Shibu Yooseph

Summary

Affiliation: J. Craig Venter Institute
Country: USA

Publications

  1. pmc The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families
    Shibu Yooseph
    J Craig Venter Institute, Rockville, Maryland, United States of America
    PLoS Biol 5:e16. 2007
  2. pmc The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific
    Douglas B Rusch
    J Craig Venter Institute, Rockville, Maryland, United States of America
    PLoS Biol 5:e77. 2007
  3. pmc The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples
    Shannon J Williamson
    J Craig Venter Institute, Rockville, Maryland, USA
    PLoS ONE 3:e1456. 2008
  4. doi request reprint Genomic and functional adaptation in surface ocean planktonic prokaryotes
    Shibu Yooseph
    J Craig Venter Institute, Rockville, Maryland 20850, USA
    Nature 468:60-6. 2010
  5. pmc Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering
    Shibu Yooseph
    J, Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    BMC Bioinformatics 9:182. 2008
  6. pmc A metagenomic framework for the study of airborne microbial communities
    Shibu Yooseph
    Informatics, J Craig Venter Institute, San Diego, California, United States of America
    PLoS ONE 8:e81862. 2013
  7. pmc Metagenomic exploration of viruses throughout the Indian Ocean
    Shannon J Williamson
    Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, California, USA
    PLoS ONE 7:e42047. 2012
  8. pmc Functional tradeoffs underpin salinity-driven divergence in microbial community composition
    Chris L Dupont
    Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, California, United States of America
    PLoS ONE 9:e89549. 2014
  9. pmc Comparative genome analysis of 19 Ureaplasma urealyticum and Ureaplasma parvum strains
    Vanya Paralanov
    J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    BMC Microbiol 12:88. 2012
  10. pmc Analyses of the microbial diversity across the human microbiome
    Kelvin Li
    J Craig Venter Institute, Rockville, Maryland, United States of America
    PLoS ONE 7:e32118. 2012

Detail Information

Publications19

  1. pmc The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families
    Shibu 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...
  2. pmc The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific
    Douglas 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...
  3. pmc The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples
    Shannon J Williamson
    J Craig Venter Institute, Rockville, Maryland, USA
    PLoS ONE 3:e1456. 2008
    ....
  4. doi request reprint Genomic and functional adaptation in surface ocean planktonic prokaryotes
    Shibu 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...
  5. pmc Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering
    Shibu 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...
  6. pmc A metagenomic framework for the study of airborne microbial communities
    Shibu Yooseph
    Informatics, J Craig Venter Institute, San Diego, California, United States of America
    PLoS ONE 8:e81862. 2013
    ..The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria. ..
  7. pmc Metagenomic exploration of viruses throughout the Indian Ocean
    Shannon 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...
  8. pmc Functional tradeoffs underpin salinity-driven divergence in microbial community composition
    Chris L Dupont
    Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, California, United States of America
    PLoS ONE 9:e89549. 2014
    ..These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity. ..
  9. pmc Comparative genome analysis of 19 Ureaplasma urealyticum and Ureaplasma parvum strains
    Vanya Paralanov
    J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    BMC Microbiol 12:88. 2012
    ....
  10. pmc Analyses of the microbial diversity across the human microbiome
    Kelvin Li
    J Craig Venter Institute, Rockville, Maryland, United States of America
    PLoS ONE 7:e32118. 2012
    ....
  11. pmc Discovery of [NiFe] hydrogenase genes in metagenomic DNA: cloning and heterologous expression in Thiocapsa roseopersicina
    Gergely 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...
  12. ncbi request reprint Zinc finger gene clusters and tandem gene duplication
    Mengxiang 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...
  13. ncbi request reprint ThurGood: evaluating assembly-to-assembly mapping
    Hagit 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)...
  14. ncbi request reprint A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome
    Richard J Mural
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 296:1661-71. 2002
    ....
  15. ncbi request reprint Viral photosynthetic reaction center genes and transcripts in the marine environment
    Itai 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...
  16. ncbi request reprint A note on efficient computation of haplotypes via perfect phylogeny
    Vineet 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)...
  17. pmc Whole-genome shotgun assembly and comparison of human genome assemblies
    Sorin 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...
  18. ncbi request reprint Haplotyping as perfect phylogeny: a direct approach
    Vineet Bafna
    The Center for Advancement of Genomics, 1901 Research Blvd, 6th Floor, Rockville, MD 20850, USA
    J Comput Biol 10:323-40. 2003
    ....
  19. pmc Evolution of allostery in the cyclic nucleotide binding module
    Natarajan 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...