JS
Jared T. Simpson
COVID-19bioinformaticsgenomicsSARS-CoV-2AlgorithmsNanoporesSoftwareGenomicsMutationq-bio.GN
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
76 papers in the corpus · 2009–2026Multi-platform reassessment of human mitochondrial DNA methylation reveals signals consistent with technical artifacts.42367956 · Basrai, Salman, Bahcheli, Alexander T, Tan, Djarren et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
A structure-selective endonuclease drives uniparental mitochondrial DNA inheritance.41889885 · Shimomura, Mayu, Yun, Hwa Young, Zuzarte, Philip C et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
Tutorial: annotation of animal genomes.41606128 · Clarke, Zoe A, Sokolowski, Dustin J, Byles-Ho, Ciaran K et al.2026 · 1 citationNature protocols. 2026;21(7):2883-2893
Rapid donor-specific single nucleotide variation detection by nanopore sequencing of ex vivo lung perfusate.41362394 · Yamamoto, Haruchika, Allen, Jonathan, Sundby, Adam et al.2025 · 1 citationJHLT open. 2026;11:100433
Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing.40909653 · Bertocchi, Uri, Grunwald, Assaf, Goldner, Gal et al.2025 · 5 citationsbioRxiv : the preprint server for biology. 2025
Detecting Protein-DNA binding in single molecules using antibody guided methylation.40598583 · Thatavarty, Apoorva, Sagy, Naor, Erdos, Michael R et al.2025 · 4 citationsEpigenetics & chromatin. 2025;18(1):39
Pathogenesis and transmission of SARS-CoV-2 D614G, Alpha, Gamma, Delta, and Omicron variants in golden hamsters.40295859 · Banete, Andra, Griffin, Bryan D, Corredor, Juan C et al.2026 · 7 citationsNpj viruses. 2025;3(1):15
Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population.39738001 · Aynaud, Marie-Ming, Caldwell, Lauren, Al-Zahrani, Khalid N et al.2024 · 2 citationsNature communications. 2024;15(1):10795
SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes.39703420 · Nasir, Jalees A, Maguire, Finlay, Smith, Kendrick M et al.2025 · 2 citationsNAR genomics and bioinformatics. 2024;6(4):lqae176
An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology.39651266 · Sokolowski, Dustin J, Miclăuș, Mihai, Nater, Alexander et al.2025 · 10 citationsbioRxiv : the preprint server for biology. 2024
Inhibiting EZH2 targets atypical teratoid rhabdoid tumor by triggering viral mimicry via both RNA and DNA sensing pathways.39472584 · Feng, Shengrui, Marhon, Sajid A, Sokolowski, Dustin J et al.2024 · 14 citationsNature communications. 2024;15(1):9321
The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.39401061 · Gill, Erin E, Jia, Baofeng, Murall, Carmen Lia et al.2024 · 4 citationsMicrobial genomics. 2024;10(10)
The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.38764594 · Gill, Erin E, Jia, Baofeng, Murall, Carmen Lia et al.2026 · 1 citationArXiv. 2024
Detecting Somatic Mutations Without Matched Normal Samples Using Long Reads.38464143 · Simpson, Jared T2026 · 5 citationsbioRxiv : the preprint server for biology. 2024
Characterizing Risk Factors for Hospitalization and Clinical Characteristics in a Cohort of COVID-19 Patients Enrolled in the GENCOV Study.37632107 · Morgan, Gregory, Casalino, Selina, Chowdhary, Sunakshi et al.2023 · 7 citationsViruses. 2023;15(8)
Somrit: The Somatic Retrotransposon Insertion Toolkit10.1101/2023.08.06.552193v2 · D'Costa, A., Simpson, J. T.2023 · 2 citationsbioRxiv
Prevalence of Low-Frequency, Antiviral Resistance Variants in SARS-CoV-2 Isolates in Ontario, Canada, 2020-2023.37477915 · Sjaarda, Calvin P, Lau, Lynette, Simpson, Jared T et al.2023 · 18 citationsJAMA network open. 2023;6(7):e2324963
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.36912329 · Kain, Dylan C, Isabel, Sandra, Abdulnoor, Mariana et al.2023 · 1 citationInfection control and hospital epidemiology. 2023;44(11):1829-1833
A Novel Approach to Detect IDH Point Mutations in Gliomas Using Nanopore Sequencing: Test Validation for the Clinical Laboratory.36565986 · Mimosa, Mashiat L, Al-Ameri, Wafa, Simpson, Jared T et al.2023 · 17 citationsThe Journal of molecular diagnostics : JMD. 2023;25(3):133-142
Genome screening, reporting, and genetic counseling for healthy populations.36331656 · Casalino, Selina, Frangione, Erika, Chung, Monica et al.2023 · 12 citationsHuman genetics. 2023;142(2):181-192
Genome Reporting for Healthy Populations-Pipeline for Genomic Screening from the GENCOV COVID-19 Study.36205462 · Frangione, Erika, Chung, Monica, Casalino, Selina et al.2022 · 6 citationsCurrent protocols. 2022;2(10):e534
Author Correction: Emergence of a mutation in the nucleocapsid gene of SARS-CoV-2 interferes with PCR detection in Canada.35986021 · Isabel, Sandra, Abdulnoor, Mariana, Boissinot, Karel et al.2022 · 1 citationScientific reports. 2022;12(1):14159
Emergence of a mutation in the nucleocapsid gene of SARS-CoV-2 interferes with PCR detection in Canada.35760824 · Isabel, Sandra, Abdulnoor, Mariana, Boissinot, Karel et al.2022 · 17 citationsScientific reports. 2022;12(1):10867
Implementation of serological and molecular tools to inform COVID-19 patient management: protocol for the GENCOV prospective cohort study.34593505 · Taher, Jennifer, Mighton, Chloe, Chowdhary, Sunakshi et al.2021 · 12 citationsBMJ open. 2021;11(9):e052842
Temporal Dynamics and Evolution of SARS-CoV-2 Demonstrate the Necessity of Ongoing Viral Genome Sequencing in Ontario, Canada.33952657 · Sjaarda, Calvin P, Guthrie, Jennifer L, Mubareka, Samira et al.2021 · 6 citationsmSphere. 2021;6(3)
Detection of the novel SARS-CoV-2 European lineage B.1.177 in Ontario, Canada.35261998 · Guthrie, Jennifer L, Teatero, Sarah, Zittermann, Sandra et al.2025 · 13 citationsJournal of clinical virology plus. 2021;1(1):100010
Revealing nascent RNA processing dynamics with nano-COP.33514943 · Drexler, Heather L, Choquet, Karine, Merens, Hope E et al.2021 · 46 citationsNature protocols. 2021;16(3):1343-1375
Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.33257764 · Bailey, Matthew H, Meyerson, William U, Dursi, Lewis Jonathan et al.2025 · 1 citationNature communications. 2020;11(1):6232
Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing.33230324 · Lee, Isac, Razaghi, Roham, Gilpatrick, Timothy et al.2021 · 227 citationsNature methods. 2020;17(12):1191-1199
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.32958763 · Bailey, Matthew H, Meyerson, William U, Dursi, Lewis Jonathan et al.2020 · 53 citationsNature communications. 2020;11(1):4748
GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis.32758139 · Gamaarachchi, Hasindu, Lam, Chun Wai, Jayatilaka, Gihan et al.2020 · 136 citationsBMC bioinformatics. 2020;21(1):343
New Twists in Detecting mRNA Modification Dynamics.32620324 · Anreiter, Ina, Mir, Quoseena, Simpson, Jared T et al.2021 · 155 citationsTrends in biotechnology. 2021;39(1):72-89
Detection of Structural Rearrangements in Embryos.32558475 · Madjunkova, Svetlana, Sundaravadanam, Yogi, Antes, Ran et al.2020 · 30 citationsThe New England journal of medicine. 2020;382(25):2472-2474
Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks.31954095 · Zhu, Helen, Uusküla-Reimand, Liis, Isaev, Keren et al.2020 · 102 citationsMolecular cell. 2020;77(6):1307-1321.e10
Author Correction: Nanopore native RNA sequencing of a human poly(A) transcriptome.31819268 · Workman, Rachael E, Tang, Alison D, Tang, Paul S et al.2024 · 5 citationsNature methods. 2020;17(1):114
A community effort to create standards for evaluating tumor subclonal reconstruction.31919445 · Salcedo, Adriana, Tarabichi, Maxime, Espiritu, Shadrielle Melijah G et al.2020 · 91 citationsNature biotechnology. 2020;38(1):97-107
Nanopore native RNA sequencing of a human poly(A) transcriptome.31740818 · Workman, Rachael E, Tang, Alison D, Tang, Paul S et al.2020 · 731 citationsNature methods. 2019;16(12):1297-1305
Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads.31011185 · Müller, Carolin A, Boemo, Michael A, Spingardi, Paolo et al.2019 · 142 citationsNature methods. 2019;16(5):429-436
Reply to 'Errors in long-read assemblies can critically affect protein prediction'.30670797 · Koren, Sergey, Phillippy, Adam M, Simpson, Jared T et al.2019 · 28 citationsNature biotechnology. 2019;37(2):127-128
Nanopore sequencing and assembly of a human genome with ultra-long reads.29431738 · Jain, Miten, Koren, Sergey, Miga, Karen H et al.2018 · 1,892 citationsNature biotechnology. 2018;36(4):338-345
Corrigendum: Shotgun metagenomics, from sampling to analysis.29220029 · Quince, Christopher, Walker, Alan W, Simpson, Jared T et al.2019 · 67 citationsNature biotechnology. 2017;35(12):1211
Shotgun metagenomics, from sampling to analysis.28898207 · Quince, Christopher, Walker, Alan W, Simpson, Jared T et al.2017 · 2,193 citationsNature biotechnology. 2017;35(9):833-844
Establishment and cryptic transmission of Zika virus in Brazil and the Americas.28538727 · Faria, N R, Quick, J, Claro, I M et al.2017 · 616 citationsNature. 2017;546(7658):406-410
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.28538739 · Quick, Joshua, Grubaugh, Nathan D, Pullan, Steven T et al.2017 · 1,187 citationsNature protocols. 2017;12(6):1261-1276
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.28396521 · Schneider, Valerie A, Graves-Lindsay, Tina, Howe, Kerstin et al.2018 · 1,186 citationsGenome research. 2017;27(5):849-864
Detecting DNA cytosine methylation using nanopore sequencing.28218898 · Simpson, Jared T, Workman, Rachael E, Zuzarte, P C et al.2017 · 1,141 citationsNature methods. 2017;14(4):407-410
De Novo Genome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis).28087693 · Lok, Si, Paton, Tara A, Wang, Zhuozhi et al.2017 · 23 citationsG3 (Bethesda, Md.). 2017;7(2):755-773
Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.27986821 · Dolle, Dirk D, Liu, Zhicheng, Cotten, Matthew et al.2018 · 18 citationsGenome research. 2017;27(2):300-309
Erratum: A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns.27851734 · Notta, Faiyaz, Chan-Seng-Yue, Michelle, Lemire, Mathieu et al.2020 · 6 citationsNature. 2017;542(7639):124
A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns.27732578 · Notta, Faiyaz, Chan-Seng-Yue, Michelle, Lemire, Mathieu et al.2017 · 530 citationsNature. 2016;538(7625):378-382
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