Position: Senior Bioinformatician

 

Skills and background:

Summary

A skilled bioinformatician with a background in cell and developmental biology. Seven years of postdoctoral research experience in bioinformatics, with particular expertise in genomics and next-generation of sequence analysis, as well as extensive experience of data-mining and integration.

 

Technical skills and experience:

Software: Sequence Assembly (Velvet, Oases, ABySS, Trinity), Short Read Alignment and Quantification (Bowtie, TopHat, Cufflinks), Genome Annotation (Maker), Galaxy, InterMine, Bioconductor.

Data Sources: Uniprot, InterPro, IntAct, Gene Ontology, ArrayExpress, KEGG, Ensembl, Treefam, Panther, Reactome, dbSNP.

Programming Languages: Perl, C++, R (bioconductor), SQL, Shell scripting.

 

Work experience

2006-2008: Postdoctoral  Researcher:  developmental & cell biology. The Gurdon Institute, University of Cambridge.

2008-2013: Postdoctoral  Researcher:  genomics and bioinformatics. Cambridge Systems Biology Centre & Department of Genetics, University of Cambridge.

 

Education

2001: BSc (Hons) 1st class Biological Science, University of Edinburgh.

2002: MPhil in Developmental Biology, University of Cambridge.

2006: PhD in Developmental Neurobiology, University of Cambridge.

 

Selected publications

Southall TD, Davidson CM, Miller C, Carr A, Brand AH (2014). Dedifferentiation of Neurons Precedes Tumor Formation in lola Mutants. Developmental Cell.

Baumgarten S, Bayer T, Aranda M, Liew YJ, Carr A, Micklem G, Voolstra CR (2013). Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. BMC Genomics

Smith RN et al (2012) InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics.

Boschetti C, Carr A, Crisp A, Eyres I, Wang-Koh Y, Lubzens E, Barraclough TG, Micklem G, Tunnacliffe A (2012).

Biochemical diversification through foreign gene expression in bdelloid rotifers.  PLoS Genetics.

Gerstein MB et al (2010). Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science.

modENCODE Consortium (2010). Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science.