MicrobeTrace integrates and analyzes multi-source public health data to support rapid outbreak response, demonstrating its utility with HIV and SARS-CoV-2 datasets.

PLoS Computational Biology · Sep 7, 2021Peer-reviewedBioinformatics

Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction

Sergey Knyazev, Viachaslau Tsyvina, Anupama Shankar, Andrew Melnyk, Alexander Artyomenko, Tatiana Malygina, Yuri B. Porozov, Ellsworth M. Campbell, William M. Switzer, Pavel Skums, Serghei Mangul, Alex Zelikovsky

This paper introduces CliqueSNV, a method to accurately identify minority viral haplotypes from NGS data by reducing sequencing noise, achieving detection at frequencies as low as 0.1%.

Nucleic Acids Research · Jun 18, 2021Peer-reviewedBioinformatics

Genome-wide patterns of gene expression in a wild primate indicate species-specific mechanisms associated with tolerance to natural simian immunodeficiency virus infection

Noah D. Simons, Geeta N. Eick, María José Ruiz‐López, David Hyeroba, Patrick A. Omeja, Geoffrey Weny, Huiyuan Zheng, Anupama Shankar, Simon D. W. Frost, James Holland Jones, Colin A. Chapman, William M. Switzer, Tony L. Goldberg, Kirstin N. Sterner, Nelson Ting

The paper analyzes gene expression in wild Ugandan red colobus to show SIV infection does not cause chronic immune activation and identifies upregulation of CD101 as a potential tolerance mechanism.

Genome Biology and Evolution · May 9, 2019Peer-reviewedGenomics