Transcript Pathdb - University of Edinburgh

Bioinformatics (and Systems Biology?)
in Biomedical Research
Donald Dunbar
Systems Biology Club
30th November 2005
Introduction
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Bioinformatics at QMRI
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Who we work with
What we do
Our focus
Systems Biology at QMRI?
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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?
November 30th 2005
Donald Dunbar: Systems Biology Club
Bioinformatics at QMRI
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Queen’s Medical Research Institute
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Centre for Cardiovascular Science
• Hypertension, atherosclerosis, thrombosis, diabetes, obesity, heart failure
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Centre for Inflammation Research
• Lung, kidney, vascular, and other diseases associated with inflammation
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Centre for Reproductive Biology
• Female and male reproductive health and disease
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We work with cardiovascular and inflammation scientists
Providing bioinformatics support in several areas
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Gene expression experiment analysis
Genome mining
Text mining
Databasing and data-mining
Bioinformatics workflows
November 30th 2005
Donald Dunbar: Systems Biology Club
Bioinformatics at QMRI
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Gene expression
November 30th 2005
Donald Dunbar: Systems Biology Club
Bioinformatics at QMRI
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Gene expression
Genome mining
November 30th 2005
Donald Dunbar: Systems Biology Club
Bioinformatics at QMRI
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Gene expression
Genome mining
Text mining
November 30th 2005
Donald Dunbar: Systems Biology Club
Bioinformatics at QMRI
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Gene expression
Genome mining
Text mining
Databasing & Datamining
November 30th 2005
Donald Dunbar: Systems Biology Club
Bioinformatics at QMRI
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Gene expression
Genome mining
Text mining
Databasing & Datamining
Bioinformatics
workflows
November 30th 2005
Donald Dunbar: Systems Biology Club
Bioinformatics at QMRI
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Focus on data integration and access
Across levels
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Across disciplines
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Molecule, cell, organism
Genomics, proteomics, genetics,
physiology, pathology, biochemistry
Use the literature as well as in-house
data
Knowledge capture
November 30th 2005
Donald Dunbar: Systems Biology Club
Systems Biology at QMRI?
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Where we’d like to apply it
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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
ACTH
GC
ALDO
Treatments & Conditions
November 30th 2005
Aldo, - Na, Kidney mass
ACTH + Na
C57Bl6 controls, 12-20weeks
Pharmaceuticals, siRNA
renin
AGT ANGII
Donald Dunbar: Systems Biology Club
Systems Biology at QMRI?
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Why?
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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)
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Use models to help us understand the biology
Use models to help us predict (eg new experiments)
Utilise multidisciplinary research
November 30th 2005
Donald Dunbar: Systems Biology Club
Systems Biology at QMRI?
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Can we do it?
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What data do we need?
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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?
November 30th 2005
Donald Dunbar: Systems Biology Club
Systems Biology at QMRI?
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Who can we work with
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Biologists (genetics, physiology…)
Bioinformaticians
Statisticians
Mathematicians
Computer scientists
Doctoral training centre
Can the Edinburgh SB community create a
network of collaborating scientists?
November 30th 2005
Donald Dunbar: Systems Biology Club
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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November 30th 2005
Donald Dunbar: Systems Biology Club
Visit our Web Pages
http://www.bioinf.mvm.ed.ac.uk
November 30th 2005
Donald Dunbar: Systems Biology Club