All Stories

  1. Identifying Context-Specific Cell-Cell Interaction Genes Without Ligand-Receptor Databases from Spatial Transcriptomics

    Article • May 2026, openRxiv

    Hyobin Kim

  2. A Generalizable Transformer Framework for Gene Regulatory Network Inference from Single‐Cell Transcriptomes

    Article • Advanced Intelligent Systems, January 2026, Wiley

    Hyobin Kim

  3. T H 17 cells converted into exT H 17 cells sustain rheumatoid-like IL-17–independent inflammatory arthritis

    Article • Science Immunology, November 2025, American Association for the Advancement of Science

    Hyobin Kim

  4. Multi-scale and multi-context interpretable mapping of cell states across heterogeneous spatial samples

    Article • Nature Communications, August 2025, Springer Science + Business Media

    Hyobin Kim

  5. SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution

    Article • BMC Bioinformatics, June 2025, Springer Science + Business Media

    Hyobin Kim

  6. Ovarian tumor cells gain competitive advantage by actively reducing the cellular fitness of microenvironment cells

    Article • Nature Biotechnology, December 2024, Springer Science + Business Media

    Hyobin Kim

  7. Integrating Prior Knowledge Using Transformer for Gene Regulatory Network Inference

    Article • Advanced Science, November 2024, Wiley

    Hyobin Kim

  8. Unveiling contact-mediated cellular crosstalk

    Article • Trends in Genetics, October 2024, Elsevier

    Hyobin Kim

  9. Data enhancement in the age of spatial biology

    Article • January 2024, Elsevier

    Hyobin Kim

  10. CellNeighborEX: deciphering neighbor‐dependent gene expression from spatial transcriptomics data

    Article • Molecular Systems Biology, October 2023, Springer Science + Business Media

    Paul B Fisher, Hyobin Kim

  11. Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis

    Article • Molecular Systems Biology, September 2022, Springer Science + Business Media

    Hyobin Kim

  12. CellNeighborEX: Deciphering Neighbor-Dependent Gene Expression from Spatial Transcriptomics Data

    Article • February 2022, Cold Spring Harbor Laboratory Press

    Hyobin Kim

  13. Basement membrane stiffness determines metastases formation

    Article • Nature Materials, January 2021, Springer Science + Business Media

    Hyobin Kim

  14. Antifragility Predicts the Robustness and Evolvability of Biological Networks through Multi-Class Classification with a Convolutional Neural Network

    Article • Entropy, September 2020, MDPI AG

    Hyobin Kim

  15. On two information-theoretic measures of random fuzzy networks

    Article • January 2020, The MIT Press

    Hyobin Kim

  16. A Multilayer Structure Facilitates the Production of Antifragile Systems in Boolean Network Models

    Article • Complexity, December 2019, Hindawi Publishing Corporation

    Professor Carlos Gershenson, Hyobin Kim

  17. Instability of Multilayer Networks Induced by Inter-Layer Coupling

    Article • December 2019, Institute of Electrical & Electronics Engineers (IEEE)

    Hyobin Kim

  18. Effects of Antimodularity and Multiscale Influence in Random Boolean Networks

    Article • Complexity, June 2019, Hindawi Publishing Corporation

    Professor Carlos Gershenson, Luis Escobar Loera , Hyobin Kim

  19. A Novel Antifragility Measure Based on Satisfaction and Its Application to Random and Biological Boolean Networks

    Article • Complexity, May 2019, Hindawi Publishing Corporation

    Hyobin Kim

  20. How Criticality of Gene Regulatory Networks Affects the Resulting Morphogenesis under Genetic Perturbations

    Article • Artificial Life, April 2018, The MIT Press

    Hiroki Sayama, Hyobin Kim

  21. Robustness and Evolvability of Multilayer Gene Regulatory Networks

    Article • January 2018, The MIT Press

    Hyobin Kim

  22. The Role of Criticality of Gene Regulatory Networks in Morphogenesis

    Article • IEEE Transactions on Cognitive and Developmental Systems, January 2018, Institute of Electrical & Electronics Engineers (IEEE)

    Hyobin Kim

  23. Criticality of gene regulatory networks and the resulting morphogenesis

    Article • September 2017, The MIT Press

    Hyobin Kim

  24. The Relationship between Microscopic and Collective Properties in Gene Regulatory Network-based Morphogenetic Systems

    Article • January 2016, The MIT Press

    Hyobin Kim