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