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 2022

  • Sequre: 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), 2022

  • 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), 2020

  • 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 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, 2021

  • 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

  • Assessing 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, 2020

  • Coexpression 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-contribution

  • Large-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-contribution

  • Generalizable 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, 2018

  • Secure 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 ] Access the recommendation on F1000Prime

  • 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-contribution

  • Diffusion 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 ]