D
Dongying Wu
Researcher at Joint Genome Institute
Publications - 22
Citations - 8614
Dongying Wu is an academic researcher from Joint Genome Institute. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 15, co-authored 17 publications receiving 7813 citations. Previous affiliations of Dongying Wu include J. Craig Venter Institute.
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Journal ArticleDOI
Environmental Genome Shotgun Sequencing of the Sargasso Sea
J. Craig Venter,Karin A. Remington,John F. Heidelberg,Aaron L. Halpern,Doug Rusch,Jonathan A. Eisen,Dongying Wu,Ian T. Paulsen,Karen E. Nelson,William C. Nelson,Derrick E. Fouts,Samuel Levy,Anthony H. Knap,Michael W. Lomas,Kenneth H. Nealson,Owen White,Jeremy Peterson,Jeff Hoffman,Rachel Parsons,Holly Baden-Tillson,Cynthia Pfannkoch,Yu-Hui Rogers,Hamilton O. Smith +22 more
TL;DR: Over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors are identified, suggesting substantial oceanic microbial diversity.
Journal ArticleDOI
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote
Jonathan A. Eisen,Robert S. Coyne,Martin Wu,Dongying Wu,Mathangi Thiagarajan,Jennifer R. Wortman,Jonathan H. Badger,Qinghu Ren,Paolo Amedeo,Kristie M. Jones,Luke J. Tallon,Arthur L. Delcher,Steven L. Salzberg,Joana C. Silva,Brian J. Haas,William H. Majoros,Maryam Farzad,Jane M. Carlton,Jane M. Carlton,Roger Smith,Jyoti Garg,Ronald E. Pearlman,Kathleen M Karrer,Lei Sun,Gerard Manning,Nels C. Elde,Aaron P. Turkewitz,David J. Asai,David E. Wilkes,Yufeng Wang,Hong-Hong Cai,Kathleen E Collins,B. Andrew Stewart,Suzanne R. Lee,Katarzyna Wilamowska,Zasha Weinberg,Walter L. Ruzzo,Dorota Wloga,Jacek Gaertig,Joseph Frankel,Che-Chia Tsao,Martin A. Gorovsky,Patrick J. Keeling,Ross F. Waller,Nicola J. Patron,J. Michael Cherry,Nicholas A. Stover,Cynthia J. Krieger,Christina del Toro,Hilary F. Ryder,Sondra Williamson,Rebecca A Barbeau,Eileen P. Hamilton,Eduardo Orias +53 more
TL;DR: The T. thermophila genome has been used for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance as mentioned in this paper, and it has been shown that the excision of DNA from the MIC to generate the macronucleus specifically targets foreign DNA as a form of genome self-defense.
Journal ArticleDOI
Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing
Patrick M. Shih,Patrick M. Shih,Dongying Wu,Amel Latifi,Seth D. Axen,David P. Fewer,Emmanuel Talla,Alexandra Calteau,Fei Cai,Nicole Tandeau de Marsac,Rosmarie Rippka,Michael Herdman,Kaarina Sivonen,Thérèse Coursin,Thierry Laurent,Lynne Goodwin,Matt Nolan,Karen W. Davenport,Cliff Han,Edward M. Rubin,Jonathan A. Eisen,Tanja Woyke,Muriel Gugger,Cheryl A. Kerfeld,Cheryl A. Kerfeld +24 more
TL;DR: This phylum-wide study highlights the benefits of diversity-driven genome sequencing, identifying more than 21,000 cyanobacterial proteins with no detectable similarity to known proteins, and foregrounds the diversity of light-harvesting proteins and gene clusters for secondary metabolite biosynthesis.
Journal ArticleDOI
Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments
Barbara A. Methé,Karen E. Nelson,Jonathan A. Eisen,Ian T. Paulsen,William C. Nelson,John F. Heidelberg,Dongying Wu,Martin Wu,Naomi L. Ward,Maureen J. Beanan,Robert J. Dodson,R. Madupu,Lauren M. Brinkac,Sean C. Daugherty,Robert T. DeBoy,Anthony S. Durkin,Michelle L. Gwinn,James F. Kolonay,Steven A. Sullivan,Daniel H. Haft,Jeremy D. Selengut,Tanja M. Davidsen,Nikhat Zafar,Owen White,Bao Tran,Claudia M. Romero,Heather Forberger,J. Weidman,H. Khouri,Tamara Feldblyum,T. Utterback,S. van Aken,Derek R. Lovley,Claire M. Fraser +33 more
TL;DR: The complete genome sequence of Geobacter sulfurreducens, a δ-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior, which suggest the organism has the potential for use in bioremediation of radioactive metals and in the generation of electricity.
Journal ArticleDOI
Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters
Dongying Wu,Sean C. Daugherty,Susan Van Aken,Grace Pai,Kisha Watkins,Hoda Khouri,Luke J. Tallon,Jennifer Zaborsky,Helen E. Dunbar,Phat L. Tran,Nancy A. Moran,Jonathan A. Eisen +11 more
TL;DR: This study, which to the authors' knowledge is the first genomic analysis of an obligate symbiosis involving multiple partners, suggests striking complementarity in the biosynthetic capabilities of the two symbionts: B. cicadellinicola and S. muelleri, both isolated from H. coagulata.