A calibrated, standardized flow-cytometry framework is proposed to reliably measure EVs for translational prostate cancer biomarker research. Analysis of transcriptomics and proteomics of EV cargo is being currently explored.

• Fabrice Lucien, Yohan Kim, Jing Qian, Jacob J Orme, Henan Zhang, Ali Arafa, Feven Abraha, Ishwor Thapa, Erik J Tryggestad, William S Harmsen, others. Tumor-derived extracellular vesicles predict clinical outcomes in oligometastatic prostate cancer and suppress antitumor immunity. International Journal of Radiation Oncology Biology* Physics*. 2022.
• Yohan Kim, Edwin Van Der Pol, Ali Arafa, Ishwor Thapa, Cameron J Britton, Jorgena Kosti, Siyang Song, Vidhu B Joshi, Ree M Erickson, Hesham Ali, others. Calibration and standardization of extracellular vesicle measurements by flow cytometry for translational prostate cancer research. Nanoscale. 2022.

Applied immunoinformatics to profile adaptive immune responses using TCR repertoire sequencing, leveraging sequence alignment to quantify TCR similarity, discover antigen-driven clusters, and performing clonotype analysis to track clonal expansion, diversity, and shared/public TCRs across conditions.

• Fransenio Clark, Anna Gil, Ishwor Thapa, Nuray Aslan, Dario Ghersi, Liisa K Selin. Cross-reactivity influences changes in human influenza A virus and Epstein Barr virus specific CD8 memory T cell receptor alpha and beta repertoires between young and old. Frontiers in Immunology. 2023.

16S sequencing analysis was performed to discern gut microbiota changes in Cldn3KO mice that were capable of modulating fatty acid metabolism and oxidative stress response. A split graph model was developed to represent the composition and interactions of a given microbiome and a pipeline that integrates genomic information and pathway analysis was developed.

• Rizwan Ahmad, Balawant Kumar, Ishwor Thapa, Geoffrey A Talmon, Jeffrey Salomon, Amanda E Ramer-Tait, Dhundy K Bastola, Punita Dhawan, Amar B Singh. Loss of claudin-3 expression increases colitis risk by promoting Gut Dysbiosis. Gut Microbes. 2023.

• Suyeon Kim, Ishwor Thapa, Ling Zhang, Hesham Ali. A novel graph theoretical approach for modeling microbiomes and inferring microbial ecological relationships. BMC genomics. 2019.

Developed a computational pipeline to identify statistically overrepresented chemical fragments in therapeutic classes and search for similar fragments in a large database of natural products. We showed that several therapeutic classes including antibacterial, antineoplastic, and drugs active on the cardiovascular system, have enriched fragments that can be found in many natural compounds. Various computational drug repurposing approaches were explored.

• Suyeon Kim, Ishwor Thapa, Ling Zhang, Hesham Ali. On Identifying Candidates for Drug Repurposing for the Treatment of Ulcerative Colitis using Gene Expression Data. International Work-Conference on Bioinformatics and Biomedical Engineering. 2019.

• Sunandini Sharma, Kritika Karri, Ishwor Thapa, Dhundy Bastola, Dario Ghersi. Identifying enriched drug fragments as possible candidates for metabolic engineering. BMC Medical Genomics. 2016.

• Akshay Balasubramanya, Ishwor Thapa, Dhundy Bastola, Dario Ghersi. A novel approach to identify shared fragments in drugs and natural products. Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2015.