I am a PhD graduate in bioinformatics, a first class honours graduate in computer engineering, an open-source software developer, an avid traveller, a singer, and an enthusiastic cook. I have sixteen years of industry and academic experience developing software in C++, Python, and R, including ten years developing high-performance parallel algorithms for genome sequence assembly, and six years developing embedded and real-time control systems. I developed ABySS 1.0, the first software tool to assemble a human genome from Illumina sequencing, as well as ABySS 2.0, the first assembler to reconstruct a twenty-gigabase conifer genome, seven times the size of the human genome. I enjoy camping, cycling, swing dancing, theatre, and cooking and sharing good food with friends, and I sing tenor with the internationally recognized Chor Leoni Men’s Choir.
Education and Employment
2019–present—Senior Computational Biologist—10x Genomics
Developed algorithms for the flagship single-cell gene expression software tool, Cell Ranger, which is implemented in Rust and Python.
2012–2019—PhD Bioinformatics—University of British Columbia
NSERC Canada Graduate Scholarship (CGS) student in bioinformatics. Published five papers as the first author. The memory-efficient genome sequence assembly tool ABySS 2.0 (2017) has received over 100 citations. Coursework in bioinformatics, statistics, machine learning, and genetics. GPA 4.26 (93%)
2008–2012—Computational Biologist—BC Cancer Genome Sciences Centre
Developed the genome sequence assembly software package, ABySS, implemented in C++. This heavily parallel and distributed software system, which uses both MPI and OpenMP for parallel computation, was the first system to assemble a human genome using short-read sequencing technology.
2004–2007—Embedded Firmware Developer—Pathway Connectivity
Developed the firmware for Pathway’s product line of lighting control devices. These devices, which use Atmel’s AVR and ARM microcontrollers, convert between a variety of lighting-control protocols. Modernized the lighting control industry in developing a device, the Pathport, to adapt legacy serial equipment to an Ethernet network. This device won an award for best new product at the industry trade show, Lighting Dimensions International.
1998–2004—BASc Computer Engineering—Simon Fraser University
First class honours scholarship student in computer engineering. Completed an honours undergraduate thesis and two years of co-op work experience at three companies. GPA 3.85
Expertise
Bioinformatics and Genomics
Analysis of DNA and RNA sequencing, including genome sequence assembly, sequence alignment, variant calling, genome annotation, visualization, and inspection of genome assemblies, variants, and rearrangements. Developed ABySS 2.0 to assemble twenty gigabase conifer genomes, seven times the size of human.
Data Analysis Pipelines
Extensive experience in constructing data analysis workflows, visualization, reporting, and communicating results effectively with aesthetic appeal.
Problem Solving and Leadership
A practiced talent to decompose complex problems into well-defined components, enabling concurrent development by a team. Daily involvement in reviewing code to provide constructive criticism with empathy, to improve both the developer’s skills as well as code quality. Use of automated testing to ensure correctness and provide timely automated feedback on code quality to developers.
Open-source Developer
Developer and member of the project leadership committee of Homebrew, the package manager for macOS and Linux. Created Homebrew for Linux, and grew its community of fifty thousand users.
Sequencing Technologies and Genomic Assays
10x Genomics Chromium, Illumina HiSeq, Oxford Nanopore, Bionano Genomics
Programming Languages
Rust, C++, C, Python, R, Ruby, shell, and assembly
Programming Methodologies
Functional, generic, and object-oriented programming
Parallel Processing
OpenMP, POSIX threads, C++ threads, and MPI
Continuous Integration
CircleCI, Travis CI, Azure Pipelines, and GitHub Actions
Cloud and Containerization
AWS, Docker, and Singularity
Version Control
Git and GitHub wizard. Proven ability to solve any git calamity.
Selected Publications
A selection from over 30 peer-reviewed publications, h-index of 21, and over 8,000 citations
ORCA: A Comprehensive Bioinformatics Container Environment for Education and Research
SD Jackman, T Mozgacheva, S Chen, et al. (2019) Bioinformatics
Tigmint: Correcting assembly errors using linked reads from large molecules
SD Jackman, L Coombe, J Chu, et al. (2018) BMC Bioinformatics
ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter
SD Jackman, BP Vandervalk, H Mohamadi, et al. (2017) Genome Research
Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation
SD Jackman, RL Warren, EA Gibb, et al. (2015) Genome Biology and Evolution
UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation
SD Jackman, J Bohlmann, I Birol. (2015) PLOS ONE
Assembling the 20 Gb white spruce (Picea glauca) genome from WGSS data
I Birol, A Raymond, SD Jackman, et al. (2013) Bioinformatics
Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins
CI Keeling, MM Yuen, …, SD Jackman, et al. (2013) Genome Biology
De novo assembly and analysis of RNA-seq data
G Robertson, J Schein, …, SD Jackman, et al. (2010) Nature Methods
Assembling genomes using short-read sequencing technology
SD Jackman, I Birol (2010) Genome Biology
De novo transcriptome assembly with ABySS
I Birol, SD Jackman, CB Nielsen, et al. (2009) Bioinformatics
ABySS-Explorer: visualizing genome sequence assemblies
CB Nielsen, SD Jackman, I Birol, et al. (2009) IEEE Transactions on Visualization and Computer Graphics
ABySS: a parallel assembler for short read sequence data
JT Simpson, K Wong, SD Jackman, et al. (2009) Genome Research