V M Markowitz

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. pmc IMG/M 4 version of the integrated metagenome 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 Microbial Genome and Metagenome Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598 USA
    Nucleic Acids Res 42:D568-73. 2014
  2. 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
  3. pmc IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project
    Victor M Markowitz
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS ONE 7:e40151. 2012
  4. 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
  5. 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
  6. pmc Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool
    Daniel Dalevi
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    BMC Bioinformatics 8:402. 2007
  7. 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
  8. doi request reprint IMG ER: a system for microbial genome annotation expert review and curation
    Victor M Markowitz
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Bioinformatics 25:2271-8. 2009
  9. ncbi request reprint Characterizing heterogeneous molecular biology database systems
    V M Markowitz
    Information and Computing Sciences Division, Lawrence Berkeley National Laboratory, CA 94720, USA
    J Comput Biol 2:547-56. 1995
  10. ncbi request reprint Microbial genome data resources
    Victor M Markowitz
    Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 50A 1148, Berkeley CA 94720, USA
    Curr Opin Biotechnol 18:267-72. 2007

Detail Information

Publications18

  1. pmc IMG/M 4 version of the integrated metagenome 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 Microbial Genome and Metagenome Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598 USA
    Nucleic Acids Res 42:D568-73. 2014
    ..jgi.doe.gov/mer) and Human Microbiome Project (HMP)-specific metagenome samples (IMG/M HMP: http://img.jgi.doe.gov/imgm_hmp). ..
  2. 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/...
  3. pmc IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project
    Victor M Markowitz
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS ONE 7:e40151. 2012
    ..IMG/M-HMP is available at http://www.hmpdacc-resources.org/imgm_hmp/...
  4. 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)...
  5. 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)...
  6. pmc Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool
    Daniel Dalevi
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    BMC Bioinformatics 8:402. 2007
    ..Hierarchical group names are typically manually assigned in trees, an approach that becomes unfeasible for very large topologies...
  7. 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...
  8. doi request reprint IMG ER: a system for microbial genome annotation expert review and curation
    Victor M Markowitz
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Bioinformatics 25:2271-8. 2009
    ..The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct...
  9. ncbi request reprint Characterizing heterogeneous molecular biology database systems
    V M Markowitz
    Information and Computing Sciences Division, Lawrence Berkeley National Laboratory, CA 94720, USA
    J Comput Biol 2:547-56. 1995
    ..In this paper, we propose criteria that would facilitate characterizing, evaluating, and comparing heterogeneous molecular biology database systems...
  10. ncbi request reprint Microbial genome data resources
    Victor M Markowitz
    Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 50A 1148, Berkeley CA 94720, USA
    Curr Opin Biotechnol 18:267-72. 2007
    ..Given their diversity, these resources cannot be used effectively without determining the scope and type of individual resources as well as the relationship between their data...
  11. 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...
  12. pmc The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions
    Victor 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...
  13. pmc The integrated microbial genomes (IMG) system
    Victor 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...
  14. pmc IMG/M: a data management and analysis system for metagenomes
    Victor 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...
  15. pmc Gene context analysis in the Integrated Microbial Genomes (IMG) data management system
    Konstantinos 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...
  16. ncbi request reprint Comparative genome analysis in the integrated microbial genomes (IMG) system
    Victor M Markowitz
    Lawrence Berkeley National Laboratory, USA
    Methods Mol Biol 395:35-56. 2007
    ..Genes can be further examined using gene neighborhoods and compared with sequence alignment tools...
  17. doi request reprint Annotation of metagenome short reads using proxygenes
    Daniel Dalevi
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Bioinformatics 24:i7-13. 2008
    ..The latter requires assignment of individual reads to protein families, which is hindered by the fact that short reads contain only a fragment, usually small, of a protein...
  18. ncbi request reprint Data management challenges for molecular and cell biology: an industry perspective
    Victor M Markowitz
    Data Management Systems, Gene Logic, Inc, Berkeley, California 94704, USA
    OMICS 7:121-2. 2003