I am a PhD candidate in bioinformatics, a first class honours graduate in computer engineering, a computer and electronics enthusiast, an open-source software developer and advocate, an avid traveller, a hiker, a singer, and an experimental cook. I have fifteen years of industry and academic experience developing software in C++ and a variety of scripting languages, including nine years developing high-performance distributed and parallel algorithms for genome sequence assembly, and six years developing embedded and real-time control systems. I have extensive experience developing portable software for POSIX systems such as Linux and macOS. When developing performance-critical software, I understand the hardware from the transistor up.
2012–present — PhD Candidate Bioinformatics
University of British Columbia
NSERC CGS-M and CGS-D scholarship student in bioinformatics. Coursework in bioinformatics, statistics, machine learning, and genetics. GPA 4.26 (93%)
1998–2004 — BASc (First Class Hons.) Computer Engineering
Simon Fraser University
Scholarship student in computer engineering. Completed an honours undergraduate thesis and two full years of co-op work experience at three companies. GPA 3.85
2008–2012 — Computational biologist
BC Cancer Agency Genome Sciences Centre
Developed the genome sequence assembly software package, ABySS. 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 Inc.
Developed the firmware for Pathway’s product line of small, low-cost lighting control devices. These small devices, which use Atmel’s AVR and ARM microcontrollers, convert between a variety of lighting-control protocols including DMX512, analog, PWM, and contact closure. Modernized the lighting control industry in developing a device, the Pathport, to adapt legacy lighting control equipment to Ethernet. This industry-changing product won an award for best new product at the industry trade show, Lighting Dimensions International.
2002 May — Co-op work experience
Vortek Industries Ltd.
Worked on the rapid thermal processing tool used in the manufacturing of semiconductor devices. Developed the temperature sensor and lamp power control system using the QNX real-time operating system.
2002–present — Open-source developer
Maintain open-source bioinformatics software packages for Homebrew and Linuxbrew. Lead developer of Linuxbrew, the Homebrew package manager for Linux.
A selection of 12 of 29 peer-reviewed publications, h-index of 20, and over 6,000 citations
ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter
Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S, Hammond SA, Jahesh G, Khan H, Coombe L, Warren RL, et al. (2017) Genome Research
Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation
Jackman SD, Warren RL, Gibb EA, Vandervalk BP, Mohamadi H, Chu J, Raymond A, Pleasance S, Coope R, Wildung MR, et al. (2015) Genome Biology and Evolution
Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism
Warren RL, Keeling CI, Yuen MMS, Raymond A, Taylor GA, Vandervalk BP, Mohamadi H, Paulino D, Chiu R, Jackman SD, et al. (2015) The Plant Journal
UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation
Jackman SD, Bohlmann J, Birol İ. (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, NY Liao, TR Docking, SK Chan, GA Taylor, DL Palmquist, SD Jackman, et al. (2013) Genome Biology
The genome and transcriptome of the pine saprophyte Ophiostoma piceae
S Haridas, Y Wang, L Lim, SM Alamouti, SD Jackman, et al. (2013) BMC Genomics
De novo assembly and analysis of RNA-seq data
G Robertson, J Schein, R Chiu, R Corbett, M Field, SD Jackman et al. (2010) Nature Methods
Assembling genomes using short-read sequencing technology
SD Jackman and 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
Techniques for analysis of whole-genome shotgun sequencing and RNA-seq, including de novo sequence assembly, sequence alignment, variant calling, genome annotation, and visualization and inspection of genome assemblies, variants, and rearrangements.
C++, C, R, Python, Ruby, shell, and assembly.
OpenMP, MPI, and POSIX threads.
macOS, Debian, Ubuntu, and other GNU/Linux distributions.
University of British Columbia
- 2013-present Natural Sciences and Engineering Research Council of Canada (NSERC) Canada Graduate Scholarship (CGS-M and CGS-D)
- 2012–2013 CIHR/MSFHR Strategic Training Program in Bioinformatics
Simon Fraser University
- 1999–2004 Open Undergraduate Scholarship
- 1998–1999 Tadeusz Specht Memorial Entrance Scholarship in Science