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


Delineation of Tumor Migration Paths by Using a Bayesian Biogeographic Approach

Cancers | 11:12 (14 pp)

A. Chroni, T. Vu, S. Miura, S. Kumar


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

The American Biology Teacher | 81:543–552

C. Babaian, S. Kumar


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


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


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


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


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


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


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


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


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


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


FlyExpress 7: An Integrated Discovery Platform to Study Coexpressed Genes Using in situ Hybridization Images in Drosophila

G3: Genes, Genomes, Genetics | 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


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


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


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


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