Visualizing Genomic Medicine: An Introduction to General Biology

The American Biology Teacher | 86:265–273 (9 pp)

C. Babaian, S. Kumar


MyESL: Sparse learning in molecular evolution and phylogenetic analysis

Bioinformatics | (submitted)

M. Sanderford, S. Sharma, G. Stecher, J. Liu, J. Ye, S. Kumar


Methods for Estimating Personal Disease Risk and Phylogenetic Diversity of Hematopoietic Stem Cells

Molecular Biology and Evolution | 41:msad279 (11 pp)

J.M. Craig, G.S. Gerhard, S. Sharma, A. Yankovskiy, S. Miura, S. Kumar


Of Phylogenies and Tumors: Cancer as a Model System to Teach Evolution

The American Biology Teacher | 86:62–70 (9 pp)

C. Babaian, S. Kumar


Analyses of Allele Age and Fitness Impact Reveal Human Beneficial Alleles to be Older than Neutral Controls


A. Pivirotto, A. Platt, R. Patel, S. Kumar, J. Hey


Split-Transformer Impute (STI): A Transformer Framework for Genotype Imputation

bioRxiv | (available)

M.E. Mowlaei, C. Li, O. Jamialahmadi, R. Dias, J. Chen, B. Jamialahmadi, T.R. Rebbeck, V. Carnevale, S. Kumar, X. Shi


Evolutionary Sparse Learning Reveals the Shared Genetic Basis of Convergent Traits

bioRxiv | (submitted)

J. Allard , S. Sharma , R. Patel , M. Sanderford , K. Tamura , S. Vucetic , G. Gerhard, S. Kumar


Discovering Fragile Clades And Causal Sequences In Phylogenomics By Evolutionary Sparse Learning

Molecular Biology and Evolution | 41:msae131 (31 pp)

S. Sharma, S. Kumar


R3F: An R Package for Evolutionary Dates, Rates, and Priors using Relative Rate Framework

bioRxiv | (available)

Q. Tao, S. Sharma, K. Tamura, S. Kumar


Some Mechanistic Underpinnings of Molecular Adaptations of SARS-COV-2 Spike Protein by Integrating Candidate Adaptive Polymorphisms with Protein Dynamics


N. Ose, P. Campitelli, T. Modi, I. Kazan, S. Kumar, B. Ozkan


Computational Reproducibility of Molecular Phylogenies

Molecular Biology and Evolution | 40:msad165 (9 pp)

S. Kumar, Q. Tao, A. P. Lamarca, K. Tamura


Completing a Molecular Timetree of Apes and Monkeys

Frontiers in Bioinformatics | 3:1284744 (8 pp)

J.M. Craig, G. Bamba, J. Barba, S.B. Hedges, S. Kumar


Molecular Timetrees using Relaxed Clocks and Uncertain Phylogenies

Frontiers in Bioinformatics | 3:1225807 (13 pp)

J. Barba-Montoya, S. Sharma, S. Kumar


The Origin of Eukaryotes and Rise in Complexity were Synchronous with the Rise in Oxygen

Frontiers in Bioinformatics | 3:1233281 (10 pp)

J. M. Craig, S. Kumar, S. B. Hedges


Discovering Research Articles Containing Evolutionary Timetrees by Machine Learning

Bioinformatics | 39:btad035 (7 pp)

M. Stanojevic, J. Andjelkovic, A. Kasprowicz, L.A. Huuki, J. Chao, S.B. Hedges, S. Kumar, Z. Obradovic


Improving Cellular Phylogenies through the Integrated Use of Mutation Order and Optimality Principles

Computational and Structural Biotechnology Journal | 21:3894–3903

S. Miura, T. Dolker, M. Sanderford, S. Kumar


Bootstrap Confidence for Molecular Evolutionary Estimates from Tumor Bulk Sequencing Data

Frontiers in Bioinformatics | 3:1090730 (11 pp)

J. Huzar, M. Shenoy, M. D. Sanderford, S. Kumar, S. Miura


Protein Dynamics Provide Mechanistic Insights about Epistasis among Common Missense Polymorphisms

Biophysical Journal | 122:2938–2947

N. J. Ose, P. Campitelli, R. Patel, S. Kumar, S. B. Ozkan


Gene Expression Study of Breast Cancer using Welch Satterthwaite t-test, Kaplan-Meier Estimator Plot and Huber Loss Robust Regression Model

Journal of King Saud University - Science | 35:102447 (9 pp)

S. Karim, M.S. Iqbal, N. Ahmad, M.S. Ansari, Z. Mirza, A. Merdad, S. Jastaniah, S. Kumar


Masatoshi Nei (1931–2023)

Nature Ecology & Evolution | 7:(2 pp)

J. Zhang, S. Kumar


Masatoshi Nei (1931–2023)

Molecular Biology and Evolution | 40:msad149 (5 pp)

S. Kumar, T. Gojobori


Embracing Green Computing in Molecular Phylogenetics

Molecular Biology and Evolution | 39:msac043 (4 pp)

S. Kumar


TimeTree 5: An Expanded Resource for Species Divergence Times

Molecular Biology and Evolution | 39:msac174 (6 pp)

S. Kumar, M. Suleski, J. M. Craig, A. E. Kasprowicz, M. Sanderford, M. Li, G. Stecher, S. B. Hedges


Taming the Selection of Optimal Substitution Models in Phylogenomics by Site Subsampling and Upsampling

Molecular Biology and Evolution | 39:msac236 (8 pp)

S. Sharma, S. Kumar


TopHap: Rapid Inference of Key Phylogenetic Structures from Common Haplotypes in Large Genome Collections with Limited Diversity

Bioinformatics | 38:2719–2726

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


Epistasis Creates Invariant Sites and Modulates the Rate of Molecular Evolution

Molecular Biology and Evolution | 39:msac106 (11 pp)

R. Patel, V. Carnevale, S. Kumar


Dynamic Coupling of Residues within Proteins as a Mechanistic Foundation of Many Enigmatic Pathogenic Missense Variants

PLoS Computational Biology | 18:e1010006 (22 pp)

N. J. Ose, B. M. Butler, A. Kumar, M. Sanderford, S. Kumar, S. B. Ozkan


Limitations of Phylogenomic Data Can Drive Inferred Speciation Rate Shifts

Molecular Biology and Evolution | 39:msac038 (11 pp)

J. M. Craig, S. Kumar, S. B. Hedges


Storyboarding for Biology: An Authentic STEAM Experience

The American Biology Teacher | 84:328–335

C. Babaian, S. Kumar


Epistasis Storyboarded

The American Biology Teacher | 84:562–569

C. Babaian, S. Kumar


Clone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and Models

Cancers | 14:4326 (13 pp)

A. Chroni, S. Miura, L. Hamilton, T. Vu, S.G. Gaffney, V. Aly, S. Karim, M. Sanderford, J.P. Townsend, S. Kumar


A Phylogenetic Approach to Study the Evolution of Somatic Mutational Processes in Cancer

Communications Biology | 5:617 (11 pp)

S. Miura, T. Vu, J. Choi, J. P. Townsend, S. Karim, S. Kumar


MOCA for Integrated Analysis of Gene Expression and Genetic Variation in Single Cells

Frontiers in Genetics | 13:831040 (8 pp)

J. Huzar, H. Kim, S. Kumar, S. Miura


Waiting for the Truth: Is Reluctance in Accepting an Early Origin Hypothesis for SARS-CoV-2 Delaying Our Understanding of Viral Emergence?

BMJ Global Health | 7:e008386 (8 pp)

M. Canuti, S. Bianchi, O. Kolbl, S.L.K. Pond, S. Kumar, M. Gori, C. Fappani, D. Colzani, E. Borghi, G.V. Zuccotti, M.C. Raviglione, E. Tanzi, A. Amendola


Molecular Evidence for SARS-CoV-2 in Samples Collected from Patients with Morbilliform Eruptions since Late Summer 2019 in Lombardy, Northern Italy

Environmental Research | 215:113979 (9 pp)

A. Amendola, M. Canuti, S. Bianchi, S. Kumar, C. Fappani, M. Gori, D. Colzani, S. L. K. Pond, S. Miura, M. Baggeri, A. Marchi, E. Borghi, G. V. Zuccotti, M. C. Raviglione, F. Magurano, E. Tanzi


Development of "Biosearch System" for Biobank Management and Storage of Disease Associated Genetic Information

Journal of King Saud University - Science | 34:101760 (10 pp)

S. Karim, M. Al-Kharraz, Z. Mirza, H. Noureldin, H. Abusamara, N. Alganmi, A. Merdad, S. Jastaniah, S. Kumar, M. Rasool, A. Abuzenadah, M. Al-Qahtani


Evolutionary Sparse Learning for Phylogenomics

Molecular Biology and Evolution | 38:4674–4682

S. Kumar, S. Sharma


Fast and Accurate Bootstrap Confidence Limits on Genome-scale Phylogenies using Little Bootstraps

Nature Computational Science | 1:573–577

S. Sharma, S. Kumar


Tumors are Evolutionary Island-like Ecosystems

Genome Biology and Evolution | 13:evab276 (11 pp)

A. Chroni, S. Kumar


Migrations of Cancer Cells through the Lens of Phylogenetic Biogeography

Scientific Reports | 11:17184 (13 pp)

A. Chroni, S. Miura, O. Oladeinde, V. Aly, S. Kumar


Data-driven Speciation Tree Prior for Better Species Divergence Times in Calibration-poor Molecular Phylogenies

Bioinformatics | 37:i102–i110

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


Epistasis Produces an Excess of Invariant Sites in Neutral Molecular Evolution

Proceedings of the National Academy of Sciences (USA) | 118:e2018767118

R. Patel and S. Kumar


MEGA11: Molecular Evolutionary Genetics Analysis Version 11

Molecular Biology and Evolution | 38:3022–3027

K. Tamura, G. Stecher, S. Kumar


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


How to Build a Super Predator: From Genotype to Phenotype

The American Biology Teacher | 83:138–146

C. Babaian, S. Kumar


Assessing Rapid Relaxed-Clock Methods for Phylogenomic Dating

Genome Biology and Evolution | 13:evab251 (14 pp)

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


Molecular and Morphological Clocks for Estimating Evolutionary Divergence Times

BMC Ecology and Evolution | 21:83 (15 pp)

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


Deep Low-Shot Learning for Biological Image Classification and Visualization from Limited Training Samples

IEEE Transactions on Neural Networks and Learning Systems | (11 pp)

L. Cai, Z. Wang, R. Kulathinal, S. Kumar, S. Ji


Common Treatment, Common Variant: Evolutionary Prediction of Functional Pharmacogenomic Variants

Journal of Personalized Medicine | 11:131 (13 pp)

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


TreeMap: A Structured Approach to Fine Mapping of eQTL Variants

Bioinformatics | 37:1125–1134

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


The Durability of Immunity against Reinfection by SARS-CoV-2: A Comparative Evolutionary Study

The Lancet Microbe | 12:e666–e675

J. P. Townsend, H. B. Hassler, Z. Wang, S. Miura, J. Singh, S. Kumar, N. Ruddle, A.P. Galvani, A. Dornburg


The Somatic Molecular Evolution of Cancer: Mutation, Selection, and Epistasis

Progress in Biophysics and Molecular Biology | 165:56–65

K. Dasari, J. A. Somarelli, S. Kumar, J. P. Townsend


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


Efficient Methods for Dating Evolutionary Divergences

in The Molecular Evolutionary Clock (ed. Ho) [Springer] | 197–219

Q. Tao, K. Tamura, S. Kumar


Where Did SARS-CoV-2 Come From?

Molecular Biology and Evolution | 37:2463–2464

T. Leitner, S. Kumar


Molecular Evolutionary Genetics Analysis (MEGA) for macOS

Molecular Biology and Evolution | 37:1237–1239

G. Stecher, K. Tamura, S. Kumar


A New Method for Inferring Timetrees from Temporally Sampled Molecular Sequences

PLoS Computational Biology | 16:e1007046 (24 pp)

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


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


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


Using a GTR+Gamma 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


The Bits and Bytes of Biology: Digitalization Fuels an Emerging Generative Platform for Biological Innovation

Handbook of Digital Innovation (ed. Nambisan, Lyytinen, Yoo) [Edward Elgar] | 253–265

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


Molecular Memories of a Cambrian Fossil

The American Biology Teacher | 82:586–595

C. Babaian, 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 | 80:4329–4341.e4

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


Beaver and Naked Mole Rat Genomes Reveal Common Paths to Longevity

Cell 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


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


Deep Model Based Transfer and Multi-task Learning for Biological Image Analysis

IEEE Transactions on Big Data | 6:322–333

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


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


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


Ecological Nitrogen Limitation Shapes the DNA Composition of Plant Genomes

Molecular Biology and Evolution | 26:953–956

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


The Timetree of Life

Oxford University Press (New York) | (551 pp)

S.B. Hedges, S. Kumar


Discovering the Timetree of Life

The TimeTree of Life (ed. Hedges, Kumar) [Oxford University Press] | 3–18

S.B. Hedges, S. Kumar

Signatures of Nitrogen Limitation in the Elemental Composition of the Proteins Involved in the Metabolic Apparatus

Proceedings of the Royal Society B: Biological Sciences | 276:2605–2610

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

Association of Orthodenticle with Natural Variation for Early Embryonic Patterning in Drosophila melanogaster

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution | 312:841–854

L.M. Goering, P.K. Hunt, C. Heighington, C. Busick, P.S. Pennings, J. Hermisson, S. Kumar, G. Gibson

Phylogenetic Construction of 17 Bacterial Phyla by New Method and Carefully Selected Orthologs

Gene | 429:59–64

T. Horiike, D. Miyata, K. Hamada, S. Saruhashi, T. Shinozawa, S. Kumar, R. Chakraborty, T. Komiyama, Y. Tateno

A Bag-of-words Approach for Drosophila Gene Expression Pattern Annotation

BMC Bioinformatics | 10:119 (16 pp)

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

Drosophila Gene Expression Pattern Annotation Using Sparse Features and Term-term Interactions

KDD-09: 15th ACM SIGKDD Conference on Knowledge Discovery and Data Mining | 407–415

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

Positional Conservation and Amino Acids Shape the Correct Diagnosis and Population Frequencies of Benign and Damaging Personal Amino Acid Mutations

Genome Research | 19:1562–1569

S. Kumar, M.P. Suleski, G.J. Markov, S. Lawrence, A. Marco, A.J. Filipski

Relationship between Gene Co-expression and Sharing of Transcription Factor Binding Sites in Drosophila Melanogasterc

Bioinformatics | 25:2473–2477

A. Marco, C. Konikoff, T.L. Karr, S. Kumar

The Origin of Metazoa: A Transition from Temporal to Spatial Cell Differentiation

BioEssays | 31:758–768

K.V. Mikhailov, A.V. Konstantinova, M.A. Nikitin, P.V. Troshin, L.Y. Rusin, V.A. Lyubetsky, Y.V. Panchin, A.P. Mylnikov, L.L. Moroz, S. Kumar, V.V. Aleoshin

Methods for Incorporating the Hypermutability of CpG Dinucleotides in Detecting Natural Selection Operating at the Amino Acid Sequence Level

Molecular Biology and Evolution | 26:2275–2284

Y. Suzuki, T. Gojobori, S. Kumar


Developmental Stage Annotation of Drosophila Gene Expression Pattern Images via an Entire Solution Path for LDA

ACM Transactions on Knowledge Discovery from Data | 2:(21 pp)

J. Ye, J. Chen, R. Janardan, S. Kumar


Biological Image Analysis via Matrix Approximation

Encyclopedia of Data Warehousing and Mining (ed. Wang) [Idea Group] | 166–170

J. Ye, R. Janadan, S. Kumar

Automated Annotation of Drosophila Gene Expression Patterns Using a Controlled Vocabulary

Bioinformatics | 24:1881–1888

S. Ji, L. Sun, R. Jin, S. Kumar, J. Ye

MEGA: A Biologist-centric Software for Evolutionary Analysis of DNA and Protein Sequences

Briefings in Bioinformatics | 9:299–306

S. Kumar, M. Nei, J. Dudley, K. Tamura


Detecting Molecular Signatures of Adaptive Evolution

Evolutionary Genomics and Proteomics (ed. Pagel, Pomiankowski) [Sinauer] | 241–254

A. Filipski, S. Prohaska, S. Kumar

Nullomers: Really a Matter of Natural Selection?

PLoS One | 2:1022–1025

C. Acquisti, G. Poste, D. Curtiss, S. Kumar

Evolution of Genes and Genomes on the Drosophila Phylogeny

Nature | 450:203–218

A.G. Clark, M.B. Eisen, D.R. Smith, C.M. Bergman, B. Oliver, T.A. Markow, T.C. Kaufman, M. Kellis, W. Gelbart, V.N. Iyer, D.A. Pollard, T.B. Sackton, S. Kumar, et al

Lower Bounds on Multiple Sequence Alignment Using Exact 3-way Alignment

BMC Bioinformatics | 8:140 (8 pp)

C.J. Colbourn, S. Kumar

Bioinformatics Software for Biologists in the Genomics Era

Bioinformatics | 23:1713–1717

S. Kumar, J. Dudley

Multiple Sequence Alignment: In Pursuit of Homologous DNA Positions

Genome Research | 17:127–135

S. Kumar, A. Filipski

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

Molecular Biology and Evolution | 24:1596–1599

K. Tamura, J. Dudley, M. Nei, S. Kumar

Constraint and Turnover in Sex-biased Gene Expression in the Genus Drosophila

Nature | 450:233–237

Y. Zhang, D. Sturgill, M. Parisi, S. Kumar, B. Oliver


Classification of Drosophila Embryonic Developmental State Range Based on Gene Expression Pattern Images

Computational Systems Bioinformatics Conference | 2006:293–298

J. Ye, J. Chen, Q. Li, S. Kumar

Codon-based Detection of Positive Selection Can be Biased by Heterogeneous Distribution of Polar Amino Acids along Protein Sequences

Computational Systems Bioinformatics Conference | 2006:335–340

X. Xia, S. Kumar

Signatures of Ecological Resource Availability in the Animal and Plant Proteomes

Molecular Biology and Evolution | 23:1946–1951

J.J. Elser, W.F. Fagan, S. Subramanian, S. Kumar

TimeTree: A Public Knowledge-base of Divergence Times among Organisms

Bioinformatics | 22:2971–2972

S.B. Hedges, J. Dudley, S. Kumar

Constraining Fossil Calibrations for Molecular Clocks

BioEssays | 28:770–771

S.B. Hedges, S. Kumar, M. Van Tuinen

Evolutionary Anatomies of Positions and Types of Disease-associated and Neutral Amino Acid Mutations in the Human Genome

BMC Genomics | 7:306 (9 pp)

S. Subramanian, S. Kumar

Higher Intensity of Purifying Selection on >90% of the Human Genes Revealed by the Intrinsic Replacement Mutation Rates

Molecular Biology and Evolution | 23:2283–2287

S. Subramanian, S. Kumar


The Evolution of the Genome: Comparative Genomics in Eukaryotes

The Evolution of the Genome (ed. Gregory) [Elsevier] | 521–583

A. Filipski, S. Kumar

Maximum Likelihood Outperforms Maximum Parsimony Even When Evolutionary Rates are Heterotachous

Molecular Biology and Evolution | 22:2139–2141

S. Gadagkar, S. Kumar

Inferring Species Phylogenies from Multiple Genes: Concatenated Sequence Tree versus Consensus Gene Tree

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution | 304:64–74

S. Gadagkar, M. Rosenberg, S. Kumar

Automatic Annotation Techniques for Gene Expression Images of the Fruit Fly Embryo

Visual Communications and Image Processing 2005, Pts 1-4 | 5960:576–583

M. Gargesha, J. Yang, B. Van Emden, S. Panchanathan, S. Kumar

Molecular Clocks: Four Decades of Evolution

Nature Reviews Genetics | 6:654–662

S. Kumar

Placing Confidence Limits on the Molecular Age of the Human-Chimpanzee Divergence

Proceedings of the National Academy of Sciences (USA) | 102:18842–18847

S. Kumar, A. Filipski, V. Swarna, A. Walker, S.B. Hedges

Pushing Back the Expansion of Introns in Animal Genomes

Cell | 123:1182–1184

S. Kumar, S.B. Hedges


Image Registration and Similarity Computation for Chicken Gene Expression Patterns

Genomic Signal Processing and Statistics | (4 pp)

M. Gargesha, P. Antin, B. Van Emden, S. Panchanathan, S. Kumar

The Spectrum of Human Rhodopsin Disease Mutations through the Lens of Interspecific Variation

Gene | 12:107–118

A. Briscoe, C. Gaur, S. Kumar

Identifying Spatially Similar Gene Expression Patterns in Early Stage Fruit Fly Embryo Images: Binary Feature versus Invariant Moment Digital Representations

BMC Bioinformatics | 16:202–214

R. Gurunathan, B. Van Emden, S. Panchanathan, S. Kumar

Precision of Molecular Time Estimates

Trends in Genetics | 20:242–247

S.B. Hedges, S. Kumar

Gene Expression Intensity Shapes Evolutionary Rates of the Proteins Encoded by the Vertebrate Genome

Genetics | 168:373–381

S. Subramanian, S. Kumar

Prospects for Inferring Very Large Phylogenies by Using the Neighbor-joining Method

Proceedings of the National Academy of Sciences (USA) | 101:11030–11035

K. Tamura, M. Nei, S. Kumar

Temporal Patterns of Fruit Fly (Drosophila) Evolution Revealed by Mutation Clocks

Molecular Biology and Evolution | 21:36–44

K. Tamura, S. Subramanian, S. Kumar

MEGA3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment

Briefings in Bioinformatics | 5:150–163

S. Kumar, K. Tamura, M. Nei


Genomic Clocks and Evolutionary Timescales

Trends in Genetics | 19:200–206

S.B. Hedges, S. Kumar

Genomic Sequence of a Ranavirus (family Iridoviridae) Associated with Salamander Mortalities in North America

Virology | 316:90–103

J. Jancovich, J. Mao, V. Chinchar, C. Wyatt, S. Case, S. Kumar, G. Valente, S. Subramanian, E. Davidson, J. Collins, B. Jacobs

Quantifying the Intragenic Distribution of Human Disease Mutations

Annals of Human Genetics | 67:567–579

M. Miller, J. Parker, S. Rissing, S. Kumar

Heterogeneity of Nucleotide Frequencies among Evolutionary Lineages and Phylogenetic Inference

Molecular Biology and Evolution | 20:610–621

M. Rosenberg, S. Kumar

Taxon Sampling, Bioinformatics, and Phylogenomics

Systematic Biology | 52:119–124

M. Rosenberg, S. Kumar

Patterns of Transitional Mutation Biases within and among Mammalian Genomes

Molecular Biology and Evolution | 20:988–993

M. Rosenberg, S. Subramanian, S. Kumar

Neutral Substitutions Occur at a Faster Rate in Exons than in Noncoding DNA in Primate Genomes

Genome Research | 13:838–844

S. Subramanian, S. Kumar


Vertebrate Genomes Compared

Science | 297:1283–1285

S.B. Hedges, S. Kumar

Measuring Conservation of Contiguous Sets of Autosomal Markers on Bovine and Porcine Genomes in relation to the Map of the Human Genome

Genome | 45:769–776

Z. Jiang, J. Melville, H. Cao, S. Kumar, A. Filipski, A. Gibbins

BEST: A Novel Computational Approach for Comparing Gene Expression Patterns from Early Stages of Drosophila melanogaster Development

Genetics | 162:2037–2047

S. Kumar, K. Jayaraman, S. Panchanathan, R. Gurunathan, A. Marti-Subirana, S. Newfeld

Mutation Rates in Mammalian Genomes

Proceedings of the National Academy of Sciences (USA) | 99:803–808

S. Kumar, S. Subramanian

Evolutionary Distance Estimation under Heterogeneous Substitution Pattern among Lineages

Molecular Biology and Evolution | 19:1727–1736

K. Tamura, S. Kumar


Elucidating Gene Interaction Networks Based on Gene Expression Pattern Image Analysis

Proceedings of the International Conference on Biomedical Engineering | 5:232–234

S. Kumar, S. Panchanathan

Does Nonneutral Evolution Shape Observed Patterns of DNA Variation in Animal Mitochondrial Genomes?

Annual Review of Genetics | 35:539–566

A. Gerber, R. Loggins, S. Kumar, T. Dowling

A Genomic Timescale for the Origin of Eukaryotes

BMC Evolutionary Biology | 1:4 (10 pp)

S.B. Hedges, H. Chen, S. Kumar, D.Y.C. Wang, A.S. Thompson, H. Watanabe

Mutation and Linkage Disequilibrium in Human mtDNA

European Journal of Human Genetics | 9:969–972

P. Hedrick, S. Kumar

Classification and Indexing of Gene Expression Images

Applications of Digital Image Processing XXIV | 4472:471–481

K. Jayaraman, S. Panchanathan, S. Kumar, A. Tescher

Disparity Index: A Simple Statistic to Measure and Test the Homogeneity of Substitution Patterns between Molecular Sequences

Genetics | 158:1321–1327

S. Kumar, S. Gadagkar

Determination of the Number of Conserved Chromosomal Segments between Species

Genetics | 157:1387–1395

S. Kumar, S. Gadagkar, A. Filipski, X. Gu

MEGA2: Molecular Evolutionary Genetics Analysis Software

Bioinformatics | 17:1244–1245

S. Kumar, K. Tamura, I. Jakobsen, M. Nei

Understanding Human Disease Mutations through the Use of Interspecific Genetic Variation

Human Molecular Genetics | 10:2319–2328

M. Miller, S. Kumar

Incomplete Taxon Sampling is Not a Problem for Phylogenetic Inference

Proceedings of the National Academy of Sciences (USA) | 98:10751–10756

M. Rosenberg, S. Kumar

Traditional Phylogenetic Reconstruction Methods Reconstruct Shallow and Deep Evolutionary Relationships Equally Well

Molecular Biology and Evolution | 18:1823–1827

M. Rosenberg, S. Kumar


Efficiency of the Neighbor-joining Method in Reconstructing Deep and Shallow Evolutionary Relationships in Large Phylogenies

Journal of Molecular Evolution | 51:544–553

S. Kumar, S. Gadagkar

Questioning Evidence for Recombination in Human Mitochondrial DNA

Science | 288:1931a (2 pp)

S. Kumar, P. Hedrick, T. Dowling, M. Stoneking

Expansion and Molecular Evolution of the Interferon-induced 2 '-5 ' Oligoadenylate Synthetase Gene Family

Molecular Biology and Evolution | 17:738–750

S. Kumar, C. Mitnik, G. Valente, G. Floyd-Smith


Molecular Evolution and Phylogenetics

Oxford University Press [New York] | (333 pp)

M. Nei, S. Kumar

Single Column Discrepancy and Dynamic Max-Mini Optimizations for Quickly Finding the Most Parsimonious Evolutionary Trees

Bioinformatics | 16:140–151

P. Purdom, P. Bradford, K. Tamura, S. Kumar


Molecular Evolution of a Developmental Pathway: Phylogenetic Analyses of Transforming Growth Factor-beta Family Ligands, Receptors and Smad Signal Transducers

Genetics | 152:783–795

S. Newfeld, R. Wisotzkey, S. Kumar

Divergence Time Estimates for the Early History of Animal Phyla and the Origin of Plants, Animals and Fungi

Proceedings of the Royal Society B: Biological Sciences | 266:163–171

D. Wang, S. Kumar, S.B. Hedges

Divergence Times of Eutherian Mammals

Science | 285:2031a (2 pp)

S.B. Hedges, S. Kumar


Genome Maps 10. Comparative Genomics. Mammalian Radiations. Wall Chart.

Science | 286:463–478

S.J. O'Brien, J.F. Eisenberg, M. Miyamoto, S.B. Hedges, S. Kumar, D.E. Wilson, M. Menotti-Raymond, W.J. Murphy, W.G. Nash, L.A. Lyons, J.C. Menninger, R. Stanyon, J. Wienberg, N.G. Copeland, N.A. Jenkins, J. Gellin, M. Yerle, L. Andersson, J. Womack, T. Broad, J. Postlethwait, et al.


A Molecular Timescale for Vertebrate Evolution

Nature | 392:917–920

S. Kumar, S.B. Hedges

The Optimization Principle in Phylogenetic Analysis Tends to Give Incorrect Topologies When the Number of Nucleotides or Amino Acids Used is Small

Proceedings of the National Academy of Sciences (USA) | 95:12390–12397

M. Nei, S. Kumar, K. Takahashi


Evolution and Functional Diversification of the Paired Box (Pax) DNA-binding Domains

Molecular Biology and Evolution | 14:829–842

K. Balczarek, Z. Lai, S. Kumar

Detection of Convergent and Parallel Evolution at the Amino Acid Sequence Level

Molecular Biology and Evolution | 14:527–536

J. Zhang, S. Kumar

Sequence Convergence in the Peptide-binding Region of Primate and Rodent MBC Class Ib Molecules

Molecular Biology and Evolution | 14:1035–1041

M. Yeager, S. Kumar, A. Hughes

Tempo and Mode of Nucleotide Substitutions in GAG and ENV Gene Fragments in Human Immunodeficiency Virus Type 1 Populations with a Known Transmission History

Journal of Virology | 71:4761–4770

T. Leitner, S. Kumar, J. Albert

Small-sample Tests of Episodic Adaptive Evolution: A Case Study of Primate Lysozymes

Molecular Biology and Evolution | 14:1335–1338

J. Zhang, S. Kumar, M. Nei


Stepwise Algorithm for Finding Minimum Evolution Trees

Molecular Biology and Evolution | 13:584–593

S. Kumar

Patterns of Nucleotide Substitution in Mitochondrial Protein Coding Genes of Vertebrates

Genetics | 143:537–548

S. Kumar

Evolutionary Relationships of Eukaryotic Kingdoms

Journal of Molecular Evolution | 42:183–193

S. Kumar, A. Rzhetsky

Evolution of the Hedgehog Gene Family

Genetics | 142:965–972

S. Kumar, K. Balczarek, Z. Lai

Approximate Methods for Estimating the Pattern of Nucleotide Substitution and the Variation of Substitution Rates among Sites

Molecular Biology and Evolution | 13:650–659

Z. Yang, S. Kumar

Continental Breakup and the Ordinal Diversification of Birds and Mammals

Nature | 381:226–229

S.B. Hedges, P. Parker, C. Sibley, S. Kumar


A New Method of Inference of Ancestral Nucleotide and Amino Acid Sequences

Genetics | 141:1641–1650

Z. Yang, S. Kumar, M. Nei

Four-cluster Analysis: A Simple Method to Test Phylogenetic Hypotheses

Molecular Biology and Evolution | 12:163–167

A. Rzhetsky, S. Kumar, M. Nei

18S Ribosomal-RNA Data Indicate that Aschelminthes are Polyphyletic in Origin and Consist of at Least Three Distinct Clades

Molecular Biology and Evolution | 12:1132–1137

B. Winnepenninckx, T. Backeljau, L. Mackey, J. Brooks, R. De Watcher, S. Kumar, J. Garey


MEGA - Molecular Evolutionary Genetics Analysis Software for Microcomputers

Computer Applications in the Biosciences | 10:189–191

S. Kumar, K. Tamura, M. Nei


A Guide to Molecular Evolutionary Genetics Analysis Program for Microcomputers

Pennsylvania State University [University Park, PA, USA] | (135 pp)

S. Kumar, K. Tamura, M. Nei


Human Origins and Analysis of Mitochondrial DNA Sequences

Science | 255:737–739

S.B. Hedges, S. Kumar, K. Tamura, M. Stoneking