people graduates rahul satija - footprinting and statistical alignment joanna davies - integrative...
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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:
€
dx dt = Fθ (x )
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dx dt = Fθ (x )
Systems and Modeling
Variation within Species
Focus
Recombination
Hein
, Sch
ieru
p a
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Wiu
f Gen
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ealo
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s, V
ar ia
tion
an
d
Evolu
tion
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
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