Research Topics
| Shibu YoosephSummaryAffiliation: J. Craig Venter Institute Country: USA Publications
| Collaborators
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Detail Information
Publications
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein familiesShibu Yooseph
J Craig Venter Institute, Rockville, Maryland, United States of America
PLoS Biol 5:e16. 2007..Our analysis indicates that new families are being discovered at a rate that is linear or almost linear with the addition of new sequences, implying that we are still far from discovering all protein families in nature...- The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samplesShannon J Williamson
J Craig Venter Institute, Rockville, Maryland, USA
PLoS ONE 3:e1456. 2008.... - The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical PacificDouglas B Rusch
J Craig Venter Institute, Rockville, Maryland, United States of America
PLoS Biol 5:e77. 2007..Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS... 
Genomic and functional adaptation in surface ocean planktonic prokaryotesShibu Yooseph
J Craig Venter Institute, Rockville, Maryland 20850, USA
Nature 468:60-6. 2010..Their genomic features also lead us to propose that one method used to avoid predation by viruses and/or bacterivores is by means of slow growth and the maintenance of low biomass...- Gene identification and protein classification in microbial metagenomic sequence data via incremental clusteringShibu Yooseph
J, Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
BMC Bioinformatics 9:182. 2008..and consequently gene identification is challenging. The vast amount of sequence data also requires faster protein family classification tools... - Metagenomic exploration of viruses throughout the Indian OceanShannon J Williamson
Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, California, USA
PLoS ONE 7:e42047. 2012..This is the first study to holistically explore virioplankton dynamics across multiple size classes and provides unprecedented insight into virus diversity, metabolic potential and virus-host interactions... - Analyses of the microbial diversity across the human microbiomeKelvin Li
J Craig Venter Institute, Rockville, Maryland, United States of America
PLoS ONE 7:e32118. 2012.... - Discovery of [NiFe] hydrogenase genes in metagenomic DNA: cloning and heterologous expression in Thiocapsa roseopersicinaGergely Maroti
J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
Appl Environ Microbiol 75:5821-30. 2009..It also provides a model for functionally analyzing novel enzymes from environmental microbes in a culture-independent manner... 
Zinc finger gene clusters and tandem gene duplicationMengxiang Tang
ACLARA BioSciences, 1288 Pear Street, Mountain View, CA 94043, USA
J Comput Biol 9:429-46. 2002..We provide algorithms to reconstruct a duplication model for a given data set. We use our method to hypothesize the series of duplication events that may have produced the ZNF45 family that appears on human chromosome 19...- ThurGood: evaluating assembly-to-assembly mappingHagit Shatkay
School of Computing, Queen s University, Kingston, Ontario, Canada
J Comput Biol 11:800-11. 2004..These tools have already proved useful in the evaluation and ranking of several methods for assembly-to-assembly mapping, which were recently used to map multiple versions of the human genome to each other (Istrail et aL, 2004)... - A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genomeRichard J Mural
Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
Science 296:1661-71. 2002.... - Evolution of allostery in the cyclic nucleotide binding moduleNatarajan Kannan
Department of Chemistry and Biochemistry, University of California, Gilman Drive, La Jolla, California 92093 0654, USA
Genome Biol 8:R264. 2007..In this study, we analyze the evolutionary information embedded in genomic sequences to explore the diversity of signaling through the CNB domain and also how the CNB domain elicits a cellular response upon binding to cAMP... - A note on efficient computation of haplotypes via perfect phylogenyVineet Bafna
Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
J Comput Biol 11:858-66. 2004..For the second problem of computing a PPH solution that minimizes the number of distinct haplotypes, we show that the problem is NP-hard using a reduction from Vertex Cover (Garey and Johnson, 1979)... - Whole-genome shotgun assembly and comparison of human genome assembliesSorin Istrail
Applied Biosystems, 45 West Gude Drive, Rockville, MD 20850, USA
Proc Natl Acad Sci U S A 101:1916-21. 2004..The Celera results provide more order and orientation, and the consortium sequence provides better coverage of exact and nearly exact repeats... - Haplotyping as perfect phylogeny: a direct approachVineet Bafna
The Center for Advancement of Genomics, 1901 Research Blvd, 6th Floor, Rockville, MD 20850, USA
J Comput Biol 10:323-40. 2003.... - Viral photosynthetic reaction center genes and transcripts in the marine environmentItai Sharon
Faculty of Biology, Technion Israel Institute of Technology, Haifa, Israel
ISME J 1:492-501. 2007..Furthermore, we show that different viral psbA genes are expressed in the environment...