The Department of Pathology is offering a fully-funded 4-year PhD studentship in computational/mathematical biology for October 2016 entry, funded by a grant from the European Research Council (ERC).The student will be based at the Division of Virology, Addenbrooke’s Hospital, Cambridge, under the supervision of Dr Andrew E. Firth.
The studentship is available to UK nationals and EU students who meet the UK residency requirements. Further information about your fee status can be found at the following website:
Title of project: Comparative genomics of RNA viruses
Details of project:
We are seeking highly motivated candidates with a strong background in mathematics and, preferably, also knowledge of computer programming and/or the biological sciences, interested in pursuing PhD research in comparative genomic analysis of RNA virus genomes.
The aim of the PhD studentship is (1) to computationally identify all functional elements in the genomes of RNA viruses and retroviruses of medical, veterinary and agricultural importance; and (2) to develop new comparative genomic software, web interfaces, and an interactive RNA virus comparative genomics database. Specific projects include RNA structure prediction and novel feature discovery using sequence alignments for ~700 virus species; (2) development of methods for automated feature annotation; and (3) development of methods for mining high-throughput sequencing data for highly divergent novel viruses, and processing their sequence information for comparative genomics. The projects are expected to feed into experimental validation/characterization work undertaken by other members of the joint computational/experimental lab.
More information on the supervisor’s research can be found on their research group websites http://www.path.cam.ac.uk/directory/andrew-firth and http://www.firthlab.path.cam.ac.uk/index.html
Information on how to apply is available at http://www.path.cam.ac.uk/graduate/firth.html.
The deadline for applications is Monday 22 February 2016 by 12 noon. Applications received after this time will not be considered.
1) Olspert A, Chung BY, Atkins JF, Carr JP, Firth AE* (2015) Transcriptional slippage in the positive-sense RNA virus family Potyviridae. EMBO Rep 16:995-1004.
2) Finch LK, Ling R, Napthine S, Olspert A, Michiels T, Lardinois C, Bell S, Loughran G, Brierley I, Firth AE* (2015) Characterization of ribosomal frameshifting in Theiler's murine encephalomyelitis virus. J Virol 89:8580-8589.
3) Firth AE* (2014) Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses. Nucleic Acids Res 42:12425-12439.
4) Cook S*, Chung BY, Bass D, Moureau G, Tang S, McAlister E, Culverwell CL, Glucksman E, Wang H, Brown TD, Gould EA, Harbach RE, de Lamballerie X, Firth AE* (2013) Novel virus discovery and genome reconstruction from field RNA samples reveals highly divergent viruses in dipteran hosts. PLoS One 8:e80720.
5) Fang Y*, Treffers EE, Li Y, Tas A, Sun Z, van der Meer Y, de Ru AH, van Veelen PA, Atkins JF, Snijder EJ*, Firth AE* (2012) Efficient -2 frameshifting by mammalian ribosomes to synthesize a previously undiscovered arterivirus protein. Proc Natl Acad Sci U S A 109:E2920-E2928.