In Review
---

Somatic Selection Distinguishes Oncogenes and Tumor Suppressor Genes (Revision invited)

P. Chandrashekar, N. Ahmadinejad, J. Wang, A. Sekulic, J. B. Egan, Y. W. Asmann, S. Kumar, C. Maley, L. Liu

---

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

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

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

B. Mello, Q. Tao, S. Kumar

2020
173

The Role of Conformational Dynamics and Allostery in Modulating Protein Evolution (accepted)

Annual Review of Biophysics

P. Campitelli, T. Modi, S. Kumar, S. B. Ozkan

172

Molecular biology and evolution of cancer: from discovery to action

Molecular Biology and Evolution | (https://doi.org/10.1093/molbev/msz242)

J. A. Somarelli, H. Gardner, V. L. Cannataro, E. F. Gunady, A. M. Boddy, N. A. Johnson, J. N. Fisk, S. G. Gaffney, J. H. Chuang, S. Li, F. D. Ciccarelli, A. R. Panchenko, K. Megquier, S. Kumar, A. Dornburg, J. DeGregori, J. P. Townsend

171

Reliable confidence intervals for RelTime estimates of evolutionary divergence times

Molecular Biology and Evolution | (https://doi.org/10.1093/molbev/msz236)

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

170

Rapid and reliable methods for molecular dating

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

Q. Tao, K. Tamura, S. Kumar

2019
169

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

The American Biology Teacher | 81:543-552

C. Babaian, S. Kumar

168

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

165

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
164

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

163

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

162

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

161

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

160

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

159

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

158

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

157

Neutral theory, disease mutations, and personal exomes

Molecular Biology and Evolution | 35:1297-1303

S. Kumar, R. Patel

156

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
155

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

154

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

153

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

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