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

Microbiota Transfer Thera... 2015 2026 2018 2022 2017 2020 2015 2021 2020 250 500 750
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.

  1. 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 →
  2. CheckV assesses the quality and completeness of metagenome-assembled viral genomes
    2020 905 citations Stephen Nayfach, Antônio Pedro Camargo et al. profile →
  3. VirSorter: mining viral signal from microbial genomic data
    2015 721 citations Simon Roux, François Enault et al. profile →
  4. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses
    2021 682 citations Benjamin Bolduc, Arvind Varsani et al. profile →
  5. DRAM for distilling microbial metabolism to automate the curation of microbiome function
    2020 580 citations Mikayla Borton, Lindsey Solden et al. profile →
  6. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
    2019 572 citations Ho Bin Jang, Benjamin Bolduc et al. profile →
  7. Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
    2015 340 citations Simon Roux, Steven Hallam et al. profile →
  8. Identification of mobile genetic elements with geNomad
    2023 301 citations Antônio Pedro Camargo, Simon Roux et al. profile →
  9. 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 →
  10. Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing
    2018 251 citations Gareth Trubl, Ho Bin Jang et al. mSystems profile →
  11. 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 →
  12. 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 →
  13. 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 →

Author Peers

Peers are selected by citation overlap in the author's most active subfields. citations · hero ref

Author Last Decade Papers Cites
Simon Roux 8.5k 5.7k 3.0k 1.6k 1.3k 129 11.7k
Matthew B. Sullivan 14.1k 1.7× 9.9k 1.7× 3.9k 1.3× 1.9k 1.1× 1.4k 1.1× 155 18.8k
Eric P. Nawrocki 4.3k 0.5× 11.1k 1.9× 3.6k 1.2× 1.1k 0.7× 973 0.8× 31 16.9k
Paramvir Dehal 4.4k 0.5× 9.1k 1.6× 3.0k 1.0× 1.5k 0.9× 811 0.6× 25 16.3k
Torbjørn Rognes 5.6k 0.7× 9.3k 1.6× 2.8k 0.9× 695 0.4× 531 0.4× 64 15.5k
Lars Hestbjerg Hansen 3.8k 0.4× 9.1k 1.6× 1.6k 0.5× 1.6k 1.0× 1.1k 0.9× 331 16.9k
Vladislav Saveliev 2.2k 0.3× 4.3k 0.7× 1.9k 0.6× 709 0.4× 900 0.7× 6 7.9k
Alexandre Lomsadze 2.8k 0.3× 6.5k 1.1× 3.2k 1.1× 528 0.3× 743 0.6× 27 10.8k
Benjamin Buchfink 3.4k 0.4× 5.6k 1.0× 2.5k 0.8× 867 0.5× 490 0.4× 5 10.7k
Sarah K. Highlander 3.0k 0.4× 5.7k 1.0× 1.2k 0.4× 1.1k 0.7× 345 0.3× 71 11.7k
Alexander F. Auch 4.7k 0.6× 7.8k 1.4× 2.3k 0.8× 360 0.2× 544 0.4× 17 10.5k

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

20 of 20 papers shown
1.
Kosina, Suzanne M., Katherine Louie, Matthew B. Sullivan, et al.. (2025). Virocell Necromass Provides Limited Plant Nitrogen and Elicits Rhizosphere Metabolites That Affect Phage Dynamics. Plant Cell & Environment. 1 indexed citations
2.
Coclet, Clément, Antônio Pedro Camargo, & Simon Roux. (2024). MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes. mSystems. 9(10). e0088824–e0088824. 6 indexed citations
3.
Singh, Kanwar, W. Berkeley Kauffman, Erin Nuccio, et al.. (2023). A standardized quantitative analysis strategy for stable isotope probing metagenomics. mSystems. 8(4). e0128022–e0128022. 8 indexed citations
4.
Vik, Dean, Benjamin Bolduc, Simon Roux, et al.. (2023). MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets. ISME Communications. 3(1). 87–87. 4 indexed citations
5.
Ndela, Éric Olo, Anja Poehlein, Heike M. Freese, et al.. (2022). New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria. Virus Evolution. 8(2). veac070–veac070. 14 indexed citations
6.
Berg, Maureen, Danielle Goudeau, Katherine D. McMahon, et al.. (2021). Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions. The ISME Journal. 15(6). 1569–1584. 18 indexed citations
7.
Bachy, Charles, David M. Needham, María Consuelo Gazitúa, et al.. (2021). Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts. The ISME Journal. 15(11). 3129–3147. 15 indexed citations
8.
Roux, Simon, Blair G. Paul, Sarah C. Bagby, et al.. (2021). Ecology and molecular targets of hypermutation in the global microbiome. Nature Communications. 12(1). 3076–3076. 43 indexed citations
9.
10.
Dutilh, Bas E., Arvind Varsani, Yigang Tong, et al.. (2021). Perspective on taxonomic classification of uncultivated viruses. Current Opinion in Virology. 51. 207–215. 35 indexed citations
11.
Džunková, Mária, Frederik Schulz, Simon Roux, et al.. (2020). Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. The ISME Journal. 14(10). 2527–2541. 47 indexed citations
12.
Hufsky, Franziska, Niko Beerenwinkel, Irmtraud M. Meyer, et al.. (2020). The International Virus Bioinformatics Meeting 2020. Viruses. 12(12). 1398–1398. 2 indexed citations
13.
Gazitúa, María Consuelo, Dean Vik, Simon Roux, et al.. (2020). Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. The ISME Journal. 15(4). 981–998. 95 indexed citations
14.
Baltrus, David A., Christina A. Cuomo, John J. Dennehy, et al.. (2019). Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity. Microbiology Resource Announcements. 8(36). 1 indexed citations
15.
Trubl, Gareth, Ho Bin Jang, Simon Roux, et al.. (2018). Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing. mSystems. 3(5). 251 indexed citations breakdown →
16.
Borton, Mikayla, David Hoyt, Simon Roux, et al.. (2018). Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales. Proceedings of the National Academy of Sciences. 115(28). E6585–E6594. 61 indexed citations
17.
Enault, François, et al.. (2016). Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses. The ISME Journal. 11(1). 237–247. 301 indexed citations
18.
Bolduc, Benjamin, Ken Youens‐Clark, Simon Roux, Bonnie L. Hurwitz, & Matthew B. Sullivan. (2016). iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. The ISME Journal. 11(1). 7–14. 78 indexed citations
19.
Howard‐Varona, Cristina, Simon Roux, Hugo Doré, et al.. (2016). Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus. The ISME Journal. 11(1). 284–295. 42 indexed citations
20.
Roux, Simon & J.G. Ferreira. (2006). Investigating an Ethical Approach to Genetically Modified Crops in Environmental Educational Processes. SHILAP Revista de lepidopterología. 1 indexed citations

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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