2020
190

Molecular and morphological clocks for estimating evolutionary divergence times

Research Square | (https://doi.org/10.21203/rs.3.rs-29165/v1)

J. Barba-Montoya, Q. Tao, S. Kumar

189

An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic

bioRxiv | (https://doi.org/10.1101/2020.09.24.311845)

S. Kumar, Q. Tao, S. Weaver, M. Sanderford, M. A. Caraballo-Ortiz, S. Sharma, S. L. K. Pond, S. Miura

188

The bits and bytes of biology: digitalization fuels an emerging generative platform for biological innovation

Handbook of Digital Innovation | 253

R. J. Kulathinal, Y. Yoo, S. Kumar

187

Functional, Morphological, and Evolutionary Characterization of Hearing in Subterranean, Eusocial African Mole-Rats

Current Biology | 30:(18 pp)

S. J. Pyott, M. van Tuinen, L. A. Screven, K. M. Schrode, J. Bai, C. M. Barone, S. D. Price, A. Lysakowski, M. Sanderford, S. Kumar, J. Santos-Sacchi, A. M. Lauer, T. J. Park

186

Interactive effect of TLR SNPs and exposure to sexually transmitted infections on prostate cancer risk in Jamaican men

The Prostate | 80:1365–1372

B. Dubey, M. Jackson, C. Zeigler-Johnson, K. Devarajan, R. E. Flores-Obando, N. McFarlane-Anderson, M. Tulloch-Reid, W. Aiken, K. Kimbro, D. Reed, L. R. Kidd, D. Gibbs, S. Kumar, C. Ragin

185

Where did SARS-CoV-2 come from?

Molecular Biology and Evolution | 37:2463–2464

T. Leitner, S. Kumar

184

Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated

Bioinformatics (accepted) | (https://doi.org/10.1101/2020.07.09.195487)

J. Barba-Montoya, Q. Tao, S. Kumar

183

PathFinder: Bayesian inference of clone migration histories in cancer

Bioinformatics (accepted) | (https://doi.org/10.1101/2020.07.10.197194)

S. Kumar, A. Chroni, K. Tamura, M. Sanderford, O. Oladeinde, V. Aly, T. Vu, S. Miura

182

TreeMap: A structured approach to fine mapping of eQTL variants

Bioinformatics (in revision) | (https://doi.org/10.1101/2020.05.31.125880)

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

181

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

180

Beaver and Naked Mole Rat Genomes Reveal Common Paths to Longevity

Cells Reports | 32:(13 pp)

X. Zhou, Q. Dou, G. Fan, Q. Zhang, M. Sanderford, A. Kaya, J. Johnson, E. Karlsson, X. Tian, A. Mikhalchenko, S. Kumar, A. Seluanov, Z. Zhang, V. Gorbunova, X. Liu, and V. N. Gladyshev

179

Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches

Molecular Ecology Resources | (https://doi.org/10.1111/1755-0998.13249)

B. Mello, Q. Tao, J. Barba-Montoya, S. Kumar

178

Relative efficiencies of simple and complex substitution models in estimating divergence times in phylogenomics

Molecular Biology and Evolution | 37:1819–1831

Q. Tao, J. Barba-Montoya, L. A. Huuki, M. K. Durnan, S. Kumar

177

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

Scientific Reports | 10:3498 (21 pp)

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

176

A new method for inferring timetrees from temporally sampled molecular sequences

PLoS Computational Biology | 16:(24 pp)

S. Miura, K. Tamura, Q. Tao, L. A. Huuki, S. L. K. Pond, J. Priest, J. Deng, S. Kumar

175

Somatic Selection Distinguishes Oncogenes and Tumor Suppressor Genes

Bioinformatics | 36:1712–1717

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

174

The Role of Conformational Dynamics and Allostery in Modulating Protein Evolution

Annual Review of Biophysics | 49:267–288

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

173

Molecular biology and evolution of cancer: from discovery to action

Molecular Biology and Evolution | 37:320–326

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

172

Molecular Evolutionary Genetics Analysis (MEGA) for macOS

Molecular Biology and Evolution | 37:1237–1239

G. Stecher, K. Tamura, S. Kumar

171

Reliable confidence intervals for RelTime estimates of evolutionary divergence times

Molecular Biology and Evolution | 37:280–290

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

2019
170

Delineation of Tumor Migration Paths by Using a Bayesian Biogeographic Approach

Cancers | 11:12 (14 pp)

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

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