Publications by authors named "Jared T Simpson"

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Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing.
Uri Bertocchi, Assaf Grunwald, Gal Goldner, Eliran Eitan, Sigal Avraham, Jared T Simpson

ACS Nano· November 2025

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Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing.
Uri Bertocchi, Assaf Grunwald, Gal Goldner, Eliran Eitan, Sigal Avraham, Jared T Simpson

bioRxiv· September 2025

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Detecting Protein-DNA binding in single molecules using antibody guided methylation.
Apoorva Thatavarty, Naor Sagy, Michael R Erdos, Isac Lee, Jared T Simpson

Epigenetics Chromatin· July 2025

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Pathogenesis and transmission of SARS-CoV-2 D614G, Alpha, Gamma, Delta, and Omicron variants in golden hamsters.
Andra Banete, Bryan D Griffin, Juan C Corredor, Emily Chien, Lily Yip, Jared T Simpson

Npj Viruses· February 2025

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SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes.
Jalees A Nasir, Finlay Maguire, Kendrick M Smith, Emily M Panousis, Sheridan J C Baker, Jared T Simpson

NAR Genom Bioinform· December 2024

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An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology.
Dustin J Sokolowski, Mihai Miclăuș, Alexander Nater, Mariela Faykoo-Martinez, Kendra Hoekzema, Jared T Simpson

bioRxiv· November 2024

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The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.
Erin E Gill, Baofeng Jia, Carmen Lia Murall, Raphaël Poujol, Muhammad Zohaib Anwar, Jared T Simpson

Microb Genom· October 2024

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Inhibiting EZH2 targets atypical teratoid rhabdoid tumor by triggering viral mimicry via both RNA and DNA sensing pathways.
Shengrui Feng, Sajid A Marhon, Dustin J Sokolowski, Alister D'Costa, Fraser Soares, Jared T Simpson

Nat Commun· October 2024

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The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.
Erin E Gill, Baofeng Jia, Carmen Lia Murall, Raphaël Poujol, Muhammad Zohaib Anwar, Jared T Simpson

ArXiv· May 2024

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Detecting Somatic Mutations Without Matched Normal Samples Using Long Reads.
Jared T Simpson

bioRxiv· February 2024

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Coronavirus disease 2019 (COVID-19) outbreak on an in-patient medical unit associated with unrecognized exposures in common areas-Epidemiological and whole-genome sequencing investigation.
Dylan C Kain, Sandra Isabel, Mariana Abdulnoor, Karel Boissinot, Richard De Borja, Jared T Simpson

Infect Control Hosp Epidemiol· November 2023

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Prevalence of Low-Frequency, Antiviral Resistance Variants in SARS-CoV-2 Isolates in Ontario, Canada, 2020-2023.
Calvin P Sjaarda, Lynette Lau, Jared T Simpson, Ramzi Fattouh, Mia J Biondi

JAMA Netw Open· July 2023

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A Novel Approach to Detect IDH Point Mutations in Gliomas Using Nanopore Sequencing: Test Validation for the Clinical Laboratory.
Mashiat L Mimosa, Wafa Al-Ameri, Jared T Simpson, Michael Nakhla, Karel Boissinot

J Mol Diagn· March 2023

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Author Correction: Emergence of a mutation in the nucleocapsid gene of SARS-CoV-2 interferes with PCR detection in Canada.
Sandra Isabel, Mariana Abdulnoor, Karel Boissinot, Marc R Isabel, Richard de Borja, Jared T Simpson

Sci Rep· August 2022

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Emergence of a mutation in the nucleocapsid gene of SARS-CoV-2 interferes with PCR detection in Canada.
Sandra Isabel, Mariana Abdulnoor, Karel Boissinot, Marc R Isabel, Richard de Borja, Jared T Simpson

Sci Rep· June 2022

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Detection of the novel SARS-CoV-2 European lineage B.1.177 in Ontario, Canada.
Jennifer L Guthrie, Sarah Teatero, Sandra Zittermann, Yao Chen, Ashleigh Sullivan, Jared T Simpson

J Clin Virol Plus· June 2021

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Temporal Dynamics and Evolution of SARS-CoV-2 Demonstrate the Necessity of Ongoing Viral Genome Sequencing in Ontario, Canada.
Calvin P Sjaarda, Jennifer L Guthrie, Samira Mubareka, Jared T Simpson, Bettina Hamelin

mSphere· May 2021

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Revealing nascent RNA processing dynamics with nano-COP.
Heather L Drexler, Karine Choquet, Hope E Merens, Paul S Tang, Jared T Simpson

Nat Protoc· March 2021

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New Twists in Detecting mRNA Modification Dynamics.
Ina Anreiter, Quoseena Mir, Jared T Simpson, Sarath C Janga, Matthias Soller

Trends Biotechnol· January 2021

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Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing.
Isac Lee, Roham Razaghi, Timothy Gilpatrick, Michael Molnar, Ariel Gershman, Jared T Simpson

Nat Methods· December 2020

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Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
Matthew H Bailey, William U Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Jared T Simpson

Nat Commun· November 2020

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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
Matthew H Bailey, William U Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Jared T Simpson

Nat Commun· September 2020

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GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis.
Hasindu Gamaarachchi, Chun Wai Lam, Gihan Jayatilaka, Hiruna Samarakoon, Jared T Simpson

BMC Bioinformatics· August 2020

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Detection of Structural Rearrangements in Embryos.
Svetlana Madjunkova, Yogi Sundaravadanam, Ran Antes, Rina Abramov, Siwei Chen, Jared T Simpson

N Engl J Med· June 2020

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Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks.
Helen Zhu, Liis Uusküla-Reimand, Keren Isaev, Lina Wadi, Azad Alizada, Jared T Simpson

Mol Cell· March 2020

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