[BiO BB] PhD post in plasmid bioinformatics, genomics and ecology

Meredith Salisbury msalisbury at genomeweb.com
Fri May 10 11:33:54 EDT 2002

Hi Dawn,

I'm with Genome Technology magazine and saw your recent post.  I'm working
on an article about what kind of training people need for bioinformatics and
what positions they should look for or expect, and was wondering if I could
talk to you for some information about what the hiring side is looking for.

Thanks so much,

Meredith Salisbury
Managing Editor, Genome Technology

> -----Original Message-----
> From: bio_bulletin_board-admin at bioinformatics.org
> [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Dawn
> Field
> Sent: Friday, May 10, 2002 9:50 AM
> To: bio_bulletin_board at bioinformatics.org
> Subject: [BiO BB] PhD post in plasmid bioinformatics, genomics and
> ecology
> Dear List,
> We recently hired a superb research programmer following a post
> he made to this list about wanting to move from staight IT into
> bioinformatics  - so we're making sure to post here for this UK
> studentship.  For more information about the
> bioinformatics/genomics aspects of the below studentship please
> feel free to contact me.
> A 3-year NERC funded studentship is available for doctoral research,
> starting 1st October 2002, to work on the ecology and functional
> genomics of plasmids,
> supervised by Professor Mark Bailey, Professor John Fry, and Dr.
> Dawn Field.
> We are seeking a motivated student able to work at the interface
> of genomics,
> bioinformatics, evolutionary and ecological genetics, and
> microbial adaptation to develop
> new approaches and methods of addressing key questions about the
> role of plasmids
> in short and long-term ecological adaptation.
> To apply, please send a CV and details of two referees (name,
> address, fax,
> and email) to Professor Mark Baily, Microbial Ecology Section, CEH Oxford,
> Mansfield Rd, Oxford OX1 3SR. Applications are invited from UK residents.
> The closing date for applications is the 31st May 2002.
> Ecological and functional genomic studies to determine the
> evolutionary contribution
> of plasmids to the horizontal gene pool of bacteria
> The revolution in genomics has already produced 60 + published
> bacterial genome
> sequences and over 230 plasmid sequences for comparison and
> study.  The study
> of bacterial genome sequences combined with the introduction of
> large-scale population
> studies of DNA sequence-level variation has led to a paradigm
> shift in our thinking about
> how fluid bacterial chromosomes are and the amounts of
> recombination they are able to
> undergo.  An extremely important aspect of this fluid gene pool
> that has received far
> less attention is the contribution of plasmids, extrachromosomal
> genetic elements that
> persist and replicate independently of the host genome.  The
> significance of
> understanding this horizontal gene pool (HGP) lies in attempting
> to understand how,
> when and why plasmids contribute to the evolution fitness,
> persistence, and ecological
> role of a given host in a specific environment.
> For the last decade we have studied the microbial genetics of
> plant associated
> pseudomonads and demonstrated the direct co-operation between
> host and plasmid
> in local adaptation to the niche.  Current questions we are
> trying to address include:
> How does plasmid host-range evolve? What selective pressures
> control plasmid
> persistence or extinction in populations? How different/similar
> is the genome structure
> and gene content of plasmids taken from the same host? Which
> plasmid genes/sequences
> are responsible for specific host phenotypes and adaptation? Do
> rates of recombination
> differ within plasmids when compared to their host chromosome?
> To answer these broad
> questions, we need to collect, analyse, and integrate information
> obtained from a variety
> of experimental and computer-based approaches including:  1)
> population-level and
> phylogenetic studies of genetic variation found in plasmid and
> host populations, 2) comparative
> genomics analysis of plasmids and their hosts, 3) transcriptomic
> studies of plasmid genes
> expressed only in certain hosts/environments, and 4) proteomic
> studies of host-specific
> and environment-specific protein profiles collected using
> state-of-the-art proteomic
> technologies.
> Students with undergraduate or MRes degrees (or significant
> research experience) in
> the fields of Ecology, Evolution, Microbiology, or Computational
> biology (Bioinformatics)
> are strongly encouraged to apply.  Students with a background in
> Computer Science,
> Maths, Statistics, or a related field with a strong desire to
> learn biological principles will
> also be considered.  The student will be located in the
> Laboratories of Mark Bailey
> (mbj at ceh.ac.uk) and Dawn Field (Dfield at ceh.ac.uk) at CEH-Oxford
> and be registered
> for a NERC funded PhD with John Fry (fry at cardiff.ac.uk) at the
> University of Cardiff.
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