D
Derek M. Bickhart
Researcher at Agricultural Research Service
Publications - 117
Citations - 6440
Derek M. Bickhart is an academic researcher from Agricultural Research Service. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 36, co-authored 104 publications receiving 4642 citations. Previous affiliations of Derek M. Bickhart include United States Department of Agriculture & University of Connecticut.
Papers
More filters
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
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.
Philippe Normand,Pascal Lapierre,Louis S. Tisa,Johann Peter Gogarten,Nicole Alloisio,Emilie Bagnarol,Carla A. Bassi,Alison M. Berry,Derek M. Bickhart,Nathalie Choisne,Arnaud Couloux,Benoit Cournoyer,Stéphane Cruveiller,Vincent Daubin,Nadia Demange,Maria Pilar Francino,Eugene Goltsman,Ying Huang,Olga R. Kopp,Laurent Labarre,Alla Lapidus,Céline Lavire,J Maréchal,Michele Martinez,Juliana E. Mastronunzio,Beth C. Mullin,James Niemann,Pierre Pujic,Tania Rawnsley,Zoé Rouy,Chantal Schenowitz,Anita Sellstedt,Fernando Tavares,Jeffrey P. Tomkins,David Vallenet,Claudio Valverde,Luis Gabriel Wall,Ying Wang,Claudine Médigue,David R. Benson +39 more
TL;DR: The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses.
Journal ArticleDOI
De novo assembly of the cattle reference genome with single-molecule sequencing.
Benjamin D. Rosen,Derek M. Bickhart,Robert D. Schnabel,Sergey Koren,Christine G. Elsik,Elizabeth Tseng,Troy N. Rowan,Wai Yee Low,Aleksey V. Zimin,Christine Couldrey,Richard Hall,Wenli Li,Arang Rhie,Jay Ghurye,Stephanie D. McKay,Françoise Thibaud-Nissen,Jinna Hoffman,Brenda M. Murdoch,Warren M Snelling,Tara G. McDaneld,John A. Hammond,John C. Schwartz,Wilson Nandolo,Wilson Nandolo,Darren E. Hagen,Christian Dreischer,Sebastian J. Schultheiss,Steven G. Schroeder,Adam M. Phillippy,John B. Cole,Curtis P. Van Tassell,George E. Liu,Timothy P. L. Smith,Juan F. Medrano +33 more
TL;DR: It is demonstrated that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this 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
metaFlye: scalable long-read metagenome assembly using repeat graphs
Mikhail Kolmogorov,Derek M. Bickhart,Bahar Behsaz,Alexey Gurevich,Mikhail Rayko,Sung Bong Shin,Kristen L. Kuhn,Jeffrey Yuan,Evgeny Polevikov,Timothy P. L. Smith,Pavel A. Pevzner +10 more
TL;DR: MetaFlye is presented, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity, and benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long- read assemblers.