Computational and RNA Biology

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  1. 2022
  2. Published

    DeepLoc 2.0: multi-label subcellular localization prediction using protein language models

    Thumuluri, V., Almagro Armenteros, J. J., Johansen, A. R., Nielsen, H. & Winther, Ole, 2022, In: Nucleic Acids Research. 50, W1, p. W228-W234

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

  3. Published

    Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA

    Dehasque, M., Chrzanová Pecnerová, Patrícia, Kempe Lagerholm, V., Ersmark, E., Danilov, G. K., Mortensen, P., Vartanyan, S. & Dalén, L., 2022, In: Genes. 13, 4, 16 p., 687.

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

  4. Published

    Disease-linked mutations cause exposure of a protein quality control degron

    Kampmeyer, Caroline, Larsen-Ledet, Sven, Wagnkilde, M. R., Michelsen, M., Iversen, Henriette Kring Mangor, Nielsen, S. V., Lindemose, Søren, Caregnato, A., Ravid, T., Stein, Amelie, Teilum, Kaare, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2022, In: Structure. 30, 9, p. 1245-1253.e5

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

  5. Published

    Efficient approaches for large-scale GWAS with genotype uncertainty

    Jørsboe, E. & Albrechtsen, Anders, 2022, In: G3: Genes, Genomes, Genetics (Bethesda). 12, 1, 9 p., jkab385.

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

  6. Published

    Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells

    Bakoulis, Stylianos, Krautz, Robert, Alcaraz, N., Salvatore, Marco & Andersson, Robin, 2022, In: Nucleic acids symposium series. 50, 4, p. 2111-2127 17 p., 088.

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

  7. Published

    Estimation of site frequency spectra from low-coverage sequencing data using stochastic EM reduces overfitting, runtime, and memory usage

    Rasmussen, Malthe Sebro, Garcia Erill, Genís, Korneliussen, Thorfinn Sand, Wiuf, Carsten & Albrechtsen, Anders, 2022, In: Genetics. 222, 4, 15 p., iyac148.

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

  8. Published

    Estimation of the covariance structure from SNP allele frequencies

    van Waaij, J., Li, Z. & Wiuf, Carsten, 2022, In: Statistical Applications in Genetics and Molecular Biology. 21, 1, 20 p., 20220005.

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

  9. Published

    Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome

    van der Valk, T., Dehasque, M., Chacón-Duque, J. C., Oskolkov, N., Vartanyan, S., Heintzman, P. D., Chrzanová Pecnerová, Patrícia, Díez-del-Molino, D. & Dalén, L., 2022, In: iScience. 25, 8, 11 p., 104826.

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

  10. Published

    Flagella disruption in Bacillus subtilis increases amylase production yield

    Fehler, A. O., Kallehauge, T. B., Geissler, Adrian Sven, González-Tortuero, E., Seemann, Ernst Stefan, Gorodkin, Jan & Vinther, Jeppe, 2022, In: Microbial Cell Factories. 21, 11 p., 131.

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

  11. Published

    Genetic guidelines for translocations: Maintaining intraspecific diversity in the lion (Panthera leo)

    Bertola, Laura, Miller, S. M., Williams, V. L., Naude, V. N., Coals, P., Dures, S. G., Henschel, P., Chege, M., Sogbohossou, E. A., Ndiaye, A., Kiki, M., Gaylard, A., Ikanda, D. K., Becker, M. S. & Lindsey, P., 2022, In: Evolutionary Applications. 15, 1, p. 22-39 18 p.

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

  12. Published

    Genetic loci and prioritization of genes for kidney function decline derived from a meta-analysis of 62 longitudinal genome-wide association studies

    Gorski, M., Rasheed, H., Teumer, A., Thomas, L. F., Graham, S. E., Sveinbjornsson, G., Winkler, T. W., Günther, F., Stark, K. J., Chai, J-F., Tayo, B. O., Wuttke, M., Li, Y., Tin, A., Ahluwalia, T. S., Ärnlöv, J., Åsvold, B. O., Bakker, S. J. L., Banas, B., Bansal, N. & 29 others, Biggs, M. L., Biino, G., Böhnke, M., Boerwinkle, E., Bottinger, E. P., Brenner, H., Brumpton, B., Carroll, R. J., Chaker, L., Chalmers, J., Chee, M., Chee, M., Cheng, C., Chu, A. Y., Ciullo, M., Cocca, M., Cook, J. P., Coresh, J., Cusi, D., de Borst, M. H., Degenhardt, F., Eckardt, K., Endlich, K., Evans, M. K., Feitosa, M. F., Franke, A., Freitag-Wolf, S., Rossing, Peter & LifeLines Cohort Study, L. C. S., 2022, In: Kidney International. 102, 3, p. 624-639 16 p.

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

  13. Published

    Genetics of early-life head circumference and genetic correlations with neurological, psychiatric and cognitive outcomes

    Vogelezang, S., Bradfield, J. P., Early Growth Genetics Consortium, Ahluwalia, T. V. S., Liu, X., Schnurr, T. M., Frithioff-Bøjsøe, C., Bønnelykke, K., Lind, M. V., Lauritzen, L., Michaelsen, K. F., Lund, M. A. V., Melbye, M., Morgen, C. S., Pedersen, O. B., Holm, J-C., Grarup, N., Hansen, T., Nohr, E. A., Bisgaard, H. & 3 others, Grant, S. F. A., Felix, J. F. & Jaddoe, V. W. V., 2022, In: BMC Medical Genomics. 15, 16 p., 124.

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

  14. Published

    Genome-wide study of early and severe childhood asthma identifies interaction between CDHR3 and GSDMB

    Eliasen, A. U., Pedersen, C. E. T., Rasmussen, M. A., Wang, N., Soverini, M., Fritz, A., Stokholm, J., Chawes, B. L., Morin, A., Bork-Jensen, J., Grarup, N., Pedersen, O., Hansen, T., Linneberg, A., Mortensen, P. B., Hougaard, D. M., Bybjerg-Grauholm, J., Bækvad-Hansen, M., Mors, O., Nordentoft, M. & 14 others, Børglum, A. D., Werge, Thomas, Agerbo, E., Söderhall, C., Altman, M. C., Thysen, A. H., McKennan, C. G., Brix, Susanne, Gern, J. E., Ober, C., Ahluwalia, Tarun Veer Singh, Bisgaard, H., Pedersen, A. G. & Bønnelykke, Klaus, 2022, In: Journal of Allergy and Clinical Immunology. 150, 3, p. 622-630

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

  15. Published

    Genomic evidence refutes the hypothesis that the Bornean banteng is a distinct species

    Sun, Xin, Ciucani, M. M., Rasmussen, Jacob Agerbo, Gilbert, M Thomas P & Sinding, Mikkel Holger Strander, 2022, In: BMC Ecology and Evolution. 22, 4 p., 110.

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

  16. Published

    Genomic stability and phenotypic characteristics of industrially-produced Lacticaseibacillus rhamnosus GG

    Strickertsson, Marianne Stage, 2022, Department of Biology, Faculty of Science, University of Copenhagen. 112 p.

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

  17. Published

    Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya

    Kuja, J. O., Kanoi, B. N., Balboa, Renzo Fidel Ferdinando, Shiluli, C., Maina, M., Waweru, H., Gathii, K., Mungai, M., Masika, M., Anzala, O., Mwau, M., Clark, T. G., Waitumbi, J. & Gitaka, J., 2022, In: BMC Genomics. 23, 1, 8 p., 627.

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

  18. Published

    Genomic variation in baboons from central Mozambique unveils complex evolutionary relationships with other Papio species

    Santander, C., Molinaro, L., Mutti, G., Martínez, F. I., Mathe, J., da Silva, M. J. F., Caldon, M., Oteo-Garcia, G., Aldeias, V., Archer, W., Bamford, M., Biro, D., Bobe, R., Braun, D. R., Hammond, P., Lüdecke, T., Pinto, M. J., Meira Paulo, L., Stalmans, M., Regala, F. T. & 6 others, Bertolini, F., Moltke, Ida, Raveane, A., Pagani, L., Carvalho, S. & Capelli, C., 2022, In: BMC Ecology and Evolution. 22, 16 p., 44.

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

  19. Published

    Grey wolf genomic history reveals a dual ancestry of dogs

    Bergström, A., Stanton, D. W. G., Taron, U. H., Frantz, L., Sinding, M. H. S., Ersmark, E., Pfrengle, S., Cassatt-Johnstone, M., Lebrasseur, O., Girdland-Flink, L., Fernandes, D. M., Ollivier, M., Speidel, L., Gopalakrishnan, S., Westbury, M. V., Ramos-Madrigal, J., Feuerborn, T. R., Reiter, E., Gretzinger, J., Münzel, S. C. & 61 others, Swali, P., Conard, N. J., Carøe, C., Haile, James Seymour, Linderholm, A., Androsov, S., Barnes, I., Baumann, C., Benecke, N., Bocherens, H., Brace, S., Carden, R. F., Drucker, D. G., Fedorov, S., Gasparik, M., Germonpré, M., Grigoriev, S., Groves, P., Hertwig, S. T., Ivanova, V. V., Janssens, L., Jennings, R. P., Kasparov, A. K., Kirillova, I. V., Kurmaniyazov, I., Kuzmin, Y. V., Kosintsev, P. A., Lázničková-Galetová, M., Leduc, C., Nikolskiy, P., Nussbaumer, M., O’Drisceoil, C., Orlando, L., Outram, A., Pavlova, E. Y., Perri, A. R., Pilot, M., Pitulko, V. V., Plotnikov, V. V., Protopopov, A. V., Rehazek, A., Sablin, M., Seguin-Orlando, A., Storå, J., Verjux, C., Zaibert, V. F., Zazula, G., Crombé, P., Hansen, Anders Johannes, Willerslev, Eske, Leonard, J. A., Götherström, A., Pinhasi, R., Schuenemann, V. J., Hofreiter, M., Gilbert, M Thomas P, Shapiro, B., Larson, G., Krause, J., Dalén, L. & Skoglund, P., 2022, In: Nature. 607, 7918, p. 313-320

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

  20. Published

    Guidelines for evaluating the conservation value of African lion (Panthera leo) translocations

    Becker, M. S., Almeida, J., Begg, C., Bertola, L., Breitenmoser, C., Breitenmoser, U., Coals, P., Funston, P., Gaylard, A., Groom, R., Henschel, P., Ikanda, D., Jorge, A., Kruger, J., Lindsey, P., Maimbo, H., Mandisodza-Chikerema, R., Maude, G., Mbizah, M., Miller, S. M. & 17 others, Mudongo, E., Mwape, H., Mweetwa, T., Naude, V., Nyirenda, V. R., Parker, A., Parker, D., Reid, C., Robson, A., Sayer, E., Selier, S. J., Sichande, M., Simukonda, C., Uiseb, K., Williams, V. L., Zimba, D. & Hunter, L., 2022, In: Frontiers in Conservation Science. 3, 13 p., 963961.

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

  21. Published

    H3K9 dimethylation safeguards cancer cells against activation of the interferon pathway

    Hansen, A. M., Ge, Y., Schuster, Mikkel Bruhn, Pundhir, Sachin, Jakobsen, J. S., Kalvisa, A., Tapia, Marta Cecylia, Gordon, Sandra, Ambri, F., Bagger, F. O., Pandey, D., Helin, K. & Porse, Bo Torben, 2022, In: Science Advances. 8, 11, eabf8627.

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

  22. Published

    Haplotype and population structure inference using neural networks in whole-genome sequencing data

    Meisner, Jonas & Albrechtsen, Anders, 2022, In: Genome Research. 32, 8, p. 1542-1552 11 p.

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

  23. Published

    Integrating convolution and self-attention improves language model of human genome for interpreting non-coding regions at base-resolution

    YANG, Meng, Huang, L., Huang, H., Tang, H., Zhang, N., Yang, H., Wu, J. & Mu, F., 2022, In: Nucleic Acids Research. 50, 14, 19 p., e81.

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

  24. Published

    JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

    Castro-Mondragon, J. A., Riudavets-Puig, R., Rauluseviciute, I., Lemma, R. B., Turchi, L., Blanc-Mathieu, R., Lucas, J., Boddie, P., Khan, A., Perez, N. M., Fornes, O., Leung, T. Y., Aguirre, A., Hammal, F., Schmelter, D., Baranasic, D., Ballester, B., Sandelin, A., Lenhard, B., Vandepoele, K. & 3 others, Wasserman, W. W., Parcy, F. & Mathelier, A., 2022, In: Nucleic acids symposium series. 50, D1, p. D165-D173 9 p.

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

  25. Published

    Joint identification of sex and sex-linked scaffolds in non-model organisms using low depth sequencing data

    Nursyifa, Casia, Brüniche-Olsen, Anna, Garcia Erill, Genís, Heller, Rasmus & Albrechtsen, Anders, 2022, In: Molecular Ecology Resources. 22, 2, p. 458-467 10 p.

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

  26. Published

    Life-threatening viral disease in a novel form of autosomal recessive IFNAR2 deficiency in the Arctic

    Duncan, C. J. A., Skouboe, M. K., Howarth, S., Hollensen, A. K., Chen, R., Børresen, M. L., Thompson, B. J., Spegarova, J. S., Hatton, C. F., Stæger, F. F., Andersen, M. K., Whittaker, J., Paludan, S. R., Jørgensen, S. E., Thomsen, M. K., Mikkelsen, J. G., Heilmann, C., Buhas, D., Øbro, N. F., Bay, J. T. & 17 others, Marquart, Hanne Vibeke Hansen, Morena, M. T. D. L., Klejka, J. A., Hirschfeld, M., Borgwardt, L., Forss, I., Masmas, T., Poulsen, A., Noya, F., Rouleau, G., Hansen, Torben, Zhou, S., Albrechtsen, Anders, Alizadehfar, R., Allenspach, E. J., Hambleton, S. & Mogensen, T. H., 2022, In: Journal of Experimental Medicine. 219, 6, 26 p., e20212427.

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

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