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

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

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

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

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

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

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

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

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