Publications

  • k-SALSA: k-Anonymous Synthetic Averaging of Retinal Images via Local Style Alignment
    Minkyu Jeon, Hyeonjin Park, Hyunwoo Kim, Michael Morley, Hyunghoon Cho
    To appear in ECCV, 2022

  • Secure and Federated Linear Mixed Model Association Tests
    Jeffrey Chen, Manaswitha Edupalli, Bonnie Berger*, Hyunghoon Cho*
    bioRxiv, 2022 [ Preprint ]
    Appeared in the Privacy and Security Workshop at RECOMB, 2022

  • Sequre: A High-Performance Framework for Rapid Development of Secure Bioinformatics Pipelines
    Haris Smajlović, Ariya Shajii, Bonnie Berger, Hyunghoon Cho, Ibrahim Numanagić
    To appear in 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

  • Density-Preserving Data Visualization Unveils Dynamic Patterns of Single-Cell Transcriptomic Variability
    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 ]