Transcript Integrating the Bioinformatic Technology Group into your research

Integrating the Bioinformatic Technology Group
into your research programme
BHRC Away day, Jan 2011
•Introduction
•People and Skills
•Examples
•Integrating the BTG
•Contacts
Introduction
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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
People and Skills
Lee Hazelwood (Group Leader)
David Westhead
(Director)
Binbin Liu
Andy Bulpitt (DepDirector)
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, multiscale 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
Examples: Standard problem
• Genome sequence analysis
• Gene expression analysis
using sequencing and array
Method
methods
• ChIP on chip and ChIP-seq
• Copy number analysis
Bioinformatics
HTnetwork analysis
• Gene
List
Black
box
Experiment
• Point mutations and SNPs
Data
• Comparative
genome studies
• Protein structure prediction
• Analysis of protein microarrays
Not usually
• High throughput
massstraightforward!
spectrometry data
• Protein-Protein
Multipledocking
methods and parameters
• Protein Interaction
Need to understand
biology and
the question
• Simulation
of cellular the
subsystems
to analyze
pathways
and regulatory/signalling networks
Question: Can we identify related genes using known
pathways and siRNA cell phenotype screens?
Path1
Cell
phenotype
Data
Bioinformatics
Black box
Great!
Wait!
P values (very small)
List
How did you identify the phenotype?
P values
Not so small
Cell area
Protocol
Cell
phenotype
P values
Analysis (not so small)
Other Technology
Groups
Path1a
Bioinformatics
Black box
List
Important to know how the
error is carried through
Question: Identify TF binding sites and genes
using Chip-Seq data
Peak
Overlaps
CHip-Seq
Data
Bioinformatics
Black box
List of
related TFs
or genes
You are really interested in cell fate!
List
Pheno
Multi-faceted problem
Novel area of research
Decision
tree
BTG involvement depends on your question?
To maximise our potential contribution you need to
think outside the black box!
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
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?