People

Graduates

Rahul Satija - Footprinting and Statistical Alignment

Joanna Davies - Integrative Genomics of Asthma

Aziz Mithani - Comparison of Metabolic Pathways

Marton Munz - Comparative Molecular Dynamics

Postdocs

Rune Lyngsø - computer scientist, RNA and algorithms

Istvan Miklos - mathematician, Statistical Alignment

Garrett Hellenthal - Geneticist, Association Mapping

Shuhei Mano - Mathematical Geneticist

Bhalchandra Thatte - Combinatorics Inference of Pedigrees

Student Projects

Plamen Turmenjev - evolution of cell cycle dynamics

Cong Xie - inference of somatic cell phylogeny

Stephen Okeefe - MCMC statistical alignment

Tian Zuo - MinARGs and Association Mapping

Markus Gerstel Evolving English Grammar

Themes: Evolution, Variation and Systems

Evolutionary model

Unknown ancestral sequences

Unknown genealogy

Evolution/Homology:

Domain Expansion:

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dx dt = Fθ (x )

Systems and Modeling

Variation within Species

Focus

Recombination

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Sequence Evolution & Hidden Structure

Genomes

Some ProjectsTheoretical Projects/Methodology Projects (Taylor, Darden,..)

The TPS Algorithm & the Evolutionary Path of Protein Structures

Evolutionary Docking of Proteins

Difficult Concepts in Systems Biology

Alternative Splicing: Functionality, Evolution and Selection

Collaboration Projects (Kay Davies, Cookson, Peter Simmonds, Iber, Decode)

Computational Promoter Analysis of non-Coding RNAs

Population Pedigree Inference from Genomic Data

Comparative Virus Annotation

Parameter and Sensitivity Analysis for Large System of ODEs

Systems Biology (Bela Novak,

Engineering Systems Biology of the Cell Cycle

Evolving Dynamical Systems

Comments

+’s: Oxford is clearly great place

Extremely good collaborations and connections can be made

-’s: We provide ideas, expertise, discussion, criticism, but are not

strong on micro-management

A very good project & a very good plan for it should be provided

The content of a project could be

Theoretical/Mathematical/Algorithmic

Software engineering

Empirical Collaboration

Some idea of yours

Outreach

Bioinformatics Days:2003 Comparative Genomics2003 Pathogen Analysis2004 Mathematical Modelling and Systems Biology2004 Expression Data Analysis2005 Regulatory Elements in Eukaryotic Genomes

2005 Bioinformatics and Network Biology2006 Bioinformatics and Protein Science2006 Computational Problems in Biology2007 Genetics of Disease

Future: Linguistic Models in Biology and Language, Prostate and Breast Cancer

Courses:

• Bioinformatics and Computational Biology (undergrad) 16*60 min

• DTC LSI & DTC SysBiol (graduate) 12*90 min

• Part Time MSc Bioinformatics (masters)

Lecture Series:2004 The Human Genome 2005 Beyond the Human Genome2005 Bioinformatics, Systems Biology and the OMICS2007 All about Drosophila

Future: Major Diseases and the Model Organisms, The Great Genetic Diseases, The Great Infectious Diseases