Computational and RNA Biology

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  1. Published

    Assembly and analysis of 100 full MHC haplotypes from the Danish population

    Jensen, J. M., Villesen, P., Friborg, R. M., Mailund, T., Besenbacher, S., Sørensen, L. M., Petersen, B., Sibbesen, J. A., Liu, S., Skov, L., Belling, K. G., Have, C. T., Izarzugaza, J. M. G., Grosjean, M., Bork-Jensen, J., Grove, J., Als, T. D., Huang, S., Chang, Y., Xu, R. & 39 others, Ye, W., Rao, J., Guo, X., Sun, J., Cao, H., Ye, C., Beusekom, J. V., Espeseth, T., Flindt, E., Halager, A. E., Hellard, S. L., Hultman, C. M., Lescai, F., Li, S., Lund, O., Løngren, P., Matey-Hernandez, M. L., Mors, O., Pedersen, C. N. S., Sicheritz-Pontén, T., Sullivan, P., Syed, A., Westergaard, D., Yadav, R., Li, N., Xu, X., Hansen, Torben, Bolund, L., Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Gupta, R., Rasmussen, Simon, Børglum, A. D., Wang, J., Eiberg, Hans Rudolf Lytchoff, Kristiansen, Karsten, Brunak, Søren & Schierup, M. H., Sep 2017, In: Genome Research. 27, 9, p. 1597-1607 11 p.

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

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

  3. Published

    Association of bacteriochlorophyll a with the CsmA protein in chlorosomes of the photosynthetic green filamentous bacterium Chloroflexus aurantiacus

    Sakuragi, Y., Frigaard, Niels-Ulrik, Shimada, K. & Matsuura, K., 1999, In: BBA General Subjects. 1413, 3, p. 172-180 9 p.

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

  4. Published

    Association testing for next-generation sequencing data using score statistics

    Skotte, L., Korneliussen, Thorfinn Sand & Albrechtsen, Anders, 2012, In: Genetic Epidemiology. 36, 5, p. 430-437 8 p.

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

  5. Published

    Association testing of novel type 2 diabetes risk alleles in the JAZF1, CDC123/CAMK1D, TSPAN8, THADA, ADAMTS9, and NOTCH2 loci with insulin release, insulin sensitivity, and obesity in a population-based sample of 4,516 glucose-tolerant middle-aged Danes.

    Grarup, Niels, Andersen, G., Krarup, N. T., Albrechtsen, Anders, Schmitz, O., Jørgensen, T., Borch-Johnsen, K., Hansen, Torben & Pedersen, Oluf Borbye, 2008, In: Diabetes. 57, 9, p. 2534-40 6 p.

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

  6. Published

    AutoCNV: a semiautomatic CNV interpretation system based on the 2019 ACMG/ClinGen Technical Standards for CNVs

    Fan, C., Wang, Z., Sun, Y., Sun, J., Liu, X., Kang, L., Xu, Y., Yang, M., Dai, W., Song, L., Wei, X., Xiang, J., Huang, H., Zhou, M., Zeng, F., Huang, L., Xu, Z. & Peng, Z., 2021, In: BMC Genomics. 22, 12 p., 721.

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

  7. Published

    Autoencoding beyond pixels using a learned similarity metric

    Larsen, A. B. L., Sønderby, S. K., Larochelle, H. & Winther, Ole, 2016, Proceedings of The 33rd International Conference on Machine Learning. Balcan, M. F. & Weinberger, K. Q. (eds.). p. 1558–1566 9 p. (JMLR: Workshop and Conference Proceedings, Vol. 48).

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

  8. Published

    Autophagy is required for stem cell mobilization by G-CSF

    Leveque-El Mouttie, L., Vu, T., Lineburg, K. E., Kuns, R. D., Bagger, F. O., Teal, B. E., Lor, M., Boyle, G. M., Bruedigam, C., Mintern, J. D., Hill, G. R., MacDonald, K. P. A. & Lane, S. W., 2015, In: Blood. 125, 19, p. 2933-2936 4 p.

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

  9. Published

    BRPF3-HBO1 regulates replication origin activation and histone H3K14 acetylation

    Feng, Y., Vlassis, A., Roques, C., Lalonde, M. E., Gonzalez Aguilera, C., Lambert, J. P., Lee, S., Zhao, X., Alabert, C., Johansen, Jens Vilstrup, Paquet, E., Yang, X. J., Gingras, A. C., Côté, J. & Groth, Anja, 2016, In: EMBO Journal. 35, 2, p. 176-192 17 p.

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

  10. Published

    Bacterial natural transformation by highly fragmented and damaged DNA

    Overballe-Petersen, S., Harms, K., Orlando, L. A. A., Moreno Mayar, J. Víctor, Rasmussen, Simon, Dahl, Tais Wittchen, Rosing, Minik Thorleif, Poole, A. M., Sicheritz-Ponten, T., Brunak, S., Inselmann, S., de Vries, J., Wackernagel, W., Pybus, O. G., Nielsen, Rasmus, Johnsen, P. J., Nielsen, K. M. & Willerslev, Eske, 3 Dec 2013, In: Proceedings of the National Academy of Sciences of the United States of America. 110, 49, p. 19860–19865 6 p.

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

  11. Published

    Bacteriochlorophyllide c C-82 and C-121 methyltransferases are essential for adaptation to low light in Chlorobaculum tepidum

    Gomez Maqueo Chew, A., Frigaard, Niels-Ulrik & Bryant, D. A., 2007, In: Journal of Bacteriology. 189, 17, p. 6176-6184 8 p.

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

  12. Published

    Bayesian inference of protein ensembles from SAXS data

    Antonov, L. D., Olsson, S., Boomsma, Wouter & Hamelryck, Thomas Wim, 2016, In: Physical Chemistry Chemical Physics. 18, 8, p. 5832-5838 7 p.

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

  13. Published

    Bayesian inference of protein structure from chemical shift data

    Bratholm, L. A., Christensen, A. S., Hamelryck, Thomas Wim & Jensen, Jan Halborg, 2015, In: PeerJ. 3, 19 p., e861.

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

  14. Published

    Bayesian methods in structural bioinformatics

    Hamelryck, Thomas Wim (ed.), Mardia, K. (ed.) & Ferkinghoff-Borg, J. (ed.), 2012, Springer. 377 p. (Statistics for Biology and Health).

    Research output: Book/Report › Book › Research › peer-review

  15. Published

    Bayesian protein superposition using Hamiltonian Monte Carlo

    Sanz Moreta, Lys, Al-Sibahi, A. S. & Hamelryck, Thomas Wim, Oct 2020, Proceedings - IEEE 20th International Conference on Bioinformatics and Bioengineering, BIBE 2020. IEEE, p. 1-11 9288019

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

  16. Published

    Bayesian transcriptome assembly

    Sørensen, L. M., Sibbesen, Jonas Andreas & Krogh, Anders, 2014, In: Genome Biology (Online Edition). 15, 10, 11 p., 501.

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

  17. 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 journal › Review › Research › peer-review

  18. Published

    Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track

    Kuo, T., Bath, T., Ma, S., Pattengale, N., YANG, Meng, Cao, Y., Hudson, C. M., Kim, J., Post, K., Xiong, L. & Ohno-Machado, L., 2021, In: International Journal of Medical Informatics. 154, 8 p., 104559.

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

  19. Published

    Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios

    Matey-Hernandez, M. L., Danish Pan Genome Consortium, D. P. G. C., Brunak, Søren, Izarzugaza, J. M. G., Sørensen, L. M., Petersen, Bent, Sibbesen, Jonas Andreas, Liu, S., Belling, K. G., Have, C. T., Bork-Jensen, J., Sun, J., Hansen, Torben, Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Wang, J., Eiberg, Hans Rudolf Lytchoff & Kristiansen, Karsten, 2018, In: BMC Bioinformatics. 19, p. 1-12 239.

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

  20. Published

    Bending during seedling emergence: Mechanochemical insight

    Bai, B., 2021, In: Trends in Plant Science. 26, 9, p. 879-881 3 p.

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

  21. 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/Report › Ph.D. thesis › Research

  22. Published

    Beyond rotamers: a generative, probabilistic model of side chains in proteins

    Harder, T., Boomsma, Wouter, Paluszewski, M., Frellsen, J., Johansson, Kristoffer Enøe & Hamelryck, Thomas Wim, 1 Jan 2010, In: B M C Bioinformatics. 11, p. 306

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

  23. Published

    Binning microbial genomes using deep learning

    Nissen, J. N., Sønderby, C. K., Armenteros, J. J. A., Grønbech, Christopher Heje, Nielsen, H. B., Petersen, T. N., Winther, Ole & Rasmussen, Simon, 2018, (bioRxiv).

    Research output: Working paper › Preprint › Research

  24. Published

    Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes

    Valen, E., Preker, P., Andersen, P. R., Zhao, X., Chen, Y., Ender, C., Dueck, A., Meister, G., Sandelin, Albin Gustav & Jensen, T. H., 2011, In: Nature Structural and Molecular Biology. 18, 9, p. 1075–1082 8 p.

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

  25. Published

    Bioinformatic Analysis of Breast Tumor Interstitial Fluids: Insights into a Pan-molecular Secretome

    Terkelsen, Thilde Bagger, 2019, Department of Biology, Faculty of Science, University of Copenhagen.

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

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