CV
Education
- Ph.D in Computer Science, McGill University, 2011
- Masters in Computer Science, Dalhousie University, 2006
- Bachelor of Computer Science, Concordia University, 2000
Work experience
- 2015-: Genomics Research Consultant
- Arenaria Software Consulting Inc.
- Develop and apply new computaitonal methods for genomics research
- Clients include the UCSC Genomics Institute and DNANexus
- 2014: Postdoc
- McGill University
- Hidden Markov Models for transosable element annotation
- Supervisor: Mathieu Blanchette
- 2011-2013: Postdoc
- University of California Santa Cruz
- Computing and storing multiple genome alignments
- Supervisor: David Haussler
- 2008: Consultant
- Flagstone Reinsurance
- Develop prototype port of catastrophe modeling pipeline for Cell-based processors
- 2000-2004: Software Developer
- CAE Inc.
- Tools research and development group member in the Visual Systems division
- Wrote software to rapidly generate flight simulator terrain and models from satellite and GIS data
Skills
- Programming and scripting
- C, C++
- Python, bash
- HPC and cloud
- Slurm
- Google Cloud, Amazon EC2
- Genomics
- Expertise in most standard tools and formats for genome sequencing, comparison as well as pangenomics
Selected Publications
Selected Talks
Better graph variants using this one weird trick
Talk at Human Pangenome Reference Consortium (HPRC) Annual Meeting, Memphis, TN, USA (via Zoom)
Variant representation on graphs (with Heng Li)
Talk at Global Alliance for Genomics and Health (GA4GH) Connect Meeting, Cambridge, MA, USA (via Zoom)
Peer Review
- Reviewer for Bionformatics, Genome Biology, Nature Genetics and others
Hobbies
- Rock climbing
- Cross country skiing
- Crossword puzzles