In Review
173

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

The American Biology Teacher

C. Babaian, S. Kumar

172

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

bioRxiv | (https://doi.org/10.1101/697318)

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

Reliable confidence intervals for RelTime estimates of evolutionary divergence times

bioRxiv | (https://doi.org/10.1101/677286)

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

A new method for inferring timetrees from temporally sampled molecular sequences

bioRxiv | (https://doi.org/10.1101/620187)

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) | (https://doi.org/10.1101/536656)

B. Mello, Q. Tao, 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

2019
171

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

167

On estimating evolutionary probabilities of population variants

BMC Evolutionary Biology | 19:133 (14 pp)

R. Patel, S. Kumar

166

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

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

2018
163

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

162

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

161

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

160

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

159

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

158

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

157

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

156

Neutral theory, disease mutations, and personal exomes

Molecular Biology and Evolution | 35:1297-1303

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) | 7:2791-2797

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

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

151

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

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

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

148

MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets

Molecular Biology and Evolution | 33:1870-1874

S. Kumar, G. Stecher, K. Tamura

147

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

146

Advances in time estimation methods for molecular data

Molecular Biology and Evolution | 33:863-869

S. Kumar, S.B. Hedges