J
Jarrod Chapman
Researcher at Lawrence Berkeley National Laboratory
Publications - 12
Citations - 5824
Jarrod Chapman is an academic researcher from Lawrence Berkeley National Laboratory. The author has contributed to research in topics: Genome & Shotgun sequencing. The author has an hindex of 9, co-authored 12 publications receiving 5497 citations. Previous affiliations of Jarrod Chapman include University of California, Berkeley & Joint Genome Institute.
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Journal ArticleDOI
Community structure and metabolism through reconstruction of microbial genomes from the environment
Gene W. Tyson,Jarrod Chapman,Jarrod Chapman,Philip Hugenholtz,Eric E. Allen,Rachna J. Ram,Paul G. Richardson,Victor V. Solovyev,Edward M. Rubin,Daniel S. Rokhsar,Daniel S. Rokhsar,Jillian F. Banfield +11 more
TL;DR: Reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II and analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.
Journal ArticleDOI
Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes
Samuel Aparicio,Jarrod Chapman,Elia Stupka,Nik Putnam,Jer Ming Chia,Paramvir S. Dehal,Alan Christoffels,Sam Rash,Shawn Hoon,Arian F.A. Smit,Maarten D. Sollewijn Gelpke,Jared C. Roach,Tania Oh,Isaac Ho,Marie Wong,Chris Detter,Frans Verhoef,Paul Predki,Alice Tay,Susan Lucas,Paul G. Richardson,Sarah Smith,Melody S. Clark,Yvonne J. K. Edwards,Norman A. Doggett,Andrey Zharkikh,Sean V. Tavtigian,Dmitry Pruss,Mary Barnstead,Cheryl Evans,Holly Baden,Justin Powell,Gustavo Glusman,Lee Rowen,Leroy Hood,Y. H. Tan,Greg Elgar,Trevor Hawkins,Byrappa Venkatesh,Daniel S. Rokhsar,Sydney Brenner +40 more
TL;DR: The Fugu rubripes genome has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds as discussed by the authors.
Journal ArticleDOI
Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis
Brett M. Tyler,Sucheta Tripathy,Xuemin Zhang,Paramvir S. Dehal,Paramvir S. Dehal,Rays H. Y. Jiang,Rays H. Y. Jiang,Andrea Aerts,Andrea Aerts,Felipe D. Arredondo,Laura Baxter,Douda Bensasson,Douda Bensasson,Douda Bensasson,Jim Beynon,Jarrod Chapman,Jarrod Chapman,Jarrod Chapman,C. M. B. Damasceno,Anne E. Dorrance,Daolong Dou,Allan W. Dickerman,Inna Dubchak,Inna Dubchak,Matteo Garbelotto,Mark Gijzen,Stuart G. Gordon,Francine Govers,Niklaus J. Grünwald,Wayne Huang,Wayne Huang,Kelly Ivors,Kelly Ivors,Richard W. Jones,Sophien Kamoun,Konstantinos Krampis,Kurt Lamour,Mi-Kyung Lee,W. Hayes McDonald,MoÌnica Medina,Harold J. G. Meijer,Eric K. Nordberg,Donald J. Maclean,Manuel D. Ospina-Giraldo,Paul Morris,Vipaporn Phuntumart,Nicholas H. Putnam,Nicholas H. Putnam,Sam Rash,Sam Rash,Jocelyn K. C. Rose,Yasuko Sakihama,Asaf Salamov,Asaf Salamov,Alon Savidor,Chantel F. Scheuring,Brian M. Smith,Bruno W. S. Sobral,Astrid Terry,Astrid Terry,Trudy Torto-Alalibo,Joe Win,Zhanyou Xu,Hong-Bin Zhang,Igor V. Grigoriev,Igor V. Grigoriev,Daniel S. Rokhsar,Daniel S. Rokhsar,Jeffrey L. Boore +68 more
TL;DR: Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.
Journal ArticleDOI
Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78
Diego Martinez,Luis F. Larrondo,Nik Putnam,Nik Putnam,Maarten D. Sollewijn Gelpke,Katherine H. Huang,Jarrod Chapman,Jarrod Chapman,Kevin G. Helfenbein,Preethi Ramaiya,J. Chris Detter,Frank W. Larimer,Pedro M. Coutinho,Bernard Henrissat,Randy M. Berka,Dan Cullen,Daniel S. Rokhsar +16 more
TL;DR: The sequenced genome of Phanerochaete chrysosporium strain RP78 reveals an impressive array of genes encoding secreted oxidases, peroxidases and hydrolytic enzymes that cooperate in wood decay, and provides a framework for further development of bioprocesses for biomass utilization, organopollutant degradation and fiber bleaching.
Proceedings ArticleDOI
Parallel de bruijn graph construction and traversal for de novo genome assembly
Evangelos Georganas,Aydin Buluc,Jarrod Chapman,Leonid Oliker,Daniel S. Rokhsar,Katherine Yelick +5 more
TL;DR: A novel algorithm is provided that leverages one-sided communication capabilities of the Unified Parallel C (UPC) to facilitate the requisite fine-grained parallelism and avoidance of data hazards, while analytically proving its scalability properties.