Transforming Molecular Evolutionary Analyses with Protein Foundation Models

Nature Methods | 23: (Accepted in principle)

S. Kumar, R. Alibutud, J. Allard, M. E. Mowlaei, X. Shi

Tiny Subsamples and Upsampling Tame Big Data Evolutionary Analysis in Phylogenomics

Molecular Biology and Evolution | 43: (Acceptance pending minor revisions)

S. Kumar, K. Tamura, S. Sharma

The Genetic Foundations of Convergent Traits

Nature Reviews Genetics | 27:563-578

J. Allard, S. Kumar

Epistasis Plays a Limited role in Driving Entrenchment During Neutral Protein Evolution

Genome Biology | 27:(10 pp)

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

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

Bioinformatics | 42:btag197 (4 pp)

J. Allard, S. Kumar

MEGA 12.1: Cross-platform Release for macOS and Linux Operating Systems

Journal of Molecular Evolution | 94:14–18

G. Stecher, M. Suleski, Q. Tao, K. Tamura, 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 | 94:177–189

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

Evolutionary Dynamics of Early and Late Mutational Signatures in Metastatic Cancer

Frontiers in Bioinformatics | 6:(10 pp)

A. Yankovskiy, S. Kumar, S. Miura

ESL-PSC Toolkit: a Graphical Software Environment for Linking Shared Genetic Changes to Convergent Phenotypes

Molecular Biology and Evolution | (Acceptance pending minor revisions)

J. Allard, S. Kumar

Nutrigenomics: From Epicure to Epigenetics - Engaging Students with Nutrition Through the Human Genome

The American Biology Teacher | 88: (In press)

C. Babaian, S. Kumar

The Big Evolution of the Little Phage: Teaching biological interdependency through a virus

The American Biology Teacher | 88:93–102

C. Babaian, S. Kumar

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

Genome Research | (Revision invited)

C Li, M. E. Mowlaei, L. Ni, HGSVC, M. J.P. Chaisson, E. Eichler, V. Carnevale, S. Kumar, X. Shi

HyperEvoGen: Exploring deep phylogeny using non-Euclidean variational inference

arXiv | (in submission)

J. Lamanna, M. E. Mowlaei, X. Shi, S. Kumar, V. Carnevale

Multiple Versus Pairwise Sequence Alignments for Protein Phylogenetics Using Foundation Models

ICIBM | (Revision invited)

R. Alibutud, S. Kumar

GI-Joe: Taming Long-Context Genotype Imputation for Higher Accuracy and Efficiency

ICIBM | (Revision invited)

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

Gain and Loss of DNA Methylation During Tumor Evolution

ICIBM | (Revision invited)

D. Tabatabaei, S. Kumar, S. Miura

A Collaborative Genomics Platform for T1D Research in Eastern and Central Europe

Metabologia | (revision in review)

K. Shchubelka,..., S, Sharma,..., S. Kumar,..., T. K. Oleksynk

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

arXiv | (available)

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