Publications
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, 2023sfkit: 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, Web Server Issue, 2023 [ Link ]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 ]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 International Workshop on High Performance Computational Biology (HiCOMB), 2022Secure 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 ]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*
RECOMB Genome Privacy and Security Workshop, 2022 [ Link ]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 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 ]