19 June: fyi -- phd funding, UCD
Index of June 2006 | Index of year: 2006 | Full index
students are invited to apply for bioinformatics-related studentships.
Two projects are detailed below.
Could you circulate to anyone that may be looking for PhD positions in bioinformatics.
This is a competitive PhD application process. The deadline is 26th June, and students are
very strongly advised
to contact me (denis.shields@ucd.ie) before submitting applications.
Project titles:
(1) ?Genetic programming for the identification of novel signalling motifs in proteins?
(2) ?Cytoplasmic signalling near the membrane in adhesion proteins: a combined
bioinformatic and
experimental approach to identifying and characterising key signalling motifs.?
Other bioinformatics groups at UCD (http://bioinformatics.ucd.ie) may have other potential
projects.
Denis
Denis Shields, Bioinformatics, Conway Institute, University College Dublin, Dublin 4, Ireland
tel +353-1-7166831 denis.shields@ucd.ie
Details:
Project Title:
Genetic programming for the identification of novel signalling motifs in proteins.
Principal Investigator
Denis Shields (School of Medicine)
Michael O?Neill (School of Computer Science)
Email:
Denis.shields@ucd.ie ( UCD Conway Institute for Biomolecular and Biomedical Research)
m.oneill@ucd.ie (UCD Natural Computing Research and Applications Group)
Project Description:
Current approaches to identifying short critical signalling motifs in proteins are hampered by
the computational
inefficiency of motif discovery algorithms. We have previously identified computer algorithms
that allow short
motifs to be discovered that are shared between proteins. The basis for these methods are
that they manage to
eliminate similarities arising from structural similarity of related proteins. However, these
methods fail to
adequately account for motifs that have gaps. Genetic programming is a computational
technique that may be
applied to this problem, but is reasonably computationally intensive. This studentship will
address this problem
at two stages: in the first stage the student will apply genetic algorithms to the refinement
and combination of
large datasets of initially discovered motifs, to identify gapped motifs. For the second stage
of the studentship,
the student will decide either to develop de novo methods of motif discovery based on
genetic programming,
or alternatively to test experimentally in the laboratory the functions of the discovered motifs
identified. Such
motifs in the form of synthesised peptides may act as key reagents in teasing apart the
signalling pathways of
proteins in cellular models, and ultimately some of them have the potential to serve as
models of therapeutics.
Websites of the collaborating research groups: http://ncra.ucd.ie and http://
bioinformatics.ucd.ie/shields/
Qualifications/Background required:
A BSc in Science (Chemistry, Biology, Mathematics, Physics, Statistics, Computer Science, or
Engineering). An
aptitude for, and an interest in, both computational modelling and understanding biological
signalling systems.
Commencement Date
Between 1 Oct 2006 and 1 Jan 2007
Closing Date
26th June 2006 (Ad Astra scholarship application procedure, see
http://www.ucd.ie/lifesciences/graduateschool/index.html
and
http://www.ucd.ie/lifesciences/graduateschool/Ad%20Astra%20application.html
Further enquiries to: (Principal Investigator?s email)
Denis.shields@ucd.ie
M.oneill@ucd.ie
Project Title
Cytoplasmic signalling near the membrane in adhesion proteins: a combined bioinformatic
and experimental
approach to identifying and characterising key signalling motifs.
Principal Investigators (joint)
Ann Hopkins, School of Medicine
Denis Shields, School of Medicine
Email:
Denis.shields@ucd.ie
Project Description
Our previous bioinformatic and experimental work has identified a number of short
palmitylated peptides
derived from cytoplasmic regions near the membrane of transmembrane proteins. These
have the potential to
serve as reagents to tease apart the roles of different aspects of a variety of adhesion
molecules involved in
tight and adherens junctions. Design will focus on peptide subsequences that lie downstream
of naturally
palmitylated regions of human proteins. The student will work equally in the lab and in
computer modelling.
The goal will be to tease apart these signalling pathways in more detail, and the structure
and activity of
bioactive molecules, some of which may form the basis of potential therapeutics influencing
junction formation
and dissolution in the treatment of mucosal and inflammatory disease. The student would
need to have a
strong interest in laboratory research, computational modelling, and programming, and
laboratory research.
The research teams of the two supervisors provide a strongly supportive environment in
which to acquire skills
in both domains. This project will provide an ambitious student with the opportunity to
develop the trans-
disciplinary skill-set to bridge between bioinformatics and cell biology in the broad field of
drug discovery.
Qualifications/Background required (50 words max please)
A BSc in Science (Chemistry, Biology, Physics, Statistics, Computer
Science, or Engineering). An aptitude for, and an interest in, both
computational modelling and experimentation.
Commencement Date
Between 1 Oct 2006 and 1 Jan 2007
Closing Date
26th June 2006 (ad astra scholarship closing date: see
http://www.ucd.ie/lifesciences/graduateschool/index.html
and
http://www.ucd.ie/lifesciences/graduateschool/Ad%20Astra%20application.html
Index of June 2006 | Index of year: 2006 | Full index