Computational and RNA Biology

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  1. Published

    Unraveling the genetic basis of neurological diseases and thalassemia: the clinical utility of high throughput sequencing

    ZHANG, W., 2023, Department of Biology, Faculty of Science, University of Copenhagen. 117 p.

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

  2. Published

    Unrecognized circulation of SAT 1 foot-and-mouth disease virus in cattle herds around Queen Elizabeth National Park in Uganda

    Dhikusooka, M. T., Ayebazibwe, C., Namatovu, A., Belsham, G. J., Siegismund, Hans Redlef, Wekesa, S. N., Balinda, S. N., Muwanika, V. B. & Tjørnehøj, K., 2016, In: BMC Veterinary Research. 12, 13 p., 5.

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

  3. Published

    Unveiling mRNP composition by fluorescence correlation and cross-correlation spectroscopy using cell lysates

    Mateu-Regué, À., Christiansen, Jan, Bagger, F. O., Hellriegel, C. & Nielsen, Finn Cilius, 2021, In: Nucleic Acids Research. 49, 20, 15 p., e119.

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

  4. Published

    Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

    Lizio, M., Harshbarger, J., Abugessaisa, I., Noguchi, S., Kondo, A., Severin, J., Mungall, C., Arenillas, D., Mathelier, A., Medvedeva, Y. A., Lennartsson, A., Drabløs, F., Ramilowski, J. A., Rackham, O., Gough, J., Andersson, R., Sandelin, A. G., Ienasescu, H-I., Ono, H., Bono, H. & 5 others, Hayashizaki, Y., Carninci, P., Forrest, A. R. R., Kasukawa, T. & Kawaji, H., 2017, In: Nucleic Acids Research. 45, D1, p. D737-D743 7 p.

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

  5. Published

    Upper palaeolithic Siberian genome reveals dual ancestry of Native Americans

    Raghavan, M., Skoglund, P., Graf, K. E., Metspalu, M., Albrechtsen, A., Moltke, I., Rasmussen, S., Stafford jr., T., Orlando, L. A. A., Metspalu, E., Karmin, M., Tambets, K., Rootsi, S., Mägi, R., Campos, P., Balanovska, E., Balanovsky, O., Khusnutdinova, E., Litvinov, S., Osipova, L. P. & 11 others, Fedorova, S. A., Voevoda, M. I., Degiorgio, M., Sicheritz-Ponten, T., Brunak, S., Demeshchenko, S., Kivisild, T., Villems, R., Nielsen, R., Jakobsson, M. & Willerslev, Eske, 2014, In: Nature. 505, 7481, p. 87-91 4 p.

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

  6. Published

    Upregulation of alpha cell glucagon-like peptide 1 (GLP-1) in Psammomys obesus--an adaptive response to hyperglycaemia?

    Hansen, A. M. K., Bödvarsdottir, T. B., Nordestgaard, D. N. E., Heller, Rasmus, Gotfredsen, C. F., Maedler, K., Fels, J., Holst, Jens Juul & Karlsen, A., 2011, In: Diabetologia. 54, 6, p. 1379-87 9 p.

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

  7. Published

    Urinary Proteomics Identifies Cathepsin D as a Biomarker of Rapid eGFR Decline in Type 1 Diabetes

    Limonte, C. P., Valo, E., Drel, V., Natarajan, L., Darshi, M., Forsblom, C., Henderson, C. M., Hoofnagle, A. N., Ju, W., Kretzler, M., Montemayor, D., Nair, V., Nelson, R. G., O’toole, J. F., Toto, R. D., Rosas, S. E., Ruzinski, J., Sandholm, N., Schmidt, I. M., Vaisar, T. & 12 others, Waikar, S. S., Zhang, J., Rossing, Peter, Ahluwalia, Tarun Veer Singh, Groop, P. H., Pennathur, S., Snell-Bergeon, J. K., Costacou, T., Orchard, T. J., Sharma, K., de Boer, I. H. & Kidney Precision Medicine Project, K. P. M. P., 2022, In: Diabetes Care. 45, 6, p. 1416-1427 12 p.

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

  8. Published

    Variants in the 5' region of the neuropeptide Y receptor Y2 gene (NPY2R) are associated with obesity in 5,971 white subjects

    Torekov, Signe Sørensen, Larsen, L. H., Andersen, G., Albrechtsen, Anders, Glümer, C., Borch-Johnsen, K., Jørgensen, Tina, Hansen, Teis Schjals & Pedersen, Oluf Borbye, 2006, In: Diabetologia. 49, 11, p. 2653-8 6 p.

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

  9. Published

    Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population

    Li, S., Besenbacher, S., Li, Y., Kristiansen, Karsten, Grarup, Niels, Albrechtsen, Anders, Sparsø, T. H., Korneliussen, Thorfinn Sand, Hansen, Torben, Wang, J., Nielsen, Rasmus, Pedersen, Oluf Borbye, Bolund, L. & Schierup, M. H., 2014, In: European Journal of Human Genetics. 22, p. 1040-1045 6 p.

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

  10. Published

    Variational Open-Domain Question Answering

    Liévin, V., Motzfeldt, A. G., Jensen, I. R. & Winther, Ole, 2023, In: Proceedings of Machine Learning Research. 202, p. 20950-20977 28 p.

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

  11. Published

    VeTra: a tool for trajectory inference based on RNA velocity

    Weng, Guangzheng, Kim, Junil & Won, K. J., 2021, In: Bioinformatics. 37, 20, p. 3509-3513 btab364.

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

  12. Published

    Vejledning i forskning

    Brandt, Luise Ørsted, 2018

    Research output: Other contribution › Net publication - Internet publication › Education

  13. Published

    Vicariance followed by secondary gene flow in a young gazelle species complex

    Garcia Erill, Genís, Kjær, M. M., Albrechtsen, Anders, Siegismund, Hans Redlef & Heller, Rasmus, 2021, In: Molecular Ecology. 30, 2, p. 528-544

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

  14. Published

    Warthog Genomes Resolve an Evolutionary Conundrum and Reveal Introgression of Disease Resistance Genes

    Garcia Erill, Genís, Jørgensen, C. H. F., Muwanika, V. B., Wang, X., Rasmussen, Malthe Sebro, de Jong, Y. A., Gaubert, P., Olayemi, A., Salmona, J., Butynski, T. M., Bertola, Laura, Siegismund, Hans Redlef, Albrechtsen, Anders & Heller, Rasmus, 2022, In: Molecular Biology and Evolution. 39, 7, 17 p., msac134.

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

  15. Published

    Weighting sequence variants based on their annotation increases power of whole-genome association studies

    Sveinbjornsson, G., Albrechtsen, Anders, Zink, F., Gudjonsson, S. A., Oddson, A., Másson, G., Holm, H., Kong, A., Thorsteinsdottir, U., Sulem, P., Gudbjartsson, D. F. & Stefansson, K., 2016, In: Nature Genetics. 48, 3, p. 314-317 4 p.

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

  16. Published

    What are artificial neural networks?

    Krogh, Anders, 2008, In: Nature Biotechnology. 26, 2, p. 195-7 2 p.

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

  17. Published

    Whole Genome Sequencing in the Evaluation of Fetal Structural Anomalies: A Parallel Test with Chromosomal Microarray Plus Whole Exome Sequencing

    Zhou, J., Yang, Z., Sun, J., Liu, L., Zhou, X., Liu, F., Xing, Y., Cui, S., Xiong, S., Liu, X., Yang, Y., Wei, X., Zou, G., Wang, Z., Wei, X., Wang, Y., Zhang, Y., Yan, S., Wu, F., Zeng, F. & 4 others, Wang, J., Duan, T., Peng, Z. & Sun, L., 2021, In: Genes. 12, 3, 14 p., 376.

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

  18. Published

    Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes

    Lohmueller, K. E., Sparsø, T. H., Li, Q., Galijatovic, E. A. A., Korneliussen, T. S., Albrechtsen, A., Banasik, K., Grarup, N., Hallgrimsdottir, I., Kiil, K., Oskari Kilpeläinen, T., Krarup, N. T., Pers, T. H., Sanchez, G., Hu, Y., DeGiorgio, M., Jørgensen, T., Sandbæk, A., Lauritzen, T., Brunak, S. & 6 others, Kristiansen, Karsten, Li, Y., Hansen, Torben, Wang, J., Nielsen, Rasmus & Pedersen, Oluf Borbye, 5 Dec 2013, In: American Journal of Human Genetics. 93, 6, p. 1072-1086 15 p.

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

  19. Published

    Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

    Qin, C., Yu, C., Shen, Y., Fang, X., Chen, L., Min, J., Cheng, J., Zhao, S., Xu, M., Luo, Y., Yang, Y., Wu, Z., Mao, L., Wu, H., Ling-Hu, C., Zhou, H., Lin, H., Gonzalez-Morales, S., Trejo-Saavedra, D. L., Tian, H. & 53 others, Tang, X., Zhao, M., Huang, Z., Zhou, A., Yao, X., Cui, J., Li, W., Chen, Z., Feng, Y., Niu, Y., Bi, S., Yang, X., Li, W., Cai, H., Luo, X., Montes-Hernandez, S., Leyva-Gonzalez, M. A., Xiong, Z., He, X., Bai, L., Tan, S., Tang, X., Liu, D., Liu, J., Zhang, S., Chen, M., Zhang, L., Zhang, L., Zhang, Y., Liao, W., Zhang, Y., Wang, M., Lv, X., Wen, B., Liu, H., Luan, H., Zhang, Y., Yang, S., Wang, X., Xu, J., Li, X., Li, S., Wang, J., Palloix, A., Bosland, P. W., Li, Y., Krogh, Anders, Rivera-Bustamante, R. F., Herrera-Estrella, L., Yin, Y., Yu, J., Hu, K. & Zhang, Z., 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 14, p. 5135-5140 6 p.

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

  20. Published

    X-ray scattering and electron cryomicroscopy study on the effect of carotenoid biosynthesis to the structure of Chlorobium tepidum chlorosomes

    Ikonen, T. P., Li, H., Psencík, J., Laurinmäki, P. A., Butcher, S. J., Frigaard, Niels-Ulrik, Serimaa, R. E., Bryant, D. A. & Tuma, R., 2007, In: Biophysical Journal. 93, 2, p. 620-628 8 p.

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

  21. Published

    YeastFab: The design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae

    Guo, Y., Dong, J., Zhou, T., Auxillos, Jamie Yam, Li, T., Zhang, W., Wang, L., Shen, Y., Luo, Y., Zheng, Y., Lin, J., Chen, G. Q., Wu, Q., Cai, Y. & Dai, J., 27 Apr 2015, In: Nucleic Acids Research. 43, 13, p. e88

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

  22. Published

    YeastFab: High-Throughput Genetic Parts Construction, Measurement, and Pathway Engineering in Yeast

    Garcia-Ruiz, E., Auxillos, Jamie Yam, Li, T., Dai, J. & Cai, Y., 1 Jan 2018, Methods in Enzymology. Scrutton, N. (ed.). Academic Press, p. 277-306 30 p. (Methods in Enzymology, Vol. 608).

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

  23. Published

    cWords - systematic microRNA regulatory motif discovery from mRNA expression data

    Rasmussen, S. H., Jacobsen, A. & Krogh, Anders, 2013, In: Silence. 4, 2, 9 p.

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

  24. Published

    fastNGSadmix: admixture proportions and principal component analysis of a single NGS sample

    Jørsboe, E., Hanghøj, Kristian Ebbesen & Albrechtsen, Anders, 1 Oct 2017, In: Bioinformatics. 33, 19, p. 3148-3150 3 p.

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

  25. Published

    hyperTRIBER: a flexible R package for the analysis of differential RNA editing

    Rennie, Sarah, Magnusson, D. H. & Andersson, Robin, 2021, 12 p.

    Research output: Working paper › Preprint › Research

  26. 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

  27. Published

    mRNA decay of most arabidopsis miRNA targets requires slicer activity of AGO1

    Arribas Hernandez, Laura, Kielpinski, L. J. & Brodersen, Peter, 2016, In: Plant Physiology. 171, 4, p. 2620-2632 13 p.

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

  28. Published

    mRNA pseudoknot structures can act as ribosomal roadblocks

    Hansen, J. T., Oddershede, L. B. & Sørensen, Michael Askvad, 2012, In: Nucleic Acids Research. 40, 1, p. 303-313 11 p.

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

  29. Published

    mTOR complex 2 phosphorylates IMP1 cotranslationally to promote IGF2 production and the proliferation of mouse embryonic fibroblasts.

    Dai, N., Christiansen, Jan, Nielsen, F. & Avruch, J., 2013, In: Genes & Development. 27, 3, p. 301-312 12 p.

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

  30. Published

    maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences

    Menzel, K. P., Stadler, P. F. & Gorodkin, Jan, 2011, In: Bioinformatics. 27, 3, p. 317-325 9 p.

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

  31. Published

    miR-449 inhibits cell proliferation and is down-regulated in gastric cancer

    Bou Kheir, T., Futoma-Kazmierczak, E., Jacobsen, A., Krogh, Anders, Bardram, L., Hother, C., Grønbæk, Kirsten, Federspiel, B., Lund, Anders H. & Friis-Hansen, Lennart Jan, 2011, In: Molecular Cancer. 10, p. 1-12 12 p.

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

  32. Published

    miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer

    Pan, Y., Robertson, G., Pedersen, L., Lim, E., Hernandez-Herrera, A., Rowat, A. C., Patil, S. L., Chan, C. K., Wen, Y., Zhang, X., Basu-Roy, U., Mansukhani, A., Chu, A., Sipahimalani, P., Bowlby, R., Brooks, D., Thiessen, N., Coarfa, C., Ma, Y., Moore, R. A. & 8 others, Schein, J. E., Mungall, A. J., Liu, J., Pecot, C. V., Sood, A. K., Jones, S. J. M., Marra, M. A. & Gunaratne, P. H., 2016, In: OncoTarget. 7, 18, p. 25930-25948 19 p.

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

  33. Published

    miRMaid: a unified programming interface for microRNA data resources

    Jacobsen, A., Krogh, Anders, Kauppinen, S. & Lindow, M., 2010, In: BMC Bioinformatics. 11, Suppl 1, p. 29

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

  34. Published

    microRNA-101 is a potent inhibitor of autophagy

    Frankel, Lisa, Wen, J., Lees, M., Høyer-Hansen, M., Farkas, T., Krogh, Anders, Jäättelä, M. & Lund, Anders H., 2011, In: E M B O Journal. 30, p. 4628-4641 14 p.

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

  35. Published

    microRNA-143 down-regulates Hexokinase 2 in colon cancer cells

    Gregersen, Lea Haarup, Jacobsen, A., Frankel, Lisa, Wen, J., Krogh, Anders & Lund, Anders H., 2012, In: B M C Cancer. 12, 232, 23 p.

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

  36. Published

    microRNA-146a inhibits G protein-coupled receptor-mediated activation of NF-κB by targeting CARD10 and COPS8 in gastric cancer

    Crone, S. G., Jacobsen, A., Federspiel, B., Bardram, L., Krogh, Anders, Lund, Anders H. & Friis-Hansen, Lennart Jan, 2012, In: Molecular Cancer. 11, 71, p. 71 31 p.

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

  37. Published

    netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks [version 2; peer review: 2 approved]

    Pai, S., Weber, P., Isserlin, R., Kaka, H., Hui, S., Shah, M. A., Giudice, L., Giugno, R., Nøhr, A. K., Baumbach, J. & Bader, G. D., 2021, In: F1000Research. 9, 42 p., 1239.

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

  38. Published

    scVAE: variational auto-encoders for single-cell gene expression data

    Grønbech, Christopher Heje, Vording, M. F., Timshel, P., Sønderby, C. K., Pers, Tune H & Winther, Ole, 2020, In: Bioinformatics. 36, 16, p. 4415-4422 8 p.

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

  39. Published

    spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data

    Vitting-Seerup, K., Porse, Bo Torben, Sandelin, Albin Gustav & Waage, J., 2014, In: B M C Bioinformatics. 15, p. 1-7 7 p., 81.

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

  40. Published

    vcfpp: a C++ API for rapid processing of the variant call format

    Li, Z., 2024, In: Bioinformatics. 40, 2, 4 p., btae049.

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

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