Disease Systems Biology Program

  1. 2020
  2. Published

    Comparing 22 Popular Phosphoproteomics Pipelines for Peptide Identification and Site Localization

    Locard-Paulet, Marie, Bouyssié, D., Froment, C., Burlet-Schiltz, O. & Jensen, Lars Juhl, 6 Mar 2020, In : Journal of Proteome Research. 19, 3, p. 1338-1345 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Published

    Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii

    Iversen, Katrine Højholt, Rasmussen, L. H., Al-Nakeeb, K., Armenteros, J. J. A., Jensen, C. S., Dargis, R., Lukjancenko, O., Justesen, U. S., Moser, Claus Ernst, Rosenvinge, F. S., Nielsen, X. C., Christensen, J. J. & Rasmussen, Simon, 17 Feb 2020, In : Scientific Reports. 10, 1, p. 2728

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    Higher burden of rare frameshift indels in genes related to synaptic transmission separate familial hemiplegic migraine from common types of migraine

    Rasmussen, A. H., Olofsson, I., Chalmer, M. A., Olesen, Jes & Hansen, Thomas Folkmann, 1 Jan 2020, In : Journal of Medical Genetics. 106640.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Accepted/In press

    Sex differences in text-mined possible adverse drug events associated with drugs for psychosis

    Sørup, F. K. H., Eriksson, Robert, Westergaard, David, Hallas, J., Brunak, Søren & Andersen, Stig Ejdrup, 1 Jan 2020, (Accepted/In press) In : Journal of Psychopharmacology. 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. E-pub ahead of print

    Heterogeneity of treatment effect of prophylactic pantoprazole in adult ICU patients: a post hoc analysis of the SUP-ICU trial

    Granholm, A., Marker, S., Krag, M., Zampieri, F. G., Thorsen-Meyer, H., Kaas-Hansen, Benjamin Skov, van der Horst, I. C. C., Lange, Theis, Wetterslev, J., Perner, Anders & Møller, Morten Hylander, Jan 2020, In : Intensive Care Medicine.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    A draft genome sequence of the elusive giant squid, Architeuthis dux

    Rodrigues da Fonseca, Rute Andreia, Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, Â. M., Barrio-Hernandez, I., Hoving, H., Tafur-Jimenez, R., Chu, C., Frazão, B., Petersen, Bent, Peñaloza, F., Musacchia, F., Alexander, G. C., Osório, H., Winkelmann, I., Simakov, O., Rasmussen, Simon, Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., Zhang, Guojie, Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Pontén, Thomas, Nielsen, Rasmus & Gilbert, M Thomas P, 2020, In : GigaScience. 9, 1, giz152.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    CAncer bioMarker Prediction Pipeline (CAMPP) - A standardized framework for the analysis of quantitative biological data

    Terkelsen, T., Krogh, Anders & Papaleo, Elena, 2020, In : PLOS Computational Biology. 16, 3, 20 p., e1007665.

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Combined burden and functional impact tests for cancer driver discovery using DriverPower

    PCAWG Drivers and Functional Interpretation Working Group, P. D. A. F. I. W. G. & PCAWG Consortium, P. C., 2020, In : Nature Communications. 11, 1, 734.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    Conflicting associations between dietary patterns and changes of anthropometric traits across subgroups of middle-aged women and men

    Jiang, L., Audouze, K., Romero Herrera, Jose Alejandro, Ängquist, Lars, Kjærulff, S. K., Izarzugaza, J. M. G., Tjønneland, Anne, Halkjær, J., Overvad, K., Sørensen, Thorkild I.A. & Brunak, Søren, 2020, In : Clinical Nutrition. 39, 1, p. 265-275

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Accepted/In press

    Cross-sectional study identifies lower risk of Staphylococcus aureus nasal colonization in Danish blood donors with hidradenitis suppurativa symptoms

    Dinh, K. M., Erikstrup, L. T., Andersen, R. K., Andersen, P. S., Mikkelsen, S., Kjerulff, B. D., Burgdorf, K. S., Hansen, Thomas Folkmann, Nielsen, K. R., Hjalgrim, H., Jemec, Gregor, Ullum, Henrik, Erikstrup, C. & Pedersen, O. B., 2020, (Accepted/In press) In : British Journal of Dermatology.

    Research output: Contribution to journalLetterResearchpeer-review

  12. Published

    Immune Profiling of Human Gut-Associated Lymphoid Tissue Identifies a Role for Isolated Lymphoid Follicles in Priming of Region-Specific Immunity

    Fenton, T. M., Jørgensen, P. B., Niss, Kristoffer, Rubin, S. J. S., Mörbe, U. M., Riis, Lene Buhl, Da Silva, C., Plumb, A., Vandamme, J., Jakobsen, H. L., Brunak, Søren, Habtezion, A., Nielsen, Ole Haagen, Johansson-Lindbom, B. & Agace, W. W., 2020, In : Immunity. 52, 3, p. 557-570, e1-e6

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    Interpreting pathways to discover cancer driver genes with Moonlight

    Colaprico, A., Olsen, C., Bailey, M. H., Odom, G. J., Terkelsen, T., Silva, T. C., Olsen, A. V., Cantini, L., Zinovyev, A., Barillot, E., Noushmehr, H., Bertoli, G., Castiglioni, I., Cava, C., Bontempi, G., Chen, X. S. & Papaleo, Elena, 2020, In : Nature Communications. 11, 17 p., 69.

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. E-pub ahead of print

    JIB.tools 2.0 - A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools

    Friedrichs, M., Shoshi, A., Chmura, Piotr Jaroslaw, Ison, J., Schwammle, V., Schreiber, F., Hofestadt, R. & Sommer, B., 2020, In : Journal of integrative bioinformatics. 16, 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    Lipidomic profiles, lipid trajectories and clinical biomarkers in female elite endurance athletes

    V Varga, Tibor, Ali, A., Romero Herrera, Jose Alejandro, Ahonen, L. L., Mattila, I. M., Al-Sari, N. H., Legido-Quigley, C., Skouby, Sven O., Brunak, Søren & Tornberg, Å. B., 2020, In : Scientific Reports. 10, 9 p., 2349.

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. E-pub ahead of print

    Proposed new diagnostic criteria for chronic migraine

    Chalmer, M. A., Hansen, Thomas Folkmann, Lebedeva, E. R., Dodick, D. W., Lipton, R. B. & Olesen, Jes, 2020, In : Cephalalgia.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    The derived allele of a novel intergenic variant at chromosome 11 associates with lower body mass index and a favorable metabolic phenotype in Greenlanders

    Lepola, Mette Andersen, Jørsboe, Emil, Skotte, L., Hanghøj, Kristian Ebbesen, Sandholt, C. H., Moltke, Ida, Grarup, Niels, Kern, T., Mahendran, Y., Søborg, B., Bjerregaard, P., Larsen, C. V. L., Dahl-Petersen, I. K., Tiwari, H. K., Feenstra, B., Koch, A., Wiener, H. W., Hopkins, S. E., Pedersen, Oluf Borbye, Melbye, Mads, Boyer, B. B., Jørgensen, M. E., Albrechtsen, Anders & Hansen, Torben, 2020, In : PLOS Genetics. 16, 1, 17 p., e1008544.

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. 2019
  19. Published

    High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach

    Mollerup, S., Asplund, M., Friis-Nielsen, J., Kjartansdóttir, K. R., Fridholm, H., Hansen, T. A., Romero Herrera, Jose Alejandro, Barnes, Christopher James, Jensen, R. H., Richter, S. R., Nielsen, Ida Broman, Pietroni, C., Alquezar-Planas, D. E., Rey de la Iglesia, Alba, Olsen, Pernille Vibeke Selmer, Rajpert-De Meyts, E., Groth-Pedersen, L., von Buchwald, Christian, Jensen, D. H., Gniadecki, R., Høgdall, Estrid Vilma Solyom, Langhoff, J. L., Pete, I., Vereczkey, I., Baranyai, Z., Dybkaer, K., Johnsen, H. E., Steiniche, T., Hokland, P., Rosenberg, Jacob, Baandrup, U., Sicheritz-Pontén, Thomas, Willerslev, Eske, Brunak, Søren, Lund, O., Mourier, T., Vinner, Lasse, Izarzugaza, J. M. G., Nielsen, L. P. & Hansen, Anders Johannes, 15 Oct 2019, In : The Journal of Infectious Diseases. 220, 8, p. 1312-1324

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. Published

    Herpes Simplex Virus Type 1 infection is associated with suicidal behavior and first registered psychiatric diagnosis in a healthy population

    Nissen, J., Trabjerg, B., Pedersen, M. G., Banasik, Karina, Pedersen, Ole Birger Vesterager, Sørensen, E., Nielsen, K. R., Erikstrup, C., Petersen, M. S., Paarup, H. M., Bruun-Rasmussen, P., Westergaard, David, Hansen, Thomas Folkmann, Pedersen, C. B., Werge, Thomas, Torrey, F., Hjalgrim, H., Mortensen, P. B., Yolken, R., Brunak, Søren, Ullum, Henrik & Burgdorf, K. S., Oct 2019, In : Psychoneuroendocrinology. 108, p. 150-154

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Published

    DBDS Genomic Cohort, a prospective and comprehensive resource for integrative and temporal analysis of genetic, environmental and lifestyle factors affecting health of blood donors

    Hansen, Thomas Folkmann, Banasik, Karina, Erikstrup, C., Pedersen, Ole Birger Vesterager, Westergaard, David, Chmura, P. J., Nielsen, K., Thørner, L., Hjalgrim, H., Paarup, H., Larsen, M. A. H., Petersen, M., Jennum, Poul, Andersen, S., Nyegaard, M., Jemec, Gregor, Olesen, Jes, Werge, Thomas, Johansson, P. I., Sørensen, E., Brunak, Søren, Ullum, Henrik & Burgdorf, K. S., 9 Jun 2019, In : BMJ Open. 9, 6, p. 1-7 7 p., e028401.

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    Molecular dynamics-guided discovery of an ago-allosteric modulator for GPR40/FFAR1

    Lückmann, Michael, Trauelsen, Mette, Bentsen, Marie Aare, Nissen, Tinne Amalie Damgaard, Martins, J., Fallah, Z., Nygaard, Mads Mørup, Papaleo, Elena, Lindorff-Larsen, Kresten, Schwartz, Thue W. & Frimurer, Thomas Michael, 2 Apr 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 14, p. 7123-7128

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    SignalP 5.0 improves signal peptide predictions using deep neural networks

    Armenteros, J. J. A., Tsirigos, Konstantinos, Sønderby, C. K., Petersen, T. N., Winther, Ole, Brunak, Søren, von Heijne, G. & Nielsen, H., 18 Feb 2019, In : Nature Biotechnology. 37, 4, p. 420-423

    Research output: Contribution to journalJournal articleCommunication

  24. Published
  25. Published

    A Brief History of Protein Sorting Prediction

    Nielsen, H., Tsirigos, Konstantinos, Brunak, Søren & von Heijne, G., 2019, In : The Protein Journal. 38, 3, p. 200-216 17 p.

    Research output: Contribution to journalReviewResearchpeer-review

  26. Published

    A Guide to Dictionary-Based Text Mining

    Cook, H. V. & Jensen, Lars Juhl, 2019, Bioinformatics and Drug Discovery. Larson, R. S. & Oprea, T. I. (eds.). 3 ed. Humana Press, Vol. 1939. p. 73-89 17 p. (Methods in Molecular Biology).

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  27. Published

    A generic deep convolutional neural network framework for prediction of receptor–ligand interactions - NetPhosPan: application to kinase phosphorylation prediction

    Fenoy, E., Izarzugaza, J. M. G., Jurtz, V., Brunak, Søren & Nielsen, M., 2019, In : Bioinformatics. 35, 7, p. 1098-1107

    Research output: Contribution to journalJournal articleResearchpeer-review

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