2019
169

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

168

Delineation of Tumor Migration Paths by Using a Bayesian Biogeographic Approach

Cancers | 11:12 (14 pp)

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

167

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

The American Biology Teacher | 81:543–552

C. Babaian, S. Kumar

166

On Estimating Evolutionary Probabilities of Population Variants

BMC Evolutionary Biology | 19:133 (14 pp)

R. Patel, S. Kumar

165

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

164

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

2018
163

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

162

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

161

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

160

Neutral Theory, Disease Mutations, and Personal Exomes

Molecular Biology and Evolution | 35:1297–1303

S. Kumar, R. Patel

159

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

158

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

157

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

156

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

155

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

2017
154

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

153

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

152

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

151

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

2016
150

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

149

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

Molecular Biology and Evolution | 33:1870–1874

S. Kumar, G. Stecher, K. Tamura

148

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

147

Advances in Time Estimation Methods for Molecular Data

Molecular Biology and Evolution | 33:863–869

S. Kumar, S.B. Hedges