Common treatment, common variant: evolutionary prediction of functional pharmacogenomic variants

Journal of Personalized Medicine (accepted) | (https://doi.org/10.3390/jpm11020131)

L. B. Scheinfeldt, A. Brangan, D. Kusic, S. Kumar, N. Gharani


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

Molecular Ecology Resources | 21:122–136

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


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


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


Efficient Methods for Dating Evolutionary Divergences

In The Molecular Evolutionary Clock | 197–219

Q. Tao, K. Tamura, S. Kumar


Molecular Memories of a Cambrian Fossil

The American Biology Teacher | 82:586–595

C. Babaian, S. Kumar


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


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


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


Where did SARS-CoV-2 come from?

Molecular Biology and Evolution | 37:2463–2464

T. Leitner, S. Kumar


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

Bioinformatics | 36:i884–i894

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


PathFinder: Bayesian inference of clone migration histories in cancer

Bioinformatics | 36:i675–i683

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


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


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


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


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


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


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


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


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


Molecular Evolutionary Genetics Analysis (MEGA) for macOS

Molecular Biology and Evolution | 37:1237–1239

G. Stecher, K. Tamura, S. Kumar


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


Delineation of Tumor Migration Paths by Using a Bayesian Biogeographic Approach

Cancers | 11:12 (14 pp)

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


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

The American Biology Teacher | 81:543–552

C. Babaian, S. Kumar


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


On estimating evolutionary probabilities of population variants

BMC Evolutionary Biology | 19:133 (14 pp)

R. Patel, S. Kumar


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


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


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


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


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


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


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


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


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


Neutral theory, disease mutations, and personal exomes

Molecular Biology and Evolution | 35:1297–1303

S. Kumar, R. Patel


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


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


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


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


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