1. Complete genome sequence of Methanospirillum hungatei type strain JF1.

    Standards in Genomic Sciences 11:2 (2016) PMID 26744606 PMCID PMC4704411

    Methanospirillum hungatei strain JF1 (DSM 864) is a methane-producing archaeon and is the type species of the genus Methanospirillum, which belongs to the family Methanospirillaceae within the order Methanomicrobiales. Its genome was selected for sequencing due to its ability to utilize hydrogen...
  2. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

    PLoS Biology 12(8):e1001920 (2014) PMID 25093819 PMCID PMC4122341

    Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the p...
  3. Complete genome sequence of Rhodospirillum rubrum type strain (S1).

    Standards in Genomic Sciences 4(3):293 (2011) PMID 21886856 PMCID PMC3156396

    Rhodospirillum rubrum (Esmarch 1887) Molisch 1907 is the type species of the genus Rhodospirillum, which is the type genus of the family Rhodospirillaceae in the class Alphaproteobacteria. The species is of special interest because it is an anoxygenic phototroph that produces extracellular eleme...
  4. Identification of ribosomal RNA genes in metagenomic fragments.

    PMID 19346323 PMCID PMC2677747

    Identification of genes coding for ribosomal RNA (rRNA) is considered an important goal in the analysis of data from metagenomics projects. Here, we report the development of a software program designed for the identification of rRNA genes from metagenomic fragments based on hidden Markov models...
  5. Meeting Report from the Genomic Standards Consortium (GSC) Workshops 6 and 7.

    Standards in Genomic Sciences 1(1):68 (2009) PMID 21304639 PMCID PMC3035212

    This report summarizes the proceedings of the 6th and 7th workshops of the Genomic Standards Consortium (GSC), held back-to-back in 2008. GSC 6 focused on furthering the activities of GSC working groups, GSC 7 focused on outreach to the wider community. GSC 6 was held October 10-14, 2008 at the ...
  6. Building an OptIPlanet collaboratory to support microbial metagenomics

    Future Generation Computer Systems 25(2):124 (2009)

    We describe early experiments in the adoption of the OptIPuter architecture to provide data-intensive capabilities to several remote users of a large-scale, multi-year effort to organize and make publicly available data describing a wide variety of marine microbial ecologies, their genomic ...
  7. The minimum information about a genome sequence (MIGS) specification.

    Nature Biotechnology 26(5):541 (2008) PMID 18464787 PMCID PMC2409278

    With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding th...
  8. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities.

    PLoS ONE 3(8):e3042 (2008) PMID 18725995 PMCID PMC2518522

    Sequencing the expressed genetic information of an ecosystem (metatranscriptome) can provide information about the response of organisms to varying environmental conditions. Until recently, metatranscriptomics has been limited to microarray technology and random cloning methodologies. The applic...
  9. Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy.

    Journal of Bacteriology 189(11):4020 (2007) PMID 17416667 PMCID PMC1913398

    Along with methane, methanol and methylated amines represent important biogenic atmospheric constituents; thus, not only methanotrophs but also nonmethanotrophic methylotrophs play a significant role in global carbon cycling. The complete genome of a model obligate methanol and methylamine utili...
  10. Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii.

    Applied and Environmental Microbiology 73(11):3536 (2007) PMID 17400776 PMCID PMC1932680

    The complete DNA sequence of the aerobic cellulolytic soil bacterium Cytophaga hutchinsonii, which belongs to the phylum Bacteroidetes, is presented. The genome consists of a single, circular, 4.43-Mb chromosome containing 3,790 open reading frames, 1,986 of which have been assigned a tentative ...
  11. The complete genome sequence of Bacillus thuringiensis Al Hakam.

    Journal of Bacteriology 189(9):3680 (2007) PMID 17337577 PMCID PMC1855882

    Bacillus thuringiensis is an insect pathogen that is widely used as a biopesticide (E. Schnepf, N. Crickmore, J. Van Rie, D. Lereclus, J. Baum, J. Feitelson, D. R. Zeigler, and D. H. Dean, Microbiol. Mol. Biol. Rev. 62:775-806, 1998). Here we report the finished, annotated genome sequence of B. ...
  12. CAMERA: a community resource for metagenomics.

    PLoS Biology 5(3):e75 (2007) PMID 17355175 PMCID PMC1821059

  13. Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis.

    PLoS ONE 2(9):e947 (2007) PMID 17895988 PMCID PMC1978527

    Francisella tularensis is the causative agent of tularemia, which is a highly lethal disease from nature and potentially from a biological weapon. This species contains four recognized subspecies including the North American endemic F. tularensis subsp. tularensis (type A), whose genetic diversi...
  14. The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes.

    Journal of Bacteriology 188(22):7922 (2006) PMID 16980466 PMCID PMC1636319

    We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with those of Methanosarcina acetivorans and Methanosarcina mazei. The genome of M. barkeri is distinguished by having an organization that is well conserved with respect to the other Methanosarcina spp. in th...
  15. Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis.

    Journal of Bacteriology 188(9):3382 (2006) PMID 16621833 PMCID PMC1447445

    Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis are closely related gram-positive, spore-forming bacteria of the B. cereus sensu lato group. While independently derived strains of B. anthracis reveal conspicuous sequence homogeneity, environmental isolates of B. cereus and B. thu...
  16. The sequence and analysis of duplication-rich human chromosome 16.
    Joel Martin, Cliff Han, Laurie A Gordon, Astrid Terry, Shyam Prabhakar, Xinwei She, Gary Xie, Uffe Hellsten, Yee Man Chan, Michael Altherr, Olivier Couronne, Andrea Aerts, Eva Bajorek, Stacey Black, Heather Blumer, Elbert Branscomb, Nancy C Brown, William J Bruno, Judith M Buckingham, David F Callen, Connie S Campbell, Mary L Campbell, Evelyn W Campbell, Chenier Caoile, Jean F Challacombe, Leslie A Chasteen, Olga Chertkov, Han Chi, Mari Christensen, Lynn M Clark, Judith D Cohn, Mirian Denys, John C Detter, Mark Dickson, Mira Dimitrijevic-Bussod, Julio Escobar, Joseph Fawcett, Dave Flowers, Dea Fotopulos, Tijana Glavina, Maria Gomez, Eidelyn Gonzales, David Goodstein, Lynne A Goodwin, Deborah L Grady, Igor Grigoriev, Matthew Groza, Nancy Hammon, Trevor Hawkins, Lauren Haydu, Carl E Hildebrand, Wayne Huang, Sanjay Israni, Jamie Jett, Phillip B Jewett, Kristen Kadner, Heather Kimball, Arthur Kobayashi, Marie-Claude Krawczyk, Tina Leyba, Jonathan Longmire, Frederick Lopez, Yunian Lou, Steve Lowry, Thom Ludeman, Chitra F Manohar, Graham A Mark, Kimberly L, Linda J Meincke, Jenna Morgan, Robert K Moyzis, Mark O Mundt, A Christine Munk, Richard D Nandkeshwar, Sam Pitluck, Martin Pollard, Paul Predki, Beverly Parson-Quintana, Lucia Ramirez, Sam Rash, James Retterer, Darryl O Ricke, Donna L Robinson, Alex Rodriguez, Asaf Salamov, Elizabeth H Saunders, Duncan Scott, Timothy Shough, Raymond L Stallings, Malinda Stalvey, Robert D Sutherland, Roxanne Tapia, Judith G Tesmer, Nina Thayer, Linda S Thompson, Hope Tice, David C Torney, Mary Tran-Gyamfi, Ming Tsai, Levy E Ulanovsky, Anna Ustaszewska, Nu Vo, P Scott White, Albert L Williams, Patricia L Wills, Jung-Rung Wu, Kevin Wu, Joan Yang, Pieter Dejong, David Bruce, Norman A Doggett, Larry Deaven, Jeremy Schmutz, Jane Grimwood, Paul Richardson, Daniel S Rokhsar, Evan Eichler, Paul Gilna, Susan M Lucas, Richard Myers, Edward M Rubin, and Len A Pennacchio

    Nature 432(7020):988 (2004) PMID 15616553

    Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confir...
  17. [1] GenBank: Current status and future directions

    Methods in Enzymology 183:3 (1990)

    The GenBank11“GenBank” is a registered trademark of the U.S. Department of Health and Human Services. database provides a collection of nucleotide sequences as well as relevant bibliographic and biological annotation. We present an updated view of the size and scope of the database, an...