graduate school, research topics

About EBI
http://www.ebi.ac.uk/Information/About_EBI/about_ebi.html


http://www.ebi.ac.uk/Thornton/
* Elucidating and evolution enzyme function through structural analysis
* Deriving principles of protein structure
* Functional annotation of genomes, proteins and structures
* Functional genomics analysis of ageing
* Web tool and resource development

http://www.ebi.ac.uk/Rebholz/
The group focuses on extraction of facts from scientific literature in molecular biology. This is mainly based but not limited to matching of language patterns. In addition we do research on the disambiguation of semantic types, e.g. proteins, genes, species, drugs, and on automatic methods to identify language patterns. Both approaches require machine learning expertise and domain knowledge. The group has strong experience in Natural Language Processing methods (NLP) in the biomedical domain, and has applied its methods to different problems, e.g. identification of protein-protein interactions, extraction of acronyms and identification of mutations. All solutions are implemented as stand-alone modules, which can be combined and used to process text data in a pipeline. Existing modules are made available to the public through EBI's central services ('Whatizit', now as SOAP Web Service).

http://www.ebi.ac.uk/luscombe/
The Luscombe group's research focuses on the genomic analysis of regulatory systems.

We study how the biology of an organism is shaped by regulation of gene expression. We investigate this at various levels of complexity, from single-celled bacteria and yeast to complex mammals. Expression of a gene - i.e. production of a protein - is a complex exercise requiring large, gluttonous protein machines which expend the cell's energy reserves. Hence, the organism needs to be judicious in choosing which proteins to produce when and where. Furthermore, the expression of all genes at all times would be detrimental to the organism. Expression must be rigorously regulated so that the right genes are ‘switched on or off’ in response to changes in the internal and external environments of the cell.

http://www.ebi.ac.uk/chembl/
The ChEMBL group's research focuses on mapping the interactions and functional effects of small molecules binding to their macromolecular targets.

The group studies the interactions of pharmacologically active molecules and their receptors. In particular the group builds and maintains a series of drug discovery databases that are components of ChEMBL.

http://www.ebi.ac.uk/goldman/
Our main interests are in methods for the analysis of DNA and amino acid sequences to study evolution. Past work has been on the theoretical basis of phylogenetic analyses of this data, aiming to understand and improve methods, and on the development of statistical methods that test the accuracy of current mathematical models. More recent work has concentrated on devising new, better, mathematical models and the application of these models and methods to comparative genomic data.

http://www.ebi.ac.uk/panda/
The Protein and Nucleotide Database Group (PANDA) is a large group providing all the sequence resources at the EBI, from DNA through to Protein and encompassing the associated databases, such as genome databases (eg, Ensembl), protein families (eg, InterPro), protein function (eg, UniProtKB), proteomics (eg, IntAct) ontologies (eg, GOA), and pathways (eg, Reactome).

http://www.ebi.ac.uk/compneur-srv/
The interests of the group Computational Neurobiology revolve around signal transduction in neurons, ranging from the molecular structure of membrane proteins involved in neurotransmission to modelling signalling pathways. A strong focus is the molecular and cellular basis of neuroadaptation in neurons of the basal ganglia. We also provide services that facilitate our research, including database production and software development.

http://www.ebi.ac.uk/bertone/
The Bertone Group analyses genetic and biochemical mechanisms underlying cellular differentiation events, particularly in human and mouse embryonic stem (ES) cell lines.

SFU Bioinformatics Program
http://compbio.cs.sfu.ca/bio_graduate.htm

UBC Bioinformatics Program
http://www.bioinformatics.ubc.ca/

Bioinformatics at Boston University
http://bioinformatics.bu.edu/

July 15 deadline
http://www.embl.de/training/eipp/application/index.html

research groups
http://www.embl.de/training/eipp/application/recruiting_gl/index.html

research topics
http://www.embl.de/training/eipp/application/research_topics/index.html

Data integration / structural biology
http://www.embl.de/research/units/scb/schneider_reinhard/index.html

********** Data integration - disease mechanism
http://www.embl.de/research/units/scb/schneider_reinhard/index.html

******* Protein interactions and complexes - disease mechanism
http://www.embl.de/research/units/scb/russell/index.html

*** Gavin
http://www.embl.de/research/units/scb/gavin/awards/index.html

shared applicant questionnaire
https://www-db.embl.de/jss/servlet/de.embl.ml.phdProgramme.PhdApplicationExternalViewer?m=handleRequestExtView

Structural and Computational Biology:

Bork Group - Deciphering function and evolution of biological systems
Briggs Group - How proteins manipulate membranes - cryo-electron microscopy and tomography
Russell Group - Structural bioinformatics
Scheffzek Team - Signal transduction – disease proteins
Schneider (Reinhard) Group - Data integration and knowledge management

http://www.icapture.ubc.ca/who/who_mark_wilkinson.shtml
He then worked as a freelance bioinformatics consultant for one year, after which he joined the iCAPTURE Team, and now continues working in the area of bioinformatics, with a particular focus on data integration and machine-readable knowledge representation.

Visit the Wilkinson Lab Homepage (http://wilkinsonlab.ca) for up-to-date information on our research activities. The Wilkinson Laboratory is
interested in the problem of facilitating the interaction between a biologist and the data and analytical tools they require each day to make new discoveries. Our laboratory focuses on four main themes: Annotation, Interrogation, Integration, and Visualization.
http://www.biomoby.org/

CardioSHARE
http://cardioshare.icapture.ubc.ca/
CardioSHARE will use the knowledge of biologists, encoded in "Ontologies" to help interpret these kinds of questions, and automate the discovery and retrieval of the answers. When completed, CardioSHARE will be sufficiently powerful to answer questions for which the answer IS NOT KNOWN - putting it well beyond the power of keyword-style searches like Google and Entrez. CardioSHARE will accomplish this by having sufficient
understanding of biological/bioinformatics analyses that it can automatically construct and execute the pipeline of analytical tools necessary to answer the question being asked, thus finally bringing the power of in silico research into the hands of biomedical bench scientists.
- semantic web


http://www.stat.ubc.ca/~jenny/research.html
* High-throughput phenotypic experiments, genome-wide reverse genetic studies
* Finding informative sets and clusters of genes. Novel forms of meta-analysis. Using concepts from graph theory and survival analysis in the context of cluster analysis.