Genome Analysis & Bioinformatics Group

abalonestrawBiotechnology

Oct 2, 2013 (4 years and 1 month ago)

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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

Unknown
ancestral
sequences

Unknown
genealogy

Evolution/Homology:

Domain Expansion:

Systems and Modeling

Variation within Species

Focus

Recombination

Sequence Evolution & Hidden Structure

Genomes

Some Projects

Theoretical 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 Genomics

2003 Pathogen Analysis

2004 Mathematical Modelling and Systems Biology

2004 Expression Data Analysis

2005 Regulatory Elements in Eukaryotic Genomes

2005 Bioinformatics and Network Biology

2006 Bioinformatics and Protein Science

2006 Computational Problems in Biology

2007 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

Genome

2005 Bioinformatics, Systems Biology and the OMICS

2007 All about Drosophila


Future
:

Major

Diseases

and

the

Model

Organisms,

The

Great

Genetic

Diseases,

The

Great

Infectious

Diseases