Integrating the Bioinformatic Technology Group into your research programme

•Introduction•People and Skills•Examples•Integrating the BTG•Contacts

BHRC Away day, Jan 2011

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

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

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

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?

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

Question: Identify TF binding sites and genes using Chip-Seq data

BioinformaticsBlack box

Peak Overlaps

List of related TFs

or genesCHip-Seq

Data

You are really interested in cell fate!

List Decision

tree

Multi-faceted problem

Pheno

Novel area of research

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 L.D.Hazelwood@leeds.ac.uk

• Take a look at the website www.bhrc.ac.uk (click on technology groups)

Questions?