J
Josh D. Neufeld
Researcher at University of Waterloo
Publications - 157
Citations - 11306
Josh D. Neufeld is an academic researcher from University of Waterloo. The author has contributed to research in topics: Metagenomics & Temperature gradient gel electrophoresis. The author has an hindex of 47, co-authored 149 publications receiving 9441 citations. Previous affiliations of Josh D. Neufeld include University of British Columbia & University of Warwick.
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Journal ArticleDOI
PANDAseq: paired-end assembler for illumina sequences
TL;DR: PANDAseq rapidly assembles sequences and scales to billions of paired-end reads and shows significant improvements over naïve assembly with negligible loss of "good" sequence.
Journal ArticleDOI
Ecology and exploration of the rare biosphere
Michael D. Lynch,Josh D. Neufeld +1 more
TL;DR: The ecology of rare microbial populations is discussed, molecular and computational methods for targeting taxonomic 'blind spots' within the rare biosphere of complex microbial communities are highlighted, and the value of studying the biogeography of microorganisms is highlighted.
Journal ArticleDOI
Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads
Andrea K. Bartram,Michael D. Lynch,Jennifer C. Stearns,Gabriel Moreno-Hagelsieb,Josh D. Neufeld +4 more
TL;DR: This method incorporates indexed primers to enable the characterization of multiple microbial communities in a single flow cell lane, may be modified readily to target other variable regions or genes, and demonstrates unprecedented and economical access to DNAs from organisms that exist at low relative abundances.
Journal ArticleDOI
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Pelin Yilmaz,Pelin Yilmaz,Renzo Kottmann,Dawn Field,Rob Knight,Rob Knight,James R. Cole,Linda A. Amaral-Zettler,Jack A. Gilbert,Jack A. Gilbert,Jack A. Gilbert,Ilene Karsch-Mizrachi,Anjanette Johnston,Guy Cochrane,Robert Vaughan,Christopher I. Hunter,Joonhong Park,Norman Morrison,Philippe Rocca-Serra,Peter Sterk,Manimozhiyan Arumugam,Mark J. Bailey,Laura K. Baumgartner,Bruce W. Birren,Martin J. Blaser,Vivien Bonazzi,Timothy F. Booth,Peer Bork,Frederic D. Bushman,Pier Luigi Buttigieg,Pier Luigi Buttigieg,Patrick S. G. Chain,Patrick S. G. Chain,Patrick S. G. Chain,Emily S. Charlson,Elizabeth K. Costello,Heather Huot-Creasy,Peter Dawyndt,Todd Z. DeSantis,Noah Fierer,Jed A. Fuhrman,Rachel E. Gallery,Dirk Gevers,Richard A. Gibbs,Inigo San Gil,Antonio Gonzalez,Jeffrey I. Gordon,Robert P. Guralnick,Wolfgang Hankeln,Wolfgang Hankeln,Sarah K. Highlander,Philip Hugenholtz,Janet K. Jansson,Janet K. Jansson,Andrew L. Kau,Scott T. Kelley,Jerry Kennedy,Dan Knights,Omry Koren,Justin Kuczynski,Nikos C. Kyrpides,Robert Larsen,Christian L. Lauber,Teresa M. Legg,Ruth E. Ley,Catherine A. Lozupone,Wolfgang Ludwig,Donna Lyons,Eamonn Maguire,Barbara A. Methé,Folker Meyer,Brian D. Muegge,Sara Nakielny,Karen E. Nelson,Diana R. Nemergut,Josh D. Neufeld,Lindsay K. Newbold,Anna Oliver,Norman R. Pace,Giriprakash Palanisamy,Jörg Peplies,Joseph F. Petrosino,Lita M. Proctor,Elmar Pruesse,Elmar Pruesse,Christian Quast,Jeroen Raes,Sujeevan Ratnasingham,Jacques Ravel,David A. Relman,David A. Relman,Susanna Assunta-Sansone,Patrick D. Schloss,Lynn M. Schriml,Rohini Sinha,Michelle I. Smith,Erica Sodergren,Aymé Spor,Jesse Stombaugh,James M. Tiedje,Doyle V. Ward,George M. Weinstock,Doug Wendel,Owen White,Andrew S. Whiteley,Andreas Wilke,Jennifer R. Wortman,Tanya Yatsunenko,Frank Oliver Glöckner,Frank Oliver Glöckner +109 more
TL;DR: To establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, the minimum information about any (x) sequence is presented (MIxS).
Journal ArticleDOI
Bacterial biogeography of the human digestive tract
Jennifer C. Stearns,Michael D. Lynch,Michael D. Lynch,Dilani B. Senadheera,Howard C. Tenenbaum,Michael B. Goldberg,Dennis G. Cvitkovitch,Kenneth Croitoru,Gabriel Moreno-Hagelsieb,Josh D. Neufeld +9 more
TL;DR: This first comprehensive characterization of the abundant and rare microflora found along the healthy human digestive tract represents essential groundwork to investigate further how the human microbiome relates to health and disease.