Bioinformatics (and Systems Biology?) in Biomedical Research

Bioinformatics (and Systems Biology?)in Biomedical Research

Donald DunbarSystems Biology Club

30th November 2005

November 30th 2005 Donald Dunbar: Systems Biology Club

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?


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


Bioinformatics at QMRI Gene expression


Bioinformatics at QMRI Gene expression Genome mining


Bioinformatics at QMRI Gene expression Genome mining Text mining


Bioinformatics at QMRI Gene expression Genome mining Text mining Databasing & Data-

mining


Bioinformatics at QMRI Gene expression Genome mining Text mining Databasing & Data-

mining Bioinformatics

workflows


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


Systems Biology at QMRI? Where we’d like to apply it

We have systems like this

ALDO

GC

reninAGT ANGII

ACTH

Physiology & MeasurementsBlood pressureRenal clearance, GFRUrine electrolytesPlasma electrolytesPlasma steroidsPlasma AGT, reninPlasma AldosteroneBody weight, fat massDrinking, eating quantitiesMultiple tissue pathologyq-RTPCRMicroarrays, proteomics

Mouse modelsRen1 KO/TG11b KO/TGAS KO/TGHSD1 KO/Liver TG/AdiposeTG/Brain TGHSD2 KO/Kidney TG

Treatments & ConditionsAldo, - Na, Kidney massACTH + NaC57Bl6 controls, 12-20weeksPharmaceuticals, siRNA


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


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?


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?


Summary

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


Visit our Web Pages

http://www.bioinf.mvm.ed.ac.uk

Bioinformatics (and Systems Biology?) in Biomedical Research

Documents

Transcript of Bioinformatics (and Systems Biology?) in Biomedical Research