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Who Bishal Shrestha is, what the tools do, and how to cite them — in plain, direct answers.
- Who is Bishal Shrestha?
- Bishal Shrestha is a Doctoral Researcher in Computer Science at the University of Miami building AI and deep learning for the 3D architecture of life, with first-author methods spanning the folding of the genome, single cells, and protein structure, and two first-author papers in Oxford University Press journals. Curriculum vitae
- Who is Bishal Shrestha's PhD advisor?
- Bishal Shrestha is advised by Dr. Zheng Wang, Associate Professor of Computer Science at the University of Miami, whose lab studies deep learning for structural bioinformatics and the 3D genome. Wang Lab
- What makes Bishal Shrestha's research distinctive?
- Bishal Shrestha's first-author work spans three biological scales: chromatin folding across time (HiC4D-SPOT), a single cell's 3D genome to its gene expression (scHiGex), and protein interface accuracy (ARC, developed for CASP16). Two are published in Oxford University Press journals, and the tools are open source. The through-line
- What is HiC4D-SPOT?
- HiC4D-SPOT is an unsupervised deep-learning tool, first-authored by Bishal Shrestha (Briefings in Bioinformatics, 2025), that detects exactly where and when the 3D folding of the genome changes across time. It uses a ConvLSTM autoencoder to flag TAD and loop disruptions in spatiotemporal Hi-C data. HiC4D-SPOT case study
- What is scHiGex?
- scHiGex is a graph transformer, first-authored by Bishal Shrestha (NAR Genomics and Bioinformatics, 2025), that predicts a single cell's gene expression directly from that same cell's 3D genome structure (single-cell Hi-C). It is open source. scHiGex case study
- What is ARC?
- ARC is an ensemble of graph neural networks, first-authored by Bishal Shrestha, that scores how accurate a predicted protein interface really is. It was developed for CASP16, the field's community-wide blind assessment, and is under review at PROTEINS. ARC case study
- How do I cite Bishal Shrestha's work?
- Each paper's page carries a copy-pasteable BibTeX entry. HiC4D-SPOT and scHiGex are published in Oxford University Press journals with DOIs; ARC is under review; the earlier AA-LPCR work is on arXiv (2311.12857). All publications