Author

C. Ruis

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 3 Evolutionary Biology· 2

Signature Assays, Organisms & Methods

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Approach:statistical model· 5 Assay:whole-genome sequencing· 3 Assay:DNA methylation· 2 Research Focus:host-pathogen & immune response· 2 Organism:human· 2 Organism:bacteria (other)· 1 Research Focus:cell type annotation· 1 Research Focus:chromatin & epigenetic regulation· 1

Frequent Co-Authors

A. Rambaut· 2 shared A. S. Hinrichs· 2 shared J. McBroome· 2 shared J. Parkhill· 2 shared R. A. Floto· 2 shared R. Corbett-Detig· 2 shared Y. Turakhia· 2 shared A. de Bernardi Schneider· 1 shared

Activity by Year

2019-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

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2 shared papersEvolutionary Biology

A. Rambaut

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Author profile →

5 papers

Recent·Most cited

Automated Agnostic Designation of Pathogen Lineages

J. McBroome, A. de Bernardi Schneider, C. Roemer, M. T. Wolfinger, A. S. Hinrichs, A. N. O'Toole, C. Ruis, Y. Turakhia, A. Rambaut, R. Corbett-Detig

The paper introduces an automated method for pathogen lineage designation using phylogenetic trees, offering a consistent alternative to manual curation.

bioRxiv · Feb 3, 2023 · PreprintEvolutionary Biology

Mutational spectra distinguish SARS-CoV-2 replication niches

C. Ruis, T. P. Peacock, L. M. Polo, D. Masone, M. Soledad Alvarez, A. S. Hinrichs, Y. Turakhia, C. Ye, J. McBroome, R. Corbett-Detig, J. Parkhill, R. A. Floto

The paper analyzes SARS-CoV-2 mutational spectra to infer replication niches, finding reduced G>T mutations in Omicron linked to upper respiratory tract replication.

bioRxiv · Sep 27, 2022 · PreprintMicrobiology

Mutational spectra analysis reveals bacterial niche and transmission routes

C. Ruis, A. Weimann, G. Tonkin-Hill, A. P. Pandurangan, M. MATUSZEWSKA, G. G. R. Murray, R. C. Levesque, T. L. Blundell, R. A. Floto, J. Parkhill

The paper analyzes mutational spectra in bacterial lineages to infer niche-specific mutagen exposure and transmission routes.

bioRxiv · Jul 13, 2022 · PreprintMicrobiology

A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology

A. Rambaut, E. C. Holmes, V. Hill, A. OToole, J. McCrone, C. Ruis, L. du Plessis, O. Pybus

This paper proposes a dynamic nomenclature system for SARS-CoV-2 to improve genomic epidemiology by tracking active lineages and their spread.

bioRxiv · Apr 17, 2020Microbiology

Preadaptation of pandemic GII.4 noroviruses in hidden virus reservoirs years before emergence

C. Ruis, L. Lindesmith, M. Mallory, P. D. Brewer-Jensen, J. Bryant, V. Costantini, C. Monit, J. Vinje, R. S. Baric, R. A. Goldstein, J. A. Breuer

This paper shows that GII.4 noroviruses preadapt and circulate undetected for years before causing a new pandemic, with changes in host immunity enabling spread rather than genetic changes alone.

bioRxiv · Jun 3, 2019Evolutionary Biology