| 2026 | WABI | Is Level-1 Blob Reconstruction Under the Network Multispecies Coalescent Easy? | Junyan Dai, Erin K. Molloy |
| 2025 | RECOMB | Dynamic Programming Algorithms for Fast and Accurate Cell Lineage Tree Reconstruction from CRISPR-Based Lineage Tracing Data. | Junyan Dai, Erin K. Molloy |
| 2025 | RECOMB | A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing Data. | Farid Rashidi Mehrabadi, Erfan Sadeqi Azer, John D. Bridgers, Eva Prez-Guijarro, Kerrie Marie, Howard H. Yang, Charli Gruen, Chih Hao Wu, Welles Robinson, Huaitian Liu, Can Kizilkale, Michael C. Kelly, Cari Smith, Sung Chin, Jessica Ebersole, Sandra Burkett, Aydin Bulu, Maxwell P. Lee, Erin K. Molloy, Teresa M. Przytycka, Glenn Merlino, Chi-Ping Day, Salem Malikic, Funda Ergn, S. Cenk Sahinalp |
| 2023 | WABI | Leveraging Constraints Plus Dynamic Programming for the Large Dollo Parsimony Problem. | Junyan Dai, Tobias Rubel, Yunheng Han, Erin K. Molloy |
| 2023 | WABI | Quartets Enable Statistically Consistent Estimation of Cell Lineage Trees Under an Unbiased Error and Missingness Model (Abstract). | Yunheng Han, Erin K. Molloy |
| 2023 | WABI | Fast, Parallel, and Cache-Friendly Suffix Array Construction. | Jamshed Khan, Tobias Rubel, Laxman Dhulipala, Erin K. Molloy, Rob Patro |
| 2020 | RECOMB | Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss. | Brandon Legried, Erin K. Molloy, Tandy J. Warnow, Sbastien Roch |
| 2020 | WABI | Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees. | Xilin Yu, Thien Le, Sarah A. Christensen, Erin K. Molloy, Tandy J. Warnow |
| 2019 | WABI | TRACTION: Fast Non-Parametric Improvement of Estimated Gene Trees. | Sarah A. Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy J. Warnow |
| 2018 | RECOMB | NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees. | Erin K. Molloy, Tandy J. Warnow |
| 2017 | WABI | Optimal Completion of Incomplete Gene Trees in Polynomial Time Using OCTAL. | Sarah A. Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy J. Warnow |