Integrating the Bioinformatic Technology Group into your research programme
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Integrating the Bioinformatic Technology Group into your research programme
•Introduction•People and Skills•Examples•Integrating the BTG•Contacts
BHRC Away day, Jan 2011
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Introduction
• Group of quantitative researchers • We are biologists that use a different set of tools• Collaborate with you to answer biological questions• Enable you to cross technical boundaries• Enable you to ask data intensive questions
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People and Skills
Lee Hazelwood (Group Leader) David Westhead (Director)
Binbin Liu Andy Bulpitt (Dep-Director)
Michael Bentley • Biology: TF binding sites, sequence alignment, RT-PCR,
microarray analysis, CHip-Seq, RNA-seq, pathways, enzyme kinetics, electrophysiology, protein conformation, metabolic and development pathways, drug target discovery, multi-scale and tissue modelling …
• Computational: High throughput, machine learning, hidden markov models, power calculations, data mining, image analysis, molecular dynamics, simulations,
• Physical processes: Cell signalling and organisation, reaction kinetics, binding, structural biology, statistical physics of soft matter
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Examples: Standard problem
BioinformaticsBlack box List
HTExperiment
Data
Method
• Genome sequence analysis• Gene expression analysis using sequencing and array
methods• ChIP on chip and ChIP-seq• Copy number analysis• Gene network analysis• Point mutations and SNPs• Comparative genome studies• Protein structure prediction• Analysis of protein microarrays• High throughput mass spectrometry data • Protein-Protein docking• Protein Interaction• Simulation of cellular subsystems to analyze pathways
and regulatory/signalling networks
Not usually straightforward!
Multiple methods and parameters
Need to understand the biology and the question
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BioinformaticsBlack box List
Cell phenotype
Data
P values (very small)Path1
Great!
Wait!
Question: Can we identify related genes using known pathways and siRNA cell phenotype screens?
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How did you identify the phenotype?
BioinformaticsBlack box List
P values
Path1a
Protocol
Analysis
Other Technology Groups
Cellphenotype
P values(not so small)
Cell areaNot so small
Important to know how the error is carried through
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Question: Identify TF binding sites and genes using Chip-Seq data
BioinformaticsBlack box
Peak Overlaps
List of related TFs
or genesCHip-Seq
Data
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You are really interested in cell fate!
List Decision
tree
Multi-faceted problem
Pheno
Novel area of research
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BTG involvement depends on your question?
To maximise our potential contribution you need to think outside the black box!
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How to integrate us into your research?
Aim: Build long term successful research collaborations
Talk science• Meet to discuss possible projects• Invite us to your group meetings
Take forward• Write joint grants• Carry out pilot projects • BHRC pump prime funding
Develop a project proposal with help from BTG
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Contacting the group
• Based at FBS (Garstang, Level 10) and LIMM (Brenner, Level 7).
• Email Lee David Hazelwood [email protected]
• Take a look at the website www.bhrc.ac.uk (click on technology groups)
Questions?