James Emmanuel San

The paper reprocesses SARS-CoV-2 genomic data to correct systematic errors in phylogenies using a novel assembly tool, resulting in a cleaner global tree of 4.47 million samples.

The paper identifies gaps in genomic surveillance of West Nile Virus in Africa and proposes strategies to improve public health response.

The paper develops an Oxford Nanopore Technology-based protocol for HBV sequencing to improve genomic surveillance in clinical settings, generating full-genome sequences and detailed intra-patient diversity data.

SeqPanther is a tool for analyzing and modifying microbial genome sequences to identify and visualize mutations and variations in NGS data.

This study analyzes SARS-CoV-2 genomic data from Ethiopia to understand its introduction, spread, and evolution during the first four waves of the pandemic.

This study analyzes SARS-CoV-2 genetic diversity and lineage dynamics in Egypt, showing that lineage C.36 evolved into sub-lineages to maintain dominance despite immunity.

The paper uses genomic data to analyze how national and international restrictions affected SARS-CoV-2 transmission in Brazil and Paraguay, showing the spread of variants and the role of importation.

This study uses genomic data from 8746 SARS-CoV-2 genomes across 33 African countries to show that most epidemics were initiated by European importations and later driven by local transmission and mobility, leading to the spread of variants of concern.

This paper describes adapting Illumina protocols for rapid and accurate SARS-CoV-2 whole genome sequencing during a hospital outbreak, reducing library prep time and sharing protocols with a genomics surveillance network.