GABI- Genome Analysis & Bioinformaticshttp://www.stats.ox.ac.uk/mathgen/bioinformatics/

Personel

Topics

Activities

PersonelJotun Hein,

Ian Holmes

Charlotte Deane

Professor & LectureresProfessor & Lectureres

Gerton Lunter (math)

Yun Song (math)

Santiago Schnell (math.biol.)

Alex Drummond (biol/compu.sci)

Jakob Skou (biol/math)

Sumedha (compu.lab)

MacCauley (DTC)

Post.DocsPost.Docs Roald Forsberg (biol.)

Istvan Miklos (math)

Irmi Meyer (phys/genomics)

Rune Lyngsoe (com.sci)

Ph.DsPh.Ds

2-3 more very shortly2-3 more very shortly

1-2 more very shortly1-2 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

Statistical: Probability and Sum over all Paths

C T G A G G

G T - - G CCTGAGG GTGC

* probabilities

+ costs

Coalescent TheoryCoalescent Theory

SubtopicsSubtopics

Recombination Blocks (Song, Hein,..).Recombination Blocks (Song, Hein,..).

Serially sampled sequences (Forsberg, Drummond,..).Serially sampled sequences (Forsberg, Drummond,..).

Comparison in Bioinformatics

General Problem: Entities observed in Homologous Variants. Applications:

Protein Structure

RNA Structures.

Gene Finding.

Proteomics

..........

Describe its evolutionary process

Describe their evolutionary relationship

Infer hidden structure or combine observations optimally.

Future:

Alternative Splicing

Viral genesMouse Cow Human

Molecular Evolution and Gene Finding: Two HMMs

Simple Prokaryotic Simple Eukaryotic

AGTGGTACCATTTAATGCG..... Pcoding{ATG-->GTG} orAGTGGTACTATTTAGTGCG..... Pnon-coding{ATG-->GTG}

ActivitiesSeminar 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.Primary recruitment for Genome Analysis & Bioinformatics over.

Theoretical/Applied focus of groupTheoretical/Applied focus of group

CollaborationsCollaborations

Teaching students/DPhilsTeaching students/DPhils