Publications

This list is also available on Google Scholar

Preprints

Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas
Nuno R Faria, Josh Quick, Ingra Morales, Julien Theze, Jacqueline G de Jesus, Marta Giovanetti, Moritz UG Kraemer, Sarah C Hill et al.
bioRxiv (2017)

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
Joshua Quick, Nathan D Grubaugh, Steven T Pullan, Ingra M Claro, Andrew D Smith, Karthik Gangavarapu, Glenn Oliveira, Refugio Robles-Sikisaka et al.
bioRxiv (2017)

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 et al.
bioRxiv (2016)

trio-sga: facilitating de novo assembly of highly heterozygous genomes with parent-child trios
Milan Malinsky, Jared T Simpson, Richard Durbin
bioRxiv (2016)

Peer Reviewed

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
Nature Methods (2017)

De novo genome and transcriptome assembly of the Canadian beaver (Castor canadensis)
Si Lok, Tara A Paton, Zhuozhi Wang, Gaganjot Kaur, Susan Walker, Ryan KC Yuen, Wilson WL Sung, Joseph Whitney et al.
G3: Genes, Genomes, Genetics (2017)

A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns
Faiyaz Notta, Michelle Chan-Seng-Yue, Mathieu Lemire, Yilong Li, Gavin W Wilson, Ashton A Connor, Robert E Denroche, Sheng-Ben Liang et al.
Nature (2016)

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 A McCarthy, Thomas M Keane
Genome Research (2016)

A global reference for human genetic variation
1000 Genomes Project Consortium et al.
Nature (2015)

Nanocall: an open source basecaller for Oxford Nanopore sequencing data
Matei David, Lewis Jonathan Dursi, Delia Yao, Paul C Boutros, Jared T Simpson
Bioinformatics (2016)

Real-time, portable genome sequencing for Ebola surveillance
Joshua Quick, Nicholas J Loman, Sophie Duraffour, Jared T Simpson, Ettore Severi, Lauren Cowley, Joseph Akoi Bore, Raymond Koundouno et al.
Nature (2016)

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing
Tyler S Alioto, Ivo Buchhalter, Sophia Derdak, Barbara Hutter, Matthew D Eldridge, Eivind Hovig, Lawrence E Heisler, Timothy A Beck et al.
Nature communications (2015)

MinION Analysis and Reference Consortium: Phase 1 data release and analysis
Camilla LC Ip, Matthew Loose, John R Tyson, Mariateresa de Cesare, Bonnie L Brown, Miten Jain, Richard M Leggett, David A Eccles et al.
F1000Research (2015)

The khmer software package: enabling efficient nucleotide sequence analysis
Michael R Crusoe, Hussien F Alameldin, Sherine Awad, Elmar Boucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, Bede Constantinides et al.
F1000Research (2015)

A complete bacterial genome assembled de novo using only nanopore sequencing data
Nicholas J Loman, Joshua Quick, Jared T Simpson
Nature methods (2015)

The genomic and phenotypic diversity of Schizosaccharomyces pombe
Daniel C Jeffares, Charalampos Rallis, Adrien Rieux, Doug Speed, Martin P{ř}evorovsk{ỳ}, Tobias Mourier, Francesc X Marsellach, Zamin Iqbal et al.
Nature genetics (2015)

The theory and practice of genome sequence assembly
Jared T Simpson, Mihai Pop
Annual review of genomics and human genetics (2015)

A high-definition view of functional genetic variation from natural yeast genomes
Anders Bergström, Jared T Simpson, Francisco Salinas, Benjamin Barré, Leopold Parts, Amin Zia, Alex N Nguyen Ba, Alan M Moses et al.
Molecular biology and evolution (2014)

Exploring genome characteristics and sequence quality without a reference
Jared T Simpson
Bioinformatics (2014)

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Keith R Bradnam, Joseph N Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, Inan{ç} Birol, Sébastien Boisvert, Jarrod A Chapman et al.
GigaScience (2013)

Insights into hominid evolution from the gorilla genome sequence
Aylwyn Scally, Julien Y Dutheil, LaDeana W Hillier, Gregory E Jordan, Ian Goodhead, Javier Herrero, Asger Hobolth, Tuuli Lappalainen et al.
Nature (2012)

Efficient de novo assembly of large genomes using compressed data structures
Jared T Simpson, Richard Durbin
Genome research (2012)

Assemblathon 1: a competitive assessment of de novo short read assembly methods
Dent Earl, Keith Bradnam, John St John, Aaron Darling, Dawei Lin, Joseph Fass, Hung On Ken Yu, Vince Buffalo et al.
Genome research (2011)

Trait variation in yeast is defined by population history
Jonas Warringer, Enikö Zörgö, Francisco A Cubillos, Amin Zia, Arne Gjuvsland, Jared T Simpson, Annabelle Forsmark, Richard Durbin et al.
PLoS Genet (2011)

Copy number variant detection in inbred strains from short read sequence data
Jared T Simpson, Rebecca E McIntyre, David J Adams, Richard Durbin
Bioinformatics (2010)

Revealing the genetic structure of a trait by sequencing a population under selection
Leopold Parts, Francisco A Cubillos, Jonas Warringer, Kanika Jain, Francisco Salinas, Suzannah J Bumpstead, Mikael Molin, Amin Zia et al.
Genome research (2011)

Efficient construction of an assembly string graph using the FM-index
Jared T Simpson, Richard Durbin
Bioinformatics (2010)

Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels
Ian Sudbery, Jim Stalker, Jared T Simpson, Thomas Keane, Alistair G Rust, Matthew E Hurles, Klaudia Walter, Dee Lynch et al.
Genome biology (2009)

Complex landscapes of somatic rearrangement in human breast cancer genomes
Philip J Stephens, David J McBride, Meng-Lay Lin, Ignacio Varela, Erin D Pleasance, Jared T Simpson, Lucy A Stebbings, Catherine Leroy et al.
Nature (2009)

ABySS: a parallel assembler for short read sequence data
Jared T Simpson, Kim Wong, Shaun D Jackman, Jacqueline E Schein, Steven JM Jones, Inan{ç} Birol
Genome research (2009)