Iain Anderson

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. pmc Genomics of aerobic cellulose utilization systems in actinobacteria
    Iain Anderson
    U S Department of Energy Joint Genome Institute, Walnut Creek, California, USA
    PLoS ONE 7:e39331. 2012
  2. pmc A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans
    Mircea Podar
    Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
    Genome Biol 9:R158. 2008
  3. pmc Genomic characterization of methanomicrobiales reveals three classes of methanogens
    Iain Anderson
    Joint Genome Institute, Walnut Creek, California, USA
    PLoS ONE 4:e5797. 2009
  4. pmc Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction
    Iain Anderson
    Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA 94598, USA
    J Bacteriol 190:2957-65. 2008
  5. pmc The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota
    Iain J Anderson
    Genome Biology Program, Joint Genome Institute, Walnut Creek, USA
    BMC Genomics 10:145. 2009
  6. pmc Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes
    Iain Anderson
    Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 6:e20237. 2011
  7. ncbi request reprint Gene discovery in the Acanthamoeba castellanii genome
    Iain J Anderson
    Department of Parasite Genomics, The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    Protist 156:203-14. 2005
  8. pmc Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii
    Konstantinos Mavromatis
    DOE Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 4:e4192. 2009
  9. pmc Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX
    Athanasios Lykidis
    Department of Energy, Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA 94598, USA
    J Bacteriol 189:2477-86. 2007
  10. pmc IMG/M: the integrated metagenome data management and comparative analysis system
    Victor M Markowitz
    Biological Data Management and Technology Center, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California, CA 94702, USA
    Nucleic Acids Res 40:D123-9. 2012

Detail Information

Publications26

  1. pmc Genomics of aerobic cellulose utilization systems in actinobacteria
    Iain Anderson
    U S Department of Energy Joint Genome Institute, Walnut Creek, California, USA
    PLoS ONE 7:e39331. 2012
    ..Mining of genome data for cellulose degradative enzymes followed by experimental verification successfully identified several actinobacteria species which were not previously known to degrade cellulose as cellulolytic organisms...
  2. pmc A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans
    Mircea 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...
  3. pmc Genomic characterization of methanomicrobiales reveals three classes of methanogens
    Iain Anderson
    Joint Genome Institute, Walnut Creek, California, USA
    PLoS ONE 4:e5797. 2009
    ..While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens...
  4. pmc Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction
    Iain Anderson
    Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA 94598, USA
    J Bacteriol 190:2957-65. 2008
    ....
  5. pmc The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota
    Iain J Anderson
    Genome Biology Program, Joint Genome Institute, Walnut Creek, USA
    BMC Genomics 10:145. 2009
    ..It is the third heterotrophic, obligate sulfur reducing crenarchaeote to be sequenced and provides an opportunity for comparative analysis of the three genomes...
  6. pmc Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes
    Iain Anderson
    Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 6:e20237. 2011
    ..The extremely halophilic archaea are present worldwide in saline environments and have important biotechnological applications. Ten complete genomes of haloarchaea are now available, providing an opportunity for comparative analysis...
  7. ncbi request reprint Gene discovery in the Acanthamoeba castellanii genome
    Iain J Anderson
    Department of Parasite Genomics, The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    Protist 156:203-14. 2005
    ..histolytica. Serine, cysteine and metalloproteases were identified, some of which are likely involved in pathogenicity...
  8. pmc Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii
    Konstantinos Mavromatis
    DOE Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 4:e4192. 2009
    ....
  9. pmc Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX
    Athanasios Lykidis
    Department of Energy, Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA 94598, USA
    J Bacteriol 189:2477-86. 2007
    ..In addition to providing an overview of the physiology of a soil actinomycete, this study presents insights on the transcriptional regulation and secretion of cellulases which may facilitate the industrial exploitation of these systems...
  10. pmc IMG/M: the integrated metagenome data management and comparative analysis system
    Victor M Markowitz
    Biological Data Management and Technology Center, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California, CA 94702, USA
    Nucleic Acids Res 40:D123-9. 2012
    ..IMG/M is available at http://img.jgi.doe.gov/m. A companion IMG/M systems provide support for annotation and expert review of unpublished metagenomic data sets (IMG/M ER: http://img.jgi.doe.gov/mer)...
  11. pmc IMG: the Integrated Microbial Genomes database and comparative analysis system
    Victor M Markowitz
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA
    Nucleic Acids Res 40:D115-22. 2012
    ..jgi.doe.gov/er), teaching courses and training in microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu) and analysis of genomes related to the Human Microbiome Project (IMG/HMP: http://www.hmpdacc-resources.org/img_hmp)...
  12. doi request reprint IMG 4 version of the integrated microbial genomes comparative analysis system
    Victor M Markowitz
    Biological Data Management and Technology Center, Computational Research Division Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, 94720 USA and Department of Energy, Microbial Genome and Metagenome Program, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, 94598 USA
    Nucleic Acids Res 42:D560-7. 2014
    ..jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu). ..
  13. pmc Improving microbial genome annotations in an integrated database context
    I Min A Chen
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS ONE 8:e54859. 2013
    ..The IMG family of systems are available at http://img.jgi.doe.gov/...
  14. pmc Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T))
    Iain Anderson
    DOE Joint Genome Institute, Walnut Creek, California, USA
    Stand Genomic Sci 7:210-20. 2012
    ..The 4,697,343 bp long chromosome with its 3,931 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia ofBacteria andArchaea project...
  15. pmc The integrated microbial genomes system: an expanding comparative analysis resource
    Victor M Markowitz
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California, USA
    Nucleic Acids Res 38:D382-90. 2010
    ..Several companion IMG systems have been set up in order to serve domain specific needs, such as expert review of genome annotations. IMG is available at http://img.jgi.doe.gov...
  16. ncbi request reprint An experimental metagenome data management and analysis system
    Victor M Markowitz
    Biological Data Management and Technology Center, Lawrence Berkeley National Lab, USA
    Bioinformatics 22:e359-67. 2006
    ..IMG/M provides tools and viewers for analyzing both metagenomes and isolate genomes individually or in a comparative context. IMG/M is available at http://img.jgi.doe.gov/m...
  17. pmc Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach
    Sean D Hooper
    Department of Energy Joint Genome Institute DOE JGI, Genome Biology Program, Walnut Creek, CA 94598, USA
    Nucleic Acids Res 37:2096-104. 2009
    ..Our clusters can be analyzed graphically and interactively online...
  18. pmc The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader
    Athanasios Lykidis
    Department of Energy DOE Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 5:e9729. 2010
    ..Cupriavidus necator JMP134 is a Gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source...
  19. pmc Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T))
    Iain Anderson
    DOE Joint Genome Institute, Walnut Creek, California, USA
    Stand Genomic Sci 6:1-13. 2012
    ..acidophilus. The genome, which consists of one chromosome and one plasmid with a total size of 3,557,831 bp harbors 3,626 protein-coding and 69 RNA genes, and is a part of the GenomicEncyclopedia ofBacteria andArchaea project...
  20. pmc SOP for pathway inference in Integrated Microbial Genomes (IMG)
    Iain Anderson
    DOE Joint Genome Institute, Walnut Creek, CA, USA
    Stand Genomic Sci 5:420-3. 2011
    ..In the unknown category, at least one term necessary for the pathway is missing, but an ortholog in another organism has the corresponding term assigned to it. Automatic pathway inference is an important initial step in genome analysis...
  21. ncbi request reprint The genome of the protist parasite Entamoeba histolytica
    Brendan Loftus
    TIGR, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 433:865-8. 2005
    ..Analysis of the genome provides new insights into the workings and genome evolution of a major human pathogen...
  22. pmc A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
    Dongying Wu
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 462:1056-60. 2009
    ....
  23. ncbi request reprint Entamoeba histolytica: observations on metabolism based on the genome sequence
    Iain J Anderson
    Department of Parasite Genomics, The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    Exp Parasitol 110:173-7. 2005
    ..histolytica. The usual eukaryotic glucose transporters are not present, but members of a prokaryotic monosaccharide transporter family are present...
  24. ncbi request reprint Symbiosis insights through metagenomic analysis of a microbial consortium
    Tanja Woyke
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 443:950-5. 2006
    ..We propose a model that describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments that it inhabits...
  25. pmc The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans
    Brendan J Loftus
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 307:1321-4. 2005
    ..neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes...
  26. pmc Disruption of the operon encoding Ehb hydrogenase limits anabolic CO2 assimilation in the archaeon Methanococcus maripaludis
    Iris Porat
    Department of Microbiology, University of Georgia, Athens, Georgia 30602 2605, USA
    J Bacteriol 188:1373-80. 2006
    ..These observations support a role for Ehb in anabolic CO2 assimilation in methanococci...