Jonathan Eisen

Summary

Affiliation: The Institute for Genomic Research
Country: USA

Publications

  1. pmc Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements
    Martin Wu
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 2:E69. 2004
  2. pmc A phylogenomic study of DNA repair genes, proteins, and processes
    J A Eisen
    Department of Biological Sciences, Stanford University, Stanford, CA 94305 5020, USA
    Mutat Res 435:171-213. 1999
  3. ncbi Assessing evolutionary relationships among microbes from whole-genome analysis
    J A Eisen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Curr Opin Microbiol 3:475-80. 2000
  4. ncbi Horizontal gene transfer among microbial genomes: new insights from complete genome analysis
    J A Eisen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Curr Opin Genet Dev 10:606-11. 2000
  5. 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
  6. ncbi Phylogenomics: intersection of evolution and genomics
    Jonathan A Eisen
    Institute for Genomic Research, Rockville, MD 20850, USA
    Science 300:1706-7. 2003
  7. pmc The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium
    Jonathan A Eisen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 99:9509-14. 2002
  8. 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
  9. 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
  10. ncbi Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis
    John F Heidelberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nat Biotechnol 20:1118-23. 2002

Research Grants

  1. Tetrahymena Genome Sequencing Project
    Jonathan Eisen; Fiscal Year: 2005

Detail Information

Publications48

  1. pmc Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements
    Martin Wu
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 2:E69. 2004
    ..With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections...
  2. pmc A phylogenomic study of DNA repair genes, proteins, and processes
    J A Eisen
    Department of Biological Sciences, Stanford University, Stanford, CA 94305 5020, USA
    Mutat Res 435:171-213. 1999
    ..We use this phylogenomic analysis to study the evolution of repair proteins and processes and to predict the repair phenotypes of those species for which we now know the complete genome sequence...
  3. ncbi Assessing evolutionary relationships among microbes from whole-genome analysis
    J A Eisen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Curr Opin Microbiol 3:475-80. 2000
    ..These include the determination of the first genome of a Crenarchaeota, the suggestion that horizontal gene transfer may be the rule rather than the exception, and revelations about how genomes evolve on short timescales...
  4. ncbi Horizontal gene transfer among microbial genomes: new insights from complete genome analysis
    J A Eisen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Curr Opin Genet Dev 10:606-11. 2000
    ..Many of these studies, however, rely on evidence that could be generated by forces other than gene transfer including selection, variable evolutionary rates, and biased sampling...
  5. 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...
  6. 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...
  7. pmc The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium
    Jonathan A Eisen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 99:9509-14. 2002
    ..tepidum and many Archaeal species...
  8. 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...
  9. 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...
  10. ncbi Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis
    John F Heidelberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nat Biotechnol 20:1118-23. 2002
    ....
  11. pmc Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters
    Dongying Wu
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 4:e188. 2006
    ..coagulata and other sharpshooters serve as vectors of transmission...
  12. ncbi Gene synteny and evolution of genome architecture in trypanosomatids
    Elodie Ghedin
    Parasity Genomics, The Institute for Genomics Research, 9712 Medical Center Dr Rockville, MD 20850, USA
    Mol Biochem Parasitol 134:183-91. 2004
    ..major by examining the regions near breakage points of the synteny. This is the first such element found in L. major suggesting that retroelements were found in the common ancestor of all three species...
  13. 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...
  14. pmc Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901
    Martin Wu
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Genet 1:e65. 2005
    ....
  15. ncbi Genome sequence of the human malaria parasite Plasmodium falciparum
    Malcolm J Gardner
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 419:498-511. 2002
    ..The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria...
  16. pmc Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes
    Rekha Seshadri
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:5646-51. 2004
    ....
  17. ncbi The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough
    John F Heidelberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nat Biotechnol 22:554-9. 2004
    ....
  18. pmc Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)
    Naomi Ward
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 2:e303. 2004
    ..We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential...
  19. ncbi Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes
    Rekha Seshadri
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 307:105-8. 2005
    ..Genome analysis provides insights into the organism's complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph...
  20. ncbi Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales
    Jonathan H Badger
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Int J Syst Evol Microbiol 55:1021-6. 2005
    ..The possible reasons why the 16S rRNA gene sequence gives conflicting results in this case are also discussed...
  21. pmc Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83
    Karen E Nelson
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 185:5591-601. 2003
    ..gingivalis can metabolize a range of amino acids and generate a number of metabolic end products that are toxic to the human host or human gingival tissue and contribute to the development of periodontal disease...
  22. pmc Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae
    Herve Tettelin
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 99:12391-6. 2002
    ..agalactiae strains from several serotypes using whole-genome microarrays, revealed the genetic heterogeneity among S. agalactiae strains, even of the same serotype, and provided insights into the evolution of virulence mechanisms...
  23. pmc The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts
    Ian T Paulsen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 99:13148-53. 2002
    ..A limited repertoire of genes homologous to known bacterial virulence factors were identified...
  24. 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...
  25. ncbi The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria
    Timothy D Read
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 423:81-6. 2003
    ..The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis...
  26. pmc The value of complete microbial genome sequencing (you get what you pay for)
    Claire M Fraser
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 184:6403-5; discusion 6405. 2002
  27. pmc New evolutionary frontiers from unusual virus genomes
    Christopher Desjardins
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20854, USA
    Genome Biol 6:212. 2005
    ..These and other unusual features challenge the way we view the evolution and definition of viruses...
  28. 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...
  29. pmc Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance
    Masashi Tanaka
    Department of Biological Sciences, Louisiana State University, Baton Rouge 70803, USA
    Genetics 168:21-33. 2004
    ..These characterizations clearly demonstrate that novel mechanisms significantly contribute to the ionizing radiation resistance in D. radiodurans...
  30. pmc Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts
    Kevin Penn
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Appl Environ Microbiol 72:1680-3. 2006
    ..More sampling is needed to understand the basis and significance of this variation...
  31. pmc Complete genome sequence of the Q-fever pathogen Coxiella burnetii
    Rekha Seshadri
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 100:5455-60. 2003
    ..burnetii genome. These analyses suggest that the obligate intracellular lifestyle of C. burnetii may be a relatively recent innovation...
  32. pmc Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure
    Robert S Coyne
    J Craig Venter Institute formerly The Institute for Genomic Research, 9704 Medical Center Dr, Rockville, MD, USA
    BMC Genomics 9:562. 2008
    ....
  33. ncbi Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment
    Mary Ann Moran
    Department of Marine Sciences, University of Georgia, Athens, Georgia 30602, USA
    Nature 432:910-3. 2004
    ..This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean...
  34. ncbi Unsuspected diversity among marine aerobic anoxygenic phototrophs
    Oded Beja
    Monterey Bay Aquarium Research Institute, Moss Landing, California 95039 0628, USA
    Nature 415:630-3. 2002
    ....
  35. pmc Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp
    Tracy H Hazen
    School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
    Appl Environ Microbiol 73:7703-10. 2007
    ..This study provides evidence of genetic exchange between Vibrio plasmids, phages, and chromosomes among diverse Vibrio spp...
  36. 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...
  37. 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...
  38. pmc Identification of a fourth family of lycopene cyclases in photosynthetic bacteria
    Julia A Maresca
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 104:11784-9. 2007
    ..Identification of these cyclases fills a major gap in the carotenoid biosynthetic pathways of green sulfur bacteria and cyanobacteria...
  39. 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
  40. pmc Genetic and physical mapping of DNA replication origins in Haloferax volcanii
    Cedric Norais
    Institut de Genetique et Microbiologie, Universite Paris Sud, Orsay, France
    PLoS Genet 3:e77. 2007
    ..Our observations also suggest that H. volcanii is an ideal organism for studying how replication of four replicons is regulated in the context of the archaeal cell cycle...
  41. pmc Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)
    Jim Leebens-Mack
    Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
    OMICS 10:231-7. 2006
    ..Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors...
  42. pmc Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome
    Eileen P Hamilton
    Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
    Genomics 88:443-51. 2006
    ....
  43. ncbi Brouhaha over the other yeast
    Jonathan A Eisen
    Nature 415:845-8. 2002
  44. ncbi Comparative studies of resistin expression and phylogenomics in human and mouse
    Rong Ze Yang
    Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
    Biochem Biophys Res Commun 310:927-35. 2003
    ..The high expression of resistin in human leukemia cells suggests a hitherto unidentified biological function of resistin in leukocytes...
  45. pmc Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella
    Eric W Schmidt
    Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
    Proc Natl Acad Sci U S A 102:7315-20. 2005
    ..In addition, a related cluster was identified in Trichodesmium erythraeum IMS101, an important bloom-forming cyanobacterium...
  46. pmc A cut above: discovery of an alternative excision repair pathway in bacteria
    Bennett Van Houten
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Proc Natl Acad Sci U S A 99:2581-3. 2002
  47. pmc Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage
    Eric S Miller
    Department of Microbiology, North Carolina State University, Raleigh, NC 27695 7615, USA
    J Bacteriol 185:5220-33. 2003
    ..Features of the KVP40 genome that distinguish it from T4 are presented, as well as those, such as the replication and virion gene clusters, that are substantially conserved...
  48. 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...

Research Grants5

  1. Tetrahymena Genome Sequencing Project
    Jonathan Eisen; Fiscal Year: 2005
    ....