Author

Jared T Simpson

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 4 Bioinformatics· 2

Signature Assays, Organisms & Methods

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Organism:human· 3 Approach:statistical model· 3 Research Focus:variant calling· 3 Assay:whole-genome sequencing· 3 Approach:experimental assay· 2 Assay:long-read sequencing· 2 Approach:benchmark study· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Lewis Jonathan Dursi· 2 shared Matei David· 2 shared Paul C Boutros· 2 shared Richard Durbin· 2 shared Adam M. PhillippyiD· 1 shared Akihiro FujimotoiD· 1 shared Andrew G Lynch· 1 shared Anne-Sophie Sertier· 1 shared

Activity by Year

2015-2017 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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2 shared papersGenomics

Lewis Jonathan Dursi

Mutual co-authors in cluster

Author profile →

6 papers

Recent·Most cited

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

Valerie A Schneider, Tina Graves Lindsay, Kerstin Howe, Nathan Bouk, Hsiu-Chuan Chen, Paul A. Kitts, Terence D Murphy, Kim D. Pruitt, Françoise Thibaud-Nissen, Derek Albracht, Robert S Fulton, Milinn Kremitzki, Vince Magrini, Chris Markovic, Sean McGrath, , Deanna M Church

This paper evaluates GRCh38 and de novo haploid assemblies, finding that GRCh38 remains superior for complex genomic regions and coding sequences despite improvements in newer assemblies.

Genome Research · Apr 10, 2017Peer-reviewedGenomics

Using reference-free compressed data structures to analyse sequencing reads from thousands of human genomes

Dirk-Dominic Dolle, Zhicheng Liu, Matthew L Cotten, Jared T Simpson, Zamin Iqbal, Richard Durbin, Shane McCarthy, Thomas Keane

This paper introduces a population BWT data structure to efficiently store and analyze sequencing reads from thousands of human genomes, enabling variant calling and viral detection.

bioRxiv · Jun 22, 2016Genomics

Detecting DNA Methylation using the Oxford Nanopore Technologies MinION sequencer

Jared T Simpson, Rachael Workman, Philip C Zuzarte, Matei David, Lewis Jonathan Dursi, Winston Timp

This study quantifies the ability of the MinION sequencer to detect DNA methylation using synthetic DNA and demonstrates reliable prediction of CpG island methylation from single reads.

bioRxiv · Apr 4, 2016Genomics

Nanocall: An Open Source Basecaller for Oxford Nanopore Sequencing Data

Matei David, Lewis Jonathan Dursi, Delia Yao, Paul C Boutros, Jared T Simpson

Nanocall is an open-source basecaller for Oxford Nanopore sequencing data that enables offline analysis and has comparable accuracy to Metrichor's cloud-based solution.

bioRxiv · Mar 28, 2016Bioinformatics

A Comprehensive Assessment of Somatic Mutation Calling in Cancer Genomes

Tyler S Alioto, Sophia Derdak, Timothy A Beck, Paul C Boutros, Lawrence Bower, Ivo Buchhalter, Matthew D Eldridge, Nicholas J Harding, Lawrence Edward Heisler, Eivind Hovig, David T W Jones, Andrew G Lynch, Sigve Nakken, Paolo Ribeca, Anne-Sophie Sertier, , Rolf Kab

This study benchmarks somatic mutation calling in cancer genomes, identifying inconsistencies and proposing solutions to improve accuracy.

Nature Communications · Dec 9, 2015Peer-reviewedGenomics

A complete bacterial genome assembled de novo using only nanopore sequencing data

Nicholas James Loman, Joshua Quick, Jared T Simpson

This paper presents a method to assemble a complete bacterial genome using only nanopore sequencing data, achieving high accuracy without reference or other platforms.

Nature Methods · Aug 1, 2015Peer-reviewedBioinformatics