Author

João Paulo Herrera da Silva

University of MinnesotaORCID 0000-0002-3108-5313Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 5 Research Focus:phylogenetics / evolution· 2 Research Focus:cell type annotation· 1 Research Focus:differential expression· 1 Assay:DNA methylation· 1 Research Focus:ecology & biodiversity· 1 Research Focus:host-pathogen & immune response· 1 Assay:metagenomics· 1

Frequent Co-Authors

Kimberly L. VanderWaaliD· 4 shared Nakarin PamornchainavakuliD· 4 shared Cesar A. CorzoiD· 3 shared Igor A. D. PaploskiiD· 3 shared Mariana KikutiiD· 3 shared Albert RoviraiD· 1 shared Alison T. M. LimaiD· 1 shared César Augusto Diniz XavieriD· 1 shared

Activity by Year

2025-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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4 shared papersMicrobiology

Kimberly L. VanderWaalORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

MicrobiologybioRxivPreprintOct 9, 2026

Porcine epidemic diarrhea virus Whole-Genome Diversity Reveals Divergence of Contemporary Populations in the United States

João Paulo Herrera da Silva, Albert Rovira, Fabio Vannucci…·Kimberly L. VanderWaal

This study analyzes complete PEDV genomes to reveal temporal genetic differentiation and recombination in US PEDV populations, expanding the known geographic distribution of S1 clades.

DOI 10.64898/2026.10.08.757685

whole-genome sequencingstatistical model

𝕏 PostBluesky

GeneticsbioRxivPreprintJul 10, 2026

Shifts in Genetic Diversity of Porcine Reproductive and Respiratory Syndrome Virus 2 in Vietnam Before and After African Swine Fever: Increased Diversity and Novel Sub-lineages

Thanh Che Nguyen, Nakarin Pamornchainavakul, João Paulo Herrera da Silva…·Kimberly L. VanderWaal

This study analyzes shifts in PRRSV-2 genetic diversity in Vietnam before and after ASF, finding increased diversity and novel sub-lineages.

DOI 10.64898/2026.07.06.736905

statistical modelphylogenetics / evolution

𝕏 PostBluesky

EcologybioRxivPreprintMar 13, 2026

Timing the regional spread of PRRSV-2 variants across the United States

João Paulo Herrera da Silva, Igor A. D. Paploski, Mariana Kikuti…·Kimberly L. VanderWaal

This study analyzes the spread speed of PRRSV-2 variants across U.S. swine regions using genetic data and epidemiological methods.

DOI 10.64898/2026.03.12.711334

statistical modelhost-pathogen & immune response

𝕏 PostBluesky

MicrobiologybioRxivPreprintSep 10, 2025

Evolution of ssDNA plant viruses in the natural environment - a journey through time

João Paulo Herrera da Silva, César Augusto Diniz Xavier, Phedra G.S. Oliveira…·Francisco Murilo Zerbini Júnior

This study tracks begomovirus evolution in a natural environment over 12 years, finding similar substitution rates to agricultural systems and significant temporal shifts in viral communities.

DOI 10.1101/2025.09.10.675476

plant (other)DNA methylation

𝕏 PostBluesky

MicrobiologymSpherePeer-reviewedJan 23, 2025

PRRSV-2 variant classification: a dynamic nomenclature for enhanced monitoring and surveillance

Kimberly L. VanderWaal, Nakarin Pamornchainavakul, Mariana Kikuti…·Igor A. D. Paploski

This paper introduces a dynamic classification system for PRRSV-2 genetic variants using clustering algorithms and demonstrates its effectiveness in tracking genetic diversity over time.

32 citationstop 1%

virusmetagenomics

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