Published

    Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations

    Liu, X., Lin, L., Sinding, M. H. S., Bertola, L. D., Hanghøj, K., Quinn, L., Garcia-Erill, G., Rasmussen, M. S., Schubert, M., Pečnerová, P., Balboa, R. F., Li, Z., Heaton, M. P., Smith, T. P. L., Pinto, R. R., Wang, X., Kuja, J., Brüniche-Olsen, A., Meisner, J., Santander, C. G. & 8 others, Ogutu, J. O., Masembe, C., Rodrigues da Fonseca, Rute Andreia, Muwanika, V., Siegismund, Hans Redlef, Albrechtsen, Anders, Moltke, Ida & Heller, Rasmus, 2024, In: Nature Communications. 15, 1, 16 p., 2921.

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

  31. Published

    JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles

    Rauluseviciute, I., Riudavets-puig, R., Blanc-mathieu, R., Castro-mondragon, J., Ferenc, K., Kumar, V., Lemma, R. B., Lucas, J., Chèneby, J., Baranasic, D., Khan, A., Fornes, O., Gundersen, S., Johansen, M., Hovig, E., Lenhard, B., Sandelin, Albin Gustav, Wasserman, W., Parcy, F. & Mathelier, A., 2024, In: Nucleic Acids Symposium Series. 52, D1, p. D174–D182 9 p.

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

  32. Published

    MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch

    Jakobsen, S. T., Jensen, R. A. M., Madsen, M. S., Ravnsborg, T., Vaagenso, C. S., Siersbæk, M. S., Einarsson, H., Andersson, Robin, Jensen, O. N. & Siersbæk, R., 2024, In: Nature Genetics. 56, p. 663–674 12 p.

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

  33. Published

    MacroLoops for microRNAs: shall we revise the maximum allowed size?

    Arribas Hernandez, Laura, 2024, In: The Plant Cell. 36, 5, p. 1572-1573 2 p.

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

  34. Published

    Monitoring of species’ genetic diversity in Europe varies greatly and overlooks potential climate change impacts

    Pearman, P. B., Broennimann, O., Aavik, T., Albayrak, T., Alves, P. C., Aravanopoulos, F. A., Bertola, L. D., Biedrzycka, A., Buzan, E., Cubric-Curik, V., Djan, M., Fedorca, A., Fuentes-Pardo, A. P., Fussi, B., Godoy, J. A., Gugerli, F., Hoban, S., Holderegger, R., Hvilsom, C., Iacolina, L. & 32 others, Kalamujic Stroil, B., Klinga, P., Konopiński, M. K., Kopatz, A., Laikre, L., Lopes-Fernandes, M., McMahon, B. J., Mergeay, J., Neophytou, C., Pálsson, S., Paz-Vinas, I., Posledovich, D., Primmer, C. R., Raeymaekers, J. A. M., Rinkevich, B., Rolečková, B., Ruņģis, D., Schuerz, L., Segelbacher, G., Kavčič Sonnenschein, K., Stefanovic, M., Thurfjell, H., Träger, S., Tsvetkov, I. N., Velickovic, N., Vergeer, P., Vernesi, C., Vilà, C., Westergren, M., Zachos, F. E., Guisan, A. & Bruford, M., 2024, In: Nature Ecology and Evolution. 8, p. 267–281 15 p.

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

  35. Published

    Population genomics of the muskox' resilience in the near absence of genetic variation

    Pečnerová, P., Lord, E., Garcia-Erill, G., Hanghøj, K., Rasmussen, M. S., Meisner, J., Liu, X., van der Valk, T., Santander, C. G., Quinn, L., Lin, L., Liu, S., Carøe, C., Dalerum, F., Götherström, A., Måsviken, J., Vartanyan, S., Raundrup, K., Al-Chaer, A., Rasmussen, L. & 11 others, Hvilsom, C., Heide-Jørgensen, M. P., Sinding, Mikkel Holger Strander, Aastrup, P., Van Coeverden de Groot, P. J., Schmidt, N. M., Albrechtsen, Anders, Dalén, L., Heller, Rasmus, Moltke, Ida & Siegismund, Hans Redlef, 2024, In: Molecular Ecology. 33, 2, 25 p.

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

  36. 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

  37. Published

    Population structure and migration in the Eastern Highlands of Papua New Guinea, a region impacted by the kuru epidemic

    Quinn, Liam James Elgaard, Whitfield, J., Alpers, M. P., Campbell, T., Hummerich, H., Pomat, W., Siba, P., Koki, G., Moltke, Ida, Collinge, J., Hellenthal, G. & Mead, S., 2024, In: American Journal of Human Genetics. 111, 4, p. 668-679 12 p.

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

  38. Published

    Predicting peptide–MHC stability and immunogenicity with deep learning

    Prachar, Marek, 2024, Department of Biology, Faculty of Science, University of Copenhagen. 258 p.

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

  39. Published

    Recommendations for Bioinformatic Tools in lncRNA Research

    Distefano, R., Ilieva, M., Rennie, Sarah & Uchida, S., 2024, In: Current Bioinformatics. 19, 1, p. 14-20 7 p.

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

  40. Published

    Spatially resolved analysis of microenvironmental gradient impact on cancer cell phenotypes

    Auxillos, Jamie Yam, Crouigneau, R., Li, Y. F., Dai, Yifan, Stigliani, Arnaud, Tavernaro, I., Resch-Genger, U., Sandelin, Albin Gustav, Marie, R. & Pedersen, Stine Helene Falsig, 2024, In: Science Advances. 10, 18, 17 p., eadn3448.

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

  41. Published

    The nightscape of the Arctic winter shapes the diving behavior of a marine predator

    Chambault, P., Teilmann, J., Tervo, O., Sinding, Mikkel Holger Strander & Heide-Jørgensen, M. P., 2024, In: Scientific Reports. 14, 1, 9 p., 3908.

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

  42. Published

    vcfpp: a C++ API for rapid processing of the variant call format

    Li, Z., 2024, In: Bioinformatics. 40, 2, 4 p., btae049.

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

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