Simon Roux

Simon Roux

UNVERIFIED PROFILE

Are you Simon Roux?   Register this Author

Register author
Simon Roux

Simon Roux

Publications by authors named "Simon Roux"

Are you Simon Roux?   Register this Author

67Publications

2152Reads

28Profile Views

Giant virus diversity and host interactions through global metagenomics.

Nature 2020 Feb 22;578(7795):432-436. Epub 2020 Jan 22.

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41586-020-1957-xDOI Listing
February 2020

Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust.

mBio 2019 12 17;10(6). Epub 2019 Dec 17.

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.02287-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6918073PMC
December 2019

Future-Proofing Your Genome Assembly for Reproducibility and Clarity.

Microbiol Resour Announc 2019 Sep 5;8(36). Epub 2019 Sep 5.

Department of Microbiology and Plant Pathology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/MRA.00954-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6728651PMC
September 2019

A Viral Ecogenomics Framework To Uncover the Secrets of Nature's "Microbe Whisperers".

Authors:
Simon Roux

mSystems 2019 May 14;4(3). Epub 2019 May 14.

DOE Joint Genome Institute, Walnut Creek, California, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSystems.00111-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6529543PMC
May 2019

A viral reckoning: viruses emerge as essential manipulators of global ecosystems.

Environ Microbiol Rep 2019 02 30;11(1):3-8. Epub 2018 Oct 30.

Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, 70808, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/1758-2229.12700DOI Listing
February 2019

Numerous cultivated and uncultivated viruses encode ribosomal proteins.

Nat Commun 2019 02 14;10(1):752. Epub 2019 Feb 14.

Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, 75015, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-019-08672-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375957PMC
February 2019

First-generation second-generation long-acting injectable antipsychotic drugs and time to relapse.

Ther Adv Psychopharmacol 2018 Dec 25;8(12):333-336. Epub 2018 Sep 25.

Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1177/2045125318795130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6278743PMC
December 2018

Genomic variation and biogeography of Antarctic haloarchaea.

Microbiome 2018 06 20;6(1):113. Epub 2018 Jun 20.

School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40168-018-0495-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6011602PMC
June 2018

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments.

Environ Microbiol 2018 03 12;20(3):1041-1063. Epub 2018 Mar 12.

Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry Meets Biology", University of Vienna, Vienna, Austria.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/1462-2920.14043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5900883PMC
March 2018

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

Nat Commun 2017 10 11;8(1):858. Epub 2017 Oct 11.

Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-017-01086-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5636890PMC
October 2017

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

PeerJ 2017 21;5:e3817. Epub 2017 Sep 21.

Department of Microbiology, Ohio State University, Columbus, OH, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.3817DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5610896PMC
September 2017

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

Front Microbiol 2017 6;8:1241. Epub 2017 Jul 6.

Department of Microbiology, The Ohio State University, ColumbusOH, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2017.01241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5498523PMC
July 2017

Putative archaeal viruses from the mesopelagic ocean.

PeerJ 2017 15;5:e3428. Epub 2017 Jun 15.

Department of Microbiology, Ohio State University, Columbus, OH, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.3428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5474096PMC
June 2017

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

PeerJ 2017 3;5:e3243. Epub 2017 May 3.

Department of Microbiology, Ohio State University, Columbus, OH, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.3243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5419219PMC
May 2017

Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus.

ISME J 2017 01 17;11(1):284-295. Epub 2016 May 17.

Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ismej.2016.81DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5335546PMC
January 2017

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses.

ISME J 2017 01 21;11(1):237-247. Epub 2016 Jun 21.

Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ismej.2016.90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5315482PMC
January 2017

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

PeerJ 2016 8;4:e2777. Epub 2016 Dec 8.

Department of Microbiology, The Ohio State University, Columbus, OH, United States; Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.2777DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5168678PMC
December 2016

Diversity and comparative genomics of chimeric viruses in dominated peatlands.

Virus Evol 2016 Jul 3;2(2):vew025. Epub 2016 Oct 3.

Université de Rennes 1, CNRS UMR6553 EcoBio, Rennes, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/ve/vew025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5822885PMC
July 2016

Analysis of metagenomic data reveals common features of halophilic viral communities across continents.

Environ Microbiol 2016 Mar 10;18(3):889-903. Epub 2015 Dec 10.

Université Blaise Pascal, Laboratoire 'Microorganismes: Génome et Environnement', Clermont Université, Clermont-Ferrand, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/1462-2920.13084DOI Listing
March 2016

Illuminating structural proteins in viral "dark matter" with metaproteomics.

Proc Natl Acad Sci U S A 2016 Mar 16;113(9):2436-41. Epub 2016 Feb 16.

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721; Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721; Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ 85721;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1525139113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4780635PMC
March 2016

Metagenomic characterization of viral communities in corals: mining biological signal from methodological noise.

Environ Microbiol 2015 Oct 27;17(10):3440-9. Epub 2015 Mar 27.

Australian Institute of Marine Science, PMB 3 Townsville MC, Townsville, Qld, 4810, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/1462-2920.12803DOI Listing
October 2015

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

Elife 2015 Jul 22;4. Epub 2015 Jul 22.

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.08490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4533152PMC
July 2015

VirSorter: mining viral signal from microbial genomic data.

PeerJ 2015 28;3:e985. Epub 2015 May 28.

Ecology and Evolutionary Biology, University of Arizona , USA.

View Article

Download full-text PDF

Source
https://peerj.com/articles/985
Publisher Site
http://dx.doi.org/10.7717/peerj.985DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4451026PMC
June 2015

Diversity and comparative genomics of Microviridae in Sphagnum- dominated peatlands.

Front Microbiol 2015 28;6:375. Epub 2015 Apr 28.

CNRS, Laboratoire Microorganismes: Génome et Environnement - UMR 6023, Université Blaise Pascal Clermont-Ferrand, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2015.00375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412055PMC
May 2015

Ocean plankton. Patterns and ecological drivers of ocean viral communities.

Science 2015 May;348(6237):1261498

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA. Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA. Soil, Water, and Environmental Science, University of Arizona, Tucson, AZ 85721, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1261498DOI Listing
May 2015

A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole.

FEMS Microbiol Ecol 2014 Dec 15;90(3):563-74. Epub 2014 Sep 15.

INRA, UMR CARRTEL, Thonon les Bains, France; University of Savoie, UMR CARRTEL, Le Bourget du Lac, France; iEES Paris, UMR CNRS 7618-UPMC-UPEC-Paris Diderot-IRD-INRA, Paris, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/1574-6941.12416DOI Listing
December 2014

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses.

Nat Commun 2013 ;4:2700

1] Laboratoire 'Microorganismes: Génome et Environnement', Clermont Université, Université Blaise Pascal, Clermont-Ferrand 63000, France [2] CNRS UMR 6023, LMGE, Aubière 63171, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms3700DOI Listing
July 2014

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis.

BMC Bioinformatics 2014 Mar 19;15:76. Epub 2014 Mar 19.

Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France.

View Article

Download full-text PDF

Source
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
Publisher Site
http://dx.doi.org/10.1186/1471-2105-15-76DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4002922PMC
March 2014

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

Open Biol 2013 Dec 11;3(12):130160. Epub 2013 Dec 11.

Laboratoire 'Microorganismes: Génome et Environnement', Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1098/rsob.130160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3877843PMC
December 2013

Metagenomics applied to environmental viral communities.

Virologie (Montrouge) 2013 Aug;17(4):229-242

Clermont université, université Blaise-Pascal, laboratoire micro-organismes : génome et environnement, 24, avenue des Landais, 63171 Aubière, France, CNRS, UMR 6023, laboratoire micro-organismes : génome et environnement, 63171 Aubière, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1684/vir.2013.0506DOI Listing
August 2013

Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems.

FEMS Microbiol Ecol 2011 Dec 19;78(3):617-28. Epub 2011 Sep 19.

Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1574-6941.2011.01190.xDOI Listing
December 2011

Metavir: a web server dedicated to virome analysis.

Bioinformatics 2011 Nov 11;27(21):3074-5. Epub 2011 Sep 11.

Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, BP 10448, F-63000 Clermont-Ferrand, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btr519DOI Listing
November 2011