Frank Korzeniewski
Lawrence Berkeley National Laboratory
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Featured researches published by Frank Korzeniewski.
Nucleic Acids Research | 2006
Victor Markowitz; Frank Korzeniewski; Krishna Palaniappan; Ernest Szeto; Greg Werner; Anu Padki; Xueling Zhao; Inna Dubchak; Philip Hugenholtz; Iain Anderson; Athanasios Lykidis; Konstantinos Mavromatis; Natalia Ivanova; Nikos C. Kyrpides
The integrated microbial genomes (IMG) system is a new data management and analysis platform for microbial genomes provided by the Joint Genome Institute (JGI). IMG contains both draft and complete JGI genomes integrated with other publicly available microbial genomes of all three domains of life. IMG provides tools and viewers for analyzing genomes, genes and functions, individually or in a comparative context. 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 .
Nature Methods | 2007
Konstantinos Mavromatis; Natalia Ivanova; Kerrie Barry; Harris Shapiro; Eugene Goltsman; Alice C. McHardy; Isidore Rigoutsos; Asaf Salamov; Frank Korzeniewski; Miriam Land; Alla Lapidus; Igor V. Grigoriev; Paul G. Richardson; Philip Hugenholtz; Nikos C. Kyrpides
Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods presently used to process metagenomic sequences, we constructed three simulated data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate genomes. These data sets were designed to model real metagenomes in terms of complexity and phylogenetic composition. We assembled sampled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ), and predicted genes using two popular gene-finding pipelines (fgenesb and CRITICA/GLIMMER). The phylogenetic origins of the assembled contigs were predicted using one sequence similarity–based (blast hit distribution) and two sequence composition–based (PhyloPythia, oligonucleotide frequencies) binning methods. We explored the effects of the simulated community structure and method combinations on the fidelity of each processing step by comparison to the corresponding isolate genomes. The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis.Please visit methagora to view and post comments on this article
intelligent systems in molecular biology | 2006
Victor Markowitz; Natalia V. Ivanova; Krishna Palaniappan; Ernest Szeto; Frank Korzeniewski; Athanasios Lykidis; Iain Anderson; Konstantinos Mavrommatis; Victor Kunin; Hector Garcia Martin; Inna Dubchak; Phil Hugenholtz; Nikos C. Kyrpides
The application of shotgun sequencing to environmental samples has revealed a new universe of microbial community genomes (metagenomes) involving previously uncultured organisms. Metagenome analysis, which is expected to provide a comprehensive picture of the gene functions and metabolic capacity for microbial communities, needs to be conducted in the context of a comprehensive data management and analysis system. We present in this paper IMG/M, an experimental metagenome data management and analysis system that is based on the Integrated Microbial Genomes (IMG) system. 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.
Archive | 2010
Robert Otillar; Asaf Salamov; Alex Atkins; Frank Korzeniewski; Jeremy Schmutz; Erika Lindquist; Adrian Tsang; Randy M. Berka; Igor Grigoriev
Archive | 2009
Igor Grigoriev; Andrea Aerts; Frank Korzeniewski; Alan Kuo; Robert Otillar; Asaf Salamov; Xueling Zhao; Kemin Zhou
Archive | 2008
Igor Grigoriev; Andrea Aerts; Frank Korzeniewski; Alan Kuo; Asaf Salamov; Robert Otillar; Xueling Zhao; Kemin Zhou
Archive | 2006
Victor Markowitz; Frank Korzeniewski; Krishna Palaniappan; Ernest Szeto; Natalia Ivanova; Nikos C. Kyrpides; Philip Hugenholtz
Archive | 2006
Konstantinos Mavromatis; Natalia Ivanova; Kerrie Barry; Harris Shapiro; Eugene Goltsman; Alice C. McHardy; Isidore Rigoutsos; Asaf Salamov; Frank Korzeniewski; Miriam Land; Phil Hugenholtz; Nikos C. Kyrpides
Archive | 2006
Konstantinos Mavrommatis; Natalia Ivanova; Kerrie Barry; Harris Shapiro; Eugene Goltsman; Alice C. McHardy; Isidore Rigoutsos; Asaf Salamov; Frank Korzeniewski; Miriam Land; Phil Hugenholtz; Nikos C. Kyrpides
Lawrence Berkeley National Laboratory | 2006
Victor Markowitz; Frank Korzeniewski; Krishna Palaniappan; Ernest Szeto; Natalia Ivanova; Nikos C. Kyrpides; Philip Hugenholtz