Houriiyah Tegally

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.

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

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.

Disaggregation Regression and Multi-Model Evaluation for Predicting Dengue Risk in Africa

This paper uses disaggregation regression to predict dengue incidence in Africa from aggregated data, showing better alignment with reported cases than environmental suitability models.

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.

SeqPanther: Sequence manipulation and mutation statistics toolset

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

SARS-CoV-2 Genetic diversity and lineage dynamics of in Egypt

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.

Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil

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.

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

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.

Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic

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.