Publications by authors named "Jared T Simpson"

43Publications

GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis.

BMC Bioinformatics 2020 Aug 5;21(1):343. Epub 2020 Aug 5.

School of Computer Science and Engineering, UNSW Sydney, Sydney, Australia.

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http://dx.doi.org/10.1186/s12859-020-03697-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7430849PMC
August 2020

New Twists in Detecting mRNA Modification Dynamics.

Trends Biotechnol 2020 Jul 1. Epub 2020 Jul 1.

School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK. Electronic address:

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http://dx.doi.org/10.1016/j.tibtech.2020.06.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7326690PMC
July 2020

Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks.

Mol Cell 2020 03 17;77(6):1307-1321.e10. Epub 2020 Jan 17.

Computational Biology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON M5G 1L7, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.12.027DOI Listing
March 2020

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads.

Nat Methods 2019 05 22;16(5):429-436. Epub 2019 Apr 22.

Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1038/s41592-019-0394-yDOI Listing
May 2019

Reply to 'Errors in long-read assemblies can critically affect protein prediction'.

Nat Biotechnol 2019 02;37(2):127-128

School of Life Sciences, University of Nottingham, Nottingham, UK.

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http://dx.doi.org/10.1038/s41587-018-0005-yDOI Listing
February 2019

Shotgun metagenomics, from sampling to analysis.

Nat Biotechnol 2017 Sep;35(9):833-844

Centre for Integrative Biology, University of Trento, Trento, Italy.

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http://dx.doi.org/10.1038/nbt.3935DOI Listing
September 2017

Detecting DNA cytosine methylation using nanopore sequencing.

Nat Methods 2017 Apr 20;14(4):407-410. Epub 2017 Feb 20.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1038/nmeth.4184DOI Listing
April 2017

Nanocall: an open source basecaller for Oxford Nanopore sequencing data.

Bioinformatics 2017 01 10;33(1):49-55. Epub 2016 Sep 10.

Ontario Institute for Cancer Research, Toronto M5G 0A3, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btw569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408768PMC
January 2017

Real-time, portable genome sequencing for Ebola surveillance.

Authors:
Joshua Quick Nicholas J Loman Sophie Duraffour Jared T Simpson Ettore Severi Lauren Cowley Joseph Akoi Bore Raymond Koundouno Gytis Dudas Amy Mikhail Nobila Ouédraogo Babak Afrough Amadou Bah Jonathan Hj Baum Beate Becker-Ziaja Jan-Peter Boettcher Mar Cabeza-Cabrerizo Alvaro Camino-Sanchez Lisa L Carter Juiliane Doerrbecker Theresa Enkirch Isabel Graciela García Dorival Nicole Hetzelt Julia Hinzmann Tobias Holm Liana Eleni Kafetzopoulou Michel Koropogui Abigail Kosgey Eeva Kuisma Christopher H Logue Antonio Mazzarelli Sarah Meisel Marc Mertens Janine Michel Didier Ngabo Katja Nitzsche Elisa Pallash Livia Victoria Patrono Jasmine Portmann Johanna Gabriella Repits Natasha Yasmin Rickett Andrea Sachse Katrin Singethan Inês Vitoriano Rahel L Yemanaberhan Elsa G Zekeng Racine Trina Alexander Bello Amadou Alpha Sall Ousmane Faye Oumar Faye N'Faly Magassouba Cecelia V Williams Victoria Amburgey Linda Winona Emily Davis Jon Gerlach Franck Washington Vanessa Monteil Marine Jourdain Marion Bererd Alimou Camara Hermann Somlare Abdoulaye Camara Marianne Gerard Guillaume Bado Bernard Baillet Déborah Delaune Koumpingnin Yacouba Nebie Abdoulaye Diarra Yacouba Savane Raymond Bernard Pallawo Giovanna Jaramillo Gutierrez Natacha Milhano Isabelle Roger Christopher J Williams Facinet Yattara Kuiama Lewandowski Jamie Taylor Philip Rachwal Daniel Turner Georgios Pollakis Julian A Hiscox David A Matthews Matthew K O'Shea Andrew McD Johnston Duncan Wilson Emma Hutley Erasmus Smit Antonino Di Caro Roman Woelfel Kilian Stoecker Erna Fleischmann Martin Gabriel Simon A Weller Lamine Koivogui Boubacar Diallo Sakoba Keita Andrew Rambaut Pierre Formenty Stephan Gunther Miles W Carroll

Nature 2016 Feb 3;530(7589):228-232. Epub 2016 Feb 3.

The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany.

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http://dx.doi.org/10.1038/nature16996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817224PMC
February 2016

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

Nat Commun 2015 Dec 9;6:10001. Epub 2015 Dec 9.

CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1038/ncomms10001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4682041PMC
December 2015

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

Nat Methods 2015 Aug 15;12(8):733-5. Epub 2015 Jun 15.

1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nmeth.3444DOI Listing
August 2015

The Theory and Practice of Genome Sequence Assembly.

Annu Rev Genomics Hum Genet 2015 22;16:153-72. Epub 2015 Apr 22.

Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada; email:

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http://dx.doi.org/10.1146/annurev-genom-090314-050032DOI Listing
May 2016

On the representation of de Bruijn graphs.

J Comput Biol 2015 May 28;22(5):336-52. Epub 2015 Jan 28.

1 Department of Computer Science and Engineering, The Pennsylvania State University , State College, Pennsylvania.

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http://cristal.univ-lille.fr/~chikhi/pdf/recomb-14.pdf
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http://online.liebertpub.com/doi/10.1089/cmb.2014.0160
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http://dx.doi.org/10.1089/cmb.2014.0160DOI Listing
May 2015

Genome informatics 2014.

Authors:
Jared T Simpson

Genome Biol 2014 Nov 22;15(11):543. Epub 2014 Nov 22.

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http://dx.doi.org/10.1186/s13059-014-0543-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4283781PMC
November 2014

Exploring genome characteristics and sequence quality without a reference.

Authors:
Jared T Simpson

Bioinformatics 2014 May 17;30(9):1228-35. Epub 2014 Jan 17.

Ontario Institute for Cancer Research, Toronto, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btu023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998141PMC
May 2014

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Gigascience 2013 Jul 22;2(1):10. Epub 2013 Jul 22.

Genome Center, UC, Davis, CA 95616, USA.

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http://dx.doi.org/10.1186/2047-217X-2-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844414PMC
July 2013

Efficient de novo assembly of large genomes using compressed data structures.

Genome Res 2012 Mar 7;22(3):549-56. Epub 2011 Dec 7.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://genome.cshlp.org/content/22/3/549.full.pdf
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http://genome.cshlp.org/content/suppl/2011/12/12/gr.126953.1
Web Search
http://genome.cshlp.org/cgi/doi/10.1101/gr.126953.111
Publisher Site
http://dx.doi.org/10.1101/gr.126953.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3290790PMC
March 2012

Efficient construction of an assembly string graph using the FM-index.

Bioinformatics 2010 Jun;26(12):i367-73

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1093/bioinformatics/btq217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881401PMC
June 2010

Copy number variant detection in inbred strains from short read sequence data.

Bioinformatics 2010 Feb 18;26(4):565-7. Epub 2009 Dec 18.

Wellcome Trust Sanger Institute, Hinxton, CB10 1HH, UK.

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http://dx.doi.org/10.1093/bioinformatics/btp693DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820678PMC
February 2010

ABySS: a parallel assembler for short read sequence data.

Genome Res 2009 Jun 27;19(6):1117-23. Epub 2009 Feb 27.

Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada.

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http://dx.doi.org/10.1101/gr.089532.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694472PMC
June 2009