Bioinformatics 2011 BHRC Away Day presentation

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2 Οκτ 2013 (πριν από 3 χρόνια και 10 μήνες)

110 εμφανίσεις

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



Bioinformatics

Black box

List



HT

Experiment

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



Bioinformatics

Black 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?

Bioinformatics

Black box

List



P values

Path1a

Protocol

Analysis

Other Technology

Groups

Cell

phenotype

P values

(not so small)

Cell area

Not so small

Important to know how the
error is carried through

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

Bioinformatics

Black box

Peak

Overlaps

List of

related TFs

or genes

CHip
-
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?