Author

Rafael Lopes

Yale UniversityORCID 0000-0002-9416-6145Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 2 Bioinformatics· 1 Ecology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Assay:whole-genome sequencing· 4 Research Focus:phylogenetics / evolution· 2 Research Focus:benchmarking· 1 Research Focus:chromatin & epigenetic regulation· 1 Organism:virus· 1

Frequent Co-Authors

Nathan D. GrubaughiD· 4 shared Verity HilliD· 4 shared Abigail J PorzucekiD· 2 shared Colin J. CarlsoniD· 2 shared Guy BaeleiD· 2 shared Marc A. SuchardiD· 2 shared Philippe LemeyiD· 2 shared Simon DellicouriD· 2 shared

Activity by Year

2025-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 43 mutual co-author links

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4 shared papersGenomics

Nathan D. GrubaughORCID

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4 papers

Recent·Most cited

BioinformaticsbioRxivPreprintOct 4, 2026

Tracking two decades of global dengue virus lineage dynamics

Samantha Good, Abigail J Porzucek, Yi Ting Chew…·Nathan D. Grubaugh

This study tracks DENV lineage dynamics over two decades using 37,828 genomes, revealing regional diversity patterns and the impact of COVID-19 on lineage persistence and spread.

DOI 10.64898/2026.10.02.756263

whole-genome sequencingstatistical model

𝕏 PostBluesky

GenomicsbioRxivPreprintSep 30, 2026

Phylodynamic analysis reveals asymmetric and accelerating global spread of dengue virus

Verity Hill, Gytis Dudas, Xiang Ji…·Nathan D. Grubaugh

This study uses phylogeographic and phylodynamic methods to analyze DENV genome data, revealing asymmetric global spread patterns and the role of travel over climate in DENV transmission.

DOI 10.64898/2026.09.28.754967

whole-genome sequencingstatistical model

𝕏 PostBluesky

EcologybioRxivPreprintJan 10, 2026

Evolutionary history of Jamestown Canyon virus disentangles complex multi-vector ecology

Ellie Bourgikos, Simon Dellicour, Philippe Lemey…·Nathan D. Grubaugh

This study uses whole-genome sequencing and phylodynamic methods to analyze the evolutionary history and ecological dynamics of Jamestown Canyon virus, revealing its slow evolution and transmission patterns.

DOI 10.64898/2026.01.09.698726

whole-genome sequencingstatistical model

𝕏 PostBluesky

GenomicsEmerging infectious diseasesPeer-reviewedMay 1, 2025

Large-scale genomic analysis of SARS-CoV-2 Omicron BA.5 emergence in the United States

Kien Pham, Chrispin Chaguza, Rafael Lopes…·Verity Hill

This study analyzes the genomic data of SARS-CoV-2 Omicron BA.5 variants in the U.S. to understand their emergence patterns and transmission dynamics.

1 citation

viruswhole-genome sequencing

𝕏 PostBluesky