Publications
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- #35
- Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption
- Haris Smajlović, David Froelicher, Ariya Shajii, Bonnie Berger, Hyunghoon Cho, Ibrahim Numanagić
- USENIX Security (accepted)
- 2025
- Link
- #34
- TX-Phase: Secure Phasing of Private Genomes in a Trusted Execution Environment
- Natnatee Dokmai, Kaiyuan Zhu, S. Cenk Sahinalp, Hyunghoon Cho
- RECOMB (accepted)
- 2025
- Link
- #33
- Secure and Federated Genome-Wide Association Studies for Biobank-Scale Datasets
- Hyunghoon Cho, David Froelicher, Jeffrey Chen, Manaswitha Edupalli, Apostolos Pyrgelis, Juan R. Troncoso-Pastoriza, Jean-Pierre Hubaux, Bonnie Berger
- Nature Genetics
- 2025
- Link
- #32
- Learning-Augmented Sketching Offers Improved Performance for Privacy Preserving and Secure GWAS
- Junyan Xu, Kaiyuan Zhu, Jieling Cai, Can Kockan, Natnatee Dokmai, Hyunghoon Cho, David P. Woodruff, S. Cenk Sahinalp
- iScience
- 2025
- Link
- #31
- Generating Synthetic Electronic Health Record (EHR) Data: A Review with Benchmarking
- Xingran Chen, Zhenke Wu, Xu Shi, Hyunghoon Cho, Bhramar Mukherjee
- arXiv
- 2024
- Link
- #30
- Privacy of Single-Cell Gene Expression Data
- Hyunghoon Cho
- Patterns
- 2024
- Link
- Invited Preview article
- #29
- Privacy-Enhancing Technologies in Biomedical Data Science
- Hyunghoon Cho, David Froelicher, Natnatee Dokmai, Anupama Nandi, Shuvom Sadhuka, Matthew M. Hong, Bonnie Berger
- Annual Review of Biomedical Data Science
- 2024
- Link
- #28
- Secure Discovery of Genetic Relatives across Large-Scale and Distributed Genomic Datasets
- Matthew Man-Hou Hong, David Froelicher, Ricky Magner, Victoria Popic*, Bonnie Berger*, Hyunghoon Cho*
- Genome Research
- 2024
- Link
- Best Student Paper Award at RECOMB 2024
- #27
- Reconstruction of Private Genomes Through Reference-Based Genotype Imputation
- Matthew J. Mosca and Hyunghoon Cho
- Genome Biology
- 2023
- Link
- #26
- Assessing Transcriptomic Re-Identification Risks Using Discriminative Sequence Models
- Shuvom Sadhuka, Daniel Fridman, Bonnie Berger*, Hyunghoon Cho*
- Genome Research
- 2023
- Link
- Also appeared in RECOMB 2023
- #25
- 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 Research
- 2023
- Link
- #24
- Scalable and Privacy-Preserving Federated Principal Component Analysis
- David Froelicher*, Hyunghoon Cho*, Manaswitha Edupalli, Joao Sa Sousa, Jean-Philippe Bossuat, Apostolos Pyrgelis, Juan Troncoso-Pastoriza, Bonnie Berger, Jean-Pierre Hubaux
- IEEE Symposium on Security and Privacy (S&P)
- 2023
- Link
- #23
- Sequre: A High-Performance Framework for Secure Multiparty Computation Enables Biomedical Data Sharing
- Haris Smajlović, Ariya Shajii, Bonnie Berger, Hyunghoon Cho, Ibrahim Numanagić
- Genome Biology
- 2023
- Link
- Also appeared in IEEE HiCOMB 2022
- #22
- k-SALSA: k-Anonymous Synthetic Averaging of Retinal Images via Local Style Alignment
- Minkyu Jeon, Hyeonjin Park, Hyunwoo Kim, Michael Morley, Hyunghoon Cho
- ECCV
- 2022
- Link
- #21
- Secure and Federated Linear Mixed Model Association Tests
- Jeffrey Chen, Manaswitha Edupalli, Bonnie Berger*, Hyunghoon Cho*
- RECOMB Privacy Workshop
- 2022
- Link
- #20
- Mechanisms for Hiding Sensitive Genotypes with Information-Theoretic Privacy
- Fangwei Ye, Hyunghoon Cho, Salim El Rouayheb
- IEEE Transactions on Information Theory
- 2022
- Link
- Also appeared in ISIT 2020
- #19
- Truly Privacy-Preserving Federated Analytics for Precision Medicine with Multiparty Homomorphic Encryption
- David Froelicher, Juan R. Troncoso-Pastoriza, Jean Louis Raisaro, Michel A. Cuendet, Joao Sa Sousa, Hyunghoon Cho, Bonnie Berger, Jacques Fellay, Jean-Pierre Hubaux
- Nature Communications
- 2021
- Link
- #18
- Bayesian Information Sharing Enhances Detection of Regulatory Associations in Rare Cell Types
- Alexander P. Wu, Jian Peng, Bonnie Berger* and Hyunghoon Cho*
- Bioinformatics
- 2021
- Link
- Also appeared in ISMB/ECCB 2021
- #17
- Privacy-Preserving Genotype Imputation in a Trusted Execution Environment
- Natnatee Dokmai, Can Kockan, Kaiyuan Zhu, Xiaofeng Wang, S. Cenk Sahinalp* and Hyunghoon Cho*
- Cell Systems
- 2021
- Link
- Also appeared in RECOMB 2021
- #16
- Assessing Single-Cell Transcriptomic Variability through Density-Preserving Data Visualization
- Ashwin Narayan, Bonnie Berger*, Hyunghoon Cho*
- Nature Biotechnology
- 2021
- Link
- #15
- Contact Tracing Mobile Apps for COVID-19: Privacy Considerations and Related Trade-offs
- {Hyunghoon Cho, Daphne Ippolito, Yun William Yu}
- arXiv
- 2020
- Link
- #14
- Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-offs
- Hyunghoon Cho*, Sean Simmons*, Ryan Kim, Bonnie Berger
- Cell Systems
- 2020
- Link
- Also appeared in RECOMB 2020
- #13
- Coexpression Uncovers a Unified Single-Cell Transcriptomic Landscape
- Brian Hie, Hyunghoon Cho, Bryan Bryson, Bonnie Berger
- bioRxiv
- 2019
- Link
- #12
- Emerging Technologies Towards Enhancing Privacy in Genomic Data Sharing
- Bonnie Berger*, Hyunghoon Cho*
- Genome Biology
- 2019
- Link
- #11
- Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape
- Brian Hie*, Hyunghoon Cho*, Benjamin DeMeo, Bryan Bryson, Bonnie Berger
- Cell Systems
- 2019
- Link
- Also appeared in RECOMB 2019
- #10
- Large-Margin Classification in Hyperbolic Space
- Hyunghoon Cho, Benjamin DeMeo, Jian Peng, Bonnie Berger
- AISTATS
- 2019
- Link
- #9
- Realizing Private and Practical Pharmacological Collaboration
- Brian Hie*, Hyunghoon Cho*, Bonnie Berger
- Science
- 2018
- Link
- #8
- Generalizable and Scalable Visualization of Single Cell Data Using Neural Networks
- Hyunghoon Cho, Bonnie Berger, Jian Peng
- Cell Systems
- 2018
- Link
- Also appeared in RECOMB 2018
- #7
- Secure Genome-wide Association Analysis Using Multiparty Computation
- Hyunghoon Cho, David J. Wu, Bonnie Berger
- Nature Biotechnology
- 2018
- Link
- Featured in Editors' Choice, Science and MIT News
- #6
- Compact Integration of Multi-Network Topology for Functional Analysis of Genes
- Hyunghoon Cho, Bonnie Berger, Jian Peng
- Cell Systems
- 2016
- Link
- F1000Prime Recommended
- #5
- Reconstructing Causal Biological Networks through Active Learning
- Hyunghoon Cho, Bonnie Berger, Jian Peng
- PLOS One
- 2016
- Link
- #4
- Exploiting Ontology Graph for Predicting Sparsely Annotated Gene Function
- Sheng Wang*, Hyunghoon Cho*, ChengXiang Zhai, Bonnie Berger, Jian Peng
- Bioinformatics
- 2015
- Link
- Also appeared in ISMB/ECCB 2015
- #3
- Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks
- Hyunghoon Cho, Bonnie Berger, and Jian Peng
- RECOMB
- 2015
- Link
- #2
- High-Resolution Transcriptome Analysis with Long-Read RNA Sequencing
- Hyunghoon Cho, Joe Davis, Kevin S. Smith, Alexis Battle, and Stephen B. Montgomery
- PLOS One
- 2014
- Link
- #1
- Unraveling the Genetics of Human Diseases by Integrating Patterns for Epistasis Detection
- Hyunghoon Cho
- Undergraduate Honors Thesis (Stanford University)
- 2013
- Link