Director, Bioinformatics and Statistics Core
Email: vshanka@clemson.edu
Phone: 864-889-0527
Biosketch
Dr. Vijay Shankar
Dr. Vijay Shankar is a bioinformatics staff scientist that directs the Bioinformatics and Statistics core at the Clemson University’s Institute for Human Genetics. He specializes in development and application of statistical approaches and analysis pipelines for interpretation of high-throughput multivariate data generated in biomedical research. Such data include those produced from next-generation sequencing (DNA- and RNA-seq), as well as metaproteomics and metabolomics. Dr. Shankar received his PhD in 2016 from the Biomedical Sciences program at Wright State University, working with Dr. Oleg Paliy on elucidating interactions between human gut microbiome and host pathophysiology through the use of multivariate statistics. The statistical discipline acquired through doctoral research was further developed and refined through his appointment as a bioinformatics research associate (funded by NIH COBRE grant awarded to the Eukaryotic Pathogen Innovation Center) at Clemson University where he helped uncover insights in diverse biological fields and research models. These include genetic characterization in plums, chickens and in environmental microbes, transcriptional responses in biting midges and eukaryotic pathogens such as trypanosomes, and characterization of the developmental biology in swine and bovine. Dr. Shankar’s research now focuses on developing and utilizing new statistical methodologies for unraveling the complexity within single-cell RNA-seq data and integration of multiple ‘omics’ data to uncover insights at the systems-level. He also leads a team of bioinformaticians and systems administrators that manages the 40 node DELL EMC cluster at the Clemson Institute for Human Genetics. The cluster was purpose-built to serve the needs of the researchers at the institute.
Research
- Bioinformatics, GPU computing and HPC workflow management
- Development and application of multivariate statistics in a wide array of subjects and fields
- Development of new pipelines and improvement of current ones for analysis of NGS data
- ‘Omics’ approaches to single-cell high-throughput sequencing data
- Metabolic interactions in complex microbial communities
- Role of intestinal microbiota in human health and disease
Publications
Aghdam, M., Unselt, D., Adonay, M., Morozova, T., Carbone, M., Arya, G., Turlapati, L., Shankar, V., Anholt, R., & Mackay, T. (2025). Systems genetics of lifespan and senescence in Drosophila melanogaster. BMC biology.
Chaturvedi, A., Shankar, V., Simkhada, B., Lyman, R., Freymuth, P., Howansky, E., Collins, K., Mackay, T., & Anholt, R. (2025). Arsenic toxicity in the Drosophila brain at single cell resolution. Frontiers in Toxicology, 7, 1636431.
Holmberg, J., Shankar, V., Lyman, R., Mackay, T., & Feliciano, D. (2025). Single nuclei transcriptomics reveals cellular diversity in TSC subependymal giant cell astrocytomas. iScience, 28(9).
Jiamutai, F., Hatfield, A., Herbert, A., Majumdar, D., Shankar, V., & Lackey, L. (2025). Altered polyadenylation site usage in SERPINA1 3’UTR in response to cellular stress affects A1AT protein expression. Scientific Reports, 15(1), 23510.
Kunkel, D., Sørensen, P., Shankar, V., & Morgante, F. (2025). Improving polygenic prediction from summary data by learning patterns of effect sharing across multiple phenotypes. Plos Genetics, 21(1), e1011519.
Stempinski, P., Noorai, R., Shankar, V., & Kozubowski, L. (2025). Genetic determinants that permit growth without the core septin Cdc12 in Cryptococcus neoformans. bioRxiv, 2025–12.
Yan, R., Manjunatha, V., Thomas, A., Shankar, V., Lumpkins, B., Hoerr, F., Greene, A., & Jiang, X. (2025). Comparative effects of vegetarian diet and rendered animal by-product on the chicken gut health. Poultry Science, 105360.
Ates, I., Stuart, C., Rathbone, T., Barzi, M., He, G., Major, A., Shankar, V., Lyman, R., Angner, S., Mackay, T., & others (2024). Ex vivo gene editing and cell therapy for hereditary tyrosinemia type 1. Hepatology Communications, 8(5), e0424.
Collins, K., Howansky, E., Macon-Foley, S., Adonay, M., Shankar, V., Lyman, R., Nazario-Yepiz, N., Brooks, J., Lyman, R., Mackay, T., & others (2024). Drosophila Toxicogenomics: genetic variation and sexual dimorphism in susceptibility to 4-Methylimidazole. Human Genomics, 18(1), 119.
Panday, S., Shankar, V., Lyman, R., & Alexov, E. (2024). Genetic Variants Linked to Opioid Addiction: A Genome-Wide Association Study. International Journal of Molecular Sciences, 25(23), 12516.
Simkhada, B., Nazario-Yepiz, N., Freymuth, P., Lyman, R., Shankar, V., Wiggins, K., Flanagan-Steet, H., Basu, A., Weiss, R., Anholt, R., & others (2024). A Drosophila Model of Mucopolysaccharidosis IIIB. Genetics, iyae219.
MacPherson, R., Shankar, V., Anholt, R., & Mackay, T. (2023). Genetic and genomic analyses of Drosophila melanogaster models of chromatin modification disorders. Genetics, 224(4), iyad061.
Mokashi, S., Shankar, V., Johnstun, J., Mackay, T., & Anholt, R. (2023). Pleiotropic fitness effects of a Drosophila odorant-binding protein. G3, 13(2), jkac307.
Riley, V., Shankar, V., Holmberg, J., Sokolov, A., Neckles, V., Williams, K., Lyman, R., Mackay, T., & Feliciano, D. (2023). Tsc2 coordinates neuroprogenitor differentiation. iScience.
MacPherson, R., Shankar, V., Sunkara, L., Hannah, R., Campbell, M., Anholt, R., & Mackay, T. (2022). Pleiotropic fitness effects of the lncRNA Uhg4 in Drosophila melanogaster. bioRxiv.
Morozova, T., Shankar, V., MacPherson, R., Mackay, T., & Anholt, R. (2022). Modulation of the Drosophila transcriptome by developmental exposure to alcohol. BMC Genomics, 23(1), 1–14.
Rangani, G., Rouse, C., Saski, C., Noorai, R., Shankar, V., Lawton-Rauh, A., Werle, I., & Roma-Burgos, N. (2022). High Resistance to Quinclorac in Multiple-Resistant Echinochloa colona Associated with Elevated Stress Tolerance Gene Expression and Enriched Xenobiotic Detoxification Pathway. Genes, 13(3), 515.
Wang, H., Shankar, V., & Jiang, X. (2022). Compositional and Functional Changes in Microbial Communities of Composts Due to the Composting-Related Factors and the Presence of Listeria monocytogenes. Microbiology Spectrum, e01845–21.
Baker, B., Mokashi, S., Shankar, V., Hatfield, J., Hannah, R., Mackay, T., & Anholt, R. (2021). The Drosophila brain on cocaine at single-cell resolution. Genome Research.
Deaver, J., Soni, M., Diviesti, K., Finneran, K., Shankar, V., & Popat, S. (2021). Taxonomic and Functional Variations Induced by an Overloading Event in Anaerobic Codigestion of Municipal Wastewater Sludge with Fats, Oils, and Grease. ACS ES&T Engineering.
Johnstun, J., Shankar, V., Mokashi, S., Sunkara, L., Ihearahu, U., Lyman, R., Mackay, T., & Anholt, R. (2021). Functional Diversification, Redundancy, and Epistasis among Paralogs of the Drosophila melanogaster Obp50a–d Gene Cluster. Molecular Biology and Evolution.
Lackey, L., Coria, A., Ghosh, A., Grayeski, P., Hatfield, A., Shankar, V., Platig, J., Xu, Z., Ramos, S., Silverman, E., & others (2021). Alternative poly-adenylation modulates $α$1-antitrypsin expression in chronic obstructive pulmonary disease. PLoS genetics, 17(11), e1009912.
Lucius, M., Ji, H., Altomare, D., Doran, R., Torkian, B., Havighorst, A., Kaza, V., Zhang, Y., Gasparian, A., Magagnoli, J., Shankar, V., & others (2021). Genomic variation in captive deer mouse (Peromyscus maniculatus) populations. BMC genomics, 22(1), 1–15.
Mokashi, S., Shankar, V., MacPherson, R., Hannah, R., Mackay, T., & Anholt, R. (2021). Developmental Alcohol Exposure in Drosophila: Effects on Adult Phenotypes and Gene Expression in the Brain. Frontiers in Psychiatry, 12.
Mokashi, S., Shankar, V., Johnstun, J., Huang, W., Mackay, T., & Anholt, R. (2021). Systems Genetics of Single Nucleotide Polymorphisms at the Drosophila Obp56h Locus. bioRxiv.
Nazario-Yepiz, N., Fernández Sobaberas, J., Lyman, R., Campbell III, M., Shankar, V., Anholt, R., & Mackay, T. (2021). Physiological and metabolomic consequences of reduced expression of the Drosophila brummer triglyceride Lipase. PloS one, 16(9), e0255198.
Phan, I., Rice, C., Craig, J., Noorai, R., McDonald, J., Subramanian, S., Tillery, L., Barrett, L., Shankar, V., Morris, J., & others (2021). The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design. Scientific Reports, 11(1), 1–13.
Usovsky, M., Robbins, R., Fultz Wilkes, J., Crippen, D., Shankar, V., Vuong, T., Agudelo, P., & Nguyen, H. (2021). Classification methods and identification of reniform nematode resistance in known soybean cyst nematode resistant soybean genotypes. Plant Disease(ja).
Yepiz, N., Sobaberas, J., Lyman, R., Campbell, M., Shankar, V., Anholt, R., & Mackay, T. (2021). Physiological and Metabolomic Consequences of Reduced Expression of the Drosophila brummer Triglyceride Lipase. bioRxiv.
Krombeen, S., Shankar, V., Noorai, R., Saski, C., Sharp, J., Wilson, M., & Wilmoth, T. (2019). The identification of differentially expressed genes between extremes of placental efficiency in maternal line gilts on day 95 of gestation. BMC Genomics, 20(1), 254.
Nayduch, D., Shankar, V., Mills, M., Robl, T., Drolet, B., Ruder, M., Scully, E., & Saski, C. (2019). Transcriptome Response of Female Culicoides sonorensis Biting Midges (Diptera: Ceratopogonidae) to Early Infection with Epizootic Hemorrhagic Disease Virus (EHDV-2). Viruses, 11(5), 473.
Noorai, R., Shankar, V., Freese, N., Gregorski, C., & Chapman, S. (2019). Discovery of genomic variations by whole-genome resequencing of the North American Araucana chicken. PloS one, 14(12).
Wang, H., Shankar, V., Dharmasena, M., & Jiang, X. (2019). Analyzing Microbial Community Change of Turkey Litter Compost Due to Heat Exposure Using 16S High Throughput Sequencing. In IAFP 2019 Annual Meeting.
Zhebentyayeva, T., Shankar, V., Scorza, R., Callahan, A., Ravelonandro, M., Castro, S., DeJong, T., Saski, C., & Dardick, C. (2019). Genetic characterization of worldwide Prunus domestica (plum) germplasm using sequence-based genotyping. Horticulture Research, 6(1), 12.
Qiu, Y., Milanes, J., Jones, J., Noorai, R., Shankar, V., & Morris, J. (2018). Glucose signaling is important for nutrient adaptation during differentiation of pleomorphic African trypanosomes. mSphere, 3(5), e00366–18.
Qiu, Y., Shankar, V., Noorai, R., Yeung, N., McAlpine, S., & Morris, J. (2018). Identification of a post-transcriptional regulatory element that responds to glucose in the African trypanosome. bioRxiv, 327346.
Ramos-Garcia, A., Shankar, V., Saski, C., Hsiang, T., & Freedman, D. (2018). Draft Genome Sequence of the 1, 4-Dioxane-Degrading Bacterium Pseudonocardia dioxanivorans BERK-1. Genome announcements, 6(14), e00207–18.
Rouse, C., Saski, C., Noorai, R., Lawton-Rauh, A., Shankar, V., & Burgos, N. (2017). Concerted action of abiotic stress responsive genes may impart high resistance to propanil in multiple-resistant Echinochloa colona. Characterization of Multiple-Herbicide-Resistant Echinochloa colona from Arkansas, 1001, 141.
Rouse, C., Saski, C., Noorai, R., Shankar, V., & Roma-Burgos, N. (2017). High resistance to quinclorac in multiple-resistant Echinochloa colona involves adaptive co-evolution of abiotic stress-and xenobiotic detoxification genes. Characterization of Multiple-Herbicide-Resistant Echinochloa colona from Arkansas, 1001, 89.
Shankar, V., Agans, R., & Paliy, O. (2017). Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities. Scientific Reports, 7(1), 6481.
Shankar, V., Gouda, M., Moncivaiz, J., Gordon, A., Reo, N., Hussein, L., & Paliy, O. (2017). Differences in gut metabolites and microbial composition and functions between Egyptian and US children are consistent with their diets. Msystems, 2(1), e00169–16.
Paliy, O., & Shankar, V. (2016). Application of multivariate statistical techniques in microbial ecology. Molecular ecology, 25(5), 1032–1057.
Link to Google Scholar
https://scholar.google.com/citations?hl=en&user=V0Cl54wAAAAJ