Computational Reproducibility of Molecular Phylogenies

Molecular Biology and Evolution | 40:msad165 (23 pp)

S. Kumar, Q. Tao, A. P. Lamarca, K. Tamura


Molecular Timetrees using Relaxed Clocks and Uncertain Phylogenies

Frontiers in Bioinformatics | 3:1225807 (13 pp)

J. Barba-Montoya, S. Sharma, S. Kumar


The Origin of Eukaryotes and Rise in Complexity were Synchronous with the Rise in Oxygen

Frontiers in Bioinformatics | 3:1233281 (10 pp)

J. M. Craig, S. Kumar, S. B. Hedges


Improving Cellular Phylogenies through the Integrated Use of Mutation Order and Optimality Principles

Computational and Structural Biotechnology Journal | 21:3894–3903

S. Miura, T. Dolker, M. Sanderford, S. Kumar


Gene Expression Study of Breast Cancer using Welch Satterthwaite t-test, Kaplan-Meier Estimator Plot and Huber Loss Robust Regression Model

Journal of King Saud University - Science | 35:102447 (9 pp)

S. Karim, M.S. Iqbal, N. Ahmad, M.S. Ansari, Z. Mirza, A. Merdad, S. Jastaniah, S. Kumar


Bootstrap Confidence for Molecular Evolutionary Estimates from Tumor Bulk Sequencing Data

Frontiers in Bioinformatics | 3:1090730 (11 pp)

J. Huzar, M. Shenoy, M. D. Sanderford, S. Kumar, S. Miura


Protein Dynamics Provide Mechanistic Insights about Epistasis among Common Missense Polymorphisms

Biophysical Journal | 122:2938–2947

N. J. Ose, P. Campitelli, R. Patel, S. Kumar, S. B. Ozkan


Discovering Research Articles Containing Evolutionary Timetrees by Machine Learning

Bioinformatics | 39:btad035 (7 pp)

M. Stanojevic, J. Andjelkovic, A. Kasprowicz, L.A. Huuki, J. Chao, S.B. Hedges, S. Kumar, Z. Obradovic


Evolutionary Sparse Learning Reveals the Shared Genetic Basis of Convergent Traits

| (In review)

J. Allard , S. Sharma , R. Patel , M. Sanderford , K. Tamura , S. Vucetic , G. Gerhard, S. Kumar


Split-Transformer Impute (ST): Genotype Imputation Using a Transformer-Based Model

bioRxiv | (in review)

M.E. Mowlaei, C. Li, J. Chen, B. Jamialahmadi, S. Kumar, T.R. Rebbeck, X. Shi


Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics

| (in review)

N. Ose, P. Campitelli, T. Modi, I. Kazan, S. Kumar, B. Ozkan


Balancing Selection is Common for Beneficial Alleles in a Human Population

| (in review)

A. Pivirotto, A. Platt, R. Patel, S. Kumar, J. Hey


Masatoshi Nei (1931–2023)

Nature Ecology & Evolution | 7:(2 pp)

J. Zhang, S. Kumar


Masatoshi Nei (1931–2023)

Molecular Biology and Evolution | 40:msad149 (5 pp)

S. Kumar, T. Gojobori


R3F: An R Package for Evolutionary Dates, Rates, and Priors using Relative Rate Framework

bioRxiv | (available)

Q. Tao, S. Sharma, K. Tamura, S. Kumar