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Simon Roux

Lawrence Berkeley National Laboratory

77H-index
391Paper Count
3.0WCitation Count
Published Papers 113
Publication Date
Small viruses reveal bidirectional evolution between HK97-fold viruses and encapsulins via procapsids
err2026-10-14
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errOAAI
errAbelardo Aguilar; Ingrid Miranda Perez; Omer Nadel; Stephen Nayfach; Luis Ruiz Pestana; Anca M. Segall; Forest L. Rohwer; Simon Roux; Simon White; Antoni Luque
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The biogeography of giant viruses and interactions with Eukaryotes across European lakes
err2026-09-23
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errOAAI
errOlesya V. Kolmakova; Frederik Schulz; Yumary M. Vasquez; Jeremy A. Fonvielle; Lucas P. P. Braga; Simon Roux; Tanja Woyke; Andrew J. Tanentzap
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Viral genetic diversity and functional potential in polar and subarctic sea ice
err2026-07-20
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errOAAI
errKalle J Pettersson; Tatiana Demina; Eeva Eronen-Rasimus; Simon Roux; Sirja Viitamäki; Igor S Pessi; Hanna M Oksanen; Philipp Assmy; Hermanni Kaartokallio; Jenni Hultman; null; null
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Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils
err2026-06-29
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errOAAI
errJiarong Guo; Samuel T. N. Aroney; Guillermo Domínguez-Huerta; Derek Smith; Dean Vik; Carlos Owusu-Ansah; Akbar Adjie Pratama; Sergei Solonenko; Funing Tian; Cristina Howard-Varona; Zhi-Ping Zhong; Aminata Fofana; Garrett J. Smith; Suzanne B. Hodgkins; Dylan Cronin; Ben J. Woodcroft; Gene W. Tyson; Virginia I. Rich; Matthew B. Sullivan; Simon Roux; Sarah C. Bagby
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Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome
err2026-05-28
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errG. Ghiotto; G. Zampieri; E. Orellana; A. Chatzis; P. G. Kougias; A. Camargo; S. Roux; S. Campanaro; N. C. Kyrpides; L. Treu
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Changes to virus taxonomy, the international code of virus classification and nomenclature, and the ICTV statutes ratified by the International Committee on Taxonomy of Viruses (2025)
err2025-12-18
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PREAI
errSimmonds, Peter; Adriaenssens, Evelien M.; Lefkowitz, Elliot J.; Oksanen, Hanna M.; Zerbini, Francisco Murilo; Alfenas-Zerbini, Poliane; Aylward, Frank O.; Dempsey, Donald M.; Freitas-Astua, Juliana; Hendrickson, R. Curtis; Hughes, Holly R.; Krupovic, Mart; Kuhn, Jens H.; Lobocka, Malgorzata; Mayne, Richard; Mushegian, Arcady R.; Penzes, Judit J.; Reyes Munoz, Alejandro; Robertson, David L.; Roux, Simon; Rubino, Luisa; Sabanadzovic, Sead; Smith, Donald B.; Suzuki, Nobuhiro; Turner, Dann; Van Doorslaer, Koenraad; Varsani, Arvind
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Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient
err2025-12-11
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errOAAI
errGareth Trubl; Simon Roux; Mikayla A. Borton; Arvind Varsani; Yueh-Fen Li; Christine L. Sun; Ho Bin Jang; Ben J. Woodcroft; Gene W. Tyson; Kelly C. Wrighton; Scott R. Saleska; Emiley A. Eloe-Fadrosh; Matthew B. Sullivan; Virginia I. Rich
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STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies
err2025-12-01
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PREAI
errJulia M. Kelliher; Chloe Mirzayi; Sarah R. Bordenstein; Aaron Oliver; Christina A. Kellogg; Eneida L. Hatcher; Maureen Berg; Petr Baldrian; Mashael Aljumaah; Cassandra Maria Luz Miller; Christopher Mungall; Vlastimil Novak; Alexis Palucki; Ethan Smith; Nazifa Tabassum; Gregory Bonito; J. Rodney Brister; Patrick S. G. Chain; Mingfei Chen; Samuel Degregori; Jose Pablo Dundore-Arias; Joanne B. Emerson; Vanessa Moreira C. Fernandes; Roberto Flores; Antonio Gonzalez; Zoe A. Hansen; Scott A. Jackson; Ahmed M. Moustafa; Trent R. Northen; Nonia Pariente; Jennifer Pett-Ridge; Sydne Record; Linta Reji; Anna-Louise Reysenbach; Virginia I. Rich; Lorna Richardson; Simon Roux; Lynn M. Schriml; Reed S. Shabman; Maria A. Sierra; Matthew B. Sullivan; Punithavathi Sundaramurthy; Katherine M. Thibault; Luke R. Thompson; Scott Tighe; Ethell Vereen; Emiley A. Eloe-Fadrosh
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VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses
err2025-12-01
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errOAAI
errSaghaei, Shahram; Siemers, Malte; Ossetek, Kilian L.; Richter, Stephan; Edwards, Robert a; Roux, Simon; Zielezinski, Andrzej; Dutilh, Bas E.; Marz, Manja; Cassman, Noriko A.
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A call for caution in the biological interpretation of viral auxiliary metabolic genes
err2025-08-27
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errOAAI
errCody Martin; Joanne B. Emerson; Simon Roux; Karthik Anantharaman
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Quantifying the impact of workshops promoting microbiome data standards and data stewardship
err2025-03-22
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errOAAI
errKelliher, Julia M.; Rodriguez, Francisca E.; Johnson, Leah Y. D.; Roux, Simon; Smith, Montana; Clum, Alicia; Lynch, Wendi; Bias, Candace Hope; Finks, Sarai S.; Keenum, Ishi; Kiledal, E. Anders; Lin, Heng-An; Longley, Reid; Mcdonald, Ryan; Pitot, Thomas M.; Rodriguez-Ramos, Josue; Shen, Jiaxian; Sprockett, Daniel D.; Swift, Joel; Yadav, Archana; Eloe-Fadrosh, Emiley A.
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Viral niche-partitioning: comparative genomics of giant viruses across environmental gradients in a high Arctic freshwater-saltwater lake
err2024-12-08
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errOAAI
errPitot, Thomas M.; Girard, Catherine; Rapp, Josephine Z.; Somerville, Vincent; Culley, Alexander, I; Vincent, Warwick F.; Moineau, Sylvain; Roux, Simon
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Distinct and rich assemblages of giant viruses in Arctic and Antarctic lakes
err2024-03-29
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errOAAI
errPitot, Thomas M.; Rapp, Josephine Z.; Schulz, Frederik; Girard, Catherine; Roux, Simon; Culley, Alexander, I
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IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata
err2023-11-01
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errOAAI
errCamargo, Antonio Pedro; Call, Lee; Roux, Simon; Nayfach, Stephen; Huntemann, Marcel; Palaniappan, Krishnaveni; Ratner, Anna; Chu, Ken; Mukherjeep, Supratim; Reddy, T. B. K.; Chen, I-Min A.; Ivanova, Natalia N.; Eloe-Fadrosh, Emiley A.; Woyke, Tanja; Baltrus, David A.; Castaneda-Barba, Salvador; de la Cruz, Fernando; Funnell, Barbara E.; Hall, James P. J.; Mukhopadhyay, Aindrila; Rocha, Eduardo P. C.; Stalder, Thibault; Top, Eva; Kyrpides, Nikos C.
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Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem
err2023-10-27
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errOAAI
errCoclet, Clement; Sorensen, Patrick O.; Karaoz, Ulas; Wang, Shi; Brodie, Eoin L.; Eloe-Fadrosh, Emiley A.; Roux, Simon
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Identification of mobile genetic elements with geNomad
err2023-09-21
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errOAAI
errCamargo, Antonio Pedro; Roux, Simon; Schulz, Frederik; Babinski, Michal; Xu, Yan; Hu, Bin; Chain, Patrick S. G.; Nayfach, Stephen; Kyrpides, Nikos C.
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