Dr. Jared Simpson - Ontario Institute for Cancer Research

Contact

Dr. Jared Simpson

Interim Scientific Director, Computational Biology and Senior Principal Investigator

Jared.Simpson@oicr.on.ca
Twitter: @jaredtsimpson

Interim Scientific Director, Computational Biology and Senior Principal Investigator

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.

External Links

The Simpson Lab

Experience & Education

Investigator I, OICR
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

Current Affiliations

Interim Scientific Director, Computational Biology and Senior Principal Investigator, OICR
Assistant Professor, Department of Computer Science, University of Toronto

Select Publications

Jain M, Koren S, Miga KH, …, Simpson JT, Loman NJ, Loose M. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018; 36(4):338-345.
Simpson JT, Workman RE, Zuzarte PC, …, Timp W. Detecting DNA cytosine methylation using nanopore sequencing. Nat Methods. 2017; 14(4):407-410.
Quick J, Loman NJ, Duraffour S, Simpson JT, …, Carroll MW. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016; 530(7589):228-232.
Loman NJ, Quick J, Simpson JT. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods. 2015; 12(8):733-5.
Simpson JT. Exploring genome characteristics and sequence quality without a reference. Bioinformatics. 2014; 30(9):1228-35.
Simpson JT, Durbin R. Efficient de novo assembly of large genomes using compressed data structures. Genome Res. 2012; 22(3):549-56.
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res. 2009; 19(6):1117-23.

See Dr. Simpson’s recent publications on PubMed or on Google Scholar.

Research Areas

Biology Informatics and Data Standards

Disease Areas

All

Opportunities to Collaborate

Collaborate with us

If you’re interested in collaborating with Dr. Simpson, please contact him directly.

Visit OICR’s Collaborative Research Resources directory for more opportunities to collaborate with OICR researchers.

Programs

Computational Biology

Utilizes datasets from multiple sources for the development and application of algorithms for cancer genome analysis, biomarker discovery, cancer pathway discovery, data integration and tumour evolution research.

Learn More

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

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