Integrating the Bioinformatic Technology Group into your research programme

1. Integrating the Bioinformatic Technology Group into your research programme BHRC Away day, Jan 2011 • Introduction • People and Skills • Examples • Integrating the BTG • Contacts

2. 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

3. 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

4. Examples: Standard problem • 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 Method HT Experiment Data List Bioinformatics Black box Not usually straightforward! Multiple methods and parameters Need to understand the biology and the question

5. Question: Can we identify related genes using known pathways and siRNA cell phenotype screens? Path1 P values (very small) Cell phenotype Data List Bioinformatics Black box Great! Wait!

6. How did you identify the phenotype? P values Not so small Path1a Cell area List Cell phenotype Protocol Bioinformatics Black box P values (not so small) Analysis Important to know how the error is carried through Other Technology Groups

7. Question: Identify TF binding sites and genes using Chip-Seq data Peak Overlaps CHip-Seq Data List of related TFs or genes Bioinformatics Black box

8. You are really interested in cell fate! List Decision tree Pheno Multi-faceted problem Novel area of research

9. BTG involvement depends on your question? To maximise our potential contribution you need to think outside the black box!

10. 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

11. 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?