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PhD Studentships in computational/mathematical biology (Fixed Term)

PhD Studentships in computational/mathematical biology (Fixed Term)

The Department of Pathology is offering two fully-funded 4-year PhD studentships in computational/mathematical biology for October 2016 entry, funded by a grant from the European Research Council (ERC). The students will be based at the Division of Virology, Addenbrooke's Hospital, Cambridge, under the supervision of Dr Andrew E. Firth

The Department has an excellent reputation in pure biological and biomedical research. The studentships are 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 two 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 majority of pathogenic viruses have genomes composed of RNA instead of DNA. Examples include influenza, ebola, rabies, SARS, MERS, polio and dengue viruses. Further, many livestock and most plant viruses have RNA genomes. RNA virus genomes are compact and multifunctional: as well as the protein-coding genes, genomes contain signals (e.g. RNA structures and long-range interactions, and protein binding sites) to direct translation, replication, subgenomic RNA synthesis, genome packaging and other aspects of the virus replicative cycle. Many of these features differ significantly from those found in cellular genes and genomes, and features are frequently overlapping (e.g. RNA signals embedded within protein-coding genes). The advent of cheap and rapid sequencing technologies has led to great potential for comparative genomic analysis to identify and characterize genomic features. This potential has been realized most thoroughly for the human (and other vertebrate) genomes. In contrast, far less work has been done on viruses. This is surprising because - with their small genomes, high evolutionary divergence rates, and the accumulation of large numbers of sequenced isolates for pathogenic species - RNA viruses are uniquely amenable to comparative genomic analysis.

Research in our lab focuses on the development and application of computational techniques to gain a better understanding of the molecular biology of RNA viruses. Broadly speaking, the aims of the two PhD studentships are (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.



Recent Publications:

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.

6)    Jagger BW, Wise HM, Kash JC, Walters K-A, Wills NM, Xiao Y-L, Dunfee RL, Schwartzman LM, Ozinsky A, Bell GL, Dalton RM, Lo A, Efstathiou S, Atkins JF, Firth AE*, Taubenberger JK*, Digard P* (2012) An overlapping protein-coding region in influenza A virus segment 3 modulates the host response. Science 337:199-204.


More information on the supervisor’s research can be found on their research group websites and

The deadline for applications is Monday 22 February 2016 by 12 noon.  Applications received after this time will not be considered.

Fixed-term: The funds for these posts are available for 4 years. The funding will be £21,238 pa which includes University and College fees that the student will be responsible for paying.

To Apply

Copies of the form can be downloaded below:

Download form PA22

Please send applications to:

** Studentships are only 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

Applications from ineligible candidates will not be considered.

Preferred candidates will be required to apply formally through completion of a Graduate and Scholarship Application Form (GRADSAF).