GABI Genome Analysis

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GABI- Genome Analysis Bioinformatics http//www.
stats.ox.ac.uk/mathgen/bioinformatics/
Personel Topics Activities
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Personel
Jotun Hein, Ian Holmes Charlotte Deane
Professor Lectureres
Post.Docs
Gerton Lunter (math) Yun Song (math) Santiago
Schnell (math.biol.) Alex Drummond
(biol/compu.sci)
Roald Forsberg (biol.) Istvan Miklos (math) Irmi
Meyer (phys/genomics) Rune Lyngsoe (com.sci)
1-2 more very shortly
Ph.Ds
Jakob Skou (biol/math) Sumedha (compu.lab) MacCaul
ey (DTC)
2-3 more very shortly
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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
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Two kinds of alignment
Optimisation (here Parsimony) Shortest Path
costs
C T G A G G G T - - G C
CTGAGG
GTGC
probabilities
Statistical Probability and Sum over all Paths
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Coalescent Theory
Subtopics Recombination Blocks (Song,
Hein,..). Serially sampled sequences
(Forsberg, Drummond,..).
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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
genes
Human
Mouse
Cow
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Molecular Evolution and Gene Finding Two HMMs
AGTGGTACCATTTAATGCG..... PcodingATG--gtGTG
or AGTGGTACTATTTAGTGCG..... Pnon-codingATG--gtGT
G
Simple Prokaryotic
Simple Eukaryotic
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Activities
Seminar Series Monday ? Thursdays (4PM) (Hilary
term) Book study group at present MCMC
methods Journal club (compu.group/Harwell) D
TC Doctoral Training Centre. M.Sc in
Bioinformatics
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Summary
Primary recruitment for Genome Analysis
Bioinformatics over. Theoretical/Applied focus
of group Collaborations Teaching students/DPhils