2024
238

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

237

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

236

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

eLife

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

235

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

234

Evolutionary Sparse Learning Reveals the Shared Genetic Basis of Convergent Traits

| (submitted)

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

233

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

bioRxiv | (available)

S. Sharma, S. Kumar

232

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

bioRxiv | (available)

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

222

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

eLife

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

2023
231

Computational Reproducibility of Molecular Phylogenies

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

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

230

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

229

Molecular Timetrees using Relaxed Clocks and Uncertain Phylogenies

Frontiers in Bioinformatics | 3:1225807 (13 pp)

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

228

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

227

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

226

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

225

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

224

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

223

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

221

Masatoshi Nei (1931–2023)

Nature Ecology & Evolution | 7:(2 pp)

J. Zhang, S. Kumar

220

Masatoshi Nei (1931–2023)

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

S. Kumar, T. Gojobori

2022
219

Embracing Green Computing in Molecular Phylogenetics

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

S. Kumar

218

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

217

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

216

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

215

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

214

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

213

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

212

Storyboarding for Biology: An Authentic STEAM Experience

The American Biology Teacher | 84:328–335

C. Babaian, S. Kumar

211

Epistasis Storyboarded

The American Biology Teacher | 84:562–569

C. Babaian, S. Kumar

210

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

209

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

208

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

207

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

206

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

205

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

2021
203

Evolutionary Sparse Learning for Phylogenomics

Molecular Biology and Evolution | 38:4674–4682

S. Kumar, S. Sharma

202

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

Nature Computational Science | 1:573–577

S. Sharma, S. Kumar

201

Tumors are Evolutionary Island-like Ecosystems

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

A. Chroni, S. Kumar

200

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

199

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

198

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

197

MEGA11: Molecular Evolutionary Genetics Analysis Version 11

Molecular Biology and Evolution | 38:3022–3027

K. Tamura, G. Stecher, S. Kumar

196

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

195

How to Build a Super Predator: From Genotype to Phenotype

The American Biology Teacher | 83:138–146

C. Babaian, S. Kumar

194

Assessing Rapid Relaxed-Clock Methods for Phylogenomic Dating

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

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

193

Molecular and Morphological Clocks for Estimating Evolutionary Divergence Times

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

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

192

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

191

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

190

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

189

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

188

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

2020
187

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

186

Efficient Methods for Dating Evolutionary Divergences

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

Q. Tao, K. Tamura, S. Kumar

185

Where Did SARS-CoV-2 Come From?

Molecular Biology and Evolution | 37:2463–2464

T. Leitner, S. Kumar

184

Molecular Evolutionary Genetics Analysis (MEGA) for macOS

Molecular Biology and Evolution | 37:1237–1239

G. Stecher, K. Tamura, S. Kumar

183

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

182

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

181

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

180

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

179

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

178

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

177

Molecular Memories of a Cambrian Fossil

The American Biology Teacher | 82:586–595

C. Babaian, S. Kumar

176

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

175

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

174

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

173

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

172

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

171

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

170

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