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Simon Roux

Simon Roux, Ph.D., Viral Genomics Group Lead, DOE Joint Genome Institute

Dr. Roux joined the JGI in 2017 to lead viral genomics research as part of the Metagenome Program. His responsibilities include the development of novel computational tools to identify virus sequences, the design of new experimental approaches to link viruses to their host(s), collaboration with JGI users for analyzing viral datasets, and the organization of community-building efforts in the field of viral ecogenomics. For this role, Dr. Roux can rely on more than 10 years of expertise in the fields of virus ecology and virus genomics, where he has engaged in collaborative, interdisciplinary research focused around developing foundational knowledge of viral diversity and virus-host interactions in microbial systems. Through a 2021 DOE Early Career Research Program, Dr. Roux established and currently leads the Viral Genomics group at JGI to further explore the ecological and evolutionary drivers of virus-host dynamics in soil microbial communities.

Education

  • B.S. in Microbiology, Université Blaise Pascal, France
  • M.S. in Data Analysis and Modeling for Life Sciences, Université Blaise Pascal, France
  • Ph.D. in Bioinformatics, Ecology and Evolutionary Biology, Université Blaise Pascal, France

Awards and Service

  • DOE BER Early Career Research Program, 2021
  • Thomson Reuters Highly Cited Researcher (Cross-field), 2020
  • LBNL Early Career LDRD, 2018
  • Senior Editor: Microbiology Resource Announcements

Selected publications

  1. Roux et al., 2021. Ecology and molecular targets of hypermutation in the global microbiome. Nature Communications 12, 3076.
  2. Roux et al., 2018. Minimum Information about an Uncultivated Virus Genome (MIUViG). Nature Biotechnology 37, 29–37.
  3. Berg 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, 1569–1584.
  4. Nayfach et al., 2020. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nature biotechnology 39, 578-585.
  5. Roux et al., 2019. Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes. Nature Microbiology 4, 1895–1906.
  6. Schulz et al., 2020. Giant virus diversity and host interactions through global metagenomics. Nature 578, 432–436.
  7. Roux et al., 2020. IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses Nucleic acids research 49, D764-D775.
  8. Roux et al., 2016. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689–693.
  9. Brum, Roux, Ignacio-Espinoza et al., 2015. Patterns and ecological drivers of ocean viral communities. Science 348, 6237.