I am a bioinformatician working in Experimental Cancer Genetics. I help the group - mainly by running informatic pipelines, but also evaluating new tech and talking to other informatic groups on campus.
Making and running informatic pipelines for NGS data is an important part of this groups' work. We do this every day, choosing from a large palette of techniques applicable to wide range of data types. Of course, we don't work in a vacuum: we are guided by the services on campus, and our own abilities to code - or stitch together other people's code. I make informed decisions and help do the work!
I have a strong background in developing web-based systems backed by relational databases. Genetic Variant discovery typically steers away from these systems: I am curious about the possible use of a database-backed system to help this lab's work in the future, and intrigued by those brave enough to try this elsewhere.
I was involved in writing and leading the development of LIMS systems producing mutant ES Cells and mice in high throughput, for the EUCOMM, KOMP and IMPC programs - two LIMS systems (here and here) and a coordinating system (iMITS) for IMPC mouse production. That field has been revolutionised by the advent of CRISPR-based genome editing, and our software interests followed that change with WGE, a CRISPR-design tool.
WGE: a CRISPR database for genome engineering.
Bioinformatics (Oxford, England) 2015;31;18;3078-80
Off-target mutations are rare in Cas9-modified mice.
Nature methods 2015;12;6;479
The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.
Nucleic acids research 2014;42;Database issue;D802-9
A conditional knockout resource for the genome-wide study of mouse gene function.
BioMart as an integration solution for the International Knockout Mouse Consortium.
Database : the journal of biological databases and curation 2011;2011;bar028
The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium.
Nucleic acids research 2011;39;Database issue;D849-55
Nucleic acids research 2006;34;Database issue;D556-61
The otter annotation system.
Genome research 2004;14;5;963-70
Apollo: a sequence annotation editor.
Genome biology 2002;3;12;RESEARCH0082