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Author Details

Jared T Simpson
Ontario Institute for Cancer Research
2009
54
31
PMIDPaper TitleJournal TitlePublished Year
36331656Genome screening, reporting, and genetic counseling for healthy populations.Hum Genet2023
37632107Characterizing Risk Factors for Hospitalization and Clinical Characteristics in a Cohort of COVID-19 Patients Enrolled in the GENCOV Study.Viruses2023
37477915Prevalence of Low-Frequency, Antiviral Resistance Variants in SARS-CoV-2 Isolates in Ontario, Canada, 2020-2023.JAMA Netw Open2023
36912329Coronavirus disease 2019 (COVID-19) outbreak on an in-patient medical unit associated with unrecognized exposures in common areas-Epidemiological and whole-genome sequencing investigation.Infect Control Hosp Epidemiol2023
36565986A Novel Approach to Detect IDH Point Mutations in Gliomas Using Nanopore Sequencing: Test Validation for the Clinical Laboratory.J Mol Diagn2023
35986021Author Correction: Emergence of a mutation in the nucleocapsid gene of SARS-CoV-2 interferes with PCR detection in Canada.Sci Rep2022
35760824Emergence of a mutation in the nucleocapsid gene of SARS-CoV-2 interferes with PCR detection in Canada.Sci Rep2022
36205462Genome Reporting for Healthy Populations-Pipeline for Genomic Screening from the GENCOV COVID-19 Study.Curr Protoc2022
32620324New Twists in Detecting mRNA Modification Dynamics.Trends Biotechnol2021
33514943Revealing nascent RNA processing dynamics with nano-COP.Nat Protoc2021
35261998Detection of the novel SARS-CoV-2 European lineage B.1.177 in Ontario, Canada.J Clin Virol Plus2021
34593505Implementation of serological and molecular tools to inform COVID-19 patient management: protocol for the GENCOV prospective cohort study.BMJ Open2021
33952657Temporal Dynamics and Evolution of SARS-CoV-2 Demonstrate the Necessity of Ongoing Viral Genome Sequencing in Ontario, Canada.mSphere2021
32558475Detection of Structural Rearrangements in Embryos.N Engl J Med2020
31954095Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks.Mol Cell2020
31819268Author Correction: Nanopore native RNA sequencing of a human poly(A) transcriptome.Nat Methods2020
33230324Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing.Nat Methods2020
32758139GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis.BMC Bioinformatics2020
30670797Reply to 'Errors in long-read assemblies can critically affect protein prediction'.Nat Biotechnol2019
31011185Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads.Nat Methods2019
29431738Nanopore sequencing and assembly of a human genome with ultra-long reads.Nat Biotechnol2018
27614348Nanocall: an open source basecaller for Oxford Nanopore sequencing data.Bioinformatics2017
28087693<i>De Novo</i> Genome and Transcriptome Assembly of the Canadian Beaver (<i>Castor canadensis</i>).G3 (Bethesda)2017
28218898Detecting DNA cytosine methylation using nanopore sequencing.Nat Methods2017
28396521Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.Genome Res2017
29220029Corrigendum: Shotgun metagenomics, from sampling to analysis.Nat Biotechnol2017
28538739Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.Nat Protoc2017
28538727Establishment and cryptic transmission of Zika virus in Brazil and the Americas.Nature2017
28898207Shotgun metagenomics, from sampling to analysis.Nat Biotechnol2017
27986821Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.Genome Res2017
27851734Erratum: A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns.Nature2017
26840485Real-time, portable genome sequencing for Ebola surveillance.Nature2016
27732578A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns.Nature2016
25665008The genomic and phenotypic diversity of Schizosaccharomyces pombe.Nat Genet2015
26647970A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.Nat Commun2015
26535114The khmer software package: enabling efficient nucleotide sequence analysis.F1000Res2015
26834992MinION Analysis and Reference Consortium: Phase 1 data release and analysis.F1000Res2015
26076426A complete bacterial genome assembled de novo using only nanopore sequencing data.Nat Methods2015
25939056The Theory and Practice of Genome Sequence Assembly.Annu Rev Genomics Hum Genet2015
25629448On the representation of de Bruijn graphs.J Comput Biol2015
24443382Exploring genome characteristics and sequence quality without a reference.Bioinformatics2014
25418371Genome informatics 2014.Genome Biol2014
24425782A high-definition view of functional genetic variation from natural yeast genomes.Mol Biol Evol2014
23870653Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.Gigascience2013
22156294Efficient de novo assembly of large genomes using compressed data structures.Genome Res2012
22398555Insights into hominid evolution from the gorilla genome sequence.Nature2012
21422276Revealing the genetic structure of a trait by sequencing a population under selection.Genome Res2011
21926179Assemblathon 1: a competitive assessment of de novo short read assembly methods.Genome Res2011
21698134Trait variation in yeast is defined by population history.PLoS Genet2011
20022973Copy number variant detection in inbred strains from short read sequence data.Bioinformatics2010
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Collaborators

University of Cambridge
Co-authored papers 13
University of Birmingham
Co-authored papers 9
Ontario Institute for Cancer Research
Co-authored papers 6
Mount Sinai Health System and University Health Network
Co-authored papers 5
National Human Genome Research Institute, National Institutes of Health
Co-authored papers 5
UC Santa Cruz Genomics Institute, University of California
Co-authored papers 5
National Human Genome Research Institute, National Institutes of Health
Co-authored papers 5
Ontario Institute for Cancer Research
Co-authored papers 4
The Hospital for Sick Children
Co-authored papers 4
University of British Columbia
Co-authored papers 4
Wellcome Sanger Institute
Co-authored papers 4
Ontario Institute for Cancer Research
Co-authored papers 3
Ontario Institute for Cancer Research
Co-authored papers 3
Northeastern University
Co-authored papers 3
University of California los angeles
Co-authored papers 3
Ontario Institute for Cancer Research
Co-authored papers 3
Mount Sinai Hospital
Co-authored papers 3
Lunenfeld-Tanenbaum Research Institute
Co-authored papers 3
Human Longevity Inc.
Co-authored papers 3
Ontario Institute for Cancer Research
Co-authored papers 3
European Bioinformatics Institute
Co-authored papers 3
Co-authored papers 3
Moores Cancer Center, university of california san diego
Co-authored papers 2
Harvard Medical School, Brigham and Women's Hospital
Co-authored papers 2
Princess Margaret Cancer Centre, University Health Network
Co-authored papers 2
Spanish National Cancer Research Centre-CNIO
Co-authored papers 2
Rutgers Robert Wood Johnson Medical School
Co-authored papers 2
Yale School of Public Health
Co-authored papers 2
University Health Network
Co-authored papers 2
University of Washington
Co-authored papers 2