Computational and RNA Biology

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  1. 2022
  2. Published

    Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs

    Lv, W., Pan, X., Han, P., Wang, Z., Feng, W., Xing, X., Wang, Q., Qu, K., Zeng, Y., Zhang, C., Xu, Z., Li, Y., Zheng, T., Lin, L., Liu, C., Liu, X., Li, H., Henriksen, R. A., Bolund, L., Lin, L. & 7 others, Jin, X., Yang, H., Zhang, X., Yin, T., Regenberg, Birgitte, He, F. & Luo, Y., 2022, In: Clinical and Translational Medicine. 12, 4, 16 p., e817.

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

  3. Published

    Nutrient Availability Does Not Affect Community Assembly in Root-Associated Fungi but Determines Fungal Effects on Plant Growth

    Maciá-Vicente, J. G., Bai, B., Qi, R., Ploch, S., Breider, F. & Thines, M., 2022, In: mSystems. 7, 3, 14 p., e00304-22.

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

  4. Published

    Mesenchymal-epithelial crosstalk shapes intestinal regionalisation via Wnt and Shh signalling

    Maimets, Martti, Pedersen, M. T., Guiu, J., Dreier, J., Thodberg, Malte, Antoku, Yasuko, Schweiger, P. J., Rib, Leonor, Bardini Bressan, Raul, Miao, Y., Garcia, K. C., Sandelin, Albin Gustav, Serup, Palle & Jensen, Kim Bak, 2022, In: Nature Communications. 13, 12 p., 715.

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

  5. Published

    Mixture Models for Spherical Data with Applications to Protein Bioinformatics

    Mardia, K. V., Barber, S., Burdett, P. M., Kent, J. T. & Hamelryck, Thomas Wim, 2022, Directional Statistics for Innovative Applications: A Bicentennial Tribute to Florence Nightingale. Springer, p. 15-32 (Forum for Interdisciplinary Mathematics).

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

  6. Published

    Plant YTHDF proteins are direct effectors of antiviral immunity against an m6A-containing RNA virus

    Martínez-Pérez, M., Aparicio, F., Arribas Hernandez, Laura, Tankmar, Mathias Due, Rennie, Sarah, Brodersen, Peter & Pallas, V., 2022, 36 p.

    Research output: Working paper › Preprint

  7. 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

  8. Published

    A review on ethnobotany, phytochemistry, and pharmacology of the genus Didymocarpus wall. (Gesneriaceae)

    Nanjala, C., Odago, W. O., Rono, P. C., Waswa, E. N., Mutinda, E. S., Oulo, M. A., Muema, F. W., Wanga, V. O., Mkala, E. M., Kuja, J., Njire, M. M. & Hu, G. W., 2022, In: Journal of Ethnopharmacology. 295, 25 p., 115404.

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

  9. Published

    Plastome structure of 8 Calanthe s.l. species (Orchidaceae): comparative genomics, phylogenetic analysis

    Nanjala, C., Wanga, V. O., Odago, W., Mutinda, E. S., Waswa, E. N., Oulo, M. A., Mkala, E. M., Kuja, J., Yang, J., Dong, X., Hu, G. & Wang, Q., 2022, In: BMC Plant Biology. 22, 22 p., 387.

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

  10. Published

    Bioinformatics of transcription factor binding prediction

    Navarro-Delgado, E. I., Salgado-Albarrán, M., Torres-Arciga, K., Alcaraz, N., Soto-Reyes, E., Herrera, L. A. & González-Barrios, R., 2022, Bioinformatics and Human Genomics Research. CRC Press, p. 203-221 19 p.

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

  11. 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

  12. Published

    Polygenic heterogeneity in antidepressant treatment and placebo response

    Nøhr, A. K., Forsingdal, A., Moltke, Ida, Howes, O. D., Vitezic, M., Albrechtsen, Anders & Dalby, M., 2022, In: Translational Psychiatry. 12, 8 p., 456.

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

  13. Published

    Massively targeted evaluation of therapeutic CRISPR off-targets in cells

    Pan, X., Qu, K., Yuan, H., Xiang, X., Anthon, C., Pashkova, L., Liang, X., Han, P., Corsi, G. I., Xu, F., Liu, P., Zhong, J., Zhou, Y., Ma, T., Jiang, H., Liu, J., Wang, J., Jessen, N., Bolund, L., Yang, H. & 5 others, Xu, X., Church, G. M., Gorodkin, Jan, Lin, L. & Luo, Y., 2022, In: Nature Communications. 13, 14 p., 4049.

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

  14. Published

    m6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5' splice site

    Parker, M. T., Soanes, B. K., Kusakina, J., Larrieu, A., Knop, K., Joy, N., Breidenbach, F., Sherwood, Anna, Barton, G. J., Fica, S. M., Davies, B. H. & Simpson, G. G., 2022, In: eLife. 11, 34 p., 78808.

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

  15. Published

    The novel inflammatory biomarker GlycA and triglyceride-rich lipoproteins are associated with the presence of subclinical myocardial dysfunction in subjects with type 1 diabetes mellitus

    Puig-Jové, C., Julve, J., Castelblanco, E., Julián, M. T., Amigó, N., Andersen, H. U., Ahluwalia, Tarun Veer Singh, Rossing, Peter, Mauricio, D., Jensen, M. T. & Alonso, N., 2022, In: Cardiovascular Diabetology. 21, 257.

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

  16. 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

  17. Published

    African climate and geomorphology drive evolution and ghost introgression in sable antelope

    Rocha, J. L., Vaz Pinto, P., Siegismund, Hans Redlef, Meyer, M., Jansen van Vuuren, B., Veríssimo, L., Ferrand, N. & Godinho, R., 2022, In: Molecular Ecology. 31, 10, p. 2968-2984 17 p.

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

  18. Published

    Transfer learning reveals sequence determinants of regulatory element accessibility

    Salvatore, Marco, Horlacher, M., Winther, Ole & Andersson, Robin, 2022, bioRxiv, 24 p.

    Research output: Working paper › Preprint

  19. 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

  20. Published

    Transition1x: a dataset for building generalizable reactive machine learning potentials

    Schreiner, M., Bhowmik, A., Vegge, T., Busk, J. & Winther, Ole, 2022, In: Scientific Data. 9, 1, 9 p., 779.

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

  21. Published

    LocalNgsRelate: a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data

    Severson, A. L., Korneliussen, Thorfinn Sand & Moltke, Ida, 2022, In: Bioinformatics. 38, 4, p. 1159-1161 3 p.

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

  22. Published

    Somatic structural variant formation is guided by and influences genome architecture

    Sidiropoulos, N., Mardin, B. R., Rodriguez Gonzalez, Francisco G, Bochkov, I. D., Garg, S., Stuetz, A. M., Korbel, J. O., Aiden, E. L. & Weischenfeldt, Joachim Lütken, 2022, In: Genome Research. 32, 4, p. 643-655

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

  23. 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

  24. 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

  25. Published

    NanoDam identifies Homeobrain (ARX) and Scarecrow (NKX2.1) as conserved temporal factors in the Drosophila central brain and visual system

    Tang, J. L. Y., Hakes, A. E., Krautz, Robert, Suzuki, T., Contreras, E. G., Fox, P. M. & Brand, A. H., 2022, In: Developmental Cell. 57, 9, 23 p.

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

  26. Published

    In vivo, genome-wide profiling of endogenously tagged chromatin-binding proteins with spatial and temporal resolution using NanoDam in Drosophila

    Tang, J. L. Y., Krautz, Robert, Llorà-Batlle, O., Hakes, A. E., Fox, P. M. & Brand, A. H., 2022, In: STAR Protocols. 3, 4, 30 p., 101788.

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

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