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

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

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

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

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

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

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

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

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

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

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

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

FlyExpress 7: An Integrated Discovery Platform to Study Coexpressed Genes Using in situ Hybridization Images in Drosophila

G3: Genes, Genomes, Genetics | 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

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

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

e-GRASP: An Integrated Evolutionary and GRASP Resource for Exploring Disease Associations

BMC Genomics | 17:770 (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

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

Molecular Biology and Evolution | 33:1870–1874

S. Kumar, G. Stecher, K. Tamura

A Molecular Evolutionary Reference for the Human Variome

Molecular Biology and Evolution | 33:245–254

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

Advances in Time Estimation Methods for Molecular Data

Molecular Biology and Evolution | 33:863–869

S. Kumar, S.B. Hedges

Integration of Structural Dynamics and Molecular Evolution via Protein Interaction Networks: A New Era in Genomic Medicine

Current Opinion in Structural Biology | 35:135–142

A. Kumar, B.M Butler, S. Kumar, S.B. Ozkan

Using Disease-associated Coding Sequence Variation to Investigate Functional Compensation by Human Paralogous Proteins

Evolutionary Bioinformatics | 11:245–251

S. Miura, S. Tate, S. Kumar

A Protocol for Diagnosing the Effect of Calibration Priors on Posterior Time Estimates: A Case Study for the Cambrian Explosion of Animal Phyla

Molecular Biology and Evolution | 32:1907–1912

F.U. Battistuzzi, P. Billing-Ross, O. Murillo, A. Filipski, S. Kumar

Conformational Dynamics of Nonsynonymous Variants at Protein Interfaces Reveals Disease Association

Proteins | 83:428–435

B.M. Butler, Z.N. Gerek, S. Kumar, S.B. Ozkan

Phylogenetic Placement of Metagenomic Reads Using the Minimum Evolution Principle

BMC Genomics | 16:S13 (9 pp)

A. Filipski, K. Tamura, P. Billing-Ross, O. Murillo, S. Kumar

Evolutionary Diagnosis of Non-synonymous Variants Involved in Differential Drug Response

BMC Medical Genomics | 8:S6 (6 pp)

N.Z. Gerek, L. Liu, K. Gerold, P. Biparva, E.D. Thomas, S. Kumar

Tree of Life Reveals Clock-like Speciation and Diversification

Molecular Biology and Evolution | 32:835–845

S.B. Hedges, J. Marin, M. Suleski, M. Paymer, S. Kumar

Exceptional Reduction of the Plastid Genome of Saguaro Cactus (Carnegiea gigantea): Loss of the Ndh Gene Suite and Inverted Repeat

American Journal of Botany | 102:1115–1127

M. Sanderson, D. Copetti, A. Burquez, E. Bustamante, J.L.M. Charboneau, L.E. Eguiarte, S. Kumar, H.O. Lee, J. Lee, M. McMahon, K. Steele, R. Wing, T.J. Yang, D. Zwickl, M.F. Wojciechowski

Prospects for Building Large Timetrees using Molecular Data with Incomplete Gene Coverage among Species

Molecular Biology and Evolution | 31:2542–2550

A. Filipski, O. Murillo, A. Freydenzon, K. Tamura, S. Kumar

Signatures of Natural Selection on Mutations of Residues with Multiple Posttranslational Modifications

Molecular Biology and Evolution | 31:1641–1645

V.E. Gray, L. Liu, R. Nirankari, P.V. Hornbeck, S. Kumar

No Positive Selection for G Allele in a p53 Response Element in Europeans

Cell | 157:1497–1499

S. Kumar, L. Liu

Reply to: "Proper Reporting of Predictor Performance"

Nature Methods | 11:781–782

S. Kumar, J. Ye, L. Liu

myFX: A Turn-key Software for Laboratory Desktops to Analyze Spatial Patterns of Gene Expression in Drosophila Embryos

Bioinformatics | 30:1319–1321

I. Montiel, C. Konikoff, B. Braun, M. Packard, S.L. Gramates, Q. Sun, J. Ye, S. Kumar

MEGA-MD: Molecular Evolutionary Genetics Analysis Software with Mutational Diagnosis of Amino Acid Variation

Bioinformatics | 30:1305–1307

G. Stecher, L. Liu, M.D. Sanderford, D. Peterson, K. Tamura, S. Kumar

Automated Annotation of Developmental Stages of Drosophila Embryos in Images Containing Spatial Patterns of Expression

Bioinformatics | 30:266–273

L. Yuan, C. Pan, S. Ji, M. McCutchan, Z.H. Zhou, S. J. Newfeld, S. Kumar, J. Ye

Whole-genome Sequencing of the Snub-nosed Monkey Provides Insights into Folivory and Evolutionary History

Nature Genetics | 46:1303–1310

X. Zhou, B. Wang, Q. Pan, J. Zhang, S. Kumar, X. Sun, Z. Liu, H. Pan, Y. Lin, G. Liu, W. Zhan, M. Li, B. Ren, X. Ma, H. Ruan, C. Cheng, D. Wang, F. Shi, Y. Hui, Y. Tao, C. Zhang, P. Zhu, Z. Xiang, W. Jiang, J. Chang, H. Wang, Z. Cao, Z. Jiang, B. Li, G. Yang, C. Roos, P.A. Garber, M.W. Bruford, R. Li, M. Li

The Evolutionary History of Amino Acid Variations Mediating Increased Resistance of S. aureus Identifies Reversion Mutations in Metabolic Regulators

PLoS One | 8:e56466 (9 pp)

M.D. Champion, V. Gray, C. Eberhard, S. Kumar

Structural Dynamics Flexibility Informs Function and Evolution at a Proteome Scale

Evolutionary Applications | 6:423–433

Z.N. Gerek, S. Kumar, S.B. Ozkan

GRASP [Genomic Resource Access for Stoichioproteomics]: Comparative Explorations of the Atomic Content of 12 Drosophila Proteomes

BMC Genomics | 14:(14 pp)

J.D.J. Gilbert, C. Acquisti, H.M. Martinson, J.J. Elser, S. Kumar, W.F. Fagan

Evolutionary Balancing is Critical for Correctly Forecasting Disease-associated Amino Acid Variants

Molecular Biology and Evolution | 30:1252–1257

L. Liu, S. Kumar

Image-level and Group-level Models for Drosophila Gene Expression Pattern Annotation

BMC Bioinformatics | 14:350 (13 pp)

Q. Sun, S. Muckatira, L. Yuan, S. Ji, S. Newfeld, S. Kumar, J. Ye

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

Molecular Biology and Evolution | 30:2725–2729

K. Tamura, G. Stecher, D. Peterson, A. Filipski, S. Kumar

Genome-wide Profiling of Human Cap-independent Translation-enhancing Elements

Nature Methods | 10:747–750

B.P. Wellensiek, A.C. Larsen, B. Stephens, K. Kukurba, K. Waern, N. Briones, L. Liu, M. Snyder, B. L. Jacobs, S. Kumar, J.C. Chaput

A Mesh Generation and Machine Learning Framework for Drosophila Gene Expression Pattern Image Analysis

BMC Bioinformatics | 14:372 (10 pp)

W. Zhang, D. Feng, R. Li, A. Chernikov, N. Chrisochoides, C. Osgood, C. Konikoff, S. Newfeld, S. Kumar, S. Ji

Exploring Spatial Patterns of Gene Expression from Fruit Fly Embryogenesis on the iPhone

Bioinformatics | 28:2847–2848

S. Kumar, K. Boccia, M. McCutchan, J. Ye

Sharing and Re-use of Phylogenetic Trees (and associated data) to Facilitate Synthesis

BMC Research Notes | 5:574 (15 pp)

A. Stoltzfus, B. O'Meara, J. Whitacre, R. Mounce, E. L. Gillespie, S. Kumar, D.F. Rosauer, R.A. Vos

Evolutionary Meta-analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery

Molecular Biology and Evolution | 29:2087–2094

J.T. Dudley, R. Chen, M.D. Sanderford, A.J. Butte, S. Kumar

Human Genomic Disease Variants: A Neutral Evolutionary Explanation

Genome Research | 22:1383–1394

J.T. Dudley, Y. Kim, L. Liu, G. J. Markov, K. Gerold, R. Chen, A.J. Butte, S. Kumar

Performance of Computational Tools in Evaluating the Functional Impact of Laboratory-induced Amino Acid Mutations

Bioinformatics | 28:2093–2096

V.E. Gray, K.R. Kukurba, S. Kumar

Comparison of Embryonic Expression within Multigene Families using the FlyExpress Discovery Platform Reveals More Spatial than Temporal Divergence

Developmental Dynamics | 241:150–160

C. Konikoff, T.L. Karr, M. McCutchan, S.J. Newfeld, S. Kumar

Statistics and Truth in Phylogenomics

Molecular Biology and Evolution | 29:457–472

S. Kumar, A.J. Filipski, F.U. Battistuzzi, S. L. K. Pond, K. Tamura

Evolutionary Diagnosis Method for Variants in Personal Exomes

Nature Methods | 9:855–856

S. Kumar, M.D. Sanderford, V.E. Gray, J. Ye, L. Liu

MEGA-CC: Computing Core of Molecular Evolutionary Genetics Analysis Program for Automated and Iterative Data Analysis

Bioinformatics | 28:2685–2686

S. Kumar, G. Stecher, D. Peterson, K. Tamura

Drosophila Gene Expression Pattern Annotation through Multi-instance Multi-label Learning

IEEE/ACM Transactions on Computational Biology and Bioinformatics | 9:98–112

Y.X. Li, S. Ji, S. Kumar, J. Ye, Z.H. Zhou

Purifying Selection Modulates the Estimates of Population Differentiation and Confounds Genome-wide Comparisons across Single-nucleotide Polymorphisms

Molecular Biology and Evolution | 29:3617–3623

T. Maruki, S. Kumar, Y. Kim

Estimating Divergence Times in Large Molecular Phylogenies

Proceedings of the National Academy of Sciences (USA) | 109:19333–19338

K. Tamura, F.U. Battistuzzi, P. Billing-Ross, O. Murillo, A. Filipski, S. Kumar

Learning Sparse Representations for Fruit-fly Gene Expression Pattern Image Annotation and Retrieval

BMC Bioinformatics | 13:107 (15 pp)

L. Yuan, A. Woodard, S. Ji, Y. Jiang, Z.H. Zhou, S. Kumar, J. Ye

Molecular Clock: Testing

eLS | (7 pp)

F.U. Battistuzzi, A. Filipski, S. Kumar

Fast and Slow Implementations of Relaxed-clock Methods Show Similar Patterns of Accuracy in Estimating Divergence Times

Molecular Biology and Evolution | 28:2439–2442

F.U. Battistuzzi, P. Billing-Ross, A. Paliwal, S. Kumar

Stoichiogenomics: The Evolutionary Ecology of Macromolecular Elemental Composition

Trends in Ecology & Evolution | 26:38–44

J.J. Elser, C. Acquisti, S. Kumar

Rampant Purifying Selection Conserves Positions with Posttranslational Modifications in Human Proteins

Molecular Biology and Evolution | 28:1565–1568

V.E. Gray, S. Kumar

Phylomedicine: An Evolutionary Telescope to Explore and Diagnose the Universe of Disease Mutations

Trends in Genetics | 27:377–386

S. Kumar, J.T. Dudley, A. Filipski, L. Liu

TimeTree2: Species Divergence Times on the iPhone

Bioinformatics | 27:2023–2024

S. Kumar, S.B. Hedges

FlyExpress: Visual Mining of Spatiotemporal Patterns for Genes and Publications in Drosophila Embryogenesis

Bioinformatics | 27:3319–3320

S. Kumar, C. Konikoff, B. Van Emden, C. Busick, K.T. Davis, S. Ji, L.W. Wu, H. Ramos, T. Brody, S. Panchanathan, J. Ye, T. L. Karr, K. Gerold, M. McCutchan, S. J. Newfeld

Evolution of Modern Birds Revealed by Mitogenomics: Timing the Radiation and Origin of Major Orders

Molecular Biology and Evolution | 28:1927–1942

M.A. Pacheco, F.U. Battistuzzi, M. Lentino, R.F. Aguilar, S. Kumar, A. Escalante

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

Molecular Biology and Evolution | 28:2731–2739

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, S. Kumar

Performance of Relaxed-clock Methods in Estimating Evolutionary Divergence Times and Their Credibility Intervals

Molecular Biology and Evolution | 27:1289–1300

F.U. Battistuzzi, A. Filipski, S.B. Hedges, S. Kumar

Quantitative Analysis of the Drosophila Segmentation Regulatory Network Using Pattern Generating Potentials

PLoS Biology | 8:(19 pp)

M. Kazemian, C. Blatti, A. Richards, M. McCutchan, N. Wakabayashi-Ito, A.S. Hammonds, S.E. Celniker, S. Kumar, S.A. Wolfe, M.H. Brodsky, S. Sinha

More Reliable Estimates of Divergence Times in Pan Using Complete mtDNA Sequences and Accounting for Population Structure

Philosophical Transactions of the Royal Society B: Biological Sciences | 365:3277–3288

A.C. Stone, F.U. Battistuzzi, L.S. Kubatko, G.H. Perry, Jr., E. Trudeau, H. Lin, S. Kumar