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Sudhir Kumar

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Sudhir Kumar

  • College of Science and Technology

    • Biology

      • Laura H. Carnell Professor

Biography

Sudhir Kumar joined CIS as a Carnell Professor. His primary appointment is in the Department of Biology and he is the founding director of the Institute for Genomics and Evolutionary Medicine (iGEM). Dr. Kumar uses informatics as primary research tool to discover biological patterns and to make predictions in subject matters spanning the tree of life to the diagnosis of disease mutations. He has developed many algorithms, statistical methods, computer software, and web databases in biology and genomics. Recently, Thomson Reuters ScienceWatch designated him the Most Highly Cited Researcher in Computer Science in the last 10 years. Dr. Kumar has written over 150 papers, including many citation classics and hot papers. Dr. Kumar was elected Fellow of the American Association for the Advancement of Science (AAAS) for exemplary contributions in evolutionary bioinformatics, particularly in developing high-impact comparative analysis software for biologists and in illuminating the evolutionary dynamics of mutations and species through comparative genomics. He would like iGEM to catalyze strong collaborations across departments and colleges by embarking on new cross-cutting research project and recruiting faculty members in genomics, bioinformatics, and computational biology.

Courses Taught

Number

Name

Level

BIOL 3112

Fundamentals of Genomic Evolutionary Medicine

Undergraduate

BIOL 3511

Pathophysiology of Genomic Medicine

Undergraduate

BIOL 4391

Accelerated Research in Biology

Undergraduate

BIOL 5112

Fundamentals of Genomic Evolutionary Medicine

Graduate

Selected Publications

Recent

  • Allard, J.B. & Kumar, S. (2026). The genetic foundations of convergent traits. Nat Rev Genet. England. 10.1038/s41576-026-00933-7

  • Craig, J.M., Tobin, R.M., Wolfsberger, W., Oleksyk, T.K., Miura, S., Gerhard, G.S., & Kumar, S. (2025). An Evolutionary Metric for Estimating PhyloAges from Bulk Sequencing of Hematopoietic Stem Cells Reveals the Tempo of Blood Aging in Cancer and Longevity. J Mol Evol. Germany. 10.1007/s00239-025-10296-y

  • Sharma, S. & Kumar, S. (2025). Robust and Efficient Confidence Limits for Phylogenomic Inference of Organismal Relationships. Mol Biol Evol, 42(12). United States. 10.1093/molbev/msaf296

  • Stecher, G., Suleski, M., Tao, Q., Tamura, K., & Kumar, S. (2025). MEGA 12.1: Cross-Platform Release for macOS and Linux Operating Systems. J Mol Evol. Germany. 10.1007/s00239-025-10287-z

  • Sanderford, M., Sharma, S., Stecher, G., Suleski, M., Liu, J., Ye, J., & Kumar, S. (2025). MyESL: A Software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics. Mol Biol Evol, 42(10). United States. 10.1093/molbev/msaf224

  • Kumar, S. (2025). Enabling data-driven discoveries in evolutionary genetics and genomics. Genetics, 230(3). United States. 10.1093/genetics/iyaf084

  • Allard, J.B. & Kumar, S. (2025). MEGA-GPT: Artificial Intelligence Guidance and Building Analytical Protocols Using MEGA Software. Mol Biol Evol, 42(6). United States. 10.1093/molbev/msaf101

  • Allard, J.B., Sharma, S., Patel, R., Sanderford, M., Tamura, K., Vucetic, S., Gerhard, G.S., & Kumar, S. (2025). Evolutionary sparse learning reveals the shared genetic basis of convergent traits. Nat Commun, 16(1), 3217. England. 10.1038/s41467-025-58428-8

  • Li, C., Mowlaei, M.E., (HGSVC), H.G.S.V.C., Group, H.F.A.W., Carnevale, V., Kumar, S., & Shi, X. (2025). TRUHiC: A TRansformer-embedded U-2 Net to enhance Hi-C data for 3D chromatin structure characterization. BioRxiv. United States. 10.1101/2025.03.29.646133

  • Gerhard, G.S., Allard, J.B., Kaniper, S., Lynch, D., Lee, H., & Kumar, S. (2025). Genome Assembly of Arctica islandica, the Longest-Lived Non-Colonial Animal Species. Animals (Basel), 15(5). Switzerland. 10.3390/ani15050690

  • Mowlaei, M.E., Li, C., Jamialahmadi, O., Dias, R., Chen, J., Jamialahmadi, B., Rebbeck, T.R., Carnevale, V., Kumar, S., & Shi, X. (2025). STICI: Split-Transformer with integrated convolutions for genotype imputation. Nat Commun, 16(1), 1218. England. 10.1038/s41467-025-56273-3

  • Schmelkin, L., Carnevale, V., Haldane, A., Townsend, J.P., Chung, S., Levy, R.M., & Kumar, S. (2025). Entrenchment and contingency in neutral protein evolution with epistasis. BioRxiv. United States. 10.1101/2025.01.09.632266

  • Allard, J.B., Sharma, S., Patel, R., Sanderford, M., Tamura, K., Vucetic, S., Gerhard, G.S., & Kumar, S. (2025). Evolutionary sparse learning with paired species contrast reveals the shared genetic basis of convergent traits. BioRxiv. United States. 10.1101/2025.01.08.631987

  • Tobin, R.M., Singh, S., Kumar, S., & Miura, S. (2025). GenoPath: a pipeline to infer tumor clone composition, mutational history, and metastatic cell migration events from tumor DNA sequencing data. Front Bioinform, 5, 1615834. Switzerland. 10.3389/fbinf.2025.1615834

  • Barba-Montoya, J., Craig, J.M., & Kumar, S. (2025). Integrating phylogenies with chronology to assemble the tree of life. Front Bioinform, 5, 1571568. Switzerland. 10.3389/fbinf.2025.1571568

  • Kumar, S., Stecher, G., Suleski, M., Sanderford, M., Sharma, S., & Tamura, K. (2024). MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing. Mol Biol Evol, 41(12). United States. 10.1093/molbev/msae263

  • Barba-Montoya, J., Craig, J.M., & Kumar, S. (2024). Integrating Phylogenies with Chronology to Assemble the Tree of Life. BioRxiv. United States. 10.1101/2024.07.17.603989

  • Sharma, S. & Kumar, S. (2024). Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning. Mol Biol Evol, 41(7). United States. 10.1093/molbev/msae131

  • Ose, N.J., Campitelli, P., Modi, T., Kazan, I.C., Kumar, S., & Ozkan, S.B. (2024). Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. Elife, 12. England. 10.7554/eLife.92063

  • Sharma, S. & Kumar, S. (2024). Discovering Fragile Clades And Causal Sequences In Phylogenomics By Evolutionary Sparse Learning. BioRxiv. United States. 10.1101/2024.04.26.591378

  • Ose, N.J., Campitelli, P., Modi, T., Kazan, I.C., Kumar, S., & Ozkan, S.B. (2024). Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. BioRxiv. United States. 10.1101/2023.09.14.557827

  • Craig, J.M., Gerhard, G.S., Sharma, S., Yankovskiy, A., Miura, S., & Kumar, S. (2024). Methods for Estimating Personal Disease Risk and Phylogenetic Diversity of Hematopoietic Stem Cells. Mol Biol Evol, 41(1). United States. 10.1093/molbev/msad279

  • Craig, J.M., Hedges, S.B., & Kumar, S. (2024). Completing a molecular timetree of primates. Front Bioinform, 4, 1495417. Switzerland. 10.3389/fbinf.2024.1495417

  • Pivirotto, A.M., Platt, A., Patel, R., Kumar, S., & Hey, J. (2023). Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls. BioRxiv. United States. 10.1101/2023.10.09.561569

  • Zhang, J. & Kumar, S. (2023). Masatoshi Nei (1931-2023). Nat Ecol Evol, 7(9), 1347-1348. England. 10.1038/s41559-023-02119-4

  • Ose, N.J., Campitelli, P., Patel, R., Kumar, S., & Ozkan, S.B. (2023). Protein dynamics provide mechanistic insights about epistasis among common missense polymorphisms. Biophys J, 122(14), 2938-2947. United States. 10.1016/j.bpj.2023.01.037

  • Kumar, S., Tao, Q., Lamarca, A.P., & Tamura, K. (2023). Computational Reproducibility of Molecular Phylogenies. Mol Biol Evol, 40(7). United States. 10.1093/molbev/msad165

  • Kumar, S. & Gojobori, T. (2023). Obituary: Masatoshi Nei (1931-2023). Mol Biol Evol, 40(6). United States. 10.1093/molbev/msad149

  • Cai, L., Wang, Z., Kulathinal, R., Kumar, S., & Ji, S. (2023). Deep Low-Shot Learning for Biological Image Classification and Visualization From Limited Training Samples. IEEE Trans Neural Netw Learn Syst, 34(5), 2528-2538. United States. 10.1109/TNNLS.2021.3106831

  • Stanojevic, M., Andjelkovic, J., Kasprowicz, A., Huuki, L.A., Chao, J., Hedges, S.B., Kumar, S., & Obradovic, Z. (2023). Discovering research articles containing evolutionary timetrees by machine learning. Bioinformatics, 39(1). England. 10.1093/bioinformatics/btad035

  • Huzar, J., Shenoy, M., Sanderford, M.D., Kumar, S., & Miura, S. (2023). Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data. Front Bioinform, 3, 1090730. Switzerland. 10.3389/fbinf.2023.1090730

  • Miura, S., Dolker, T., Sanderford, M., & Kumar, S. (2023). Improving cellular phylogenies through the integrated use of mutation order and optimality principles. Comput Struct Biotechnol J, 21, 3894-3903. Netherlands. 10.1016/j.csbj.2023.07.018

  • Barba-Montoya, J., Sharma, S., & Kumar, S. (2023). Molecular timetrees using relaxed clocks and uncertain phylogenies. Front Bioinform, 3, 1225807. Switzerland. 10.3389/fbinf.2023.1225807

  • Craig, J.M., Kumar, S., & Hedges, S.B. (2023). The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen. Front Bioinform, 3, 1233281. Switzerland. 10.3389/fbinf.2023.1233281

  • Craig, J.M., Bamba, G.L., Barba-Montoya, J., Hedges, S.B., & Kumar, S. (2023). Completing a molecular timetree of apes and monkeys. Front Bioinform, 3, 1284744. Switzerland. 10.3389/fbinf.2023.1284744

  • Kumar, S. (2022). A Report by the Editor-in-Chief for Molecular Biology and Evolution (MBE), Volume 38. Mol Biol Evol, 39(12). United States. 10.1093/molbev/msac260

  • Amendola, A., Canuti, M., Bianchi, S., Kumar, S., Fappani, C., Gori, M., Colzani, D., Pond, S.L.K., Miura, S., Baggieri, M., Marchi, A., Borghi, E., Zuccotti, G., Raviglione, M.C., Magurano, F., & Tanzi, E. (2022). Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy. Environ Res, 215(Pt 1), 113979. Netherlands. 10.1016/j.envres.2022.113979

  • Sharma, S. & Kumar, S. (2022). Taming the Selection of Optimal Substitution Models in Phylogenomics by Site Subsampling and Upsampling. Mol Biol Evol, 39(11). United States. 10.1093/molbev/msac236

  • Chroni, A., Miura, S., Hamilton, L., Vu, T., Gaffney, S.G., Aly, V., Karim, S., Sanderford, M., Townsend, J.P., & Kumar, S. (2022). Clone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and Models. Cancers (Basel), 14(17). Switzerland. 10.3390/cancers14174326

  • Kumar, S., Suleski, M., Craig, J.M., Kasprowicz, A.E., Sanderford, M., Li, M., Stecher, G., & Hedges, S.B. (2022). TimeTree 5: An Expanded Resource for Species Divergence Times. Mol Biol Evol, 39(8). United States. 10.1093/molbev/msac174

  • Miura, S., Vu, T., Choi, J., Townsend, J.P., Karim, S., & Kumar, S. (2022). A phylogenetic approach to study the evolution of somatic mutational processes in cancer. Commun Biol, 5(1), 617. England. 10.1038/s42003-022-03560-0

  • Caraballo-Ortiz, M.A., Miura, S., Sanderford, M., Dolker, T., Tao, Q., Weaver, S., Pond, S.L., & Kumar, S. (2022). TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. Bioinformatics, 38(10), 2719-2726. England. 10.1093/bioinformatics/btac186

  • Patel, R., Carnevale, V., & Kumar, S. (2022). Epistasis Creates Invariant Sites and Modulates the Rate of Molecular Evolution. Mol Biol Evol, 39(5). United States. 10.1093/molbev/msac106

  • Ose, N.J., Butler, B.M., Kumar, A., Kazan, I.C., Sanderford, M., Kumar, S., & Ozkan, S.B. (2022). Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants. PLoS Comput Biol, 18(4), e1010006. United States. 10.1371/journal.pcbi.1010006

  • Caraballo-Ortiz, M.A., Miura, S., Sanderford, M., Dolker, T., Tao, Q., Weaver, S., Pond, S.L., & Kumar, S. (2022). TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. Bioinformatics. England. 10.1093/bioinformatics/btac186

  • Craig, J.M., Kumar, S., & Hedges, S.B. (2022). Limitations of Phylogenomic Data Can Drive Inferred Speciation Rate Shifts. Mol Biol Evol, 39(3). United States. 10.1093/molbev/msac038

  • Kumar, S. (2022). Embracing Green Computing in Molecular Phylogenetics. Mol Biol Evol, 39(3). United States. 10.1093/molbev/msac043

  • Canuti, M., Bianchi, S., Kolbl, O., Pond, S.L.K., Kumar, S., Gori, M., Fappani, C., Colzani, D., Borghi, E., Zuccotti, G., Raviglione, M.C., Tanzi, E., & Amendola, A. (2022). Waiting for the truth: is reluctance in accepting an early origin hypothesis for SARS-CoV-2 delaying our understanding of viral emergence? BMJ Glob Health, 7(3). England. 10.1136/bmjgh-2021-008386

  • Karim, S., Al-Kharraz, M., Mirza, Z., Noureldin, H., Abusamara, H., Alganmi, N., Merdad, A., Jastaniah, S., Kumar, S., Rasool, M., Abuzenadah, A., & Al-Qahtani, M. (2022). Development of "Biosearch System" for biobank management and storage of disease associated genetic information. JOURNAL of KING SAUD UNIVERSITY SCIENCE, 34(2). 10.1016/j.jksus.2021.101760

  • Huzar, J., Kim, H., Kumar, S., & Miura, S. (2022). MOCA for Integrated Analysis of Gene Expression and Genetic Variation in Single Cells. Front Genet, 13, 831040. Switzerland. 10.3389/fgene.2022.831040

  • Caraballo-Ortiz, M.A., Miura, S., Sanderford, M., Dolker, T., Tao, Q., Weaver, S., Pond, S.L., & Kumar, S. (2021). TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. BioRxiv. United States. 10.1101/2021.12.13.472454

  • Kumar, S. (2021). A Report by the Editor-in-Chief for Molecular Biology and Evolution (MBE), Volume 37. Mol Biol Evol, 38(12), 5830. United States. 10.1093/molbev/msab319

  • Chroni, A. & Kumar, S. (2021). Tumors Are Evolutionary Island-Like Ecosystems. Genome Biol Evol, 13(12). England. 10.1093/gbe/evab276

  • Townsend, J.P., Hassler, H.B., Wang, Z., Miura, S., Singh, J., Kumar, S., Ruddle, N.H., Galvani, A.P., & Dornburg, A. (2021). The durability of immunity against reinfection by SARS-CoV-2: a comparative evolutionary study. Lancet Microbe, 2(12), e666-e675. England. 10.1016/S2666-5247(21)00219-6

  • Barba-Montoya, J., Tao, Q., & Kumar, S. (2021). Assessing Rapid Relaxed-Clock Methods for Phylogenomic Dating. Genome Biol Evol, 13(11). England. 10.1093/gbe/evab251

  • Singh, D., Pandey, A., Choudhary, S.B., Kumar, S., Tribhuvan, K., Mishra, D., Bhati, J., Kumar, M., Tomar, J., Bishnoi, S., Mallick, M., Bhadana, V., Sharma, T., Pattanayak, A., & Singh, B. (2021). Development of genic-SSR markers and their application in revealing genetic diversity and population structure in an Eastern and North-Eastern Indian collection of Jack (Artocarpus heterophyllus Lam.) Ecological Indicators, 131. doi: 10.1016/j.ecolind.2021.108143.

  • Kumar, S. & Sharma, S. (2021). Evolutionary Sparse Learning for Phylogenomics. Mol Biol Evol, 38(11), 4674-4682. United States. 10.1093/molbev/msab227

  • Dasari, K., Somarelli, J.A., Kumar, S., & Townsend, J.P. (2021). The somatic molecular evolution of cancer: Mutation, selection, and epistasis. Prog Biophys Mol Biol, 165, 56-65. England. 10.1016/j.pbiomolbio.2021.08.003

  • Sharma, S. & Kumar, S. (2021). Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps. Nat Comput Sci, 1(9), 573-577. United States. 10.1038/s43588-021-00129-5

  • Chroni, A., Miura, S., Oladeinde, O., Aly, V., & Kumar, S. (2021). Migrations of cancer cells through the lens of phylogenetic biogeography. Sci Rep, 11(1), 17184. England. 10.1038/s41598-021-96215-9

  • Kumar, S., Tao, Q., Weaver, S., Sanderford, M., Caraballo-Ortiz, M.A., Sharma, S., Pond, S.L., & Miura, S. (2021). An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic. Mol Biol Evol, 38(8), 3046-3059. United States. 10.1093/molbev/msab118

  • Tao, Q., Barba-Montoya, J., & Kumar, S. (2021). Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies. Bioinformatics, 37(Suppl_1), i102-i110. England. 10.1093/bioinformatics/btab307

  • Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol, 38(7), 3022-3027. United States. 10.1093/molbev/msab120

  • Liu, L., Chandrashekar, P., Zeng, B., Sanderford, M.D., Kumar, S., & Gibson, G. (2021). TreeMap: a structured approach to fine mapping of eQTL variants. Bioinformatics, 37(8), 1125-1134. England. 10.1093/bioinformatics/btaa927

  • Barba-Montoya, J., Tao, Q., & Kumar, S. (2021). Molecular and morphological clocks for estimating evolutionary divergence times. BMC Ecol Evol, 21(1), 83. England. 10.1186/s12862-021-01798-6

  • Patel, R. & Kumar, S. (2021). Epistasis produces an excess of invariant sites in neutral molecular evolution. Proc Natl Acad Sci U S A, 118(18). United States. 10.1073/pnas.2018767118

  • Babaian, C. & Kumar, S. (2021). How to Build a Super Predator: From Genotype to Phenotype. Am Biol Teach, 83(3), 138-146. United States. 10.1525/abt.2021.83.3.138

  • Scheinfeldt, L.B., Brangan, A., Kusic, D.M., Kumar, S., & Gharani, N. (2021). Common Treatment, Common Variant: Evolutionary Prediction of Functional Pharmacogenomic Variants. J Pers Med, 11(2). Switzerland. 10.3390/jpm11020131

  • Kumar, S., Tao, Q., Weaver, S., Sanderford, M., Caraballo-Ortiz, M.A., Sharma, S., Pond, S.L., & Miura, S. (2021). An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic. BioRxiv. United States. 10.1101/2020.09.24.311845

  • Rowe, H. & Kumar, S. (2021). MBE Emerging Classics 2021. Mol Biol Evol, 38(1), 1. United States. 10.1093/molbev/msaa310

  • Mello, B., Tao, Q., Barba-Montoya, J., & Kumar, S. (2021). Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches. Mol Ecol Resour, 21(1), 122-136. England. 10.1111/1755-0998.13249