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Experience

2017 —
Sr. Bioinformatics Software Engineer
GenapSys, Redwood City, CA

2016 — 2017
Bioinformatics Scientist II, Software
Fluidigm, South San Francisco, CA

• Lead developer for interactive & scalable web platform that enables biologists to analyze and visualize single-cell RNA-seq data.

• Designed optimized cloud infrastructure for RNA-seq analysis; reduced runtime/costs by 30X compared to out-of-the-box solutions.

2014 — 2016
Consultant

• Developed web applications for data analysis and visualization, with a focus on genomics, single-cell sequencing and neuroscience.

• Contributed to several projects, including Pcaso, DNA.Land, and a neuroscience game.

2014 — 2016
Co-Founder & CEO
11factorial, Toronto, ON

• Co-founded company that provides same-day solutions for event organizers, including nametag assembly & live Twitter analytics.

• Developed infrastructure to automate nametag assembly, order management, inventory management, and generation of shipping labels.

• Processed 100,000+ nametags through automated infrastructure since company inception.


Education

2011 — 2016
PhD, Biological Sciences
Elucidating Cancer Evolution using Single-Cell Sequencing and Comparative Genomics

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

• Developed Ginkgo, a suite of software tools to analyze & visualize single-cell DNA sequencing data.

• Built machine learning tools to better understand tumor development, identify defining genomic events & retrace their order.

• Performed large-scale analysis of thousands of single-cell datasets, to inform experimental protocols & evaluate various tradeoffs.

• Gained extensive experience with DNA sequencing technologies and analyzing NGS data.

2007 — 2011
B.Eng., Computer Engineering
McGill University, Montreal, QC

• Investigated the distribution and evolutionary conservation of tumor suppressor genes in the genome.

• Developed image analysis software to analyze microscopy data from single-molecule experiments on Hep C RNA polymerase binding.


Awards

2016
Insight Data Science Fellowship (declined)
Insight Data Science, San Francisco, CA

2011 – 2015
Starr Centennial Scholar
The Starr Foundation, New York, NY

NIH NRSA Pre-doctoral Fellowship
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

2014
NASW Idea Grant (declined)
National Association of Science Writers, Berkeley, CA

2013
ASCB Local Meeting Grant
American Society of Cell Biology, Bethesda, MD

ScienceBorealis.ca Logo Competition – 2nd Runner Up
ScienceBorealis.ca, Ottawa, ON

More

2012
Featured in IEEE TryComputing.org Video
TryComputing.org

Grant for Technophilic Magazine Conference
IEEE Canadian Foundation

Science Communication Competition
NASA FameLab, Washington, DC.

2011
Dean’s Honors List
McGill University, Montreal, QC.

2010
Robert H. P. Olney Fellowship
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.

Publication of the Year Award for Technophilic Magazine
McGill Engineering Undergraduate Society, Montreal, QC.

2009
McGill Science Research Ambassador
McGill University, Montreal, QC.

Undergraduate Summer Research Award
Natural Sciences and Engineering Research Council of Canada

Scholarship in Engineering Excellence
CAE, Montreal, QC.

2008
Undergraduate Summer Research Award
Natural Sciences and Engineering Research Council of Canada

Louis C. Ho Scholarship in Engineering
McGill University, Montreal, QC.

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Skills

Web Development

PHP, Node.js, HTML/CSS, Bootstrap, JavaScript, jQuery, D3.js, MySQL, SQLite, MongoDB, Electron, Docker, Git

Data Science

Bash, awk, jq, R, python (including scipy, numpy, pandas, scikit-learn)

Bioinformatics Tools

Bowtie 2, BWA, Tophat, Cufflinks, SAMtools, bedtools, bcftools, Picard, IGV, CNVnator, etc.

Cloud and HPC

Google Cloud Platform, Amazon AWS, Sun Grid Engine (SGE), Univa Grid Engine (UGE)


Publications & Talks


Peer Reviewed Publications

• Garvin* & Aboukhalil* et al, Ginkgo: Interactive analysis and quality assessment of single-cell copy number variations. Nature Methods 2015

• Ganapathy et al., High-coverage sequencing and annotated assemblies of the budgerigar genome. GigaScience 2014

Aboukhalil et al., Kerfuffle: a web tool for multi-species gene colocalization. BMC Bioinformatics 2013

Talks

• A deep dive into R, for Python developers, O’Reilly OSCON Webcast, San Francisco, CA, 2016.

• Single-Cell Sequencing: Analysis & Visualization of Copy Number Variations, Festival of Genomics, San Francisco, CA, 2015.

• Ginkgo: Interactive analysis and quality assessment of single-cell CNV data, Genome Informatics, Cold Spring Harbor, NY, 2015.

• Ginkgo: Cloud-based single-cell copy-number analysis tool, VIZBI: Visualizing Biological Data, Cambridge, MA, 2015.

• Adventures in Data Science with Bash, O’Reilly OSCON, Portland, OR, 2015.

• Building data analysis and visualization tools with PHP, OpenWest Conference, Orem, UT, 2015.

Books

Adventures in Data Science with Bash

Magazine articles & blog posts

Build data analysis and visualization tools, php[architect], 2016.

The elephant in the lab, Naturejobs Blog, 2015.

Data-Driven Journalism 102, Canadian Science Writers’ Association Blog, 2014.

Using the Twitter API to explore the Twitterverse, ACM XRDS: Crossroads, 19 (4), 2013.

Q&A: Joe Incandela on the Higgs Boson, Technophilic Magazine, 2013.


Extracurriculars

2013 — 2016
Founder & Editor-In-Chief
CSHL Current Exchange, Cold Spring Harbor, NY

• Started CSHL’s Current Exchange magazine as a vehicle for students & postdocs to communicate science to a broader audience.

• Recruited writers, edited articles, wrote editorials and interviewed leaders in various fields.

• Copies are printed and distributed to CSHL’s Meetings & Courses attendees twice a year.

2013 — 2016
Vice-President
CSHL Bioscience Entreprise Club, Cold Spring Harbor, NY

• Organized several talks and whole-day career symposia to expose students & postdocs to careers opportunities.

• Organized business workshops to develop entrepreneurial skills (elevator pitch, business plan writing, and mock VC pitch).

2013 — 2015
Invited Guest Writer
Canadian Science Writers’ Association, Toronto, ON

• Contribute articles about applying the principles of data science to journalism.

2012 — 2014
Science Writing Mentor
Journal of Young Investigators, Washington, DC

• Guide undergraduate students in creatively communicating new science/technological innovations to a lay audience.

• Articles mentored: 1, 2, 3, 4, 5.

2012
Instructor
DNA Learning Center, Cold Spring Harbor, NY

• Taught interactive classes to middle/high school students about the science behind DNA restriction analysis, gel electrophoresis and bacterial transformation.