Jones lab

Dr. Jones' team uses bioinformatics to investigate the landscape of mutations present in cancer genomes and the early genomic events that give rise to and promote the progression of cancer. To achieve these goals, his laboratory analyzes Next Generation Sequencing data and develops novel computational approaches and methodologies. A significant aim of Dr. Jones’ research program is to find innovative ways to exploit specific genomic profiles within an individual cancer for therapeutic purposes. For example, his team has identified a number of epigenetic modifications that may potentially be targeted to reverse the effects of cancer initiating mutations. His lab is using computational approaches, such as molecular docking and molecular dynamics, to identify and refine compounds that can modify the cancer epigenome. 



The Jones Lab is located at Canada's Michael Smith Genome Sciences Centre, Echelon Technology Platform.
570 West 7th Avenue 
Vancouver, British Columbia 
V5Z 4S6 


Selected Publications

An approach to rapid characterization of DMD copy number variants for prenatal risk assessment

American Journal of Medical Genetics, 2021
Hui-Lin Chin, Kieran O'Neill, Kristal Louie, Lindsay Brown, Kamilla Schlade-Bartusiak, Patrice Eydoux, Rosemarie Rupps, Ali Farahani, Cornelius F Boerkoel, Steven J M Jones

Prenatal detection of structural variants of uncertain significance, including copy number variants (CNV), challenges genetic counseling, and creates ambiguity for expectant parents. In Duchenne muscular dystrophy, variant classification and phenotypic severity of CNVs are currently assessed by familial segregation, prediction of the effect on the reading frame, and precedent data. Delineation of pathogenicity by familial segregation is limited by time and suitable family members, whereas analytical tools can rapidly delineate potential consequences of variants. We identified a duplication of uncertain significance encompassing a portion of the dystrophin gene (DMD) in an unaffected mother and her male fetus. Using long-read whole genome sequencing and alignment of short reads, we rapidly defined the precise breakpoints of this variant in DMD and could provide timely counseling. The benign nature of the variant was substantiated, more slowly, by familial segregation to a healthy maternal uncle. We find long-read whole genome sequencing of clinical utility in a prenatal setting for accurate and rapid characterization of structural variants, specifically a duplication involving DMD.

Gene Fusions Are Recurrent, Clinically Actionable Gene Rearrangements in Wild-Type Pancreatic Ductal Adenocarcinoma.

Clinical cancer research : an official journal of the American Association for Cancer Research, 2019
Jones, Martin R, Williamson, Laura M, Topham, James T, Lee, Michael K C, Goytain, Angela, Ho, Julie, Denroche, Robert E, Jang, GunHo, Pleasance, Erin, Shen, Yaoquing, Karasinska, Joanna M, McGhie, John P, Gill, Sharlene, Lim, Howard J, Moore, Malcolm J, Wong, Hui-Li, Ng, Tony, Yip, Stephen, Zhang, Wei, Sadeghi, Sara, Reisle, Carolyn, Mungall, Andrew J, Mungall, Karen L, Moore, Richard A, Ma, Yussanne, Knox, Jennifer J, Gallinger, Steven, Laskin, Janessa, Marra, Marco A, Schaeffer, David F, Jones, Steven J M, Renouf, Daniel J
Gene fusions involving neuregulin 1 () have been noted in multiple cancer types and have potential therapeutic implications. Although varying results have been reported in other cancer types, the efficacy of the HER-family kinase inhibitor afatinib in the treatment of fusion-positive pancreatic ductal adenocarcinoma is not fully understood.

Genomic characterization of a well-differentiated grade 3 pancreatic neuroendocrine tumor.

Cold Spring Harbor molecular case studies, 2019
Williamson, Laura M, Steel, Michael, Grewal, Jasleen K, Thibodeau, My Lihn, Zhao, Eric Y, Loree, Jonathan M, Yang, Kevin C, Gorski, Sharon M, Mungall, Andrew J, Mungall, Karen L, Moore, Richard A, Marra, Marco A, Laskin, Janessa, Renouf, Daniel J, Schaeffer, David F, Jones, Steven J M
Pancreatic neuroendocrine neoplasms (PanNENs) represent a minority of pancreatic neoplasms that exhibit variability in prognosis. Ongoing mutational analyses of PanNENs have found recurrent abnormalities in chromatin remodeling genes (e.g., and ), and mTOR pathway genes (e.g., , , and ), some of which have relevance to patients with related familial syndromes. Most recently, grade 3 PanNENs have been divided into two groups based on differentiation, creating a new group of well-differentiated grade 3 neuroendocrine tumors (PanNETs) that have had a limited whole-genome level characterization to date. In a patient with a metastatic well-differentiated grade 3 PanNET, our study utilized whole-genome sequencing of liver metastases for the comparative analysis and detection of single-nucleotide variants, insertions and deletions, structural variants, and copy-number variants, with their biologic relevance confirmed by RNA sequencing. We found that this tumor most notably exhibited a -disrupting fusion, showed a novel fusion, and lacked any somatic variants in , , and .

Application of a Neural Network Whole Transcriptome-Based Pan-Cancer Method for Diagnosis of Primary and Metastatic Cancers.

JAMA network open, 2019
Grewal, Jasleen K, Tessier-Cloutier, Basile, Jones, Martin, Gakkhar, Sitanshu, Ma, Yussanne, Moore, Richard, Mungall, Andrew J, Zhao, Yongjun, Taylor, Michael D, Gelmon, Karen, Lim, Howard, Renouf, Daniel, Laskin, Janessa, Marra, Marco, Yip, Stephen, Jones, Steven J M
A molecular diagnostic method that incorporates information about the transcriptional status of all genes across multiple tissue types can strengthen confidence in cancer diagnosis.

Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples.

Nucleic acids research, 2019
Haile, Simon, Corbett, Richard D, Bilobram, Steve, Bye, Morgan H, Kirk, Heather, Pandoh, Pawan, Trinh, Eva, MacLeod, Tina, McDonald, Helen, Bala, Miruna, Miller, Diane, Novik, Karen, Coope, Robin J, Moore, Richard A, Zhao, Yongjun, Mungall, Andrew J, Ma, Yussanne, Holt, Rob A, Jones, Steven J, Marra, Marco A
Tissues used in pathology laboratories are typically stored in the form of formalin-fixed, paraffin-embedded (FFPE) samples. One important consideration in repurposing FFPE material for next generation sequencing (NGS) analysis is the sequencing artifacts that can arise from the significant damage to nucleic acids due to treatment with formalin, storage at room temperature and extraction. One such class of artifacts consists of chimeric reads that appear to be derived from non-contiguous portions of the genome. Here, we show that a major proportion of such chimeric reads align to both the 'Watson' and 'Crick' strands of the reference genome. We refer to these as strand-split artifact reads (SSARs). This study provides a conceptual framework for the mechanistic basis of the genesis of SSARs and other chimeric artifacts along with supporting experimental evidence, which have led to approaches to reduce the levels of such artifacts. We demonstrate that one of these approaches, involving S1 nuclease-mediated removal of single-stranded fragments and overhangs, also reduces sequence bias, base error rates, and false positive detection of copy number and single nucleotide variants. Finally, we describe an analytical approach for quantifying SSARs from NGS data.

The Genome of the Beluga Whale (Delphinapterus leucas).

Genes, 2017
Jones, Steven J M, Taylor, Gregory A, Chan, Simon, Warren, René L, Hammond, S Austin, Bilobram, Steven, Mordecai, Gideon, Suttle, Curtis A, Miller, Kristina M, Schulze, Angela, Chan, Amy M, Jones, Samantha J, Tse, Kane, Li, Irene, Cheung, Dorothy, Mungall, Karen L, Choo, Caleb, Ally, Adrian, Dhalla, Noreen, Tam, Angela K Y, Troussard, Armelle, Kirk, Heather, Pandoh, Pawan, Paulino, Daniel, Coope, Robin J N, Mungall, Andrew J, Moore, Richard, Zhao, Yongjun, Birol, Inanc, Ma, Yussanne, Marra, Marco, Haulena, Martin
The beluga whale is a cetacean that inhabits arctic and subarctic regions, and is the only living member of the genus . The genome of the beluga whale was determined using DNA sequencing approaches that employed both microfluidic partitioning library and non-partitioned library construction. The former allowed for the construction of a highly contiguous assembly with a scaffold N50 length of over 19 Mbp and total reconstruction of 2.32 Gbp. To aid our understanding of the functional elements, transcriptome data was also derived from brain, duodenum, heart, lung, spleen, and liver tissue. Assembled sequence and all of the underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the Bioproject accession number PRJNA360851A.

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.

Bioinformatics (Oxford, England), 2013
Birol, Inanc, Raymond, Anthony, Jackman, Shaun D, Pleasance, Stephen, Coope, Robin, Taylor, Greg A, Yuen, Macaire Man Saint, Keeling, Christopher I, Brand, Dana, Vandervalk, Benjamin P, Kirk, Heather, Pandoh, Pawan, Moore, Richard A, Zhao, Yongjun, Mungall, Andrew J, Jaquish, Barry, Yanchuk, Alvin, Ritland, Carol, Boyle, Brian, Bousquet, Jean, Ritland, Kermit, Mackay, John, Bohlmann, Jörg, Jones, Steven J M
White spruce (Picea glauca) is a dominant conifer of the boreal forests of North America, and providing genomics resources for this commercially valuable tree will help improve forest management and conservation efforts. Sequencing and assembling the large and highly repetitive spruce genome though pushes the boundaries of the current technology. Here, we describe a whole-genome shotgun sequencing strategy using two Illumina sequencing platforms and an assembly approach using the ABySS software. We report a 20.8 giga base pairs draft genome in 4.9 million scaffolds, with a scaffold N50 of 20,356 bp. We demonstrate how recent improvements in the sequencing technology, especially increasing read lengths and paired end reads from longer fragments have a major impact on the assembly contiguity. We also note that scalable bioinformatics tools are instrumental in providing rapid draft assemblies.

Circos: an information aesthetic for comparative genomics.

Genome research, 2009
Krzywinski, Martin, Schein, Jacqueline, Birol, Inanç, Connors, Joseph, Gascoyne, Randy, Horsman, Doug, Jones, Steven J, Marra, Marco A
We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.


Dr. Erin Pleasance

Staff Scientist

Dr. Jianhong An

Staff Scientist

Dr. Mikhail (Misha) Bilenky

Staff Scientist

Dr. Gordon Robertson

Staff Scientist

Dr. Veronika Csizmok

Research Associate

Dr. Chandra Lebovitz

Research Associate

Dr. Kathleen Wee

Research Associate

Dr. Rohan Abraham

Research Associate

Dr. Jahanshah Ashkani

Research Associate

Dr. Jean-Michel Garant

Research Associate

Dr. Sreeja Leelakumari

Research Associate

Dr. Cameron Grisdale

Research Associate

Dr. Cathy Zhang

Research Associate

Dr. Kieran O'Neill

Process Development Coordinator

Sitanshu Gakkhar

Computational Biologist

Melika Bonakdar

Computational Biologist

Greg Taylor

Computational Biologist

Emma Titmuss

Research Programmer

Courtney Gosselin

Research Programmer

Jimmy Li

Research Programmer

Postdoctoral Fellows

Dr. Katherine Dixon

Postdoctoral Fellow

Dr. Jasleen Grewal

Postdoctoral Fellow


Vahid Akbari

Graduate Student

Sarah Dada

Graduate Student

Luka Culibrk

Graduate Student

Faeze Keshavarz

Graduate Student

Tyler Kolisnik

Graduate Student

Caralyn Reisle

Graduate Student

Sina Hossein Zadeh

Student Researcher - M.D. Flex Program

Daniel Shirvani

Student Volunteer

Open Positions

Research Programmer

Canada’s Michael Smith Genome Sciences Centre (GSC)

Today’s Research. Tomorrow’s Medicine.

The GSC is a department of the BC Cancer Research Institute and a high-throughput genome sequencing facility. We are leaders in genomics, proteomics and bioinformatics in pursuit of novel treatment strategies for cancers and other diseases.

Among the world’s first genome centres to be established within a cancer clinic, for more than two decades our scientists and innovators have been designing and deploying cutting-edge technologies to benefit health and advance clinical research.

Among the GSC’s most significant accomplishments are the first publication to demonstrate the use of whole-genome sequencing to inform cancer treatment planning, the first published sequence of the SARS coronavirus genome and major contributions to the first physical map of the human genome as part of the Human Genome Project.

By joining the GSC you will become part of an exceptional and diverse team of scientists, clinicians, experts and professionals operating at the leading edge of clinical research. We look for people who share our core values—science, timeliness, respect—to join us on our mission to use genome science for the betterment of health and society.


Job Reference No: RP_R00008_2021_07_30

The GSC is looking for an enthusiastic and self-motivated Research Programmer to work on the next generation of federated genome and health data sharing platform, CanDIG—a Canadian data-sharing platform contributing to the development of an international effort to facilitate information exchange as part of the Global Alliance for Genomics & Health (GA4GH). CanDIG also supports large-scale provincial and national data sharing projects, including BC Cancer’s Personalized OncoGenomics program, the Terry Fox Research Institute's (TFRI) PROFYLE project and the TFRI-led Marathon of Hope Cancer Centres Network—a major federal initiative to accelerate the adoption of precision medicine for cancer in Canada. This role requires a combination of interest in DNA technology and a strong background in software development.


The successful candidate will have an undergraduate degree in computer science, bioinformatics or a related subject.


  • 2+ years of experience in Python programming.
  • Previous experience or exposure in the bioinformatics settings.
  • Full stack web development experience with web frameworks such as Flask or Django.
  • Previous experience in designing, implementing and testing REST APIs.
  • General understanding or previous experience in microservice architecture and development.
  • General knowledge in Unix environment, Version Control (Git), and Agile methodologies. 
  • The position requires working with a wide variety of researchers, software developers and clinicians, thus excellent communication skills are essential.


  • Experience or knowledge in handling genomics data files.
  • Prior experience in developing front-end applications using React.js.
  • Experience building rich queries using GraphQL or other data query language.
  • Experience working with distributed systems.
  • Basic understanding of DNA technology or previous work experience with genetic data is a plus, but not required for the position.


Please submit a detailed cover letter and resume to, using Job Reference No: RP_R00008_2021_07_30 in the subject line of your email.

This posting will remain online until filled.


We believe that diversity and inclusivity are essential for the advancement of human knowledge and science.

We welcome all applicants and provide all employees with equal opportunity for advancement, regardless of race, colour, ancestry, place of origin, political belief, religion, marital status, family status, physical or mental disability, sex, sexual orientation, gender identity or expression, age, conviction of a criminal or summary conviction offence unrelated to their employment.

All qualified candidates are encouraged to apply; however, Canadian citizens and permanent residents will be given priority.

Due to COVID-19 restrictions, the position would require working remotely on a temporary basis. This restriction would be re-evaluated upon re-contracting.

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