A Viral Ecogenomics Framework To Uncover the Secrets of Nature’s “Microbe Whisperers”

by Simon Roux
Published 2019-05-01

Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics

by Gareth Trubl, Paul Hyman, Simon Roux, Stephen T. Abedon
Published 2020-04-01

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

by Simon Roux, Steven J Hallam, Tanja Woyke, Matthew B Sullivan
Published 2015-07-01

Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.

by Simon Roux, Mart Krupovic, Axel Poulet, Didier Debroas, François Enault
Published 2012-01-01

Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences

by Simon Roux, Mart Krupovic, Didier Debroas, Patrick Forterre, François Enault
Published 2013-01-01

VirSorter: mining viral signal from microbial genomic data

by Simon Roux, Francois Enault, Bonnie L. Hurwitz, Matthew B. Sullivan
Published 2015-05-01

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

by Simon Roux, Joanne B. Emerson, Emiley A. Eloe-Fadrosh, Matthew B. Sullivan
Published 2017-09-01

Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust

by Marc W. Van Goethem, Tami L. Swenson, Gareth Trubl, Simon Roux, Trent R. Northen
Published 2019-12-01

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

by Benjamin Bolduc, Ho Bin Jang, Guilhem Doulcier, Zhi-Qiang You, Simon Roux, Matthew B. Sullivan
Published 2017-05-01

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics

by Simon Roux, Leong-Keat Chan, Rob Egan, Rex R. Malmstrom, Katherine D. McMahon, Matthew B. Sullivan
Published 2017-10-01

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept

by Melissa B. Duhaime, Natalie Solonenko, Simon Roux, Nathan C. Verberkmoes, Antje Wichels, Matthew B. Sullivan, Matthew B. Sullivan
Published 2017-07-01

Assessing the diversity and specificity of two freshwater viral communities through metagenomics.

by Simon Roux, Francois Enault, Agnès Robin, Viviane Ravet, Sébastien Personnic, Sébastien Theil, Jonathan Colombet, Télesphore Sime-Ngando, Didier Debroas
Published 2012-01-01

Numerous cultivated and uncultivated viruses encode ribosomal proteins

by Carolina M. Mizuno, Charlotte Guyomar, Simon Roux, Régis Lavigne, Francisco Rodriguez-Valera, Matthew B. Sullivan, Reynald Gillet, Patrick Forterre, Mart Krupovic
Published 2019-02-01

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

by Simon Roux, Alyse K Hawley, Monica Torres Beltran, Melanie Scofield, Patrick Schwientek, Ramunas Stepanauskas, Tanja Woyke, Steven J Hallam, Matthew B Sullivan
Published 2014-08-01

Putative archaeal viruses from the mesopelagic ocean

by Dean R. Vik, Simon Roux, Jennifer R. Brum, Ben Bolduc, Joanne B. Emerson, Cory C. Padilla, Frank J. Stewart, Matthew B. Sullivan
Published 2017-06-01

Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems

by Paula Dalcin Martins, Robert E. Danczak, Simon Roux, Jeroen Frank, Mikayla A. Borton, Richard A. Wolfe, Marie N. Burris, Michael J. Wilkins
Published 2018-08-01

Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

by Alec Vallota-Eastman, Eleanor C. Arrington, Siobhan Meeken, Simon Roux, Krishna Dasari, Sydney Rosen, Jeff F. Miller, David L. Valentine, Blair G. Paul
Published 2020-09-01

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

by Simon Roux, Natalie E. Solonenko, Vinh T. Dang, Bonnie T. Poulos, Sarah M. Schwenck, Dawn B. Goldsmith, Maureen L. Coleman, Mya Breitbart, Matthew B. Sullivan
Published 2016-12-01

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils

by Gareth Trubl, Simon Roux, Natalie Solonenko, Yueh-Fen Li, Benjamin Bolduc, Josué Rodríguez-Ramos, Emiley A. Eloe-Fadrosh, Virginia I. Rich, Matthew B. Sullivan
Published 2019-07-01

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

by Kristopher Kieft, Zhichao Zhou, Rika E. Anderson, Alison Buchan, Barbara J. Campbell, Steven J. Hallam, Matthias Hess, Matthew B. Sullivan, David A. Walsh, Simon Roux, Karthik Anantharaman
Published 2021-06-01