2019
168

Molecular dating for phylogenies containing a mix of populations and species

Molecular Ecology Resources (submitted) (https://doi.org/10.1101/536656)

B. Mello, Q. Tao, S. Kumar

167

On estimating evolutionary probabilities of population variants

BMC Evolutionary Biology (submitted) (https://doi.org/10.1101/475475)

R. Patel, S. Kumar

166

A new method for detecting autocorrelation of evolutionary rates in large phylogenies

Molecular Biology and Evolution (https://doi.org/10.1093/molbev/msz014)

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

165

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

164

Biological relevance of computationally predicted pathogenicity of noncoding variants

Nature Communications 10(1):330

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

2018
163

Accurate timetrees require accurate calibrations

Proceedings of the National Academy of Sciences (USA) 115(41):E9510-E9511

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

162

Computational enhancement of single-cell sequences for inferring tumor evolution

Bioinformatics 34(17):i917-i926

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

161

Predicting clone genotypes from tumor bulk sequencing of multiple samples

Bioinformatics 34(23):4017-4026

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

160

Adaptive landscape of protein variation in human exomes

Molecular Biology and Evolution 35(8):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

159

RelTime relaxes the strict molecular clock throughout the phylogeny

Genome Biology and Evolution 10(6):1631-1636

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

158

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

Molecular Biology and Evolution 35(7):1770-1782

K. Tamura, Q. Tao, S. Kumar

157

MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms

Molecular Biology and Evolution 35(6):1547-1549

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

156

Neutral theory, disease mutations, and personal exomes

Molecular Biology and Evolution 35(6):1297-1303

S. Kumar, R. Patel

155

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

2017
154

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

Genes, Genomes, Genetics (G3) 7(8):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(7):1812-1819

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

152

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

Molecular Biology and Evolution 34(3):718-723

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

151

Fast and accurate estimates of divergence times from big data

Molecular Biology and Evolution 34(1):45-50

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

2016
150

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

BMC Genomics 17(9):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

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

Transactions on Big Data

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

148

MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets

Molecular Biology and Evolution 33(7):1870-1874

S. Kumar, G. Stecher, K. Tamura

147

A molecular evolutionary reference for the human variome

Molecular Biology and Evolution 33(1):245-254

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

146

Advances in time estimation methods for molecular data

Molecular Biology and Evolution 33(4):863-869

S. Kumar, S.B. Hedges