iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria von Roux, Simon, Camargo, Antonio Pedro, Coutinho, Felipe H, Dabdoub, Shareef M, Dutilh, Bas E, Nayfach, Stephen, Tritt, Andrew

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Global overview and major challenges of host prediction methods for uncultivated phages von Coclet, Clément, Roux, Simon

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CheckV assesses the quality and completeness of metagenome-assembled viral genomes von Nayfach, Stephen, Camargo, Antonio Pedro, Schulz, Frederik, Eloe-Fadrosh, Emiley, Roux, Simon, Kyrpides, Nikos C.

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VirSorter: mining viral signal from microbial genomic data von Roux, Simon, Enault, Francois, Hurwitz, Bonnie L, Sullivan, Matthew B

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Viral dark matter and virus-host interactions resolved from publicly available microbial genomes von Roux, Simon, Hallam, Steven J, Woyke, Tanja, Sullivan, Matthew B

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A Viral Ecogenomics Framework To Uncover the Secrets of Nature's "Microbe Whisperers" von Roux, Simon

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Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks von Bin Jang, Ho, Bolduc, Benjamin, Zablocki, Olivier, Kuhn, Jens H., Roux, Simon, Adriaenssens, Evelien M., Brister, J. Rodney, Kropinski, Andrew M, Krupovic, Mart, Lavigne, Rob, Turner, Dann, Sullivan, Matthew B.

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Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes von Liu, Ying, Demina, Tatiana A, Roux, Simon, Aiewsakun, Pakorn, Kazlauskas, Darius, Simmonds, Peter, Prangishvili, David, Oksanen, Hanna M, Krupovic, Mart

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The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities von Chen, I-Min A, Chu, Ken, Palaniappan, Krishnaveni, Ratner, Anna, Huang, Jinghua, Huntemann, Marcel, Hajek, Patrick, Ritter, Stephan, Varghese, Neha, Seshadri, Rekha, Roux, Simon, Woyke, Tanja, Eloe-Fadrosh, Emiley A, Ivanova, Natalia N, Kyrpides, Nikos C

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VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses von Guo, Jiarong, Bolduc, Ben, Zayed, Ahmed A, Varsani, Arvind, Dominguez-Huerta, Guillermo, Delmont, Tom O, Pratama, Akbar Adjie, Gazitúa, M Consuelo, Vik, Dean, Sullivan, Matthew B, Roux, Simon

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DRAM for distilling microbial metabolism to automate the curation of microbiome function von Shaffer, Michael, Borton, Mikayla A, McGivern, Bridget B, Zayed, Ahmed A, La Rosa, Sabina Leanti, Solden, Lindsey M, Liu, Pengfei, Narrowe, Adrienne B, Rodríguez-Ramos, Josué, Bolduc, Benjamin, Gazitúa, M Consuelo, Daly, Rebecca A, Smith, Garrett J, Vik, Dean R, Pope, Phil B, Sullivan, Matthew B, Roux, Simon, Wrighton, Kelly C

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IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses von Roux, Simon, Páez-Espino, David, Chen, I-Min A, Palaniappan, Krishna, Ratner, Anna, Chu, Ken, Reddy, T B K, Nayfach, Stephen, Schulz, Frederik, Call, Lee, Neches, Russell Y, Woyke, Tanja, Ivanova, Natalia N, Eloe-Fadrosh, Emiley A, Kyrpides, Nikos C

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Giant virus diversity and host interactions through global metagenomics von Schulz, Frederik, Roux, Simon, Paez-Espino, David, Jungbluth, Sean, Walsh, David A., Denef, Vincent J., McMahon, Katherine D., Konstantinidis, Konstantinos T., Eloe-Fadrosh, Emiley A., Kyrpides, Nikos C., Woyke, Tanja

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Metavir 2: new tools for viral metagenome comparison and assembled virome analysis von Roux, Simon, Tournayre, Jeremy, Mahul, Antoine, Debroas, Didier, Enault, François

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Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages von Kieft, Kristopher, Zhou, Zhichao, Anderson, Rika E., Buchan, Alison, Campbell, Barbara J., Hallam, Steven J., Hess, Matthias, Sullivan, Matthew B., Walsh, David A., Roux, Simon, Anantharaman, Karthik

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Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses von Roux, Simon, Brum, Jennifer R., Dutilh, Bas E., Sunagawa, Shinichi, Duhaime, Melissa B., Loy, Alexander, Poulos, Bonnie T., Solonenko, Natalie, Lara, Elena, Poulain, Julie, Pesant, Stéphane, Kandels-Lewis, Stefanie, Dimier, Céline, Picheral, Marc, Searson, Sarah, Cruaud, Corinne, Alberti, Adriana, Duarte, Carlos M., Gasol, Josep M., Vaqué, Dolors, Bork, Peer, Acinas, Silvia G., Wincker, Patrick, Sullivan, Matthew B.

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Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity von Roux, Simon, Emerson, Joanne B, Eloe-Fadrosh, Emiley A, Sullivan, Matthew B

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Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study von Kang, Dae-Wook, Adams, James B, Gregory, Ann C, Borody, Thomas, Chittick, Lauren, Fasano, Alessio, Khoruts, Alexander, Geis, Elizabeth, Maldonado, Juan, McDonough-Means, Sharon, Pollard, Elena L, Roux, Simon, Sadowsky, Michael J, Lipson, Karen Schwarzberg, Sullivan, Matthew B, Caporaso, J Gregory, Krajmalnik-Brown, Rosa

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vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria von Bolduc, Benjamin, Jang, Ho Bin, Doulcier, Guilhem, You, Zhi-Qiang, Roux, Simon, Sullivan, Matthew B

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Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads von Roux, Simon, Krupovic, Mart, Poulet, Axel, Debroas, Didier, Enault, François

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