Computational and RNA Biology

  1. 2023
  2. Published

    Global determinants of insect mitochondrial genetic diversity

    French, C. M., Bertola, Laura, Carnaval, A. C., Economo, E. P., Kass, J. M., Lohman, D. J., Marske, K. A., Meier, R., Overcast, I., Rominger, A. J., Staniczenko, P. P. A. & Hickerson, M. J., 2023, In: Nature Communications. 14, 1, 15 p., 5276.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Published

    Deep-sequencing of viral genomes from a large and diverse cohort of treatment-naive HIV-infected persons shows associations between intrahost genetic diversity and viral load

    INSIGHT START Study Group, I. S. S. G., 2023, In: PLOS Computational Biology. 19, 1, 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. 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 journalJournal articleResearchpeer-review

  5. 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 journalJournal articleResearchpeer-review

  6. Published

    CRISPRi screen for enhancing heterologous alpha-amylase yield in Bacillus subtilis

    Geissler, Adrian Sven, Fehler, A. O., Poulsen, L. D., Gonzalez-Tortuero, E., Kallehauge, T. B., Alkan, F., Anthon, Christian, Seemann, Ernst Stefan, Rasmussen, M. D., Breuener, A., Hjort, C., Vinther, Jeppe & Gorodkin, Jan, 2023, In: Journal of Industrial Microbiology and Biotechnology. 50, 1, 16 p., kuac028.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    DNA metabarcoding illuminates the contribution of small and very small prey taxa to the diet of lions

    Groen, K., Beekenkamp, S., de Iongh, H. H., Lesilau, F., Chege, M., Narisha, L., Veldhuis, M., Bertola, Laura, van Bodegom, P. M. & Trimbos, K. B., 2023, In: Environmental DNA. 5, 6, p. 1321-1331 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    Identifying the genetic causes of phenotypically diagnosed Pakistani mucopolysaccharidoses patients by whole genome sequencing

    Gul, Rutaba, Firasat, S., Schubert, Mikkel, Ullah, A., Peña, E., Thuesen, Anne Cathrine Baun, Hussain, M., Stæger, Frederik Filip Vinggaard, Gjesing, A. P., Albrechtsen, Anders & Hansen, Torben, 2023, In: Frontiers in Genetics. 14, 13 p., 1128850.

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Genomic diversity and differentiation between island and mainland populations of white-tailed eagles (Haliaeetus albicilla)

    Hansen, C. C. R., Láruson, Á. J., Rasmussen, Jacob Agerbo, Ballesteros, J. A. C., Sinding, Mikkel Holger Strander, Hallgrimsson, G. T., von Schmalensee, M., Stefansson, R. A., Skarphédinsson, K. H., Labansen, A. L., Leivits, M., Sonne, C., Dietz, R., Skelmose, K., Boertmann, D., Eulaers, I., Martin, M. D., Helgason, A. S., Gilbert, M Thomas P & Pálsson, S., 2023, In: Molecular Ecology. 32, 8, p. 1925-1942 18 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    Between inflammation, homeostasis and adaptation: Systemic and tissue-specific responses to maternal immune activation

    Hansen, Signe Schmidt Kjølner, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 177 p.

    Research output: Book/ReportPh.D. thesisResearch

  11. Published

    Quantitative Evaluation of Stem-like Markers of Human Glioblastoma Using Single-Cell RNA Sequencing Datasets

    He, Yue, Døssing, Kristina Benedikte V, Sloth, Ane Beth, He, Xuening, Rossing, M. & Kjær, Andreas, 2023, In: Cancers. 15, 5, 16 p., 1557.

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. 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 journalJournal articleResearchpeer-review

  13. Published

    Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences

    Hernández Alonso, Germán, Ramos Madrigal, Jazmin, van Grouw, H., Ciucani, Marta Maria, Cavill, Emily Louisa, Sinding, Mikkel Holger Strander, Gopalakrishnan, Shyam, Antunes Pacheco, George & Gilbert, M Thomas P, 2023, In: Molecular Biology and Evolution. 40, 11, 17 p., msad243.

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. Published

    Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning

    Horlacher, M., Wagner, N., Moyon, L., Kuret, K., Goedert, N., Salvatore, Marco, Ule, J., Gagneur, J., Winther, Ole & Marsico, A., 2023, In: Genome Biology. 24, 1, 37 p., 180.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    DermX: An end-to-end framework for explainable automated dermatological diagnosis

    Jalaboi, R., Faye, F., Orbes-Arteaga, M., Jørgensen, D., Winther, Ole & Galimzianova, A., 2023, In: Medical Image Analysis. 83, 12 p., 102647.

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. Published

    Explainable Image Quality Assessments in Teledermatological Photography

    Jalaboi, R., Winther, Ole & Galimzianova, A., 2023, In: Telemedicine and e-Health. 29, 9, p. 1342-1348 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    Limited historical admixture between European wildcats and domestic cats

    Jamieson, A., Carmagnini, A., Howard-McCombe, J., Doherty, S., Hirons, A., Dimopoulos, E., Lin, A. T., Allen, R., Anderson-Whymark, H., Barnett, R., Batey, C., Beglane, F., Bowden, W., Bratten, J., De Cupere, B., Drew, E., Foley, N. M., Fowler, T., Fox, A., Geigl, E-M. & 35 others, Gotfredsen, Anne Birgitte, Grange, T., Griffiths, D., Groß, D., Haruda, A., Hjermind, J., Knapp, Z., Lebrasseur, O., Librado, P., Lyons, L. A., Mainland, I., McDonnell, C., Muñoz-Fuentes, V., Nowak, C., O'Connor, T., Peters, J., Russo, I. M., Ryan, H., Sheridan, A., Sinding, Mikkel Holger Strander, Skoglund, P., Swali, P., Symmons, R., Thomas, G., Jensen, Theis Zetner Trolle, Kitchener, A. C., Senn, H., Lawson, D., Driscoll, C., Murphy, W. J., Beaumont, M., Ottoni, C., Sykes, N., Larson, G. & Frantz, L., 2023, In: Current Biology. 33, 21, p. 4751-4760.e14

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Published

    Association of SLC12A1 and GLUR4 Ion Transporters with Neoadjuvant Chemoresistance in Luminal Locally Advanced Breast Cancer

    Justo-Garrido, M., López-Saavedra, A., Alcaraz, N., Cortés-González, C. C., Oñate-Ocaña, L. F., Caro-Sánchez, C. H. S., Castro-Hernández, C., Arriaga-Canon, C., Díaz-Chávez, J. & Herrera, L. A., 2023, In: International Journal of Molecular Sciences. 24, 22, 16 p., 16104.

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. Published

    Genetics as a novel tool in mining impact assessment and biomonitoring of critically endangered western chimpanzees in the Nimba Mountains, Guinea

    Koops, K., Humle, T., Frandsen, P., Fitzgerald, M., D'Auvergne, L., Jackson, H. A., Børsting, Claus, Siegismund, Hans Redlef, Soumah, A. G. & Hvilsom, C., 2023, In: Conservation Science and Practice. 5, 4, 17 p., e12898.

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. Published

    Mind the gap

    Larsen-Ledet, Sven & Stein, Amelie, 2023, In: Structure. 31, 6, p. 641-643 3 p.

    Research output: Contribution to journalComment/debateResearchpeer-review

  21. 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 journalJournal articleResearchpeer-review

  22. Published

    Fast and accurate out-of-core PCA framework for large scale biobank data

    Li, Z., Meisner, Jonas & Albrechtsen, Anders, 2023, In: Genome Research. 33, 9, p. 1599-1608 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    The history of Coast Salish “woolly dogs” revealed by ancient genomics and Indigenous Knowledge

    Lin, A. T., Hammond-Kaarremaa, L., Liu, H-L., Stantis, C., McKechnie, I., Pavel, M., Pavel, S. S. M., Wyss, S. S., Sparrow, D. Q., Carr, K., Aninta, S. G., Perri, A., Hartt, J., Bergström, A., Carmagnini, A., Charlton, S., Dalén, L., Feuerborn, T. R., France, C. A. M., Gopalakrishnan, S. & 13 others, Grimes, V., Harris, A., Kavich, G., Sacks, B. N., Sinding, Mikkel Holger Strander, Skoglund, P., Stanton, D. W. G., Ostrander, E. A., Larson, G., Armstrong, C. G., Frantz, L. A. F., Hawkins, M. T. R. & Kistler, L., 2023, In: Science. 382, 6676, p. 1303-1309 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. 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 journalJournal articleResearchpeer-review

  25. 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 journalConference articleResearchpeer-review

  26. Published

    Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

    Louis, Marie Georgette Yolande J, Korlević, P., Nykänen, M., Archer, F., Berrow, S., Brownlow, A., Lorenzen, Eline, O'Brien, J., Post, K., Racimo, Fernando, Rogan, E., Rosel, P. E., Sinding, Mikkel Holger Strander, van der Es, H., Wales, N., Fontaine, M. C., Gaggiotti, O. E. & Foote, A. D., 2023, In: Nature Communications. 14, 13 p., 4020.

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Published
  28. Published

    Regulation of plant immunity via small RNA-mediated control of NLR expression

    López Márquez, Diego, Del-Espino, Á., Ruiz-Albert, J., Bejarano, E. R., Brodersen, Peter & Beuzón, C. R., 2023, In: Journal of Experimental Botany. 74, 19, p. 6052-6068 17 p.

    Research output: Contribution to journalReviewResearchpeer-review

  29. Published

    Plant YTHDF proteins are direct effectors of antiviral immunity against an N6-methyladenosine-containing RNA virus

    Martínez-Pérez, M., Aparicio, F., Arribas Hernandez, Laura, Tankmar, Mathias Due, Rennie, Sarah, von Bülow, Sören, Lindorff-Larsen, Kresten, Brodersen, Peter & Pallas, V., 2023, In: EMBO Journal. 42, 18, 17 p., e113378.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Published

    Pooled analysis of frontal lobe transcriptomic data identifies key mitophagy gene changes in Alzheimer's disease brain

    Mei, T., Li, Yuan, Orduña Dolado, A., Li, Zhiquan, Andersson, Robin, Berliocchi, Laura & Rasmussen, Lene Juel, 2023, In: Frontiers in Aging Neuroscience. 15, 14 p., 1101216.

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. Published

    Benchmarking RNA Editing Detection Tools

    Morales, D. R., Rennie, Sarah & Uchida, S., 2023, In: BioTech. 12, 3, 18 p., 56.

    Research output: Contribution to journalReviewResearchpeer-review

  32. Published

    Application of whole genome sequencing data in population genetics: identifying sex-linked scaffolds and inferring admixture in a unique cattle population

    Nursyifa, Casia, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 225 p.

    Research output: Book/ReportPh.D. thesisResearch

  33. Published

    Exploring antidepressant treatment response using biological and clinical measurements

    Nøhr, A. K., 2023, Department of Biology, Faculty of Science, University of Copenhagen. 125 p.

    Research output: Book/ReportPh.D. thesisResearch

  34. Published

    CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network

    Pan, X., Ma, Z., Sun, X., Li, H., Zhang, T., Zhao, C., Wang, N., Heller, Rasmus, Hung Wong, W., Wang, W., Jiang, Y. & Wang, Y., 2023, In: Genomics, Proteomics and Bioinformatics. 21, 3, p. 632-648 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Published
  36. Published

    Functions of m6A-YTH modules in plants: Lessons from high-throughput sequencing analyses

    Porcelli, C., 2023, Department of Biology, Faculty of Science, University of Copenhagen. 178 p.

    Research output: Book/ReportPh.D. thesisResearch

  37. Published

    Systematic Analysis of Long Non-Coding RNAs in Inflammasome Activation in Monocytes/Macrophages

    Qian, N., Distefano, R., Ilieva, M., Madsen, J. H., Rennie, Sarah & Uchida, S., 2023, In: Non-coding RNA. 9, 5, 16 p., 50.

    Research output: Contribution to journalJournal articleResearchpeer-review

  38. Published

    A population of stem cells with strong regenerative potential discovered in deer antlers

    Qin, T., Zhang, G., Zheng, Y., Li, S., Yuan, Y., Li, Q., Hu, M., Si, H., Wei, G., Gao, X., Cui, X., Xia, B., Ren, J., Wang, K., Ba, H., Liu, Z., Heller, R., Li, Z., Wang, W., Huang, J. & 2 others, Li, C. & Qiu, Q., 2023, In: Science (New York, N.Y.). 379, 6634, p. 840-847 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. Published
  40. Published

    Probabilistic modelling in genomics

    Rasmussen, Malthe Sebro, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 158 p.

    Research output: Book/ReportPh.D. thesisResearch

  41. 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 journalJournal articleResearchpeer-review

  42. Published

    Potential usages of A-to-I RNA editing patterns as diagnostic biomarkers

    Rodriguez Morales, D., Ilieva, M., Rennie, Sarah & Uchida, S., 2023, In: American journal of physiology. Cell physiology. 324, 4, p. C837-C842 6 p.

    Research output: Contribution to journalReviewResearchpeer-review

  43. Published

    Chronic acidosis rewires cancer cell metabolism through PPARα signaling

    Rolver, M. G., Holland, L. K. K., Ponniah, M., Prasad, N. S., Yao, Jiayi, Schnipper, J., Kramer, S., Elingaard-Larsen, L., Pedraz-Cuesta, E., Liu, B., Pardo, L. A., Maeda, K., Sandelin, Albin Gustav & Pedersen, Stine Helene Falsig, 2023, In: International Journal of Cancer. 152, 8, 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. 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 journalJournal articleResearchpeer-review

  45. Published

    Genetic Loss of Sucrase-Isomaltase Function: Mechanisms, Implications, and Future Perspectives

    Senftleber, N. K., Ramne, Stina, Moltke, Ida, Jørgensen, M. E., Albrechtsen, Anders, Hansen, Torben & Lepola, Mette Andersen, 2023, In: Application of Clinical Genetics. 16, p. 31-39 9 p.

    Research output: Contribution to journalReviewResearchpeer-review

  46. Published

    Bridging the gap in African biodiversity genomics and bioinformatics

    Sharaf, A., Ndiribe, C. C., Omotoriogun, T. C., Abueg, L., Badaoui, B., Badiane Markey, F. J., Beedessee, G., Diouf, D., Duru, V. C., Ebuzome, C., Eziuzor, S. C., Jaufeerally Fakim, Y., Formenti, G., Ghanmi, N., Guerfali, F. Z., Houaga, I., Ideozu, J. E., Katee, S. M., Khayi, S., Kuja, J. O. & 16 others, Kwon-Ndung, E. H., Marks, R. A., Moila, A. M., Mungloo-Dilmohamud, Z., Muzemil, S., Nigussie, H., Osuji, J. O., Ras, V., Tchiechoua, Y. H., Zoclanclounon, Y. A. B., Tolley, K. A., Ziyomo, C., Mapholi, N., Muigai, A. W. T., Djikeng, A. & Ebenezer, T. G. E., 2023, In: Nature Biotechnology. 41, 9, p. 1348-1354 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. Published

    Hepatitis C virus RNA is 5'-capped with flavin adenine dinucleotide

    Sherwood, A. V., Rivera-Rangel, L. R., Ryberg, L. A., Larsen, H. S., Anker, K. M., Costa, R., Vågbø, C. B., Jakljevič, E., Pham, L. V., Fernandez-Antunez, C., Indrisiunaite, G., Podolska-Charlery, A., Grothen, J. E. R., Langvad, N. W., Fossat, N., Offersgaard, A., Al-Chaer, A., Nielsen, L., Kuśnierczyk, A., Sølund, C. & 8 others, Weis, Nina, Gottwein, Judith Margarete, Holmbeck, Kenn, Bottaro, S., Ramirez Almeida, Santseharay, Bukh, Jens, Scheel, Troels Kasper Høyer & Vinther, Jeppe, 2023, In: Nature. 619, p. 811-818

    Research output: Contribution to journalJournal articleResearchpeer-review

  48. Published

    Deep integrative models for large-scale human genomics

    Sigurdsson, Arnór Ingi, Louloudis, Ioannis, Banasik, Karina, Westergaard, David, Winther, Ole, Lund, O., Ostrowski, Sisse Rye, Erikstrup, C., Pedersen, Ole Birger Vesterager, Nyegaard, Mette, Brunak, Søren, Vilhjálmsson, B. & Rasmussen, Simon, 2023, In: Nucleic Acids Symposium Series. 51, 12, 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. Published

    Characterization of industrially-produced Lacticaseibacillus rhamnosus GG and Lactobacillus acidophilus LA-5: Analysis of genomic integrity, transcriptome and phenotypes

    Strickertsson, Marianne Stage, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 206 p.

    Research output: Book/ReportPh.D. thesisResearch

  50. Published

    Possible signs of recovery of the nearly extirpated Spitsbergen bowhead whales: calves observed in east Greenland

    Tervo, O. M., Louis, Marie Georgette Yolande J, Sinding, Mikkel Holger Strander, Heide-Jørgensen, M. P. & Hansen, R. G., 2023, In: Polar Research. 42, 4 p., 8809.

    Research output: Contribution to journalJournal articleResearchpeer-review

  51. Published

    DeepPeptide predicts cleaved peptides in proteins using conditional random fields

    Teufel, Felix Georg, Refsgaard, J. C., Madsen, C. T., Stahlhut, C., Grønborg, M., Winther, Ole & Madsen, D., 2023, In: Bioinformatics (Oxford, England). 39, 10, 6 p., btad616.

    Research output: Contribution to journalJournal articleResearchpeer-review

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