Natera
Principal Engineer — May 2024–present
Principal Engineer. Work covers production bioinformatics infrastructure, clinical interpretation platforms, and regulatory strategy in a matrixed organization of 60+ engineers, SQAs, and PMs.
Invitae
Principal Engineer / Engineering Lead — June 2017–May 2024
Engineering lead for the Interpretation Platform, the clinical analysis and reporting engine processing >1M NGS samples/year. Scaled throughput from hundreds to thousands of samples per day. Initiated and delivered the Next Generation Sample Data Store and the Invitae Variant Effect Predictor. Selected by CTO as one of ten engineers to lead Engineering Excellence across Invitae.
RCSB Protein Data Bank, UC San Diego
Technical and Scientific Team Lead — February 2008–May 2017
Senior Scientist and technical lead at the RCSB PDB (San Diego site). The RCSB PDB serves 350,000+ unique users/month from 160+ countries; its primary citation ranks in Nature’s top 100 most-cited research of all time. Built a multi-omics analytics framework mapping NGS data onto protein sequence, structure, function, and interaction data.
Wellcome Trust Sanger Institute
Postdoctoral Researcher — 2004–2008
Postdoc in the lab of Dr. Tim Hubbard. Participated in large-scale genome and protein annotation projects in national and international collaborations.
Professional Activities
Biocommons — Steering Committee, 2023–present
Community fostering collaboration on bioinformatics open-source software and data for biological sequence analysis and interpretation.
GA4GH Variation Representation Specification (VRS) — Leadership team, 2021–2024
Developing the specification and implementation for describing genomic variation. vrs.ga4gh.org
PLOS Computational Biology — Software Section Editor, 2011–2017
Built up the software section with an emphasis on publishing open-source software with large scientific impact.
BioJava — Project Leader, 2009–2017
Open-source library for processing biological data. 500+ citation publications; 600+ GitHub stars. github.com/biojava/biojava
Education
PhD, Bioinformatics/Genetics — University of Salzburg, Austria
Thesis: WILMA — a platform for the automated annotation of protein sequences
Diploma, Biology/Genetics (Bioinformatics focus) — University of Salzburg, Austria
Thesis: Deriving substitution matrices for amino acids and secondary structure