Research on SARS-CoV-2 Evolution
An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic (2020)
Authors: S. Kumar, Q. Tao, S. Weaver, M. Sanderford, M. A. Caraballo-Ortiz, S. Sharma, S. L. K. Pond, S. Miura
Molecular Biology and Evolution
Research on Big Data Phylogenomics
Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps (2021)
Authors: S. Sharma, & S. Kumar
Nature Computational Science
DOI: https://doi.org/10.1038/s43588-021-00129-5
Taming the selection of optimal substitution models in Phylogenomics by site subsampling and upsampling
Authors: S. Sharma, & S. Kumar
Molecular Biology and Evolution
DOI: https://doi.org/10.1093/molbev/msac236
Molecular timetrees using relaxed clocks and uncertain phylogenies
Authors: J. Barba, S. Sharma, & S. Kumar
Frontiers in Bioinformatics
Research on Machine Learning in Phylogenomics
Evolutionary Sparse Learning for Phylogenomics (2021)
Authors: S. Kumar, & S. Sharma
Molecular Biology and Evolution
DOI: https://doi.org/10.1093/molbev/msab227
Discovering fragile clades and Causal Sequences in phylogenomics by Evolutionary sparse learning (2024)
Authors: S. Sharma & S. Kumar
In Review (2024)
Evolutionary sparse learning reveals the shared genetic basis of convergent traits (2024)
Authors: J. Allard, S. Sharma, R. Patel, S. Maxwell, K Tamura, S. Vucetic, G. Gerhard & S. Kumar
In Review (2024)
Research on Cancer Evolution
Methods for Estimating Personal Disease Risk and Phylogenetic Diversity of Hematopoietic Stem Cells (2024)
Authors: J. Craig, G. Gerhard, S. Sharma, A. Yankovskiy, S. Miura, & S. Kumar
Molecular Biology and Evolution
DOI: https://doi.org/10.1093/molbev/msab227