Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment.
Moran MA (2004) Nature.Phylogenomics: intersection of evolution and genomics.
Eisen JA (2003) Science.WATERS: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences.
Hartman AL (2010) BMC Bioinformatics.The genome of the natural genetic engineer Agrobacterium tumefaciens C58.
Wood DW (2001) Science.Horizontal gene transfer among microbial genomes: new insights from complete genome analysis.
Eisen JA (2000) Curr Opin Genet Dev.The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.
Yooseph S (2007) PLoS Biol.Cloning and characterization of HARP/SMARCAL1: a prokaryotic HepA-related SNF2 helicase protein from human and mouse.
Coleman MA (2000) Genomics.Assessing evolutionary relationships among microbes from whole-genome analysis.
Eisen JA (2000) Curr Opin Microbiol.The age of the Arabidopsis thaliana genome duplication.
Ermolaeva MD (2003) Plant Mol Biol.Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis.
Eisen JA (1998) Genome Res.Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis.
Heidelberg JF (2002) Nat Biotechnol.Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon.
Dassarma S (2001) Photosynth Res.Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains.
Fleischmann RD (2002) J Bacteriol.Identification of a fourth family of lycopene cyclases in photosynthetic bacteria.
Maresca JA (2007) Proc Natl Acad Sci U S A.Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp.
Hazen TH (2007) Appl Environ Microbiol.Comparative genomics of emerging human ehrlichiosis agents.
Hotopp JC (2006) PLoS Genet.Complete genome sequence of Conexibacter woesei type strain (ID131577T).
Pukall Rüdiger (2010) Stand. Genomic Sci..Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum.
Wu D (2009) PLoS One.Unsuspected diversity among marine aerobic anoxygenic phototrophs.
Béjà O (2002) Nature.Genomics of emerging infectious disease: A PLoS collection.
Eisen JA (2009) PLoS Biol.Complete genome sequence of Neisseria meningitidis serogroup B strain MC58.
Tettelin H (2000) Science.Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis.
Alland D (2003) J Bacteriol.A simple, fast, and accurate method of phylogenomic inference.
Wu M (2008) Genome Biol.A cut above: discovery of an alternative excision repair pathway in bacteria.
Van Houten B (2002) Proc Natl Acad Sci U S A.A phylogenomic study of the MutS family of proteins.
Eisen JA (1998) Nucleic Acids Res.Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences.
Eisen JA (1994) Nucleic Acids Res.The complete genome sequence of Haloferax volcanii DS2, a model archaeon.
Hartman AL (2010) PLoS One.TIGRFAMs: a protein family resource for the functional identification of proteins.
Haft DH (2001) Nucleic Acids Res.Second gene for gonadotropin-releasing hormone in humans.
White RB (1998) Proc Natl Acad Sci U S A.Human gut microbiome adopts an alternative state following small bowel transplantation.
Hartman AL (2009) Proc Natl Acad Sci U S A.In silico-initiated cloning and molecular characterization of a novel human member of the L1 gene family of neural cell adhesion molecules.
Wei MH (1998) Hum Genet.Gastrogenomic delights: a movable feast.
Eisen JA (1997) Nat Med.Genome of Thermotoga maritima MSB8.
Nelson KE (2001) Methods Enzymol.Comparative studies of resistin expression and phylogenomics in human and mouse.
Yang RZ (2003) Biochem Biophys Res Commun.Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage.
Miller ES (2003) J Bacteriol.Sequence and analysis of the Arabidopsis genome.
Bevan M (2001) Curr Opin Plant Biol.Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath).
Ward N (2004) PLoS Biol.Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).
Leebens-Mack J (2006) OMICS.Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes.
Eisen JA (2007) PLoS Biol.The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria.
Read TD (2003) Nature.Evolution of sensory complexity recorded in a myxobacterial genome.
Goldman BS (2006) Proc Natl Acad Sci U S A.Environmental genome shotgun sequencing of the Sargasso Sea.
Venter JC (2004) Science.Microbial genes in the human genome: lateral transfer or gene loss?.
Salzberg SL (2001) Science.New evolutionary frontiers from unusual virus genomes.
Desjardins C (2005) Genome Biol.DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.
Heidelberg JF (2000) Nature.A phylogenomic study of DNA repair genes, proteins, and processes.
Eisen JA (1999) Mutat Res.Phylogenetic analysis and gene functional predictions: phylogenomics in action.
Eisen JA (2002) Theor Popul Biol.Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters.
Wu D (2006) PLoS Biol.Metagenomic sequencing of an in vitro-simulated microbial community.
Morgan JL (2010) PLoS One.Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83.
Nelson KE (2003) J Bacteriol.Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.
Eisen JA (2006) PLoS Biol.Genome sequence of the human malaria parasite Plasmodium falciparum.
Gardner MJ (2002) Nature.Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements.
Wu M (2004) PLoS Biol.Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes.
Seshadri R (2004) Proc Natl Acad Sci U S A.recA mutations that reduce the constitutive coprotease activity of the RecA1202(Prtc) protein: possible involvement of interfilament association in proteolytic and recombination activities.
Liu SK (1993) J Bacteriol.Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales.
Badger JH (2005) Int J Syst Evol Microbiol.Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.
Lin X (1999) Nature.Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella.
Schmidt EW (2005) Proc Natl Acad Sci U S A.The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium.
Eisen JA (2002) Proc Natl Acad Sci U S A.A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.
Wu D (2009) Nature.Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions.
Eisen JA (1995) Nucleic Acids Res.An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).
Wu D (2008) PLoS One.Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes.
Seshadri R (2005) Science.Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901.
Wu M (2005) PLoS Genet.Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.
White O (1999) Science.Genome of Geobacter sulfurreducens: metal reduction in subsurface environments.
Methé BA (2003) Science.Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome.
Hamilton EP (2006) Genomics.On the taxonomic status of the intracellular bacterium Wolbachia pipientis: should this species name include the intracellular bacteria of filarial nematodes?.
Pfarr K (2007) Int J Syst Evol Microbiol.The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species.
Eisen JA (1995) J Mol Evol.Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications.
Valdés J (2008) BMC Genomics.The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms).
Yang JC (2009) PLoS One.Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure.
Coyne RS (2008) BMC Genomics.Brouhaha over the other yeast.
Eisen JA (2002) Nature.The Calyptogena magnifica chemoautotrophic symbiont genome.
Newton IL (2007) Science.The phylogenetic relationships of Chlorobium tepidum and Chloroflexus aurantiacus based upon their RecA sequences.
Gruber TM (1998) FEMS Microbiol Lett.CompostBin: A DNA composition-based algorithm for binning environmental
shotgun reads.
Sourav Chatterji (2007) arXiv [q-bio.GN].Evidence for symmetric chromosomal inversions around the replication origin in bacteria.
Eisen JA (2000) Genome Biol.BioTorrents: a file sharing service for scientific data.
Langille MG (2010) PLoS One.Complete genome sequence of the Q-fever pathogen Coxiella burnetii.
Seshadri R (2003) Proc Natl Acad Sci U S A.A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.
Pollock DD (2000) Mol Biol Evol.Microbial genome sequencing 2000: new insights into physiology, evolution and expression analysis.
Nierman W (2000) Res Microbiol.Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae.
Tettelin H (2002) Proc Natl Acad Sci U S A.Sequence and drug susceptibility of subtype C reverse transcriptase from human immunodeficiency virus type 1 seroconverters in Zimbabwe.
Shafer RW (1997) J Virol.Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola.
Campbell BJ (2009) PLoS Genet.A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans.
Podar M (2008) Genome Biol.Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis.
Paulsen IT (2003) Science.Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.
Nelson KE (1999) Nature.The value of complete microbial genome sequencing (you get what you pay for).
Fraser CM (2002) J Bacteriol.The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts.
Paulsen IT (2002) Proc Natl Acad Sci U S A.Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440.
Nelson KE (2002) Environ Microbiol.Microbial genome sequencing.
Fraser CM (2000) Nature.Phylogenetic relationships of chemoautotrophic bacterial symbionts of Solemya velum say (Mollusca: Bivalvia) determined by 16S rRNA gene sequence analysis.
Eisen JA (1992) J Bacteriol.Assembling the marine metagenome, one cell at a time.
Woyke T (2009) PLoS One.Going to extremes. Archaea: bridging the gap between bacteria and eukarya (A Keystone Symposia), Taos, NM, USA, 9-14 January 1999.
Eisen JA (1999) Trends Genet.The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.
Heidelberg JF (2004) Nat Biotechnol.Genetic and physical mapping of DNA replication origins in Haloferax volcanii.
Norais C (2007) PLoS Genet.Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts.
Penn K (2006) Appl Environ Microbiol.The Genetic Data Environment. A user modifiable and expandable multiple sequence analysis package.
Eisen JA (1997) Methods Mol Biol.Complete genome sequence of Caulobacter crescentus.
Nierman WC (2001) Proc Natl Acad Sci U S A.Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.
Tettelin H (2001) Science.Lateral gene transfer or viral colonization?.
Salzberg SL (2001) Science.Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance.
Tanaka M (2004) Genetics.The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific.
Rusch DB (2007) PLoS Biol.