Experience

Congenica

• United Kingdom
• Biotechnology Research
• 1 - 100 Employee

• Bioinformatics Analyst

  • Sep 2021 - Present



European Bioinformatics Institute | EMBL-EBI

• United Kingdom
• Software Development
• 700 & Above Employee

• Senior Bioinformatician

  • Sep 2012 - Aug 2021

  Senior Bioinformatician in the VEuPathDB project, which facilitates the use of genetic data in the understanding of invertebrate vectors of human pathogens, to prevent diseases such as malaria. VEuPathDB is highly collaborative team with partners in USA and UK. I am an integral part of the bioinformatics team with responsibility for data production, software and database engineering. The production includes running and maintaining bioinformatic workflows (eHive pipelines using the LSF batch scheduler) on high-performance computing clusters. The analysis pipelines are performing tasks such as: integration of genomic annotation form a large number of sources, large scale DNA and protein alignment and comparative genomics. I have taken a leading role in supporting the manual gene annotation by the scientific community. This has involved writing high-quality software applications (Python, PERL) for processing, as well as quality control of gene annotation. In addition, I am using visualisation tools (python matplotlib) to communicate the outcome of gene annotation updates. I have also taken part in outreach to understand the needs of the biologist that performs the manual curation of gene annotation and created tutorials for our global users. Show less



University of Cambridge

• United Kingdom
• Research Services
• 700 & Above Employee

• • Feb 2009 - Sep 2012

  Developing “www.T1DBase.org”, “www.immunobase.org” and assisting the DIL researchers in bioinformatics. Processing of variation data from the Mouse Genomes Project for the analysis of differences between insulin-dependent diabetes susceptibility (idd) regions in susceptible or resistance mouse strains. This included using tools such as SAMtools, LookSeq and GBrowse. • Comparing SNP calls from NGS(Pileup format) to known SNPs in idd regions.• Quality control and determine a QC threshold for which SNPs to use.• Displaying and summarising the SNPs in GBrowse Developed plugins within the GDxBase framework, an example is “Mouse Strain Search”, which allow researchers to search for congenic mouse strains and retrieve both tabular and graphical display of mouse genetic data (https://doi.org/10.1093/nar/gkq912). The mouse congenic strain project had three major goals:• Designing a relational database with an audit system for in-house storage and data curation. • Building a web-application for T1Dbase: the database and query mechanism is built on the BioPerl module “DB::SeqFeature::Store” API. • Exporting DIL data to www.dkcoin.org, writing PERL modules using SOAP-Lite to upload the data via the dkcoin SOAP web-service. Show less

• • 2007 - 2009

  • Developed application "XenMARK" for Image annotation. The application consists of an interactive web interface (DHTML), server program (CGI, C++) and database (SQL server). It enables fast manual annotation and subsequent analysis of gene expression, visualized of in situ hybridization images. (https://doi.org/10.1002/dvdy.21940)• Xenopus Literature Search tool: Wrote PERL scripts for data extraction from public data resources (Genbank, Refseq, flybase, worm, yeast) and updated in-house databases.• Contributed to the development of PNGwriter (http://pngwriter.sourceforge.net). Show less



King's College London

• United Kingdom
• Research Services
• 700 & Above Employee

• Postdoctoral Research Associate

  • 2005 - 2007

  The overall aim of the project was to find SNPs that predisposes people to infectious diseases. Gained experience with setting up and optimising DNA microarrays using different DNA amplification techniques. The overall aim of the project was to find SNPs that predisposes people to infectious diseases. Gained experience with setting up and optimising DNA microarrays using different DNA amplification techniques.



University of Southampton

• United Kingdom
• Higher Education
• 700 & Above Employee

• Bioinformatician

  • 2002 - 2005

  Supported the group in bioinformatics and statistics. Designed and optimised assays for high-throughput genotyping. Genome-wide in silicon mapping of allele-specific DNA oligonucleotides. Prepared genotyping data for statistical analysis for both our collaborators in Bristol as well as my own research and performed statistical analysis on my own data. Writing PERL pipelines for data management of SNP and sequence datasets. Supported the group in bioinformatics and statistics. Designed and optimised assays for high-throughput genotyping. Genome-wide in silicon mapping of allele-specific DNA oligonucleotides. Prepared genotyping data for statistical analysis for both our collaborators in Bristol as well as my own research and performed statistical analysis on my own data. Writing PERL pipelines for data management of SNP and sequence datasets.