Computational and RNA Biology

  1. 2023
  2. 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

  3. 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

  4. 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

  5. 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

  6. 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 paperPreprintResearch

  7. Published
  8. 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 journalJournal articleResearchpeer-review

  9. 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 journalJournal articleResearchpeer-review

  10. 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

  11. 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

  12. Published

    Crosstalk between tumor acidosis, p53 and extracellular matrix regulates pancreatic cancer aggressiveness

    Czaplinska, D., Ialchina, Renata, Andersen, Henriette Berg, Yao, Jiayi, Stigliani, Arnaud, Dannesboe, Johs, Flinck, M., Chen, X., Mitrega, J., Gnosa, S. P., Dmytriyeva, O., Alves, F., Napp, J., Sandelin, Albin Gustav & Pedersen, Stine Helene Falsig, 2023, In: International Journal of Cancer. 152, 6, p. 1210-1225 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. 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

  14. Published

    Deciphering regulatory mechanisms underlying gene co-activity

    van Duin, Lucas, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 131 p.

    Research output: Book/ReportPh.D. thesisResearch

  15. Published

    Deep integrative models for large-scale human genomics

    Sigurdsson, Arnór Ingi, Louloudis, Ioannis, Banasik, Karina, Westergaard, D., 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

  16. 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

  17. 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

  18. Published

    Deorphanizing Peptides Using Structure Prediction

    Teufel, Felix Georg, Refsgaard, J. C., Kasimova, M. A., Deibler, K., Madsen, C. T., Stahlhut, C., Grønborg, M., Winther, Ole & Madsen, D., 2023, In: Journal of Chemical Information and Modeling. 63, 9, 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. 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

  20. Published

    Detecting host responses to microbial stimulation using primary epithelial organoids

    Lange, Jette Bornholdt, Müller, C. V., Nielsen, M. J., Strickertsson, J., Rago, D., Chen, Y., Maciag, Grzegorz Jerzy, Skov, Jonathan, Wellejus, A., Schweiger, P. J., Hansen, Stine Lind, Broholm, C., Gögenur, Ismail, Maimets, Martti, Sloth, S., Hendel, J., Baker, A., Sandelin, Albin Gustav & Jensen, Kim Bak, 2023, In: Gut Microbes. 15, 2, 16 p., 2281012.

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Published

    DoxoDB: A Database for the Expression Analysis of Doxorubicin-Induced lncRNA Genes

    Distefano, R., Ilieva, M., Madsen, J. H., Rennie, Sarah & Uchida, S., 2023, In: Non-coding RNA. 9, 4, 24 p., 39.

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    Editorial: Long-read sequencing—Pitfalls, benefits and success stories

    Wohlers, I., Garg, S. & Hehir-Kwa, J. Y., 2023, In: Frontiers in Genetics. 13, 3 p., 1114542.

    Research output: Contribution to journalEditorialResearchpeer-review

  23. 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

  24. Published

    Evaluation of population structure inferred by principal component analysis or the admixture model

    Van Waaij, J., Li, Song, Garcia Erill, Genís, Albrechtsen, Anders & Wiuf, Carsten, 2023, In: Genetics. 225, 2, 14 p., iyad157.

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. Published

    Evidence for early domestic yak, taurine cattle, and their hybrids on the Tibetan Plateau

    Chen, N., Zhang, Z., Hou, J., Chen, J., Gao, X., Tang, L., Wangdue, S., Zhang, X., Sinding, Mikkel Holger Strander, Liu, X., Han, J., Lü, H., Lei, C., Marshall, F. & Liu, X., 2023, In: Science Advances. 9, 50, 13 p., eadi6857.

    Research output: Contribution to journalJournal articleResearchpeer-review

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. Published

    Genomics of adaptive evolution in the woolly mammoth

    Díez-del-Molino, D., Dehasque, M., Chacón-Duque, J. C., Chrzanová Pecnerová, Patrícia, Tikhonov, A., Protopopov, A., Plotnikov, V., Kanellidou, F., Nikolskiy, P., Mortensen, P., Danilov, G. K., Vartanyan, S., Gilbert, M Thomas P, Lister, A. M., Heintzman, P. D., van der Valk, T. & Dalén, L., 2023, In: Current Biology. 33, 9, 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. 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

  35. Published

    Global dispersal and adaptive evolution of domestic cattle: a genomic perspective

    Xia, X., Qu, K., Wang, Y., Sinding, Mikkel Holger Strander, Wang, F., Hanif, Q., Ahmed, Z., Lenstra, J. A., Han, J., Lei, C. & Chen, N., 2023, In: Stress Biology. 3, 1, 13 p., 8.

    Research output: Contribution to journalReviewResearchpeer-review

  36. Published

    Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing

    Chen, N., Xia, X., Hanif, Q., Zhang, F., Dang, R., Huang, B., Lyu, Y., Luo, X., Zhang, H., Yan, H., Wang, S., Wang, F., Chen, J., Guan, X., Liu, Y., Li, S., Jin, L., Wang, P., Sun, L., Zhang, J. & 37 others, Liu, J., Qu, K., Cao, Y., Sun, J., Liao, Y., Xiao, Z., Cai, M., Mu, L., Siddiki, A. Z., Asif, M., Mansoor, S., Babar, M. E., Hussain, T., Silva, G. L. L. P., Gorkhali, N. A., Terefe, E., Belay, G., Tijjani, A., Zegeye, T., Gebre, M. G., Ma, Y., Wang, Y., Huang, Y., Lan, X., Chen, H., Migliore, N. R., Colombo, G., Semino, O., Achilli, A., Sinding, Mikkel Holger Strander, Lenstra, J. A., Cheng, H., Lu, W., Hanotte, O., Han, J., Jiang, Y. & Lei, C., 2023, In: Nature Communications. 14, 1, 13 p., 7803.

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. Published

    Graph neural network interatomic potential ensembles with calibrated aleatoric and epistemic uncertainty on energy and forces

    Busk, J., Schmidt, M. N., Winther, Ole, Vegge, T. & Jørgensen, P. B., 2023, In: Physical Chemistry Chemical Physics. 25, p. 25828-25837 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  38. Published

    GraphPart: homology partitioning for biological sequence analysis

    Teufel, Felix Georg, Gíslason, M. H., Almagro Armenteros, J. J., Johansen, A. R., Winther, Ole & Nielsen, H., 2023, In: NAR Genomics and Bioinformatics. 5, 4, 9 p., lqad088.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. 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

  40. 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

  41. Published

    Insights into the conservation and diversification of the molecular functions of YTHDF proteins

    Flores-Téllez, D., Tankmar, Mathias Due, von Bülow, Sören, Chen, Junyu, Lindorff-Larsen, Kresten, Brodersen, Peter & Arribas Hernandez, Laura, 2023, In: PLOS Genetics. 19, 10, 37 p., e1010980.

    Research output: Contribution to journalJournal articleResearchpeer-review

  42. Published

    Interpreting the molecular mechanisms of disease variants in human transmembrane proteins

    Tiemann, Johanna Katarina Sofie, Zschach, Henrike, Lindorff-Larsen, Kresten & Stein, Amelie, 2023, In: Biophysical Journal. 122, 11, 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Published
  44. Published

    Limited genetic variations of the Rh5-CyRPA-Ripr invasion complex in Plasmodium falciparum parasite population in selected malaria-endemic regions, Kenya

    Waweru, H., Kanoi, B. N., Kuja, J. O., Maranga, M., Kongere, J., Maina, M., Kinyua, J. & Gitaka, J., 2023, In: Frontiers in Tropical Diseases. 4, 9 p., 1102265.

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. 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

  46. Published

    Long divergent haplotypes introgressed from wild sheep are associated with distinct morphological and adaptive characteristics in domestic sheep

    Cheng, H., Zhang, Z., Wen, J., Lenstra, J. A., Heller, Rasmus, Cai, Y., Guo, Y., Li, M., Li, R., Li, W., He, S., Wang, J., Shao, J., Song, Y., Zhang, L., Billah, M., Wang, X., Liu, M. & Jiang, Y., 2023, In: PLOS Genetics. 19, 2, 27 p., e1010615.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. 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

  48. Published

    Molecular Representations in Machine-Learning-Based Prediction of PK Parameters for Insulin Analogs

    Einarson, K. A., Bendtsen, K. M., Li, K., Thomsen, M., Kristensen, N. R., Winther, Ole, Fulle, S., Clemmensen, L. & Refsgaard, H. H. F., 2023, In: ACS Omega. 8, 26, p. 23566-23578 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. Published

    Multiple paths toward repeated phenotypic evolution in the spiny-leg adaptive radiation (Tetragnatha; Hawai'i)

    Cerca, J., Cotoras, D. D., Santander, Cindy, Bieker, V. C., Hutchins, L., Morin-Lagos, J., Prada, C. F., Kennedy, S., Krehenwinkel, H., Rominger, A. J., Meier, J., Dimitrov, D., Struck, T. H. & Gillespie, R. G., 2023, In: Molecular Ecology. 32, 18, p. 4971-4985 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  50. 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/ReportPh.D. thesisResearch

  51. 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

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