| 2025 | ICML | Reconstructing Cell Lineage Trees from Phenotypic Features with Metric Learning. | Da Kuang, Guanwen Qiu, Junhyong Kim |
| 2021 | BIBE | A subspace clustering method for satisfying stoimetric constraints in scRNA -seq. | Angela Huang, Junhyong Kim |
| 2020 | BIBE | Resistant Fit Regression Normalization for Single-cell RNA-seq Data. | Da Kuang, Junhyong Kim |
| 2006 | RECOMB | Efficient Enumeration of Phylogenetically Informative Substrings. | Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim |
| 2006 | VLDB | Crimson: A Data Management System to Support Evaluating Phylogenetic Tree Reconstruction Algorithms. | Yifeng Zheng, Stephen Fisher, Shirley Cohen, Sheng Guo, Junhyong Kim, Susan B. Davidson |
| 2005 | SSDBM | Efficiently Supporting Structure Queries on Phylogenetic Trees. | Susan B. Davidson, Junhyong Kim, Yifeng Zheng |
| 2004 | WABI | Genome Identification and Classification by Short Oligo Arrays. | Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim, Li-San Wang |
| 2001 | ISAAC | A Combinatorial Toolbox for Protein Sequence Design and Landscape Analysis in the Grand Canonical Model. | James Aspnes, Julia Hartling, Ming-Yang Kao, Junhyong Kim, Gauri Shah |
| 2001 | PSB | A Tree Obscured By Vines: Horizontal Gene Transfer and the Median Tree Method of Estimating Species Phylogeny. | Junhyong Kim, Benjamin A. Salisbury |