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 at the Clemson University’s Center for Human Genetics, who 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.
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
I. Ates, C. Stuart, T. Rathbone, M. Barzi, G. He, A. M. Major, V. Shankar, R. A. Lyman, S. S. Angner, T. F. C. Mackay, S. Srinivasan, A. B. Farris, K. Bissig, and R. N. Cottle. (2024). Ex vivo gene editing and cell therapy for hereditary tyrosinemia type 1. Hepatology Communications 8(5): e0424
V.A. Riley, V. Shankar, J. C. Holmberg, A. M. Sokolov, V. M. Neckles, K. Williams, R. A. Lyman, T. F. C. Mackay, and D. M. Feliciano. (2023). Tsc2 coordinates neuroprogenitor differentiation. Iscience 26(12).
R. A. MacPherson, V. Shankar, R. R. H. Anholt and T. F. C. Mackay. (2023). Genetic and genomic analyses of Drosophila melanogaster models of chromatin modification disorders. Genetics 224(4), iyad061.
S. S. Mokashi, V. Shankar, J. A. Johnstun, T. F. C. Mackay, and R. R. H. Anholt. (2023). Pleiotropic fitness effects of a Drosophila odorant-binding protein. G3 13(2), jkac307.
T. V. Morozova, V. Shankar*, R. A. MacPherson, T. F. C. Mackay, and R. R. H. Anholt. (2022). Modulation of the Drosophila transcriptome by developmental exposure to alcohol. BMC Genomics 23(1), 1-14. *co-first author – equal contribution with T. V. Morozova.
H. Wang, V. Shankar, X. Jiang. (2022). Compositional and Functional Changes in Microbial Communities of Composts Due to the Composting-Related Factors and the Presence of Listeria monocytogenes. Microbiology Spectrum Aug 31;10(4):e0184521.
G. Rangani, C. E. Rouse, C. Saski, R. E. Noorai, V. Shankar, A. L. Lawton-Rauh, I. S. Werle and N. Roma-Burgos. (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.
L. Lackey, A. Coria, A. J. Ghosh, P. Grayeski, A. Hatfield, V. Shankar, J. Platig, Z. Xu, S. B. V. Ramos, E. K. Silverman, V. E. Ortega, M. H. Cho, C. P. Hersh, B. D. Hobbs, P. Castaldi and A. Laederach. (2021). Alternative poly-adenylation modulates α1-antitrypsin expression in chronic obstructive pulmonary disease. PLoS Genetics 17(11), e1009912.
S. S. Mokashi, V. Shankar, J. A. Johnstun, W. Huang, T. F. C. Mackay and R. R. H. Anholt. (2021). Systems Genetics of Single Nucleotide Polymorphisms at the Drosophila obp56h Locus. bioRxiv
M. D. Lucius, H. Ji, D. Altomare, R. Doran, B. Torkian, A. Havighorst, V. Kaza, Y. Zhang, A. V. Gasparian, J. Magagnoli, V. Shankar, M. Shtutman and H. Kiaris. (2021). Genomic variation in captive deer mouse (Peromyscus maniculatus) populations. BMC Genomics 22(1), 1-15.
N. O. Nazario-Yepiz, J. F. Sobaberas, R. Lyman, M. R. Campbell III, V. Shankar, R. R. H. Anholt and T. F. C. Mackay. (2021). Physiological and metabolomics consequences of reduced expression of the Drosophila bummer triglyceride Lipase. PLOS ONE 16(9), e0255198.
M. Usovsky, R. Robbins, J. F. Wilkes, D. Crippen, V. Shankar, T. Vuong, P. Agudelo and H. T. Nguyen. (2021) Classification methods and identification of reniform nematode resistance in known soybean cyst nematode resistant soybean genotypes. Plant Disease doi: 10.1094/PDIS-01-21-0051-RE.
J. A. Deaver, M, N, Soni, K. I. Diviesti, K. T. Finneran, V. Shankar, S. C. Popat. (2021) Taxonomic and Functional Variants Induced by an Overloading Event in Anaerobic Codigestion of Municipal Wastewater Sludge with Fats, Oils, and Grease. ACS ES&T Engineering 1: 1205-1216.
S. S. Mokashi, V. Shankar*, R. A. MacPherson, R. C. Hannah, T. F. C. Mackay and R. R. H. Anholt. (2021) Developmental Alchol Exposure in Drosophila: Effects on Adult Phenotypes and Gene Expression in the Brain. Frontiers in Psychiatry 12:699033. doi: 10.3389/fpsyt.2021.699033. PMC8341641. *co-first author – equal contribution with S. S. Mokashi.
B. M. Baker, S. S. Mokashi, V. Shankar*, J. S. Hatfield, R. C. Hannah, T. F. C. Mackay and R. R. H. Anholt. (2021) The Drosophila brain on cocaine at single cell resolution. Genome Research doi: 10.1101/gr.268037.120. *co-first author – equal contribution with B. M. Baker and S. S. Mokashi.
J. A. Johnstun, V. Shankar, S. Mokashi, L. T. Sunkara, U. E. Ihearahu, R. L. Lyman, T. F. C. Mackay and R. H. A. Anholt. (2021) Functional Diversification, Redundancy, and Epistasis among Paralogs of the Drosophila melanogaster Obp50a-d Gene Cluster. Molecular Biology and Evolution 38(5): 2030-2044.
Phan IQ, Rice CA, Craig J, Noorai RE, McDonald J, Subramanian S, Tillery L, Barrett LK, Shankar V, Morris JC and Van Voorhis WC. 2020. The transcriptome of Balamuthia mandrillaris trophozoites for structure based drug design. bioRxiv. doi: 10.1101/2020.06.29.178905.
Krombeen SK, Shankar V, Noorai RE, Saski CA, Sharp JL, Wilson ME and Wilmoth TA. 2019. The identification of differentially expressed genes between extremes of placental efficiency in maternal line gilts on day 95 of gestation. BMC Genomics 20: 254. doi: 10.1186/s12864-019-5626-0.
Nayduch D, Shankar V, Mills MK, Robl T, Drolet BS, Ruder MG, Scully ED and Saski CA. 2019. Transcriptome response of female Culicoides sonorensis biting midges (Diptera: Ceratopogonidae) to early infection with Epizootic Hemorrhagic Disease Virus (EHDV-2). Viruses 11: 473. doi: 10.3390/v11050473.
Noorai RE, Shankar V, Freese NH, Gregorski CM and Chapman SC. 2019. Discovery of genomic variants by whole-genome resequencing of the North American Araucana chicken. PLoS One 14: e0225834. doi: 10.1371/journal.pone.0225834.
Zhebentyayeva T, Shankar V, Scorza R, Callahan A, Ravelonandro M, Castro S, DeJong T, Saski CA, Dardick C. 2019. Genetic characterization of world-wide Prunus domestica (plum) germplasm using sequence-based genotyping. Hortic Res 6: 12. doi: 10.1038/s41438-018-0090-6.
Qiu Y, Milanes JE, Jones JA, Noorai RE, Shankar V, Morris J. 2018. Glucose signalling is important for nutrient adaptation during differentiation of pleomorphic African trypanosomes. mSphere 3: e00366-18.
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 Announc 6: e00207-18.
Shankar V, Agans R, Paliy O. 2017. Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities. Sci Rep 7: 6481.
Shankar V, Gouda M, Moncivaiz J, Gordon A, Reo NV, Hussein L, Paliy O. 2017. Differences in gut metabolites and microbial composition and functions between Egyptian and US teenagers are consistent with consumed diets. mSystems 2: e00169-16.
Paliy O, Shankar V. 2016. Application of multivariate statistical techniques in microbial ecology. Mol Ecol 25: 1032-1057.
Link to Google Scholar
https://scholar.google.com/citations?hl=en&user=V0Cl54wAAAAJ