Evidence for SARS-CoV-2 infection since late summer 2019 in northern Italy

medRxiv | (In review)

A. Amendola, M. Canuti, S. Bianchi, S. Kumar, C. Fappani, M. Gori, D. Colzani, S. L. K. Pond, S. Miura, M. Baggeri, A. Marchi, E. Borghi, G. V. Zuccotti, M. C. Raviglione, F. Magurano, E. Tanzi

An Evolutionary Portrait of the Progenitor SARS-CoV-2 and its Dominant Offshoots in COVID-19 Pandemic

Molecular Biology and Evolution | (In press):(https://doi.org/10.1093/molbev/msab118)

S. Kumar, Q. Tao, S. Weaver, M. Sanderford, M. A. Caraballo-Ortiz, S. Sharma, S. L. K. Pond, S. Miura

Evolutionary sparse learning for phylogenomics

Molecular Biology and Evolution | (accepted, pending minor revisions):(https://doi.org/10.1101/2021.07.19.452974)

S. Kumar, S. Sharma

Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps

Nature Computational Science | (accepted in principle):(https://doi.org/10.1101/2021.07.21.453255)

S. Sharma, S. Kumar

Migrations of cancer cells through the lens of phylogenetic biogeography

Scientific Reports | (revision in review)

A. Chroni A, S. Miura, O. Oladeinde, V. Aly, S. Kumar

Evolution of somatic mutational processes in cancer

bioRxiv | (Submitted):(https://doi.org/10.1101/2021.04.02.438268)

S. Miura, T. Vu, J. Choi, Townsend JP, S. Kumar

Data-driven Speciation Tree Prior for Better Species Divergence Times in Calibration-poor Molecular Phylogenies

Bioinformatics | 37:i02–i110

Q. Tao, J. Barba-Montoya, S. Kumar

Tumors are evolutionary islands

Genome Biology and Evolution | (revision invited)

Chroni A, Kumar S

Epistasis Produces an Excess of Invariant Sites in Neutral Molecular Evolution

Proceedings of the National Academy of Sciences (USA) | 118:e2018767118

R. Patel and S. Kumar

MEGA11: Molecular Evolutionary Genetics Analysis version 11

Molecular Biology and Evolution | 38:3022–3027

K. Tamura, G. Stecher, S. Kumar

Molecular Dating for Phylogenies Containing a Mix of Populations and Species by Using Bayesian and RelTime Approaches

Molecular Ecology Resources | 21:122–136

B. Mello, Q. Tao, J. Barba-Montoya, S. Kumar

How to Build a Super Predator: From Genotype to Phenotype

The American Biology Teacher | 83:138–146

C. Babaian, S. Kumar

Assessing rapid methods for phylogenomic dating

Genome Biology and Evolution | (in review)

J. Barba-Montoya, Q. Tao, S. Kumar

Molecular and Morphological Clocks for Estimating Evolutionary Divergence Times

BMC Ecology and Evolution | 21:83 (15 pp)

J. Barba-Montoya, Q. Tao, S. Kumar

Common Treatment, Common Variant: Evolutionary Prediction of Functional Pharmacogenomic Variants

Journal of Personalized Medicine | 11:131 (13 pp)

L. B. Scheinfeldt, A. Brangan, D. Kusic, S. Kumar, N. Gharani

TreeMap: A Structured Approach to Fine Mapping of eQTL Variants

Bioinformatics | 37:1125–1134

L. Liu, P. Chandrashekar, B. Zeng, M. D. Sanderford, S. Kumar, G. Gibson

Durability of immunity against reinfection by SARS-CoV-2

| (revision in review)

J. P. Townsend, H. B. Hassler, Z. Wang, S. Miura, J. Singh, S. Kumar, N. Ruddle, A.P. Galvani, A. Dornburg

The somatic molecular evolution of cancer: mutation, selection, and epistasis

Progress in Biophysics and Molecular Biology | (revision in review)

K. Dasari, J. A. Somarelli, S. Kumar, J. P. Townsend