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GABI - Genome Analysis & Bioinformatics stats.ox.ac.uk/mathgen/bioinformatics/

GABI - Genome Analysis & Bioinformatics http://www.stats.ox.ac.uk/mathgen/bioinformatics/. Personel Topics Activities. Personel. Professor & Lectureres. Jotun Hein, Ian Holmes Charlotte Deane. Post.Docs. Gerton Lunter (math) Yun Song (math) Santiago Schnell ( math.biol.)

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GABI - Genome Analysis & Bioinformatics stats.ox.ac.uk/mathgen/bioinformatics/

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  1. GABI- Genome Analysis & Bioinformatics http://www.stats.ox.ac.uk/mathgen/bioinformatics/ Personel Topics Activities

  2. Personel Professor & Lectureres Jotun Hein, Ian Holmes Charlotte Deane 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) MacCauley (DTC) 2-3 more very shortly

  3. 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

  4. 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

  5. Coalescent Theory Subtopics Recombination Blocks (Song, Hein,..). Serially sampled sequences (Forsberg, Drummond,..).

  6. 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

  7. Molecular Evolution and Gene Finding:Two HMMs AGTGGTACCATTTAATGCG..... Pcoding{ATG-->GTG} or AGTGGTACTATTTAGTGCG..... Pnon-coding{ATG-->GTG} Simple Prokaryotic Simple Eukaryotic

  8. 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

  9. Summary Primary recruitment for Genome Analysis & Bioinformatics over. Theoretical/Applied focus of group Collaborations Teaching students/DPhils

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