Skip to content

Hoon Cho Lab

  • Home
  • People
  • News
  • Publications
  • Contact
  • Wiki (Internal)
Menu
  • Home
  • People
  • News
  • Publications
  • Contact
  • Wiki (Internal)

Publications

  • All
  • Biomedical Privacy
  • Single-Cell Genomics
  • Network Biology
Menu
  • All
  • Biomedical Privacy
  • Single-Cell Genomics
  • Network Biology
  • #35
  • Generating Synthetic Electronic Health Record (EHR) Data: A Review with Benchmarking
  • Xingran Chen, Zhenke Wu, Xu Shi, Hyunghoon Cho, Bhramar Mukherjee
  • Journal of the American Medical Informatics Association (in press)
  • 2025
  • Link
  • #34
  • 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
  • 2025
  • Link
  • #33
  • TX-Phase: Secure Phasing of Private Genomes in a Trusted Execution Environment
  • Natnatee Dokmai, Kaiyuan Zhu, S. Cenk Sahinalp, Hyunghoon Cho
  • RECOMB
  • 2025
  • Link
  • #32
  • 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
  • #31
  • 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
  • #30
  • Privacy of Single-Cell Gene Expression Data
  • Hyunghoon Cho
  • Patterns
  • 2024
  • Link
  • Invited Preview article for Walker et al. (Cell, 2024)
  • #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

Hoon Cho Lab
Department of Biomedical Informatics and Data Science
Yale School of Medicine
101 College St, New Haven, CT 06510, USA

  • GitHub
  • Twitter
  • Instagram