Bioinformatics (and Systems Biology?) in Biomedical Research

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Bioinformatics (and Systems Biology?)in
Biomedical Research

• Donald Dunbar
• Systems Biology Club
• 30th November 2005

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Introduction

• Bioinformatics at QMRI
• Who we work with
• What we do
• Our focus
• Systems Biology at QMRI?
• Where wed 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?

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Bioinformatics at QMRI

• Queens 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

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Bioinformatics at QMRI

• Gene expression

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Bioinformatics at QMRI

• Gene expression
• Genome mining

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Bioinformatics at QMRI

• Gene expression
• Genome mining
• Text mining

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Bioinformatics at QMRI

• Gene expression
• Genome mining
• Text mining
• Databasing Data-mining

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Bioinformatics at QMRI

• Gene expression
• Genome mining
• Text mining
• Databasing Data-mining
• Bioinformatics workflows

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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

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Systems Biology at QMRI?

• Where wed 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
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Systems Biology at QMRI?

• Why?
• The biology is very complex
• More information available from system
• Reduced systems lose meaning context
• Dont 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

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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?

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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?

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Summary

• Bioinformatics at QMRI being established
• Working with two large research centres
• Want to apply systems biology approach
• Can we do it?

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Visit our Web Pages
http//www.bioinf.mvm.ed.ac.uk