| 2025 | Scalable and Interpretable Identification of Minimal Undesignable RNA Structure Motifs with Rotational Invariance. | Tianshuo Zhou, Apoorv Malik, Wei Yu Tang, David H. Mathews, Liang Huang |
| 2025 | Joint Imputation and Deconvolution of Gene Expression Across Spatial Transcriptomics Platforms. | Hongyu Zheng, Hirak Sarkar, Benjamin J. Raphael |
| 2025 | ScisTree2: An Improved Method for Large-Scale Inference of Cell Lineage Trees and Genotype Calling from Noisy Single Cell Data. | Haotian Zhang, Yiming Zhang, Teng Gao, Yufeng Wu |
| 2025 | Rag2Mol: Structure-Based Drug Design Based on Retrieval Augmented Generation. | Peidong Zhang, Xingang Peng, Rong Han, Ting Chen, Jianzhu Ma |
| 2025 | Active Learning for Protein Structure Prediction. | Zexin Xue, Michael Bailey, Abhinav Gupta, Ruijiang Li, Alejandro Corrochano-Navarro, Sizhen Li, Lorenzo Kogler-Anele, Qui Yu, Ziv Bar-Joseph, Sven Jager |
| 2025 | Hierarchical Spatio-Temporal State-Space Modeling for fMRI Analysis. | Yuxiang Wei, Anees Abrol, Vince D. Calhoun |
| 2025 | Pharming: Joint Clonal Tree Reconstruction of SNV and CNA Evolution from Single-Cell DNA Sequencing of Tumors. | Leah L. Weber, Anna Hart, Idoia Ochoa, Mohammed El-Kebir |
| 2025 | DualGOFiller: A Dual-Channel Graph Neural Network with Contrastive Learning for Enhancing Function Prediction in Partially Annotated Proteins. | Shaojun Wang, Hancheng Liu, Weiqi Zhai, Shanfeng Zhu |
| 2025 | cfDecon: Accurate and Interpretable Methylation-Based Cell Type Deconvolution for Cell-Free DNA. | Yixuan Wang, Jiayi Li, Jingqi Li, Shen Yang, Yuhan Huang, Xinyuan Liu, Yimin Fan, Irwin King, Yumei Li, Yu Li |
| 2025 | GeneCover: A Combinatorial Approach for Label-Free Marker Gene Selection. | An Wang, Stephanie Hicks, Donald Geman, Laurent Younes |
| 2025 | Accurate Detection of Tandem Repeats from Error-Prone Sequences with EquiRep. | Zhezheng Song, Tasfia Zahin, Xiang Li, Mingfu Shao |
| 2025 | Synthetic Control Removes Spurious Discoveries from Double Dipping in Single-Cell and Spatial Transcriptomics Data Analyses. | Dongyuan Song, Siqi Chen, Christy Lee, Kexin Li, Xinzhou Ge, Jingyi Jessica Li |
| 2025 | Decoding the Functional Interactome of Non-model Organisms with PHILHARMONIC. | Samuel Sledzieski, Charlotte Versavel, Rohit Singh, Faith Ocitti, Kapil Devkota, Lokender Kumar, Polina Shpilker, Liza Roger, Jinkyu Yang, Nastassja Lewinski, Hollie Putnam, Bonnie Berger, Judith Klein-Seetharaman, Lenore Cowen |
| 2025 | Devider: Long-Read Reconstruction of Many Diverse Haplotypes. | Jim Shaw, Christina Boucher, Yun William Yu, Noelle R. Noyes, Heng Li |
| 2025 | Dynamic μ-PBWT: Dynamic Run-Length Compressed PBWT for Biobank Scale Data. | Pramesh Shakya, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang |
| 2025 | The Tree Labeling Polytope: A Unified Approach to Ancestral Reconstruction Problems. | Henri Schmidt, Benjamin J. Raphael |
| 2025 | Inferring Cell Differentiation Maps from Lineage Tracing Data. | Palash Sashittal, Richard Y. Zhang, Benjamin K. Law, Henri Schmidt, Alexander Strzalkowski, Adriano Bolondi, Michelle M. Chan, Benjamin J. Raphael |
| 2025 | An Exact and Fast SAT Formulation for the DCJ Distance. | Aaryan M. Sarnaik, Ke Chen, Austin Diaz, Mingfu Shao |
| 2025 | Alignment-Free Estimation of Read to Genome Distances and Its Applications. | Ali Osman Berk Sapci, Siavash Mirarab |
| 2025 | Characterizing the Solution Space of Migration Histories of Metastatic Cancers with MACH2. | Mrinmoy Saha Roddur, Vikram Ramavarapu, Abigail Bunkum, Ariana Huebner, Roman Mineyev, Nicholas McGranahan, Simone Zaccaria, Mohammed El-Kebir |
| 2025 | 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 |
| 2025 | GEM-Finder: Dissecting GWAS Variants via Long-Range Interacting Cis-Regulatory Elements with Differentiationspecific Genes. | Gyeongsik Park, Andrew J. Lee, Inkyung Jung |
| 2025 | Prokrustean Graph: A Substring Index for Rapid K-Mer Size Analysis. | Adam Park, David Koslicki |
| 2025 | An Adversarial Scheme for Integrating Multi-modal Data on Protein Function. | Rami Nasser, Leah V. Schaffer, Trey Ideker, Roded Sharan |
| 2025 | Bayesian Aggregation of Multiple Annotations Enhances Rare Variant Association Testing. | Antonio Nappi, Na Cai, Francesco Paolo Casale |