Bishal Shrestha

University of Miami · Coral Gables, FL

• Advisor: Dr. Zheng Wang

Tribhuvan University · Nepal

• Undergraduate thesis mentor: Dr. Badri Adhikari (University of Missouri–St. Louis)

University of Miami · Coral Gables, FL

• Led ARC (first author, under review at PROTEINS): an ensemble of graph neural networks estimating per-residue local accuracy of predicted protein structures, developed for CASP16.
• Applied Geometric Algebra Transformers (GATr) to annotate protein function from 3D structure via E(3)-equivariant geometric deep learning on atomic coordinates.
• Co-developed a graph transformer to assess predicted protein-RNA complex structures, published in Bioinformatics (2026).
• Built HiC4D-SPOT (first author): a ConvLSTM-based autoencoder detecting spatiotemporal anomalies in 3D chromatin (Hi-C) data, published in Briefings in Bioinformatics (2025).
• Built scHiGex (first author): a graph transformer predicting single-cell gene expression from single-cell Hi-C 3D structure, published in NAR Genomics and Bioinformatics (2025).
• Contributed to SCW (BMC Bioinformatics 2026) and the CITED2 study (EMBO Molecular Medicine 2026).

University of Missouri–St. Louis · MO

• Researched adversarial sample generation for Nepal's embossed license-plate recognition, using adversarial training to harden models against attacks.
• Designed CNN experiments in PyTorch, including collecting and preprocessing a novel real-world dataset.

Research and Innovation Unit, Tribhuvan University

• Studied machine-learning techniques for customer-churn prediction with a leading Nepali ISP.
• Presented findings at the Himalaya International Conference on academia-industry partnerships.

• Shrestha B, Siciliano AJ, Huang G, Bao Y, Wang Z. ARC: Assessment of Interface Residue Conformation using an Ensemble of Graph Neural Networks. PROTEINS: Structure, Function, and Bioinformatics, Manuscript ID 5704351. 2026 (under review).
• Siciliano AJ, Bao Y, Shrestha B, Wang Z. Inferring the qualities of protein-RNA models with graph transformers. Bioinformatics, 2026. 2026.
• Müller F, McLachlan E, Costa A, Qu J, Shrestha B, Wang Z, et al.. CITED2 is a druggable epigenetic switch coupling neuronal maturation to regenerative decline. EMBO Molecular Medicine, 2026. 2026.
• Zhu H, Liu T, Shrestha B, Wang Z. SCW: building the whole-genome 3D structures based on extremely sparse single-cell Hi-C data. BMC Bioinformatics, 27(1), 90. 2026.

• Shrestha B, Wang Z. HiC4D-SPOT: a spatiotemporal outlier detection tool for Hi-C data. Briefings in Bioinformatics, 26(4), bbaf341. 2025.
• Shrestha B, Siciliano AJ, Zhu H, Liu T, Wang Z. scHiGex: predicting single-cell gene expression based on single-cell Hi-C data. NAR Genomics and Bioinformatics, 7(1), lqaf002. 2025.

• Shrestha B, Khakurel G, Simkhada K, Adhikari B. Adversarial sample generation and training using geometric masks for accurate and resilient license plate character recognition. arXiv preprint, cs.CV. 2023.

• Prajapati S, Engelhardt M, Shrestha A, Khakurel G, Shrestha B, Simkhada K. Industry-Academia Collaboration in Nepal, A case study of Customer Churn Prediction for Worldlink. Research and Innovation Unit, 2021.