Tuesday, October 6, 2009

Interview with Evolutionary Bioinformatics editorial board member Dr John Hancock

This interview is with Evolutionary Bioinformatics editorial board member Dr John Hancock. Evolutionary Bioinformatics is an open access journal published by Libertas Academica.

Editor in Chief Dr Dennis Wall has recently issued a call for papers.

What is the primary focus of your work and main areas of expertise?

I run a bioinformatics group at MRC Harwell, which is a major international centre in mouse genetics. My background is in molecular evolution, particularly the evolution of repetitive (simple) sequences and since 1993 I have had a strong interest in amino acid repeats in proteins. My current group also has a wider remit. We are very interested in the collection, dissemination and representation (using ontologies) of phenotype data and in the relationship between genotype and phenotype which we address using both sequence analysis techniques and systems modelling.

What are the most exciting and cutting-edge developments in your area?

Our work on amino acid repeats has recently shown that these repeats tend very strongly to occur in unstructured regions of proteins. This is a novel insight into the context in which amino acid repeats evolve and brings together the two areas of repeat and unstructured region evolution. The two other major bioinformatics challenges I'm involved in are the sharing of phenotype data and the application of Next-Generation Sequencing in mouse genetics. We are now in an exciting phase in which we establish the basic technology for sharing phenotype data between laboratories internationally. This is as much a political and sociological issue as a technical one but we believe it will provide a very powerful resource if we can succeed. Next-Generation Sequencing provides with a major computational challenges, partly from the infrastructure we require to establish pipelines, but it also provides us with exciting!
opportunities to develop new areas of analysis.

Who are your main formal and informal collaborators and/or networks? Please describe your work with them.

I am a member of a number of international collaborations. Many of these are funded by the European Commission, such as CASIMIR, which deals with interoperability and sustainability of mouse databases, EUMODIC, which is a large project to phenotype knockout mouse models, and ENFIN, which is a systems biology collaborative project. I also lead a transcontinental discussion group on phenotype data sharing, Interphenome, and am involved in the International Mouse Phenotyping Consortium.

How did you come to be working in your research area?

I first got into molecular evolution when I moved to Gabriel Dover's lab in Cambridge in the mid-80s. I had been working on the determination of RNA secondary and tertiary structure and in Gabby's lab I started working on the evolution of ribosomal RNA sequence and structure. This led eventually to an interest in repeats in proteins as these were the only ones that appeared to have the potential for having any effect on phenotype. Having an interest in comutational methods and applications has led to me being tagged as a "bioinformatician" and has led to interesting opportunities to work in disparate ares in the last few years.

What do you think about the development of open access publishing? Have you published in an open access journal? What motivated you to do so?

One of the main conclusions of our discussions in CASIMIR has been the conclusion that we should be working towards a "scientific commons" in which information should flow as freely as possible. I am therefore strongly in favour of open access publishing. The MRC, who pay my salary, insist that all papers published by them should be freely accessible within six months of publication but I would support this initiative irrespective of who paid me!

What articles and/or books have you published recently?
  • Simon, M. & Hancock, J.M.. (2009) Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins. Genome Biol. 10(6): R59 [Pubmed]
  • Beck, T., Morgan, H., Blake, A., Wells, S., Hancock, J.M. & Mallon, A.-M. (2009) Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data. BMC Bioinformatics 10(Suppl 5): S2 [Pubmed]
  • Smedley, D., Swertz, M.A., Wolstencroft, K., Proctor, G., Zouberakis, M., Bard, J., Hancock, J.M., Schofield, P. (2008) Solutions for data integration in functional genomics: a critical assessment and case study. Briefings in Bioinformatics 9(6): 532-544. [Pubmed]
  • Hancock, J.M. & Mallon, A.-M. (2007) Phenobabelomics: Mouse phenotype data resources. Brief Funct Genomic Proteomic 6: 292-301. [Pubmed]
  • Mallon, A.-M, Blake, A. & Hancock, J.M. (2008) EuroPhenome and EMPReSS: online mouse phenotyping resource. Nucleic Acids Res. 36 (Database Issue): D715-D718. [Pubmed]
  • Jiang, N., Cox, R.D. & Hancock, J.M.. (2007) A kinetic core model of the glucose-stimulated insulin secretion network of pancreatic β-cells. Mamm. Genome 18(6-7): 508-520. [Pubmed]
  • Hancock, J.M. et al. (The Mouse Phenotype Database Integration Consortium) (2007) Integration of mouse phenome data resources. Mamm. Genome 18(3): 157-163. [Pubmed]
Further information about Dr Hancock: