| 2025 | 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 |
| 2025 | Hyper-k-mers: Efficient Streaming k-mers Representation. | Igor Martayan, Lucas Robidou, Yoshihiro Shibuya, Antoine Limasset |
| 2025 | Learning Maximally Spanning Representations Improves Protein Function Annotation. | Jiaqi Luo, Yunan Luo |
| 2025 | mcRigor: A Statistical Method to Enhance the Rigor of Metacell Partitioning in Single-Cell RNA-seq and ATAC-seq Data Analysis. | Pan Liu, Jingyi Jessica Li |
| 2025 | ML-MAGES: A Machine Learning Framework for Multivariate Genetic Association Analyses with Genes and Effect Size Shrinkage. | Xiran Liu, Lorin Crawford, Sohini Ramachandran |
| 2025 | Learning Multi-cellular Representations of Single-Cell Transcriptomics Data Enables Characterization of Patient-Level Disease States. | Tianyu Liu, Edward De Brouwer, Tony Kuo, Nathaniel Diamant, Alsu Missarova, Hanchen Wang, Minsheng Hao, Hctor Corrada Bravo, Gabriele Scalia, Aviv Regev, Graham Heimberg |
| 2025 | Integration and Querying of Multimodal Single-Cell Data with PoE-VAE. | Anastasia Litinetskaya, Maiia Schulman, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi, Fabian J. Theis |
| 2025 | Orientation-Aware Networks for Protein Structure Representation Learning. | Jiahan Li, Shitong Luo, Congyue Deng, Chaoran Cheng, Jiaqi Guan, Leonidas J. Guibas, Jian Peng, Jianzhu Ma |
| 2025 | Rewiring Protein Sequence and Structure Generative Models to Enhance Protein Stability Prediction. | Ziang Li, Yunan Luo |
| 2025 | Steamboat: Attention-Based Multiscale Delineation of Cellular Interactions in Tissues. | Shaoheng Liang, Junjie Tang, Guanghan Wang, Jian Ma |
| 2025 | ALPINE: An Interpretable Approach for Decoding Phenotypes from Multi-condition Sequencing Data. | Wei-Hao Lee, Lechuan Li, Ruth Dannenfelser, Vicky Yao |
| 2025 | TissueMosaic Enables Cross-Sample Differential Analysis of Spatial Transcriptomics Datasets Through Self-supervised Representation Learning. | Sandeep Kambhampati, Luca D'Alessio, Fedor Grab, Stephen Fleming, Fei Chen, Mehrtash Babadi |
| 2025 | TarDis: Achieving Robust and Structured Disentanglement of Multiple Covariates. | Kemal Inecik, Aleyna Kara, Antony Rose, Muzlifah Haniffa, Fabian J. Theis |
| 2025 | Sequence-Based TCR-Peptide Representations Using Cross-Epitope Contrastive Fine-Tuning of Protein Language Models. | Chiho Im, Ryan Zhao, Scott D. Boyd, Anshul Kundaje |
| 2025 | Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal Transport. | Peter Halmos, Julian Gold, Xinhao Liu, Benjamin J. Raphael |
| 2025 | Unified Integration of Spatial Transcriptomics Across Platforms. | Ellie Haber, Ajinkya Deshpande, Jian Ma, Spencer Krieger |
| 2025 | Learning a CoNCISE Language for Small-Molecule Binding. | Mert Erden, Kapil Devkota, Lia Varghese, Lenore Cowen, Rohit Singh |
| 2025 | Untying Rates of Gene Gain and Loss Leads to a New Phylogenetic Approach. | Yoav Dvir, Sagi Snir |
| 2025 | TX-Phase: Secure Phasing of Private Genomes in a Trusted Execution Environment. | Natnatee Dokmai, Kaiyuan Zhu, S. Cenk Sahinalp, Hyunghoon Cho |
| 2025 | OMKar: Optical Map Based Automated Karyotyping of Genomes to Identify Constitutional Disorders. | Siavash Raeisi Dehkordi, Zhaoyang Jia, Joey Estabrook, Jen Hauenstein, Neil Miller, Naz Gleray-Lafci, Jrgen Neesen, Alex Hastie, Andy Wing Chun Pang, Paul Dremsek, Vineet Bafna |
| 2025 | Dynamic Programming Algorithms for Fast and Accurate Cell Lineage Tree Reconstruction from CRISPR-Based Lineage Tracing Data. | Junyan Dai, Erin K. Molloy |
| 2025 | Integer Programming Framework for Pangenome-Based Genome Inference. | Ghanshyam Chandra, Md. Helal Hossen, Stephan Scholz, Alexander T. Dilthey, Daniel Gibney, Chirag Jain |
| 2025 | Improved Pangenomic Classification Accuracy with Chain Statistics. | Nathaniel K. Brown, Vikram Shivakumar, Ben Langmead |
| 2025 | Old Dog, New Tricks: Exact Seeding Strategy Improves RNA Design Performances. | Tho Boury, Leonhard Sidl, Ivo L. Hofacker, Yann Ponty, Hua-Ting Yao |
| 2025 | Optimal Marker Genes for c-Separated Cell Types. | Bartol Borozan, Luka Borozan, Domagoj Severdija, Domagoj Matijevic, Stefan Canzar |