Publications
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
bioRxiv, 2022 [ Link ]Accurate Evaluation of Transcriptomic Re-Identification Risks Using Discriminative Sequence Models
Shuvom Sadhuka, Daniel Fridman, Bonnie Berger, Hyunghoon Cho
RECOMB 2023 (accepted)k-SALSA: k-Anonymous Synthetic Averaging of Retinal Images via Local Style Alignment
Minkyu Jeon, Hyeonjin Park, Hyunwoo Kim, Michael Morley, Hyunghoon Cho
European Conference on Computer Vision (ECCV), 2022 [ Link ]Secure and Federated Linear Mixed Model Association Tests
Jeffrey Chen, Manaswitha Edupalli, Bonnie Berger*, Hyunghoon Cho*
bioRxiv, 2022 [ Preprint ]
Genome Privacy and Security Workshop, RECOMB 2022Sequre: A High-Performance Framework for Rapid Development of Secure Bioinformatics Pipelines
Haris Smajlović, Ariya Shajii, Bonnie Berger, Hyunghoon Cho, Ibrahim Numanagić
IEEE International Workshop on High Performance Computational Biology (HiCOMB), 2022Mechanisms 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 IEEE International Symposium on Information Theory (ISIT), 2020Truly 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 12(5910), 2021 [ Link ]Bayesian Information Sharing Enhances Detection of Regulatory Associations in Rare Cell Types
Alexander P. Wu, Jian Peng, Bonnie Berger* and Hyunghoon Cho*
Bioinformatics 37, 2021 [ Link ]
Also appeared in ISMB/ECCB, 2021Privacy-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, 2021Assessing Single-Cell Transcriptomic Variability through Density-Preserving Data Visualization
Ashwin Narayan, Bonnie Berger*, Hyunghoon Cho*
Nature Biotechnology, 2021 [ Link ]Contact Tracing Mobile Apps for COVID-19: Privacy Considerations and Related Trade-offs
{Hyunghoon Cho, Daphne Ippolito, Yun William Yu}
arXiv, 2020 [ Link ]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, 2020Coexpression Uncovers a Unified Single-Cell Transcriptomic Landscape
Brian Hie, Hyunghoon Cho, Bryan Bryson, Bonnie Berger
bioRxiv, 2019 [ Link ]Emerging Technologies Towards Enhancing Privacy in Genomic Data Sharing
Bonnie Berger*, Hyunghoon Cho*
Genome Biology, Editorial, 2019 [ Link ]Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape
Brian Hie*, Hyunghoon Cho*, Benjamin DeMeo, Bryan Bryson, Bonnie Berger
Cell Systems 8(6), 2019 [ Link ]
Also appeared in RECOMB, 2019
*equal-contributionLarge-Margin Classification in Hyperbolic Space
Hyunghoon Cho, Benjamin DeMeo, Jian Peng, Bonnie Berger
AISTATS, 2019 [ Link ]Realizing Private and Practical Pharmacological Collaboration
Brian Hie*, Hyunghoon Cho*, Bonnie Berger
Science 362(6412), 2018 [ Link ]
Featured in MIT News [ Link ]
*equal-contributionGeneralizable and Scalable Visualization of Single Cell Data Using Neural Networks
Hyunghoon Cho, Bonnie Berger, Jian Peng
Cell Systems 7(2), 2018 [ Link ]
Also appeared in RECOMB, 2018Secure Genome-wide Association Analysis Using Multiparty Computation
Hyunghoon Cho, David J. Wu, Bonnie Berger
Nature Biotechnology 36(6), 2018 [ Link ]
Featured in Editors’ Choice, Science 360(6393) [ Link ] and MIT News [ Link ]Compact Integration of Multi-Network Topology for Functional Analysis of Genes
Hyunghoon Cho, Bonnie Berger, Jian Peng
Cell Systems 3(6), 2016 [ Link ]
Reconstructing Causal Biological Networks through Active Learning
Hyunghoon Cho, Bonnie Berger, Jian Peng
PLOS One 11(3), 2016 [ Link ]Exploiting Ontology Graph for Predicting Sparsely Annotated Gene Function
Sheng Wang*, Hyunghoon Cho*, ChengXiang Zhai, Bonnie Berger, Jian Peng
Bioinformatics 31(12), 2015 [ Link ]
Also appeared in ISMB/ECCB, 2015
*equal-contributionDiffusion Component Analysis: Unraveling Functional Topology in Biological Networks
Hyunghoon Cho, Bonnie Berger, and Jian Peng
RECOMB, 2015 [ Link ]High-Resolution Transcriptome Analysis with Long-Read RNA Sequencing
Hyunghoon Cho, Joe Davis, Kevin S. Smith, Alexis Battle, and Stephen B. Montgomery
PLOS One 9(9), 2014 [ Link ]Unraveling the Genetics of Human Diseases by Integrating Patterns for Epistasis Detection
Hyunghoon Cho
Undergraduate Honors Thesis, Stanford University, 2013 [ Link ]