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SickKids

Jared Simpson

Title:
Senior Scientist
Designations:
PhD
Phone:
416-471-1257
U of T Positions:
Associate Professor
Other Positions:
Scientific Director of Computational Biology and Senior Principal Investigator, Ontario Institute for Cancer Research

Biography

Dr. Jared Simpson is the Scientific Director of Computational Biology and a Senior Principal Investigator at the Ontario Institute for Cancer Research. He also holds an appointment as a Senior Scientist at The Hospital for Sick Children (SickKids), and is an Associate Professor in the Department of Molecular Genetics at the University of Toronto. Dr. Simpson completed his PhD at the University of Cambridge and the Wellcome Sanger Institute, where he developed computational methods for analysing sequencing data using compressed data structures. He is internationally recognized for his contributions to genome assembly and long-read sequencing analysis. His work includes developing one of the first methods for detecting DNA methylation using Oxford Nanopore sequencing reads, as well as widely used bioinformatics tools such as ABySS, SGA and Nanopolish. 

Research

The Simpson Lab develops algorithms, statistical methods and open-source software to analyze high-throughput DNA sequencing data, with a focus on long-read and other emerging sequencing technologies. Current research includes de novo genome assembly and annotation, detecting genetic and epigenetic variation, and developing rapid sequencing assays. The lab is also exploring the use of nanopore-based liquid biopsies for early, minimally invasive disease detection. Working closely with experimental and clinical collaborators, the lab aims to translate advances in sequencing technology into practical tools that deepen our understanding of human genetics and improve the diagnosis and treatment of disease in children and adults.
 

Education and experience

  • 2026–present: Scientific Director, Computational Biology, Ontario Institute for Cancer Research, Toronto, ON
  • 2025–present: Senior Scientist, Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON
  • 2025–present: Associate Professor, Department of Molecular Genetics, University of Toronto, Toronto, ON
  • 2024–present: Senior Principal Investigator, Computational Biology, Ontario Institute for Cancer Research, Toronto, ON
  • 2022–2025: Assistant Professor, Department of Molecular Genetics, University of Toronto, Toronto, ON
  • 2015–2024: Assistant Professor, Department of Computer Science, University of Toronto, Toronto, ON
  • 2012: PhD, Computational Biology, University of Cambridge / Wellcome Sanger Institute, Cambridge, UK
  • 2007–2008: Bioinformatician, Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
  • 2004–2007: Software Engineer, Electronic Arts, Burnaby, BC
  • 2004: B.Sc., Computer Science, University of British Columbia, Vancouver, BC

Publications

  1. Jain M, Koren S, Miga KH, Quick J, Rand AC, +17 co-authors, and Simpson JT, Loman NJ, and Loose M. (2018). Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology 36, 338–345. 
  2. Simpson JT, Workman RE, Zuzarte PC, David M, Dursi LJ, and Timp W. (2017). Detecting DNA cytosine methylation using nanopore sequencing. Nature Methods 14, 407–410. 
  3. *Loman NJ, Quick J, and Simpson JT. (2015). A complete bacterial genome assembled de novo using only nanopore sequencing data. Nature Methods 12, 733–735.
  4. *Simpson JT, and Durbin R. (2012). Efficient de novo assembly of large genomes using compressed data structures. Genome Research 22, 549–556. 
  5. *Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, and Birol I. (2009). ABySS: a parallel assembler for short read sequence data. Genome Research 19, 1117–1123. 

Relevant pages

Jared Simpson - University of Toronto staff page

Ontario Institute for Cancer Research - OICR page

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