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Timothy P L Smith
Researcher at Agricultural Research Service
Publications - 19
Citations - 1410
Timothy P L Smith is an academic researcher from Agricultural Research Service. The author has contributed to research in topics: Genome & Reference genome. The author has an hindex of 11, co-authored 19 publications receiving 967 citations. Previous affiliations of Timothy P L Smith include United States Department of Agriculture.
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Journal ArticleDOI
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
Derek M. Bickhart,Benjamin D. Rosen,Sergey Koren,B.L. Sayre,Alex Hastie,Saki Chan,Joyce Lee,Ernest T. Lam,Ivan Liachko,Shawn T. Sullivan,Joshua N. Burton,Heather J. Huson,John C Nystrom,Christy M. Kelley,J.L. Hutchison,Yang Zhou,Yang Zhou,Jiajie Sun,Alessandra Crisà,F. Abel Ponce de León,John C. Schwartz,John A. Hammond,Geoffrey C. Waldbieser,Steven G. Schroeder,George E. Liu,Maitreya J. Dunham,Jay Shendure,Jay Shendure,Tad S. Sonstegard,Adam M. Phillippy,Curtis P. Van Tassell,Timothy P L Smith +31 more
TL;DR: This assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.
Journal ArticleDOI
De novo assembly of haplotype-resolved genomes with trio binning.
Sergey Koren,Arang Rhie,Brian P. Walenz,Alexander T. Dilthey,Alexander T. Dilthey,Derek M. Bickhart,Sarah B. Kingan,Stefan Hiendleder,John L. Williams,Timothy P L Smith,Adam M. Phillippy +10 more
TL;DR: This work used trio binning to recover both haplotypes of a diploid human genome and identified complex structural variants missed by alternative approaches, topping the quality of current cattle reference genomes.
Journal ArticleDOI
An improved pig reference genome sequence to enable pig genetics and genomics research
Amanda Warr,Nabeel A. Affara,Bronwen Aken,Hamid Beiki,Derek M. Bickhart,Konstantinos Billis,William Chow,Lel Eory,Heather Finlayson,Paul Flicek,Carlos García Girón,Darren K. Griffin,Richard Hall,Gregory Hannum,Thibaut Hourlier,Kerstin Howe,David A. Hume,David A. Hume,Osagie G. Izuogu,Kristi Kim,Sergey Koren,Haibo Liu,Nancy Manchanda,Fergal J. Martin,Dan J. Nonneman,Rebecca E. O’Connor,Adam M. Phillippy,Gary A. Rohrer,Benjamin D. Rosen,Laurie A. Rund,Carole A. Sargent,Lawrence B. Schook,Steven G. Schroeder,Ariel S. Schwartz,Benjamin M. Skinner,Richard Talbot,Elizabeth Tseng,Christopher K. Tuggle,Mick Watson,Timothy P L Smith,Alan Archibald +40 more
TL;DR: These highly contiguous assemblies plus annotation of a further 11 short-read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species.
Journal ArticleDOI
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
Derek M. Bickhart,Mick Watson,Sergey Koren,Kevin Panke-Buisse,Laura M. Cersosimo,Maximilian O. Press,Curtis P. Van Tassell,Jo Ann S. Van Kessel,Bradd J. Haley,Seon Woo Kim,Cheryl Heiner,Garret Suen,Kiranmayee Bakshy,Ivan Liachko,Shawn T. Sullivan,Phillip R. Myer,Jay Ghurye,Mihai Pop,Paul J. Weimer,Paul J. Weimer,Adam M. Phillippy,Timothy P L Smith +21 more
TL;DR: Novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community are demonstrated.
Journal ArticleDOI
Prevalence of the prion protein gene E211K variant in U.S. cattle.
Michael P. Heaton,John W. Keele,Gregory P. Harhay,Jürgen A. Richt,Mohammad Koohmaraie,Mohammad Koohmaraie,Tommy L. Wheeler,Steven D. Shackelford,Eduardo Casas,D. Andy King,Tad S. Sonstegard,Curtis P. Van Tassell,Holly L. Neibergs,Chad C. Chase,Theodore S. Kalbfleisch,Timothy P L Smith,Michael L. Clawson,William W. Laegreid,William W. Laegreid +18 more
TL;DR: A high-throughput matrix-associated laser desorption/ionization-time-of-flight mass spectrometry assay for scoring the Prnp E211K variant and its use to determine an upper limit for the K211 allele frequency in U.S. cattle found the upper bounds for prevalence was estimated to be extremely low.