| 2025 | RECOMB | A Phylogenetic Approach to Genomic Language Modeling. | Carlos Albors, Jianan Canal Li, Gonzalo Benegas, Chengzhong Ye, Yun S. Song |
| 2025 | RECOMB | Tree Reconstruction Guarantees from CRISPR-Cas9 Lineage Tracing Data Using Neighbor-Joining. | Sebastian Prillo, Kevin An, Wilson Wu, Ivan Kristanto, Matthew G. Jones, Yun S. Song, Nir Yosef |
| 2024 | RECOMB | CELL-E: A Text-to-Image Transformer for Protein Image Prediction. | Emaad Khwaja, Yun S. Song, Bo Huang |
| 2017 | AISTATS | Tensor Decompositions via Two-Mode Higher-Order SVD (HOSVD). | Miaoyan Wang, Yun S. Song |
| 2014 | RECOMB | Changepoint Analysis for Efficient Variant Calling. | Adam E. Bloniarz, Ameet Talwalkar, Jonathan Terhorst, Michael I. Jordan, David A. Patterson, Bin Yu, Yun S. Song |
| 2014 | RECOMB | Decoding Coalescent Hidden Markov Models in Linear Time. | Kelley Harris, Sara Sheehan, John A. Kamm, Yun S. Song |
| 2010 | FPGA | Application of a reconfigurable computing cluster to ultra high throughput genome resequencing (abstract only). | Kristian Stevens, Henry Chen, Terry Filiba, Peter L. McMahon, Yun S. Song |
| 2010 | FPL | SeqHive: A Reconfigurable Computer Cluster for Genome Re-sequencing. | Kristian Stevens, Henry Chen, Terry Filiba, Peter L. McMahon, Yun S. Song |
| 2010 | RECOMB | naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing. | Wei-Chun Kao, Yun S. Song |
| 2010 | RECOMB | On the Genealogy of Asexual Diploids. | Fumei Lam, Charles H. Langley, Yun S. Song |
| 2008 | RECOMB | Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony. | Rune B. Lyngs, Yun S. Song, Jotun Hein |
| 2006 | RECOMB | Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. | Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu |
| 2005 | ISMB | Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. | Yun S. Song, Yufeng Wu, Dan Gusfield |
| 2005 | WABI | Minimum Recombination Histories by Branch and Bound. | Rune B. Lyngs, Yun S. Song, Jotun Hein |
| 2005 | WABI | Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event. | Yun S. Song, Yufeng Wu, Dan Gusfield |
| 2003 | WABI | Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks. | Yun S. Song, Jotun Hein |