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Transcript 
GABI- Genome Analysis & Bioinformatics
http://www.stats.ox.ac.uk/mathgen/bioinformatics/
Personel
Topics
Activities
Personel
Jotun Hein,
Professor & Lectureres
Ian Holmes
Charlotte Deane
Post.Docs Gerton Lunter (math)
Roald Forsberg (biol.)
Yun Song (math)
Istvan Miklos (math)
Santiago Schnell (math.biol.)
Irmi Meyer
Alex Drummond (biol/compu.sci)
Rune Lyngsoe (com.sci)
(phys/genomics)
1-2 more very shortly
Ph.Ds
Jakob Skou (biol/math)
Sumedha (compu.lab)
MacCauley (DTC)
2-3 more very shortly
Topics
Statistical Alignment – Hein, Song, Lunter, IHolmes,Miklos
Coalescent Theory – Hein, Drummond,Forsberg
RNA Secondary Structure – Lyngsoe, Meyer,
Expression Analysis – Lyngsoe, Miklos
Metabolic Pathways, Regulatory Networks - -Schnell
Pathogen Analysis – Drummond, Forsberg, Hein,
Genome Annotation – Hein, IHolmes, Jakob Skou, Meyer,
Proteomics - Deane
Two kinds of alignment
Optimisation (here Parsimony): Shortest Path
+ costs
C T G A G G
CTGAGG
GTGC
* probabilities
Statistical: Probability and Sum over all Paths
G T - - G C
Coalescent Theory
Subtopics
Recombination Blocks (Song, Hein,..).
Serially sampled sequences (Forsberg, Drummond,..).
Comparison in Bioinformatics
General Problem: Entities observed in Homologous Variants.
Applications:
Describe its evolutionary process
Describe their evolutionary relationship
Protein Structure
Infer hidden structure or combine
observations optimally.
RNA Structures.
Gene Finding.
Proteomics
..........
Future:
Alternative Splicing
Mouse
Cow
Human
Viral genes
Molecular Evolution and Gene Finding: Two HMMs
AGTGGTACCATTTAATGCG.....
AGTGGTACTATTTAGTGCG.....
Simple Prokaryotic
Pcoding{ATG-->GTG} or
Pnon-coding{ATG-->GTG}
Simple Eukaryotic
Activities
Seminar Series Monday  Thursdays (4PM) (Hilary term)
Book study group: at present MCMC methods
Journal club (compu.group/Harwell)
DTC – Doctoral Training Centre.
M.Sc in Bioinformatics
Summary
Primary recruitment for Genome Analysis & Bioinformatics over.
Theoretical/Applied focus of group
Collaborations
Teaching students/DPhils
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