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 | 16:1218 (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: Sparse Learning in Molecular Evolution and Phylogenetic analysis

Molecular Biology and Evolution | (in review)

M. Sanderford, S. Sharma, G. Stecher, 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