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Evguenia Kopylova
Researcher at University of California, San Diego
Publications - 20
Citations - 6185
Evguenia Kopylova is an academic researcher from University of California, San Diego. The author has contributed to research in topics: Ribosomal RNA & Genome. The author has an hindex of 12, co-authored 17 publications receiving 3951 citations. Previous affiliations of Evguenia Kopylova include University of Colorado Boulder & French Institute for Research in Computer Science and Automation.
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Journal ArticleDOI
SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.
TL;DR: SortMeRNA, a new software designed to rapidly filter rRNA fragments from metatranscriptomic data, is presented, capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time.
Journal ArticleDOI
A communal catalogue reveals Earth’s multiscale microbial diversity
Luke R. Thompson,Luke R. Thompson,Luke R. Thompson,Jon G. Sanders,Daniel McDonald,Amnon Amir,Joshua Ladau,Kenneth J. Locey,Robert J. Prill,Anupriya Tripathi,Sean M. Gibbons,Sean M. Gibbons,Gail Ackermann,Jose A. Navas-Molina,Stefan Janssen,Evguenia Kopylova,Yoshiki Vázquez-Baeza,Antonio Gonzalez,James T. Morton,Siavash Mirarab,Zhenjiang Zech Xu,Lingjing Jiang,Mohamed F. Haroon,Jad N. Kanbar,Qiyun Zhu,Se Jin Song,Tomasz Kosciolek,Nicholas A. Bokulich,Joshua P Lefler,Colin J. Brislawn,Gregory Humphrey,Sarah M. Owens,Jarrad T. Hampton-Marcell,Jarrad T. Hampton-Marcell,Donna Berg-Lyons,Valerie J. McKenzie,Noah Fierer,Noah Fierer,Jed A. Fuhrman,Aaron Clauset,Rick Stevens,Rick Stevens,Ashley Shade,Katherine S. Pollard,Kelly D. Goodwin,Janet K. Jansson,Jack A. Gilbert,Jack A. Gilbert,Rob Knight +48 more
TL;DR: A meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project is presented, creating both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
Journal ArticleDOI
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
Amnon Amir,Daniel McDonald,Jose A. Navas-Molina,Evguenia Kopylova,James T. Morton,Zhenjiang Zech Xu,Eric P. Kightley,Luke R. Thompson,Embriette R. Hyde,Antonio Gonzalez,Rob Knight +10 more
TL;DR: A novel sub-operational-taxonomic-unit (sOTU) approach that uses error profiles to obtain putative error-free sequences from Illumina MiSeq and HiSeq sequencing platforms, Deblur, which substantially reduces computational demands relative to similar sOTU methods and does so with similar or better sensitivity and specificity.
Journal ArticleDOI
Microbiome analyses of blood and tissues suggest cancer diagnostic approach
Gregory D. Poore,Evguenia Kopylova,Qiyun Zhu,Carolina S. Carpenter,Serena Fraraccio,Stephen Wandro,Tomasz Kosciolek,Tomasz Kosciolek,Stefan Janssen,Stefan Janssen,Jessica L. Metcalf,Se Jin Song,Jad N. Kanbar,Sandrine Miller-Montgomery,Robert K. Heaton,Rana R. McKay,Sandip Pravin Patel,Austin D. Swafford,Rob Knight +18 more
TL;DR: Microbial nucleic acids are detected in samples of tissues and blood from more than 10,000 patients with cancer, and machine learning is used to show that these can be used to discriminate between and among different types of cancer, suggesting a new microbiome-based diagnostic approach.
Journal ArticleDOI
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.
Francesco Asnicar,Andrew Maltez Thomas,Francesco Beghini,Claudia Mengoni,Serena Manara,Paolo Manghi,Qiyun Zhu,Mattia Bolzan,Fabio Cumbo,Uyen May,Jon G. Sanders,Jon G. Sanders,Moreno Zolfo,Evguenia Kopylova,Edoardo Pasolli,Edoardo Pasolli,Rob Knight,Siavash Mirarab,Curtis Huttenhower,Nicola Segata +19 more
TL;DR: PhyloPhlAn 3.0 can assign genomes from isolate sequencing or MAGs to species-level genome bins built from >230,000 publically available sequences, and reconstructs strain-level phylogenies from among the closest species using clade-specific maximally informative markers.