Simon Roux

30.3k total citations · 13 hit papers
129 papers, 11.7k citations indexed

About

Simon Roux is a scholar working on Ecology, Molecular Biology and Plant Science. According to data from OpenAlex, Simon Roux has authored 129 papers receiving a total of 11.7k indexed citations (citations by other indexed papers that have themselves been cited), including 110 papers in Ecology, 61 papers in Molecular Biology and 56 papers in Plant Science. Recurrent topics in Simon Roux's work include Bacteriophages and microbial interactions (94 papers), Plant Virus Research Studies (50 papers) and Genomics and Phylogenetic Studies (49 papers). Simon Roux is often cited by papers focused on Bacteriophages and microbial interactions (94 papers), Plant Virus Research Studies (50 papers) and Genomics and Phylogenetic Studies (49 papers). Simon Roux collaborates with scholars based in United States, France and Germany. Simon Roux's co-authors include Matthew B. Sullivan, François Enault, Emiley A. Eloe‐Fadrosh, Nikos C. Kyrpides, Stephen Nayfach, Frederik Schulz, Benjamin Bolduc, Antônio Pedro Camargo, Bonnie L. Hurwitz and Tanja Woyke and has published in prestigious journals such as Nature, Cell and Proceedings of the National Academy of Sciences.

In The Last Decade

Simon Roux

124 papers receiving 11.7k citations

Hit Papers

5 papers align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study

2017 979 citations Ann Gregory, Simon Roux et al. profile →
CheckV assesses the quality and completeness of metagenome-assembled viral genomes

2020 905 citations Stephen Nayfach, Antônio Pedro Camargo et al. profile →
VirSorter: mining viral signal from microbial genomic data

2015 721 citations Simon Roux, François Enault et al. profile →
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

2021 682 citations Benjamin Bolduc, Arvind Varsani et al. profile →
DRAM for distilling microbial metabolism to automate the curation of microbiome function

2020 580 citations Mikayla Borton, Lindsey Solden et al. profile →
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

2019 572 citations Ho Bin Jang, Benjamin Bolduc et al. profile →
Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

2015 340 citations Simon Roux, Steven Hallam et al. profile →
Identification of mobile genetic elements with geNomad

2023 301 citations Antônio Pedro Camargo, Simon Roux et al. profile →
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities

2020 287 citations Neha Varghese, Simon Roux et al. profile →
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

2018 251 citations Gareth Trubl, Ho Bin Jang et al. mSystems profile →
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses

2020 221 citations Simon Roux, David Páez-Espino et al. profile →
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

2022 199 citations Antônio Pedro Camargo, Stephen Nayfach et al. profile →
iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria

2023 182 citations Simon Roux, Antônio Pedro Camargo et al. profile →

Peers

Countries citing papers authored by Simon Roux

Since Specialization

Citations

This map shows the geographic impact of Simon Roux's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Simon Roux with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Simon Roux more than expected).

Fields of papers citing papers by Simon Roux

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Simon Roux. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Simon Roux. The network helps show where Simon Roux may publish in the future.

Co-authorship network of co-authors of Simon Roux

This figure shows the co-authorship network connecting the top 25 collaborators of Simon Roux. A scholar is included among the top collaborators of Simon Roux based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Simon Roux. Simon Roux is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

#	Work	Indexed citations
1	Beneath the surface: Unsolved questions in soil virus ecology 2025 ·Soil Biology and Biochemistry ·Christina Hazard, Karthik Anantharaman, Luke S. Hillary, Uri Neri, Simon Roux, Gareth Trubl, (unknown), Jennifer Pett‐Ridge, Graeme W. Nicol, Joanne Emerson	3
2	MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes 2024 ·mSystems ·Clément Coclet, Antônio Pedro Camargo, Simon Roux	6
3	A standardized quantitative analysis strategy for stable isotope probing metagenomics 2023 ·mSystems ·(unknown), (unknown), Kanwar Singh, (unknown), W. Berkeley Kauffman, Erin Nuccio, Steven J. Blazewicz, Jennifer Pett‐Ridge, Katherine Louie, Neha Varghese, Matthew Kellom, Alicia Clum, Robert Riley, Simon Roux, Emiley A. Eloe‐Fadrosh, Ryan Ziels, Rex R. Malmstrom	8
4	New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria 2022 ·Virus Evolution ·(unknown), (unknown), Éric Olo Ndela, (unknown), Anja Poehlein, Heike M. Freese, Simon Roux, Meinhard Simon, François Enault, Cristina Moraru	14
5	Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions 2021 ·The ISME Journal ·Maureen Berg, Danielle Goudeau, (unknown), Katherine D. McMahon, (unknown), (unknown), Donald A. Bryant, Emiley A. Eloe‐Fadrosh, Rex R. Malmstrom, Simon Roux	18
6	Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts 2021 ·The ISME Journal ·Charles Bachy, (unknown), David M. Needham, María Consuelo Gazitúa, Simon Roux, (unknown), Chang Jae Choi, Danielle M. Jorgens, Matthew B. Sullivan, Alexandra Z. Worden	15
7	Perspective on taxonomic classification of uncultivated viruses 2021 ·Current Opinion in Virology ·Bas E. Dutilh, Arvind Varsani, Yigang Tong, Peter Simmonds, Sead Sabanadzovic, Luisa Rubino, Simon Roux, Alejandro Reyes, Cédric Lood, Elliot J. Lefkowitz, Jens H. Kuhn, Mart Krupovìč, Robert A. Edwards, J. Rodney Brister, Evelien M. Adriaenssens, Matthew B. Sullivan	35
8	Ecology and molecular targets of hypermutation in the global microbiome 2021 ·Nature Communications ·Simon Roux, Blair G. Paul, Sarah C. Bagby, Stephen Nayfach, Michelle A. Allen, Graeme T. Attwood, Ricardo Cavicchioli, Ludmila Chistoserdova, Robert J. Gruninger, Steven Hallam, Maria Hernandez, Matthias Hess, Wen‐Tso Liu, Tim A. McAllister, Michelle O’Malley, Xuefeng Peng, Virginia I. Rich, S. R. Saleska, Emiley A. Eloe‐Fadrosh	43
9	Insights into the dynamics between viruses and their hosts in a hot spring microbial mat 2020 ·The ISME Journal ·(unknown), Mária Džunková, Frederik Schulz, Simon Roux, David Páez-Espino, Emiley A. Eloe‐Fadrosh, Sean P. Jungbluth, Natalia Ivanova, John R. Spear, Stephanie Carr, (unknown), Frank A. Corsetti, Hope A. Johnson, Eric D. Becraft, Nikos C. Kyrpides, Ramūnas Stepanauskas, Tanja Woyke	47
10	Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters 2020 ·The ISME Journal ·María Consuelo Gazitúa, Dean Vik, Simon Roux, Ann Gregory, Benjamin Bolduc, Brittany Widner, Margaret R. Mulholland, Steven Hallam, Osvaldo Ulloa, Matthew B. Sullivan	95
11	The International Virus Bioinformatics Meeting 2020 2020 ·Viruses ·Franziska Hufsky, Niko Beerenwinkel, Irmtraud M. Meyer, Simon Roux, (unknown), Cormac M. Kinsella, Kevin Lamkiewicz, Mike Marquet, David F. Nieuwenhuijse, (unknown), Sofia Paraskevopoulou, (unknown), Ronald Dijkman, Bashar Ibrahim, Jenna N. Kelly, Philippe Le Mercier, Manja Marz, Alban Ramette, Volker Thiel	2
12	Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber 2020 ·The ISME Journal ·Live H. Hagen, Charles Brooke, Claire Shaw, Angela Norbeck, Hailan Piao, Magnus Ø. Arntzen, Heather Olson, Alex Copeland, Nancy Isern, Anil Shukla, Simon Roux, Vincent Lombard, Bernard Henrissat, Michelle O’Malley, Igor V. Grigoriev, Susannah G. Tringe, Roderick I. Mackie, Ljiljana Paša‐Tolić, Phillip B. Pope, Matthias Hess	71
13	Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems 2020 ·mSystems ·Robert Danczak, Rebecca A. Daly, Mikayla Borton, James Stegen, Simon Roux, Kelly Wrighton, Michael J. Wilkins	22
14	Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity 2019 ·Microbiology Resource Announcements ·David A. Baltrus, Christina A. Cuomo, John J. Dennehy, Julie C. Dunning Hotopp, Julia A. Maresca, Irene L. G. Newton, David A. Rasko, Antonis Rokas, Simon Roux, Jason Stajich	1
15	Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing breakdown → 2018 ·mSystems ·Gareth Trubl, Ho Bin Jang, Simon Roux, Joanne Emerson, Natalie Solonenko, Dean Vik, Lindsey Solden, Jared Ellenbogen, (unknown), Benjamin Bolduc, Ben J. Woodcroft, S. R. Saleska, Gene W. Tyson, Kelly Wrighton, Matthew B. Sullivan, Virginia I. Rich	251
16	Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales 2018 ·Proceedings of the National Academy of Sciences ·Mikayla Borton, David Hoyt, Simon Roux, Rebecca A. Daly, Susan A. Welch, Carrie Nicora, Samuel Purvine, Elizabeth Eder, Andrea Hanson, (unknown), David M. L. Morgan, Richard Wolfe, Shikha Sharma, Timothy R. Carr, David R. Cole, Paula Mouser, Mary Lipton, Michael J. Wilkins, Kelly Wrighton	61
17	iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure 2016 ·The ISME Journal ·Benjamin Bolduc, Ken Youens‐Clark, Simon Roux, Bonnie L. Hurwitz, Matthew B. Sullivan	78
18	Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses 2016 ·The ISME Journal ·François Enault, Arnaud Briet, (unknown), Simon Roux, Matthew B. Sullivan, Marie‐Agnès Petit	301
19	Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus 2016 ·The ISME Journal ·Cristina Howard‐Varona, Simon Roux, Hugo Doré, Natalie Solonenko, Karin Holmfeldt, Lye Meng Markillie, Galya Orr, Matthew B. Sullivan	42
20	Investigating an Ethical Approach to Genetically Modified Crops in Environmental Educational Processes 2006 ·SHILAP Revista de lepidopterología ·Simon Roux, J.G. Ferreira	1

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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