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Bioinformatics (and Systems Biology?) in Biomedical Research

Bioinformatics (and Systems Biology?) in Biomedical Research. Donald Dunbar Systems Biology Club 30th November 2005. Introduction. Bioinformatics at QMRI Who we work with What we do Our focus Systems Biology at QMRI? Where we’d like to apply systems biology Can we do it?

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Bioinformatics (and Systems Biology?) in Biomedical Research

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  1. Bioinformatics (and Systems Biology?)in Biomedical Research Donald Dunbar Systems Biology Club 30th November 2005

  2. Introduction • Bioinformatics at QMRI • Who we work with • What we do • Our focus • Systems Biology at QMRI? • Where we’d like to apply systems biology • Can we do it? • what data do we have and what do we need? • can we build useful models for these data? • can we find collaborators? Donald Dunbar: Systems Biology Club

  3. Bioinformatics at QMRI • Queen’s Medical Research Institute • Centre for Cardiovascular Science • Hypertension, atherosclerosis, thrombosis, diabetes, obesity, heart failure • Centre for Inflammation Research • Lung, kidney, vascular, and other diseases associated with inflammation • Centre for Reproductive Biology • Female and male reproductive health and disease • We work with cardiovascular and inflammation scientists • Providing bioinformatics support in several areas • Gene expression experiment analysis • Genome mining • Text mining • Databasing and data-mining • Bioinformatics workflows Donald Dunbar: Systems Biology Club

  4. Bioinformatics at QMRI • Gene expression Donald Dunbar: Systems Biology Club

  5. Bioinformatics at QMRI • Gene expression • Genome mining Donald Dunbar: Systems Biology Club

  6. Bioinformatics at QMRI • Gene expression • Genome mining • Text mining Donald Dunbar: Systems Biology Club

  7. Bioinformatics at QMRI • Gene expression • Genome mining • Text mining • Databasing & Data-mining Donald Dunbar: Systems Biology Club

  8. Bioinformatics at QMRI • Gene expression • Genome mining • Text mining • Databasing & Data-mining • Bioinformatics workflows Donald Dunbar: Systems Biology Club

  9. Bioinformatics at QMRI • Focus on data integration and access • Across levels • Molecule, cell, organism • Across disciplines • Genomics, proteomics, genetics, physiology, pathology, biochemistry • Use the literature as well as in-house data • Knowledge capture Donald Dunbar: Systems Biology Club

  10. ACTH GC ALDO renin AGT ANGII Systems Biology at QMRI? • Where we’d like to apply it • We have systems like this Physiology & Measurements Blood pressure Renal clearance, GFR Urine electrolytes Plasma electrolytes Plasma steroids Plasma AGT, renin Plasma Aldosterone Body weight, fat mass Drinking, eating quantities Multiple tissue pathology q-RTPCR Microarrays, proteomics Mouse models Ren1 KO/TG 11b KO/TG AS KO/TG HSD1 KO/Liver TG/Adipose TG/Brain TG HSD2 KO/Kidney TG Treatments & Conditions Aldo, - Na, Kidney mass ACTH + Na C57Bl6 controls, 12-20weeks Pharmaceuticals, siRNA Donald Dunbar: Systems Biology Club

  11. Systems Biology at QMRI? • Why? • The biology is very complex • More information available from system • Reduced systems lose meaning & context • Don’t want to study components separately • Want to identify missing links (indirect interactions) • Use models to help us understand the biology • Use models to help us predict (eg new experiments) • Utilise multidisciplinary research Donald Dunbar: Systems Biology Club

  12. Systems Biology at QMRI? • Can we do it? • What data do we need? • Genes (sequence and level), proteins, metabolites • Interactions • Physiology, pathology • Time courses (short, long), end points • In vivo, cell culture, in vitro • Does “classical” SB scale to tissues, organs etc…? • Are these “systems” too complex? • What would models look like? Donald Dunbar: Systems Biology Club

  13. Systems Biology at QMRI? • Who can we work with • Biologists (genetics, physiology…) • Bioinformaticians • Statisticians • Mathematicians • Computer scientists • Doctoral training centre • Can the Edinburgh SB community create a network of collaborating scientists? Donald Dunbar: Systems Biology Club

  14. Summary • Bioinformatics at QMRI being established • Working with two large research centres • Want to apply systems biology approach • Can we do it? Donald Dunbar: Systems Biology Club

  15. Visit our Web Pages http://www.bioinf.mvm.ed.ac.uk Donald Dunbar: Systems Biology Club

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