Jonathan Eisen

Summary

Affiliation: UC Davis
Location: Davis, USA
URL: http://phylogenomics.wordpress.com

Publications

  1. pmc Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T))
    Iain Anderson
    DOE Joint Genome Institute, Walnut Creek, California, USA
    Stand Genomic Sci 6:1-13. 2012
  2. pmc Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing
    Patrick M Shih
    US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
    Proc Natl Acad Sci U S A 110:1053-8. 2013
  3. pmc Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance
    Steven W Kembel
    Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
    PLoS Comput Biol 8:e1002743. 2012
  4. pmc Gene conservation among endospore-forming bacteria reveals additional sporulation genes in Bacillus subtilis
    Bjorn A Traag
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
    J Bacteriol 195:253-60. 2013
  5. pmc Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource
    Thomas J Sharpton
    The J David Gladstone Institutes, University of California San Francisco, San Francisco, CA 94158, USA
    BMC Bioinformatics 13:264. 2012
  6. pmc Functional biogeography of ocean microbes revealed through non-negative matrix factorization
    Xingpeng Jiang
    College of Information Science and Technology, Drexel University, Philadelphia, Pennsylvania, USA
    PLoS ONE 7:e43866. 2012
  7. ncbi Genome of Geobacter sulfurreducens: metal reduction in subsurface environments
    B A Methé
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 302:1967-9. 2003
  8. ncbi Phylogenomics: intersection of evolution and genomics
    Jonathan A Eisen
    Institute for Genomic Research, Rockville, MD 20850, USA
    Science 300:1706-7. 2003
  9. ncbi The age of the Arabidopsis thaliana genome duplication
    Maria D Ermolaeva
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Plant Mol Biol 51:859-66. 2003
  10. pmc Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis
    David Alland
    Department of Medicine, Center for Emerging Pathogens, New Jersey Medical School, Newark, New Jersey 07103, USA
    J Bacteriol 185:3392-9. 2003

Collaborators

Detail Information

Publications63

  1. pmc Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T))
    Iain Anderson
    DOE Joint Genome Institute, Walnut Creek, California, USA
    Stand Genomic Sci 6:1-13. 2012
    ..acidophilus. The genome, which consists of one chromosome and one plasmid with a total size of 3,557,831 bp harbors 3,626 protein-coding and 69 RNA genes, and is a part of the GenomicEncyclopedia ofBacteria andArchaea project...
  2. pmc Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing
    Patrick M Shih
    US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
    Proc Natl Acad Sci U S A 110:1053-8. 2013
    ..Given the exponentially growing number of sequenced genomes, this diversity-driven study demonstrates the perspective gained by comparing disparate yet related genomes in a phylum-wide context and the insights that are gained from it...
  3. pmc Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance
    Steven W Kembel
    Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
    PLoS Comput Biol 8:e1002743. 2012
    ..Our approach will allow microbial ecologists to make more accurate inferences about microbial diversity and abundance based on 16S sequence data...
  4. pmc Gene conservation among endospore-forming bacteria reveals additional sporulation genes in Bacillus subtilis
    Bjorn A Traag
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
    J Bacteriol 195:253-60. 2013
    ..This work demonstrates the power of combining phylogenetic profiling with reverse genetics and gene-regulatory studies to identify unrecognized genes that contribute to a conserved developmental process...
  5. pmc Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource
    Thomas J Sharpton
    The J David Gladstone Institutes, University of California San Francisco, San Francisco, CA 94158, USA
    BMC Bioinformatics 13:264. 2012
    ..We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences...
  6. pmc Functional biogeography of ocean microbes revealed through non-negative matrix factorization
    Xingpeng Jiang
    College of Information Science and Technology, Drexel University, Philadelphia, Pennsylvania, USA
    PLoS ONE 7:e43866. 2012
    ..We conclude by discussing how NMF, and other dimension reduction methods, can help enable a macroscopic functional description of marine ecosystems...
  7. ncbi Genome of Geobacter sulfurreducens: metal reduction in subsurface environments
    B A Methé
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 302:1967-9. 2003
    ..As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity...
  8. ncbi Phylogenomics: intersection of evolution and genomics
    Jonathan A Eisen
    Institute for Genomic Research, Rockville, MD 20850, USA
    Science 300:1706-7. 2003
    ..Much has been gained from genomic and evolutionary studies of species. Combining the perspectives of these different approaches suggests that an integrated phylogenomic approach will be beneficial...
  9. ncbi The age of the Arabidopsis thaliana genome duplication
    Maria D Ermolaeva
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Plant Mol Biol 51:859-66. 2003
    ..In each case, our estimate places the age of the genome duplication as significantly younger than previously reported...
  10. pmc Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis
    David Alland
    Department of Medicine, Center for Emerging Pathogens, New Jersey Medical School, Newark, New Jersey 07103, USA
    J Bacteriol 185:3392-9. 2003
    ..Finally, we present population-based evidence that KasA, an important component of mycolic acid biosynthesis, develops G312S polymorphisms under selective pressure...
  11. ncbi Phylogenetic analysis and gene functional predictions: phylogenomics in action
    Jonathan A Eisen
    Department of Microbial Genomics, The Instiute for Genomic Research, Rockville, Maryland 20850, USA
    Theor Popul Biol 61:481-7. 2002
    ..Examples that are discussed include phylogenetic determination of orthology, the use of character state reconstruction analysis of gene function, and evolutionary analysis of rates and patterns of gene evolution...
  12. ncbi Microbial genes in the human genome: lateral transfer or gene loss?
    S L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 292:1903-6. 2001
    ..Gene loss combined with sample size effects and evolutionary rate variation provide an alternative, more biologically plausible explanation...
  13. pmc Evidence for symmetric chromosomal inversions around the replication origin in bacteria
    J A Eisen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 1:RESEARCH0011. 2000
    ..Until recently, however, comparisons were mainly possible only between distantly related species. Complete genome sequences are now becoming available from multiple sets of closely related strains or species...
  14. ncbi Environmental genome shotgun sequencing of the Sargasso Sea
    J Craig Venter
    Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
    Science 304:66-74. 2004
    ..2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity...
  15. pmc Comparative genomics of emerging human ehrlichiosis agents
    Julie C Dunning Hotopp
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Genet 2:e21. 2006
    ..These discoveries provide significant insights into the biology of these obligate intracellular pathogens...
  16. pmc The genome sequence of Methanohalophilus mahii SLP(T) reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments
    Stefan Spring
    DSMZ German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
    Archaea 2010:690737. 2010
    ..A comparison of the reconstructed energy metabolism in the halophilic species Mhp. mahii with other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species...
  17. pmc The complete genome sequence of Haloferax volcanii DS2, a model archaeon
    Amber L Hartman
    Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
    PLoS ONE 5:e9605. 2010
    ..This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general...
  18. pmc Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications
    Jorge Valdes
    Center for Bioinformatics and Genome Biology, Fundación Ciencia para la Vida, Facultad de Ciencias de la Salud, Universidad Andres Bello, Santiago, Chile
    BMC Genomics 9:597. 2008
    ..Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism...
  19. pmc An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP)
    Dongying Wu
    UC Davis Genome Center, University of California Davis, Davis, California, United States of America
    PLoS ONE 3:e2566. 2008
    ..Most importantly, this automated process yields results comparable to those achievable by manual analysis, yet offers speed and capacity that are unattainable by manual efforts...
  20. pmc Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes
    Jonathan A Eisen
    University of California Davis Genome Center, Section of Evolution and Ecology and the Department of Medical Microbiology and Immunology, Davis, California, United States of America
    PLoS Biol 5:e82. 2007
  21. 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...
  22. pmc Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote
    Jonathan A Eisen
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Biol 4:e286. 2006
    ..thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance...
  23. pmc Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions
    J A Eisen
    Department of Biological Sciences, Stanford University, CA 94305 5020, USA
    Nucleic Acids Res 23:2715-23. 1995
    ..We discuss possible implications of this evolutionary analysis on the general properties and evolution of the SNF2 family...
  24. pmc Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence
    Chris M Rands
    Department of Physiology, Anatomy, and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, OX1 3PT, UK
    BMC Genomics 14:95. 2013
    ..Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris...