Rosen Center for Advanced Computing

Arun Seetharam

Arun S Seetharam's Profile Photo

Lead Bioinformatics Scientist

  • aseethar@purdue.edu
  • genome assembly, gene annotation, comparative and population genomics, NGS data analyses

About Me:

Dr. Arun Seetharam is a lead bioinformatics scientist at Purdue University’s Rosen Center for Advanced Computing. With extensive expertise in comparative genomics, genome assembly, annotation, single-cell genomics,  NGS data analysis, metagenomics, proteomics, and metabolomics. Arun supports a diverse range of bioinformatics projects across various organisms, including human model systems.

Arun leads the Bioinformatics Service Line, offering bioinformatics support, cyberinfrastructure assistance, and advanced computational resources. His work empowers researchers by providing custom bioinformatics solutions, generating preliminary results for grant proposals, and mentoring students and postdoctoral fellows in cutting-edge bioinformatics techniques.

Arun is passionate about fostering collaborations across Purdue's research community, advancing research through innovative computational methodologies.

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Publications:

Hufford, M. B., Seetharam, A. S., Woodhouse, M. R., Chougule, K. M., Ou, S., Liu, J., Ricci, W. A., Guo, T., Olson, A., Qiu, Y., & others. (2021). De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science, 373(6555), 655–662. https://doi.org/10.1126/science.abg5289

Xue, C., Seetharam, A. S., Musharova, O., Severinov, K., Brouns, S. J., Severin, A. J., & Sashital, D. G. (2015). CRISPR interference and priming varies with individual spacer sequences. Nucleic Acids Research, 43(22), 10831–10847. https://doi.org/10.1093/nar/gkv1269

Seetharam, A. S., & Stuart, G. W. (2013). Whole genome phylogeny for 21 Drosophila species using predicted 2b-RAD fragments. PeerJ, 1, e226. https://doi.org/10.7717/peerj.226

Cao, M., Gao, M., Lopez-Garcia, C. L., Wu, Y., Seetharam, A. S., Severin, A. J., & Shao, Z. (2017). Centromeric DNA facilitates nonconventional yeast genetic engineering. ACS Synthetic Biology, 6(8), 1545–1553. https://doi.org/10.1021/acssynbio.7b00158

Purcell, C. M., Seetharam, A. S., Snodgrass, O., Ortega-García, S., Hyde, J. R., & Severin, A. J. (2018). Insights into teleost sex determination from the Seriola dorsalis genome assembly. BMC Genomics, 19(31). https://doi.org/10.1186/s12864-018-4436-6

Masonbrink, R., Maier, T. R., Muppirala, U., Seetharam, A. S., Lord, E., Juvale, P. S., Schmutz, J., Johnson, N. T., Korkin, D., & Mitchum, M. G. (2019). The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC Genomics, 20, 1–14. https://doi.org/10.1186/s12864-019-5982-5

Ou, S., Liu, J., Chougule, K. M., Fungtammasan, A., Seetharam, A. S., Stein, J. C., Llaca, V., Manchanda, N., Gilbert, A. M., & Wei, S. (2020). Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature Communications, 11(1), 2288. https://doi.org/10.1038/s41467-020-16147-9

Murugan, K., Seetharam, A. S., Severin, A. J., & Sashital, D. G. (2020). CRISPR-Cas12a has widespread off-target and dsDNA-nicking effects. Journal of Biological Chemistry, 295(17), 5538–5553. https://doi.org/10.1074/jbc.RA119.012218

Manchanda, N., Portwood, J. L., Woodhouse, M. R., Seetharam, A. S., Lawrence-Dill, C. J., Andorf, C. M., & Hufford, M. B. (2020). GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations. BMC Genomics, 21, 1–9. https://doi.org/10.1186/s12864-020-06851-2

Liu, J., Seetharam, A. S., Chougule, K., Ou, S., Swentowsky, K. W., Gent, J. I., Llaca, V., Woodhouse, M. R., Manchanda, N., & Presting, G. G. (2020). Gapless assembly of maize chromosomes using long-read technologies. Genome Biology, 21, 1–17. https://doi.org/10.1186/s13059-020-02185-0

Khan, T., Seetharam, A. S., Zhou, J., Bivens, N. J., Schust, D. J., Ezashi, T., Tuteja, G., & Roberts, R. M. (2021). Single nucleus RNA sequence (snRNAseq) analysis of the spectrum of trophoblast lineages generated from human pluripotent stem cells in vitro. Frontiers in Cell and Developmental Biology, 9, 695248. https://doi.org/10.3389/fcell.2021.695248

Seetharam, A. S., Vu, H. T., Choi, S., Khan, T., Sheridan, M. A., Ezashi, T., Roberts, R. M., & Tuteja, G. (2022). The product of BMP-directed differentiation protocols for human primed pluripotent stem cells is placental trophoblast and not amnion. Stem Cell Reports, 17(6), 1289–1302. https://doi.org/10.1016/j.stemcr.2022.05.011

Kinkade, J. A., Seetharam, A. S., Sachdev, S., Bivens, N. J., Phinney, B. S., Grigorean, G., Roberts, R. M., Tuteja, G., & Rosenfeld, C. S. (2024). Extracellular vesicles from mouse trophoblast cells: Effects on neural progenitor cells and potential participants in the placenta-brain axis. Biology of Reproduction, 110(2), 310–328. https://doi.org/10.1093/biolre/ioad164

Singh, U., Haltom, J. A., Guarnieri, J. W., Li, J., Seetharam, A., Beheshti, A., Aronow, B., & Wurtele, E. S. (2024). A pan-tissue, pan-disease compendium of human orphan genes. bioRxiv, 2024–02. https://doi.org/10.1101/2024.02.04.432934

For a complete list of publications, visit my Google Scholar profile.