Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Point mutation wikipedia , lookup
Epigenetics of human development wikipedia , lookup
Genome evolution wikipedia , lookup
Site-specific recombinase technology wikipedia , lookup
Vectors in gene therapy wikipedia , lookup
Minimal genome wikipedia , lookup
Pathogenomics wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Metagenomics wikipedia , lookup
Gene expression profiling wikipedia , lookup
Integrating the Bioinformatic Technology Group into your research programme BHRC Away day, Jan 2011 •Introduction •People and Skills •Examples •Integrating the BTG •Contacts 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 (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?