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Integrative Systems Biology

Group leader: Søren Brunak
Members: Agnieszka Sierakowska Juncker, Andreas Bok Andersen, Caroline Anna Brorsson, David Westergaard, Helle Krogh Pedersen, Jens Friis-Nielsen, Jon Ison, Jose Maria Gonzalez-Izarzugaza, Kirstine Christensen Belling, Klaus Højgaard Jensen, Li Jiang, Mette Kristina Beck, Peter Løngreen, Pope Moseley, Tune Hannes Pers, Valborg Gudmundsdottir
Guest members: Anders Boeck Jensen, Chris Workman, Christian Simon, Hanne Østergaard Jarmer, Henrik Bjørn Nielsen, Isa Kirk

Catalog of previous student projects.


About the group

The Integrative Systems Biology Group is at the leading edge of these developments, focusing mainly on understanding how intracellular networks of genes, proteins, metabolites and other small molecules regulate cellular behavior and how perturbations to these regulatory systems may lead to disease for the individual.

Our research strategies typically rely on integration of massive amounts of experimental data. Pathways and protein complexes are key levels of analysis helping to understand how genetic changes in many different molecular components lead to the same or similar phenotypes. The group also works on combining molecular level systems biology data with medical informatics data from the healthcare sector, such as for example electronic patient records and biobank questionnaires. The aim is to combine and stratify patients not only from their genotypes, but also phenotypically based on the clinical descriptions in the medical records which describe disease development in detail. The groups has specific focus on treatment related disease correlations and other comorbidities.



Group member profiles from recent years. We tend to hire PhD-students and postdoc which either have a strong biological/medical or computational background (see the recent distribution in the figure to the left).

   

Research project profiles in recent years. The project profiles can be placed on a space spanned by bioinformatics, systems biology, medical informatics and computational, chemical biology (see the recent distribution in the figure to the left).



If you are interested in learning more about the group or our work, please contact the group coordinator Kirstine Belling.

Selected Publications

  • Concordance of gene expression in human protein complexes reveals tissue specificity and pathology
    Bornigen D, Pers TH, Thorrez L, Huttenhower C, Moreau Y, Brunak S
    Nucleic Acids Research 2013, 41:e171. PMID:23921638

  • A computational approach to chemical etiologies of diabetes
    Audouze, K, Brunak, S, Grandjean, P
    Scientific reports 2013, 3:2712. PMID:24048418

  • A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk
    Blair DR, Lyttle CS, Mortensen JM, Bearden CF, Jensen AB, Khiabanian H, Melamed R, Rabadan R, Bernstam EV, Brunak S, Jensen LJ, Nicolae D, Shah NH, Grossman RL, Cox NJ, White KP, Rzhetsky A
    Cell 2013, 155:70-80. PMID:24074861

  • Mining electronic health records: towards better research applications and clinical care
    Jensen PB, Jensen LJ, Brunak S
    Nature Review Genetics 2012, 13:395-405. PMID:22549152

  • SignalP 4.0: discriminating signal peptides from transmembrane regions
    Petersen TN, Brunak S, von Heijne G, Nielsen H
    Nature Methods 2011, 8:785-6. PMID:21959131

  • Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes
    Pers TH, Hansen NT, Lage K, Koefoed P, Dworzynski P, Miller ML, Flint TJ, Mellerup E, Dam H, Andreassen OA, Djurovic S, Melle I, Boerglum AD, Werge T, Purcell S, Ferreira MA, Kouskoumvekaki I, Workman CT, Hansen T, Mors O, Brunak S
    Genetic Epidemiology 2011, 35:318-32. PMID:21484861

  • ChemProt: a disease chemical biology database
    Taboureau O, Nielsen SK, Audouze K, Weinhold N, Edsgaard D, Roque FS, Kouskoumvekaki I, Bora A, Curpan R, Jensen TS, Brunak S, Oprea TI
    Nucleic Acids Research 2011, 39(Database issue):D367-72. PMID: 20935044

  • Protein annotation in the era of personal genomics
    Blicher T, Gupta R, Wesolowska A, Jensen LJ, Brunak S
    Curr Opin Struct Biol. 2010, 20:335-41. PMID:20403684

  • Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
    Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M
    Science Signalling 2010, 3:ra3. PMID:20068231

  • Dissecting spatio-temporal protein networks driving human heart development and related disorders
    Lage K, Moellgard K, Greenway S, Wakimoto H, Gorham JM, Workman CT, Bendsen E, Hansen NT, Rigina O, Roque FS, Wiese C, Christoffels VM, Roberts AE, Smoot LB, Pu WT, Donahoe PK, Tommerup N, Brunak S, Seidman CE, Seidman JG, Larsen LA
    Molecular Systems Biology 2010 6:381. PMID:20571530

  • Generating genome-scale candidate gene lists for pharmacogenomics
    Hansen N, Brunak S, Altman R
    Clin Pharmacol Ther. 2009, 86:183-89. PMID:19369935

  • Sequence-based feature prediction and annotation of proteins
    Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S
    Genome Bioliology 2009, 10:206. PMID:19226438

  • Linear motif atlas for phosphorylation-dependent signaling
    Miller ML, Jensen LJ, Diella F, Joergensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R
    Science Signaling 2008, 1:ra2. PMID:18765831

  • A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes
    Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque FS, Donahoe PK, Szallasi Z, Jensen TS, Brunak S
    Proc Natl Acad Sci U S A. 2008, 105:20870-5. PMID:19104045

  • A human phenome-interactome network of protein complexes implicated in genetic disorders
    Lage K, Karlberg EO, Stoerling ZM, Olason PI, Pedersen AG, Rigina O, Hinsby AM, Tumer Z, Pociot F, Tommerup N, Moreau Y, Brunak S
    Nature Biotechnology 2007, 25:309-16. PMID:17344885

  • Co-evolution of transcriptional and post-translational cell-cycle regulation
    Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S and Bork P
    Nature 2006, 443:594-7. PMID:17006448

  • A wiring of the human nucleolus
    Hinsby AM, Kiemer L, Karlberg EO, Lage K, Fausboell A, Juncker AS, Andersen JS, Mann M and Brunak S
    Molecular Cell 2006, 22:285-295. PMID:16630896

  • Dynamics of complex formation during the yeast cell cycle
    de Lichtenberg U, Jensen LJ, Brunak S and Bork P
    Science 2005, 307:724-7. PMID:15692050

  • Protein feature based identification of cell cycle regulated proteins in yeast
    de Lichtenberg U, Jensen TS, Jensen LJ and Brunak S
    Journal of Molecular Biology 2003, 329:663-74. PMID:12787668

  • Prediction of human protein function from post-translational modifications and localization features
    Jensen LJ, Gupta R, Blom N, Devos D, Tamames J, Kesmir C, Nielsen H, Staerfeldt HH, Rapacki L, Workman C, Andersen CA, Knudsen S, Krogh A, Valencia A and Brunak S
    Journal of Molecular Biology 2002, 319:1257-1265. PMID:12079362
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