Research Topics
| Jonathan EisenSummaryAffiliation: The Institute for Genomic Research Country: USA Publications
Research Grants
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Detail Information
Publications
Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elementsMartin 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...
A phylogenomic study of DNA repair genes, proteins, and processesJ 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...
Assessing evolutionary relationships among microbes from whole-genome analysisJ 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...- Horizontal gene transfer among microbial genomes: new insights from complete genome analysisJ 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... - Evidence for symmetric chromosomal inversions around the replication origin in bacteriaJ 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... - Phylogenomics: intersection of evolution and genomicsJonathan 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... - The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacteriumJonathan 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... - Phylogenetic analysis and gene functional predictions: phylogenomics in actionJonathan 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... - Environmental genome shotgun sequencing of the Sargasso SeaJ 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... - Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensisJohn F Heidelberg
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Nat Biotechnol 20:1118-23. 2002.... - Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshootersDongying Wu
The Institute for Genomic Research, Rockville, Maryland, USA
PLoS Biol 4:e188. 2006..coagulata and other sharpshooters serve as vectors of transmission... - Gene synteny and evolution of genome architecture in trypanosomatidsElodie 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... - Comparative genomics of emerging human ehrlichiosis agentsJulie 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... - Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901Martin Wu
The Institute for Genomic Research, Rockville, Maryland, United States of America
PLoS Genet 1:e65. 2005.... - Genome sequence of the human malaria parasite Plasmodium falciparumMalcolm 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... - Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomesRekha 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.... - The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris HildenboroughJohn F Heidelberg
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Nat Biotechnol 22:554-9. 2004.... - 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... - Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenesRekha 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... - Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and CaulobacteralesJonathan 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... - Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83Karen 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... - Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiaeHerve 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... - The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbiontsIan 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... - The age of the Arabidopsis thaliana genome duplicationMaria 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... - The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteriaTimothy 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... - 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 - New evolutionary frontiers from unusual virus genomesChristopher 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... - Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryoteJonathan 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... - Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistanceMasashi 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... - Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamountsKevin 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... - Complete genome sequence of the Q-fever pathogen Coxiella burnetiiRekha 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... - Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closureRobert S Coyne
J Craig Venter Institute formerly The Institute for Genomic Research, 9704 Medical Center Dr, Rockville, MD, USA
BMC Genomics 9:562. 2008.... - Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environmentMary 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... - Unsuspected diversity among marine aerobic anoxygenic phototrophsOded Beja
Monterey Bay Aquarium Research Institute, Moss Landing, California 95039 0628, USA
Nature 415:630-3. 2002.... - Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio sppTracy 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... - 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... - Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesisDavid 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... - Identification of a fourth family of lycopene cyclases in photosynthetic bacteriaJulia 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... - Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbesJonathan 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 - Genetic and physical mapping of DNA replication origins in Haloferax volcaniiCedric 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... - 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... - Use of HAPPY mapping for the higher order assembly of the Tetrahymena genomeEileen 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.... - Brouhaha over the other yeastJonathan A Eisen
Nature 415:845-8. 2002 - Comparative studies of resistin expression and phylogenomics in human and mouseRong 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... - Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patellaEric 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... - A cut above: discovery of an alternative excision repair pathway in bacteriaBennett 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 - Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophageEric 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... - 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...
Research Grants
- Tetrahymena Genome Sequencing ProjectJonathan Eisen; Fiscal Year: 2005....