Computational and RNA Biology

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  1. 2024
  2. 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

  3. 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

  4. 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

  5. Published

    Mitogenomic Characterization of South African Leopards and the Effect of Past Climatic Events

    Tensen, Laura Nicole, Emami-Khoyi, A., Khan, Anubhab, Camacho, G., Swanepoel, L. & Fischer, K., 2024, In: Journal of Zoological Systematics and Evolutionary Research. 2024, 14 p., 2174469.

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

  6. 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

  7. 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

  8. 2023
  9. 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/Report › Ph.D. thesis › Research

  10. Published

    Proteomic Profiling of Colorectal Adenomas Identifies a Predictive Risk Signature for Development of Metachronous Advanced Colorectal Neoplasia

    Bech, J. M., Terkelsen, Thilde Bagger, Bartels, Annette Snejbjerg, Coscia, F., Doll, S., Zhao, S., Zhang, Z., Brünner, N., Lindebjerg, J., Madsen, G. I., Fang, X., Mann, Matthias & Moreira, José, 2023, In: Gastroenterology. 165, 1, p. 121-132.e5

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

  11. Published

    Rapid protein stability prediction using deep learning representations

    Blaabjerg, Lasse Møller, Kassem, M. M., Good, L. L., Jonsson, Nicolas, Cagiada, Matteo, Johansson, Kristoffer Enøe, Boomsma, Wouter, Stein, Amelie & Lindorff-Larsen, Kresten, 2023, In: eLife. 12, 19 p., e82593.

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

  12. 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 journal › Journal article › Research › peer-review

  13. Published

    The N-coil and the globular N-terminal domain of plant ARGONAUTE1 are interaction hubs for regulatory factors

    Bressendorff, Simon, Kausika, S., Sjøgaard, Ida Marie Zobbe, Oksbjerg, Emilie Duus, Michels, A., Poulsen, C. & Brodersen, Peter, 2023, In: Biochemical Journal. 480, 13, p. 957-974 18 p.

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

  14. 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 journal › Journal article › Research › peer-review

  15. 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 journal › Journal article › Research › peer-review

  16. 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 journal › Journal article › Research › peer-review

  17. 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 journal › Journal article › Research › peer-review

  18. 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 journal › Journal article › Research › peer-review

  19. Published

    The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs

    Ciucani, M. M., Ramos-Madrigal, J., Hernández-Alonso, G., Carmagnini, A., Aninta, S. G., Sun, X., Scharff-Olsen, C. H., Lanigan, L. T., Fracasso, I., Clausen, C. G., Aspi, J., Kojola, I., Baltrūnaitė, L., Balčiauskas, L., Moore, J., Åkesson, M., Saarma, U., Hindrikson, M., Hulva, P., Bolfíková, B. Č. & 19 others, Nowak, C., Godinho, R., Smith, S., Paule, L., Nowak, S., Mysłajek, R. W., Lo Brutto, S., Ciucci, P., Boitani, L., Vernesi, C., Stenøien, H. K., Smith, O., Frantz, L., Rossi, L., Angelici, F. M., Cilli, E., Sinding, Mikkel Holger Strander, Gilbert, M Thomas P & Gopalakrishnan, Shyam, 2023, In: iScience. 26, 8, 22 p., 107307.

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

  20. 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 journal › Journal article › Research › peer-review

  21. 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

  22. 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 journal › Journal article › Research › peer-review

  23. Published

    T2DB: A Web Database for Long Non-Coding RNA Genes in Type II Diabetes

    Distefano, R., Ilieva, M., Madsen, J. H., Ishii, H., Aikawa, M., Rennie, Sarah & Uchida, S., 2023, In: Non-coding RNA. 9, 3, 20 p., 30.

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

  24. 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

  25. Published

    A YTHDF–PABP interaction is required for m6A-mediated organogenesis in plants

    Tankmar, Mathias Due, Reichel, M., Arribas Hernandez, Laura & Brodersen, Peter, 2023, In: EMBO Reports. 24, 12, 19 p., e57741.

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

  26. 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 journal › Journal article › Research › peer-review

  27. 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 journal › Journal article › Research › peer-review

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