Research Topics
| K MavromatisSummaryAffiliation: Lawrence Berkeley National Laboratory Country: USA Publications
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Detail Information
Publications
Use of simulated data sets to evaluate the fidelity of metagenomic processing methodsKonstantinos Mavromatis
Department of Energy Joint Genome Institute DOE JGI, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
Nat Methods 4:495-500. 2007..The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis...
Annotation of metagenome short reads using proxygenesDaniel Dalevi
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Bioinformatics 24:i7-13. 2008..We introduce a clustering method which significantly reduces the size of a metagenome dataset while maintaining a faithful representation of its functional and taxonomic content...
The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotationKonstantinos Mavromatis
DOE Joint Genome Institute, Walnut Creek, California, United States of America
PLoS ONE 7:e48837. 2012..The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation...- 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... - Microbial co-habitation and lateral gene transfer: what transposases can tell usSean D Hooper
Department of Energy Joint Genome Institute, Genome Biology Program, Mitchell Drive, Walnut Creek, CA 94598, USA
Genome Biol 10:R45. 2009..In this study, we explore an approach using the history of lateral gene transfer recorded in microbial genomes to begin to answer two key questions: where have you been and who have you been with?.. - Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescensMark W Silby
Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Centre for Adaptation Genetics and Drug Resistance, Boston, MA 02111, USA
Genome Biol 10:R51. 2009..A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species... - The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic CrenarchaeotaIain 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... - Gene context analysis in the Integrated Microbial Genomes (IMG) data management systemKonstantinos Mavromatis
Genome Biology Program, Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
PLoS ONE 4:e7979. 2009..These computations are now maintained as part of IMG's regular genome content update cycle. IMG is available at: http://img.jgi.doe.gov... - The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion strategiesK Mavromatis
Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
J Bacteriol 188:4015-23. 2006..Genes associated with pathogen-host interactions were identified, including a small group encoding proteins (n = 12) with tandem repeats and another group encoding proteins with eukaryote-like ankyrin domains (n = 7)... - Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix oreniiKonstantinos Mavromatis
DOE Joint Genome Institute, Walnut Creek, California, United States of America
PLoS ONE 4:e4192. 2009.... - The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadataKonstantinos Liolios
University of Chicago, Department of Medicine, Chicago, Genome Biology Program, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, USA
Nucleic Acids Res 36:D475-9. 2008..GOLD is available at http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece at http://gold.imbb.forth.gr/.. - The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensionsVictor M Markowitz
Biological Data Management and Technology Center, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA
Nucleic Acids Res 36:D528-33. 2008..IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov... - IMG/M: a data management and analysis system for metagenomesVictor M Markowitz
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA
Nucleic Acids Res 36:D534-8. 2008..IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m... - Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YXAthanasios 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... - An experimental metagenome data management and analysis systemVictor 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... - The integrated microbial genomes (IMG) systemVictor M Markowitz
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
Nucleic Acids Res 34:D344-8. 2006..IMG allows users to focus their analysis on subsets of genes and genomes of interest and to save the results of their analysis. IMG is available at http://img.jgi.doe.gov... - Peptidoglycan N-acetylglucosamine deacetylases from Bacillus cereus, highly conserved proteins in Bacillus anthracisEmmanuel Psylinakis
Department of Biology, Enzyme Biotechnology Group, University of Crete, P O Box 2208, Vasilika Vouton 714 09, Heraklion, Crete, Greece
J Biol Chem 280:30856-63. 2005..cereus by BC1960 and BC3618 resulted in increased resistance to lysozyme digestion. This is the first biochemical study of bacterial peptidoglycan N-acetylglucosamine deacetylases...