Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks. - Hyunghoon Cho; Bonnie Berger; Jian Peng 001 (RECOMB, 2015)

Exploiting ontology graph for predicting sparsely annotated gene function. - Sheng Wang 001; Hyunghoon Cho; ChengXiang Zhai; Bonnie Berger; Jian Peng 001 (Bioinform., 2015)

Generalizable Visualization of Mega-Scale Single-Cell Data. - Hyunghoon Cho; Bonnie Berger; Jian Peng 001 (RECOMB, 2018)

Large-Margin Classification in Hyperbolic Space. - Hyunghoon Cho; Benjamin Demeo; Jian Peng 001; Bonnie Berger (AISTATS, 2019)

Geometric Sketching of Single-Cell Data Preserves Transcriptional Structure. - Brian Hie; Hyunghoon Cho; Benjamin Demeo; Bryan Bryson; Bonnie Berger (RECOMB, 2019)

Biomedical data sharing and analysis at scale: privacy, compaction, and integration. - Hyunghoon Cho (2019)

Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs. - Hyunghoon Cho; Sean Simmons 001; Ryan Kim; Bonnie Berger (RECOMB, 2020)

Contact Tracing Mobile Apps for COVID-19: Privacy Considerations and Related Trade-offs. - Hyunghoon Cho; Daphne Ippolito; Yun William Yu (CoRR, 2020)

Bayesian information sharing enhances detection of regulatory associations in rare cell types. - Alexander P. Wu; Jian Peng 001; Bonnie Berger; Hyunghoon Cho (Bioinform., 2021)

k-SALSA: k-Anonymous Synthetic Averaging of Retinal Images via Local Style Alignment. - Minkyu Jeon; Hyeon-Jin Park; Hyunwoo J. Kim; Michael Morley; Hyunghoon Cho (ECCV (21), 2022)

Sequre: a high-performance framework for rapid development of secure bioinformatics pipelines. - Haris Smajlovic; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (IPDPS Workshops, 2022)

Mechanisms for Hiding Sensitive Genotypes With Information-Theoretic Privacy. - Fangwei Ye; Hyunghoon Cho; Salim El Rouayheb (IEEE Trans. Inf. Theory, 2022)

Scalable and Privacy-Preserving Federated Principal Component Analysis. - David Froelicher; Hyunghoon Cho; Manaswitha Edupalli; Joao Sa Sousa; Jean-Philippe Bossuat; Apostolos Pyrgelis; Juan Ramón Troncoso-Pastoriza; Bonnie Berger; Jean-Pierre Hubaux (SP, 2023)

sfkit: a web-based toolkit for secure and federated genomic analysis. - Simon Mendelsohn; David Froelicher; Denis Loginov; David Bernick; Bonnie Berger; Hyunghoon Cho (Nucleic Acids Res., 2023)

Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets. - Matthew M. Hong; David Froelicher; Ricky Magner; Victoria Popic; Bonnie Berger; Hyunghoon Cho (RECOMB, 2024)

Generating Synthetic Electronic Health Record (EHR) Data: A Review with Benchmarking. - Xingran Chen; Zhenke Wu; Xu Shi; Hyunghoon Cho; Bhramar Mukherjee (CoRR, 2024)

Privacy of single-cell gene expression data. - Hyunghoon Cho (Patterns, 2024)

TX-Phase: Secure Phasing of Private Genomes in a Trusted Execution Environment. - Natnatee Dokmai; Kaiyuan Zhu; S. Cenk Sahinalp; Hyunghoon Cho (RECOMB, 2025)

Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. - Haris Smajlovic; David Froelicher; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (Zenodo, 2025)

Generating synthetic electronic health record data: a methodological scoping review with benchmarking on phenotype data and open-source software. - Xingran Chen; Zhenke Wu; Xu Shi; Hyunghoon Cho; Bhramar Mukherjee (J. Am. Medical Informatics Assoc., 2025)

Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. - Haris Smajlovic; David Froelicher; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (Zenodo, 2025)

Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. - Haris Smajlovic; David Froelicher; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (Zenodo, 2025)

Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. - Haris Smajlovic; David Froelicher; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (Zenodo, 2025)

ByzSFL: Achieving Byzantine-Robust Secure Federated Learning with Zero-Knowledge Proofs. - Yongming Fan; Rui Zhu; Zihao Wang; Chenghong Wang; Haixu Tang; Ye Dong; Hyunghoon Cho; Lucila Ohno-Machado (CoRR, 2025)

Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. - Haris Smajlovic; David Froelicher; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (Zenodo, 2025)