In Review

Adventures in Evolution: The Narrative of Tardigrada, Trundlers in Time

The American Biology Teacher

C. Babaian, S. Kumar


Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data

bioRxiv | (

S. Miura, T. Vu, J. Deng, T. Buturla, J. Choi, S. Kumar

Reliable confidence intervals for RelTime estimates of evolutionary divergence times

bioRxiv | (

Q. Tao, K. Tamura, B. Mello, S. Kumar

A new method for inferring timetrees from temporally sampled molecular sequences

bioRxiv | (

S. Miura, K. Tamura, S. Pond, L. A. Huuki, J. Priest, J. Deng, S. Kumar

Molecular dating for phylogenies containing a mix of populations and species

Molecular Ecology Resources (submitted) | (

B. Mello, Q. Tao, S. Kumar


Rapid and reliable methods for molecular dating

In The Molecular Evolutionary Clock. Theory and Practice, edited by Simon Ho (submitted)

Q. Tao, K. Tamura, S. Kumar


Genome-wide analysis indicates association between heterozygote advantage and healthy aging in humans

BMC Genetics | 20:52 (14 pp)

K. Xu, R. Kosoy, K. Shameer, S. Kumar, L. Liu, B. Readhead, G. M. Belbin, H. C. Lee, R. Chen, J. T. Dudley


On estimating evolutionary probabilities of population variants

BMC Evolutionary Biology | 19:133 (14 pp)

R. Patel, S. Kumar


A machine learning method for detecting autocorrelation of evolutionary rates in large phylogenies

Molecular Biology and Evolution | 36:811-824

Q. Tao, K. Tamura, F. Battistuzzi, S. Kumar


Biological relevance of computationally predicted pathogenicity of noncoding variants

Nature Communications | 10:330 (11 pp)

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


Accurate timetrees require accurate calibrations

Proceedings of the National Academy of Sciences (USA) | 115:E9510-E9511

S. B. Hedges, Q. Tao, M. Walker, S. Kumar


Computational enhancement of single-cell sequences for inferring tumor evolution

Bioinformatics | 34:i917-i926

S. Miura, L. A. Huuki, T. Buturla, T. Vu, K. Gomez, S. Kumar


Predicting clone genotypes from tumor bulk sequencing of multiple samples

Bioinformatics | 34:4017-4026

S. Miura, K. Gomez, O. Murillo, L. A. Huuki, T. Vu, T. Buturla, S. Kumar


Adaptive landscape of protein variation in human exomes

Molecular Biology and Evolution | 35:2015-2025

R. Patel, L. B. Scheinfeldt, M. D. Sanderford, T. R. Lanham, K. Tamura, A. Platt, B. S. Gilksberg, K. Xu, J. T. Dudley, S. Kumar


RelTime relaxes the strict molecular clock throughout the phylogeny

Genome Biology and Evolution | 10:1631-1636

F. U. Battistuzzi, Q. Tao, L. Jones, K. Tamura, S. Kumar


Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates

Molecular Biology and Evolution | 35:1770-1782

K. Tamura, Q. Tao, S. Kumar


MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms

Molecular Biology and Evolution | 35:1547-1549

S. Kumar, G. Stecher, M. Li, C. Knyaz, K. Tamura


Neutral theory, disease mutations, and personal exomes

Molecular Biology and Evolution | 35:1297-1303

S. Kumar, R. Patel


Somatic evolutionary timings of driver mutations

BMC Cancer | 18:85 (10 pp)

K. Gomez, S. Miura, L. A. Huuki, B.S. Spell, J.P. Townsend, S. Kumar


FlyExpress 7: an integrated discovery platform to study coexpressed genes using in situ hybridization images in Drosophila

Genes, Genomes, Genetics (G3) | 7:2791-2797

S. Kumar, C. Konikoff, M. Sanderford, L. Liu, S. Newfeld, J. Ye, R.J. Kulathinal


TimeTree: A resource for timelines, timetrees, and divergence times

Molecular Biology and Evolution | 34:1812-1819

S. Kumar, G. Stecher, M. Suleski, S. B. Hedges


The reliability and stability of an inferred phylogenetic tree from empirical data

Molecular Biology and Evolution | 34:718-723

Y. Katsura, C. Stanley, S. Kumar, M. Nei


Fast and accurate estimates of divergence times from big data

Molecular Biology and Evolution | 34:45-50

B. Mello, Q. Tao, K. Tamura, S. Kumar


e-GRASP: an integrated evolutionary and GRASP resource for exploring disease associations

BMC Genomics | 17:770 (8 pp)

S. Karim, H.F. Nour Eldin, H. Abusamra, N. Salem, E. Alhathli, J. Dudley, M.D. Sanderford, L.B. Scheinfeldt A.G. Chaudhary, M.H. Al-Qahtani, S. Kumar


Deep model based transfer and multi-task learning for biological image analysis

Transactions on Big Data | 20 pp

W. Zhang, R. Li, T. Zeng, Q. Sun, S. Kumar, J. Ye, S. Ji


MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets

Molecular Biology and Evolution | 33:1870-1874

S. Kumar, G. Stecher, K. Tamura


A molecular evolutionary reference for the human variome

Molecular Biology and Evolution | 33:245-254

L. Liu, K. Tamura, M.D. Sanderford, V. Gray, S. Kumar


Advances in time estimation methods for molecular data

Molecular Biology and Evolution | 33:863-869

S. Kumar, S.B. Hedges