Laboratory of Sudhir Kumar :: Publications 2016-2019



A new method for detecting autocorrelation of evolutionary rates in large phylogenies

bioRxiv (preprint) (

Q. Tao, K. Tamura, F. Battistuzzi, S. Kumar



Accurate timetrees require accurate calibrations

Proceedings of the National Academy of Sciences (USA) 115(41):E9510-E9511

S. B. Hedges, Q. Tao, M. Walker, S. Kumar


Computational enhancement of single-cell sequences for inferring tumor evolution

Bioinformatics 34(17):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(23):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(8):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(6):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(7):1770-1782

K. Tamura, Q. Tao, S. Kumar


MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms

Molecular Biology and Evolution 35(6):1547-1549

S. Kumar, G. Stecher, M. Li, C. Knyaz, K. Tamura


Neutral theory, disease mutations, and personal exomes

Molecular Biology and Evolution 35(6):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(8):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(7):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(3):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(1):45-50

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



e-GRASP: an integrated evolutionary and GRASP resource for exploring disease associations

BMC Genomics 17(9):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


Deep model based transfer and multi-task learning for biological image analysis

Transactions on Big Data

W. Zhang, R. Li, T. Zeng, Q. Sun, S. Kumar, J. Ye, S. Ji


MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets

Molecular Biology and Evolution 33(7):1870-1874

S. Kumar, G. Stecher, K. Tamura


A molecular evolutionary reference for the human variome

Molecular Biology and Evolution 33(1):245-254

L. Liu, K. Tamura, M.D. Sanderford, V. Gray, S. Kumar


Advances in time estimation methods for molecular data

Molecular Biology and Evolution 33(4):863-869

S. Kumar, S.B. Hedges