Taming the Selection of Optimal Substitution Models in Phylogenomics

Molecular Biology and Evolution | (in review)

S. Sharma, 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


Embracing Green Computing in Molecular Phylogenetics

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

S. Kumar


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


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


Storyboarding for Biology: An Authentic STEAM Experience

The American Biology Teacher | 84:328-335

C. Babaian, S. Kumar


Epistasis Storyboarded

The American Biology Teacher | (accepted)

C. Babaian, 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


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


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


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


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

ScienceDirect | 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


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

Preprint in bioRxiv

Q. Tao, . Sharma, S. Kumar