Dr. Jared Simpson

Investigator I

The Simpson lab develops algorithms and software for the analysis of high-throughput sequencing data. The lab, led by Dr. Jared Simpson, works primarily on de novo genome assembly, the detection of somatic mutations in cancer and, most recently, the development of algorithms for nanopore-based sequencers.

Current affiliations

  • Investigator I, OICR.
  • Assistant Professor, Department of Computer Science, University of Toronto;

Research Interests

  • Bioinformatics;
  • Sequence analysis;
  • Genomics;
  • DNA sequencing technology;
  • Algorithms.

Select publications

Quick et al.
Real-time, portable genome sequencing for Ebola surveillance.
Nature, 2016


J. Loman, J. Quick and J. T. Simpson
A complete bacterial genome assembled de novo using only nanopore sequencing data.
Nature Methods, 2015


J.T. Simpson
Exploring Genome Characteristics and Sequence Quality Without a Reference.
Bioinformatics, 2014.


J.T. Simpson and R. Durbin.
Efficient de novo assembly of large genomes using compressed data structures.
Genome Research, 22(3):549–556, 2012.


J.T. Simpson, K. Wong, S.D. Jackman, J.E. Schein, S.J.M. Jones, and I. Birol.
Abyss: a parallel assembler for short read sequence data.
Genome Research, 19(6):1117–1123, 2009.

Software

  • ABySS
    ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads;
  • SGA
    SGA is a de novo genome assembler based on the concept of string graphs;
  • Nanopolish
    A nanopore consensus algorithm using a signal-level hidden Markov model.

Previous experience

  • Doctor of Philosophy, University of Cambridge/Wellcome Trust Sanger Institute;
  • Computational Biologist, Genome Sciences Centre, BC Cancer Agency;
  • Software Engineer, Electronic Arts;
  • Bachelor of Science, Computer Science, University of British Columbia.

Related links

Opportunities to collaborate and contact

Dr. Simpson welcomes collaboration. Contact him at jared.simpson@oicr.on.ca for more information.