G
Genivaldo G. Z. Silva
Researcher at San Diego State University
Publications - 34
Citations - 2723
Genivaldo G. Z. Silva is an academic researcher from San Diego State University. The author has contributed to research in topics: Metagenomics & Genome. The author has an hindex of 20, co-authored 34 publications receiving 2100 citations. Previous affiliations of Genivaldo G. Z. Silva include Federal University of Pernambuco & Federal University of Rio de Janeiro.
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Journal ArticleDOI
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
Bas E. Dutilh,Noriko A. Cassman,Katelyn McNair,Savannah E. Sanchez,Genivaldo G. Z. Silva,Lance Boling,Jeremy J. Barr,Daan R. Speth,Victor Seguritan,Ramy K. Aziz,Ramy K. Aziz,Ben Felts,Elizabeth A. Dinsdale,John L. Mokili,Robert Edwards +14 more
TL;DR: The discovery of a previously unidentified bacteriophage present in the majority of published human faecal metagenomes, which is referred to as crAssphage and predicted to have a Bacteroides host for this phage, consistent with Bactseroides-related protein homologues and a unique carbohydrate-binding domain encoded in the phage genome.
Journal ArticleDOI
Critical Assessment of Metagenome Interpretation - A benchmark of metagenomics software
Alexander Sczyrba,Peter Hofmann,Peter Hofmann,Peter Belmann,David Koslicki,Stefan Janssen,Johannes Dröge,Johannes Dröge,Ivan Gregor,Ivan Gregor,Stephan Majda,Jessika Fiedler,Eik Dahms,Eik Dahms,Andreas Bremges,Adrian Fritz,Ruben Garrido-Oter,Tue Sparholt Jørgensen,Tue Sparholt Jørgensen,Tue Sparholt Jørgensen,Nicole Shapiro,Philip D. Blood,Alexey Gurevich,Yang Bai,Dmitrij Turaev,Matthew Z. DeMaere,Rayan Chikhi,Niranjan Nagarajan,Christopher Quince,Fernando Meyer,Monika Balvočiūtė,Lars Hestbjerg Hansen,Søren J. Sørensen,Burton Kuan Hui Chia,Bertrand Denis,Jeff Froula,Zhong Wang,Robert Egan,Dongwan Don Kang,Jeffrey J. Cook,Charles Deltel,Michael Beckstette,Claire Lemaitre,Pierre Peterlongo,Guillaume Rizk,Dominique Lavenier,Yu Wei Wu,Yu Wei Wu,Steven W. Singer,Steven W. Singer,Chirag Jain,Marc Strous,Heiner Klingenberg,Peter Meinicke,Michael D. Barton,Thomas Lingner,Hsin-Hung Lin,Yu-Chieh Liao,Genivaldo G. Z. Silva,Daniel A. Cuevas,Robert Edwards,Surya Saha,Vitor C. Piro,Vitor C. Piro,Bernhard Y. Renard,Mihai Pop,Hans-Peter Klenk,Markus Göker,Nikos C. Kyrpides,Tanja Woyke,Julia A. Vorholt,Paul Schulze-Lefert,Edward M. Rubin,Aaron E. Darling,Thomas Rattei,Alice C. McHardy +75 more
TL;DR: The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups as discussed by the authors.
Journal ArticleDOI
Lytic to temperate switching of viral communities
Ben Knowles,Cynthia B. Silveira,Barbara A. Bailey,Katie L. Barott,Vito Adrian Cantu,Ana G Cobián-Güemes,Felipe H. Coutinho,Elizabeth A. Dinsdale,Ben Felts,Kathryn A. Furby,Emma E. George,Kevin Green,Gustavo B. Gregoracci,Andreas F. Haas,John M. Haggerty,Eric R. Hester,Nao Hisakawa,Linda Wegley Kelly,Yan Wei Lim,Mark Little,Antoni Luque,T. McDole-Somera,Katelyn McNair,L. S. de Oliveira,Steven D. Quistad,N. L. Robinett,Enric Sala,Peter Salamon,Peter Salamon,Savannah E. Sanchez,Stuart A. Sandin,Genivaldo G. Z. Silva,Jennifer E. Smith,Christopher C. Sullivan,C. Thompson,Mark J. A. Vermeij,Merry Youle,C. Young,Brian J. Zgliczynski,R. Brainard,Robert Edwards,Jim Nulton,Fabiano L. Thompson,Forest Rohwer,Forest Rohwer +44 more
TL;DR: The Piggyback-the-Winner model wherein temperate dynamics become increasingly important in ecosystems with high microbial densities is proposed; thus ‘more microbes, fewer viruses’ is proposed.
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SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data
TL;DR: SUPERFOCUS is introduced, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances, and is up to 1000 times faster than other tools.
Journal ArticleDOI
Metagenomic Analysis of Healthy and White Plague-Affected Mussismilia braziliensis Corals
Gizele D. Garcia,Gustavo B. Gregoracci,Eidy de O. Santos,Pedro M. Meirelles,Genivaldo G. Z. Silva,Genivaldo G. Z. Silva,Robert Edwards,Robert Edwards,Tomoo Sawabe,Kazuyoshi Gotoh,Shota Nakamura,Tetsuya Iida,Rodrigo L. Moura,Fabiano L. Thompson +13 more
TL;DR: The results suggest that WP disease in M. braziliensis is caused by a polymicrobial consortium, and Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria and Actinomycetes are the main groups in all healthy and WP-affected corals.