Enabling Data-driven Discoveries in Evolutionary Genetics and Genomics

Genetics | 230:iyaf084 (4 pp)

S. Kumar

Evolutionary Sparse Learning Reveals the Shared Genetic Basis of Convergent Traits

Nature Communications | 16:3217 (14 pp)

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

Genome Assembly of Arctica islandica, the Longest-Lived Non-Colonial Animal Species

Animals | 15:ani15050690 (13 pp)

G. Gerhard, J. Allard, S. Kaniper, D. Lynch, H. Lee, S. Kumar

MEGA-GPT: Artificial Intelligence Guidance and Building Analytical Protocols using MEGA software

Molecular Biology and Evolution | 42:msaf101 (5 pp)

J. Allard, S. Kumar

STICI: Split-Transformer with Integrated Convolutions for Genotype Imputation

Nature Communications | 16:(14 pp)

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

MyESL: A software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics

Molecular Biology and Evolution | 42:msaf224 (16 pp)

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

Teaching Biology & Evolution Through the Watery Matrix of Life: A Genomic Medicine Perspective

The American Biology Teacher | 87:84–92

C. Babaian, S. Kumar, S. Miura

Integrating Phylogenies with Chronology to Assemble the Tree of Life

Frontiers in Bioinformatics | 5:1571568 (14 pp)

J. Barba-Montoya, J.M. Craig, S. Kumar

Entrenchment and Contingency in Neutral Protein Evolution with Epistasis

bioRxiv | (available)

L. Schmelkin , V. Carnevale, A. Haldane, J. Townsend, S. Chung, R. Levy, S. Kumar

GenoPath: A Pipeline to Infer Tumor Clone Composition, Mutational History, and Metastatic Cell Migration Events from Tumor DNA Sequencing Data

Frontiers in Bioinformatics | 5:1615834 (10 pp)

R. Tobin, S. Singh, S. Kumar, S. Miura

TRUHiC: A TRansformer-Embedded U-2 Net to Enhance Hi-C Data for 3D Chromatin Structure Characterization

bioRxiv | (available)

C. Li, M.E. Mowlaei, V. Carnevale, S. Kumar, X. Shi

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

arXiv | (available)

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

Treemble: A Graphical Tool to Generate Newick Strings from Phylogenetic Tree Images

Bioinformatics | in review

J. Allard, S. Kumar

Robust and Efficient Method for Estimating Confidence Limits for Phylogenomic Inferences of Organismal Relationships

Molecular Biology and Evolution | revision in review

S. Sharma, S. Kumar

The Genetic Foundations of Convergent Traits

Nature Reviews Genetics | in review

J. Allard, S. Kumar

An Evolutionary Metric for Estimating PhyloAges from Bulk Sequencing of Hematopoietic Stem Cells Reveals the Tempo of Blood Aging in Cancer and Longevity

Journal of Molecular Evolution | in review

J. M. Craig, R. M. Tobin, W. Wolfsberger, T. K. Oleksyk, S. Miura, G. S. Gerhard, S. Kumar

Completing a Molecular Timetree of Afrotheria

Frontiers in Bioinformatics | in review

J. M. Craig, W. Fisher, A. Thomas, S. Hedges, S. Kumar