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Genomes and GenesSpecies | Jonathan A EisenSummaryAffiliation: University of California Country: USA Publications
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Publications
Badomics words and the power and peril of the ome-memeJonathan A Eisen
Genome Center, University of California, Davis, CA, USA
Gigascience 1:6. 2012..I focus on a bad aspect of this spread the use of what I refer to as "badomics" words. I discuss why these should be considered bad and how to distinguish badomics words from good ones...
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...- A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitansMircea Podar
Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
Genome Biol 9:R158. 2008..Little is known about the mechanisms that enable this relationship... - Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applicationsJorge 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... - 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... - 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 - 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... 
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...- The complete genome sequence of Haloferax volcanii DS2, a model archaeonAmber 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... - 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... - 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 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... - 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.... - 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 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.... - Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseumDongying Wu
University of California Davis Genome Center, Davis, California, USA
PLoS ONE 4:e4207. 2009..Analyses of published metagenomic sequences from two hot springs similar to the one from which this strain was isolated, show that close relatives of T. roseum DSM 5159 are present but have some key differences from the strain sequenced... - 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... - 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... - 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... - Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic treesDongying Wu
Department of Evolution and Ecology, University of California Davis Genome Center, University of California Davis, Davis, California, United States of America
PLoS ONE 6:e18011. 2011..Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of 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... - 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.... - 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... - 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... - Assembling the marine metagenome, one cell at a timeTanja Woyke
DOE Joint Genome Institute, Walnut Creek, California, United States of America
PLoS ONE 4:e5299. 2009..A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa... - 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... - Yeast communities of diverse Drosophila species: comparison of two symbiont groups in the same hostsJames Angus Chandler
Department of Evolution and Ecology and Center for Population Biology, University of California Davis, Davis, California, USA
Appl Environ Microbiol 78:7327-36. 2012..Future work on the role of symbiont communities in animal physiology, ecological adaptation, and evolution would benefit from a similarly holistic approach... - An integrated pipeline for de novo assembly of microbial genomesAndrew Tritt
Genome Center, University of California Davis, Davis, California, United States of America
PLoS ONE 7:e42304. 2012..Finally, A5 has modest compute requirements, and can assemble a typical bacterial genome on current desktop or laptop computer hardware in under two hours, depending on depth of coverage... - Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequencesAmber L Hartman
Department of Medical Microbiology and Immunology, Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
BMC Bioinformatics 11:317. 2010..As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly... - 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... - A simple, fast, and accurate method of phylogenomic inferenceMartin Wu
Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
Genome Biol 9:R151. 2008.... - 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 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.... - Drivers of bacterial beta-diversity depend on spatial scaleJennifer B H Martiny
Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
Proc Natl Acad Sci U S A 108:7850-4. 2011..These results highlight the importance of considering multiple spatial scales for understanding microbial biogeography... - 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 - 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... - 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... - BioTorrents: a file sharing service for scientific dataMorgan G I Langille
Genome Center, University of California Davis, Davis, California, United States of America
PLoS ONE 5:e10071. 2010..BioTorrents contains multiple features, including keyword searching, category browsing, RSS feeds, torrent comments, and a discussion forum. BioTorrents is available at http://www.biotorrents.net... - Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria)Zachary A Bendiks
University of California at Davis, Genome Center, Davis, California, USA
Genome Announc 1:e0012013. 2013..The assembly contains 3,746,321 bp (in 8 scaffolds). This strain was isolated from a residential toilet as part of an undergraduate student research project to sequence reference genomes of microbes from the built environment... - Bacterial communities of diverse Drosophila species: ecological context of a host-microbe model systemJames Angus Chandler
Center for Population Biology, Department of Evolution and Ecology, University of California Davis, Davis, California, USA
PLoS Genet 7:e1002272. 2011..Bacterial taxa used in experimental studies are rare or absent in wild Drosophila populations, while the most abundant associates of natural Drosophila populations are rare in the lab... - Mauve assembly metricsAaron E Darling
Genome Center, University of California Davis, Davis, CA 95616, USA
Bioinformatics 27:2756-7. 2011.... - 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... - 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... - PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic dataThomas J Sharpton
The J David Gladstone Institutes, University of California San Francisco, San Francisco, California, United States of America
PLoS Comput Biol 7:e1001061. 2011..Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity?.. - 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... - 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... - Draft Genome Sequence of an Actinobacterium, Brachybacterium muris Strain UCD-AY4Jonathon R Lo
University of California at Davis, Genome Center, Davis, California, USA
Genome Announc 1:e0008613. 2013..The assembly contains 3,257,338 bp and has a GC content of 70%. This strain was isolated from a residential bath towel and has a 16S rRNA gene 99.7% identical to that of the original B. muris strain, C3H-21... - 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... - 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.... - 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... - 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... - 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... - 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... - 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... - Brouhaha over the other yeastJonathan A Eisen
Nature 415:845-8. 2002 - Unsuspected diversity among marine aerobic anoxygenic phototrophsOded Beja
Monterey Bay Aquarium Research Institute, Moss Landing, California 95039 0628, USA
Nature 415:630-3. 2002.... - 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... - 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