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Rob Egan
Researcher at Lawrence Berkeley National Laboratory
Publications - 20
Citations - 3140
Rob Egan is an academic researcher from Lawrence Berkeley National Laboratory. The author has contributed to research in topics: Metagenomics & Genome. The author has an hindex of 10, co-authored 17 publications receiving 2570 citations. Previous affiliations of Rob Egan include Joint Genome Institute.
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Journal ArticleDOI
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
TL;DR: MetaBAT as mentioned in this paper integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning, and automatically forms hundreds of high quality genome bins on a very large assembly consisting millions of contigs.
Journal ArticleDOI
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.
Matthias Hess,Matthias Hess,Alexander Sczyrba,Alexander Sczyrba,Rob Egan,Rob Egan,Tae-Wan Kim,Harshal A. Chokhawala,Gary P. Schroth,Shujun Luo,Douglas S. Clark,Feng Chen,Feng Chen,Tao Zhang,Tao Zhang,Roderick I. Mackie,Len A. Pennacchio,Len A. Pennacchio,Susannah G. Tringe,Susannah G. Tringe,Axel Visel,Axel Visel,Tanja Woyke,Tanja Woyke,Zhong Wang,Zhong Wang,Edward M. Rubin,Edward M. Rubin +27 more
TL;DR: To characterize biomass-degrading genes and genomes, this work sequenced and analyzed 268 gigabases of metagenomic DNA from microbes adherent to plant fiber incubated in cow rumen and identified 27,755 putative carbohydrate-active genes and expressed 90 candidate proteins, of which 57% were enzymatically active against cellulosic substrates.
Posted ContentDOI
De novoIdentification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing
Marcus H. Stoiber,Josh Quick,Rob Egan,Eun Lee J,Susan E. Celniker,Robert K. Neely,Nicholas J. Loman,Len A. Pennacchio,James B. Brown +8 more
TL;DR: The first algorithm for the identification of modified nucleotides without the need for prior training data is presented along with the open source software implementation, nanoraw, which accurately assigns contiguous raw nanopore signal to genomic positions, enabling novel data visualization and increasing power and accuracy for the discovery of covalently modified bases in native DNA.
Journal ArticleDOI
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
TL;DR: The ALE framework provides a comprehensive, reference-independent and statistically rigorous measure of single genome and metagenome assembly accuracy, which can be used to identify misassemblies or to optimize the assembly process.
Proceedings ArticleDOI
HipMer: an extreme-scale de novo genome assembler
Evangelos Georganas,Aydin Buluc,Jarrod Chapman,Steven Hofmeyr,Chaitanya Aluru,Rob Egan,Leonid Oliker,Daniel S. Rokhsar,Katherine Yelick +8 more
TL;DR: HipMer is presented, the first high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code, and significantly improves scalability of parallel k-mer analysis for complex repetitive genomes that exhibit skewed frequency distributions.