Cheryl Baxter

Anniemap: Vector Search for Viral Short Read Alignment

Anniemap improves viral short-read alignment by using vector similarity search, achieving higher sensitivity and throughput, especially for divergent genomes like HIV and HCV.

Alignment Free Viral Sequence Classification

This study evaluates alignment-free methods for viral sequence classification, showing high accuracy and efficiency on SARS-CoV-2, dengue, and HIV datasets.

Craft: A Machine Learning Approach to Dengue Subtyping

Craft is a machine learning framework for dengue subtyping that achieves high accuracy and speed, outperforming existing tools in classification efficiency.

Identifying genomic surveillance gaps in Africa for the global public health response to West Nile Virus

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

An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable For Genomic Surveillance Within Clinical Diagnostic Settings.

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.

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020-2022

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.