| 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 Pérez-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 Buluç, Maxwell P. Lee, Erin K. Molloy, Teresa M. Przytycka, Glenn Merlino, Chi-Ping Day, Salem Malikic, Funda Ergün, S. Cenk Sahinalp |
| 2025 | A Phylogenetic Approach to Genomic Language Modeling. Carlos Albors, Jianan Canal Li, Gonzalo Benegas, Chengzhong Ye, Yun S. Song |
| 2025 | ALPINE: An Interpretable Approach for Decoding Phenotypes from Multi-condition Sequencing Data. Wei-Hao Lee, Lechuan Li, Ruth Dannenfelser, Vicky Yao |
| 2025 | Accurate Detection of Tandem Repeats from Error-Prone Sequences with EquiRep. Zhezheng Song, Tasfia Zahin, Xiang Li, Mingfu Shao |
| 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 | Alignment-Free Estimation of Read to Genome Distances and Its Applications. Ali Osman Berk Sapci, Siavash Mirarab |
| 2025 | An Adversarial Scheme for Integrating Multi-modal Data on Protein Function. Rami Nasser, Leah V. Schaffer, Trey Ideker, Roded Sharan |
| 2025 | An Exact and Fast SAT Formulation for the DCJ Distance. Aaryan M. Sarnaik, Ke Chen, Austin Diaz, Mingfu Shao |
| 2025 | Bayesian Aggregation of Multiple Annotations Enhances Rare Variant Association Testing. Antonio Nappi, Na Cai, Francesco Paolo Casale |
| 2025 | Causal Disentanglement of Treatment Effects in Single-Cell RNA Sequencing Through Counterfactual Inference. Shaokun An, Jae-Won Cho, Kai Cao, Jiankang Xiong, Martin Hemberg, Lin Wan |
| 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 | 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 | Detecting Antimicrobial Resistance Through MALDI-TOF Mass Spectrometry with Statistical Guarantees Using Conformal Prediction. Nina Corvelo Benz, Lucas Miranda, Dexiong Chen, Janko Sattler, Karsten M. Borgwardt |
| 2025 | Devider: Long-Read Reconstruction of Many Diverse Haplotypes. Jim Shaw, Christina Boucher, Yun William Yu, Noelle R. Noyes, Heng Li |
| 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 | Dynamic Programming Algorithms for Fast and Accurate Cell Lineage Tree Reconstruction from CRISPR-Based Lineage Tracing Data. Junyan Dai, Erin K. Molloy |
| 2025 | Dynamic μ-PBWT: Dynamic Run-Length Compressed PBWT for Biobank Scale Data. Pramesh Shakya, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang |
| 2025 | GEM-Finder: Dissecting GWAS Variants via Long-Range Interacting Cis-Regulatory Elements with Differentiationspecific Genes. Gyeongsik Park, Andrew J. Lee, Inkyung Jung |
| 2025 | GeneCover: A Combinatorial Approach for Label-Free Marker Gene Selection. An Wang, Stephanie Hicks, Donald Geman, Laurent Younes |
| 2025 | Hierarchical Spatio-Temporal State-Space Modeling for fMRI Analysis. Yuxiang Wei, Anees Abrol, Vince D. Calhoun |
| 2025 | Hyper-k-mers: Efficient Streaming k-mers Representation. Igor Martayan, Lucas Robidou, Yoshihiro Shibuya, Antoine Limasset |
| 2025 | Improved Pangenomic Classification Accuracy with Chain Statistics. Nathaniel K. Brown, Vikram Shivakumar, Ben Langmead |
| 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 | Integer Programming Framework for Pangenome-Based Genome Inference. Ghanshyam Chandra, Md. Helal Hossen, Stephan Scholz, Alexander T. Dilthey, Daniel Gibney, Chirag Jain |
| 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 | Joint Imputation and Deconvolution of Gene Expression Across Spatial Transcriptomics Platforms. Hongyu Zheng, Hirak Sarkar, Benjamin J. Raphael |
| 2025 | Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal Transport. Peter Halmos, Julian Gold, Xinhao Liu, Benjamin J. Raphael |
| 2025 | Learning Maximally Spanning Representations Improves Protein Function Annotation. Jiaqi Luo, Yunan Luo |
| 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, Héctor Corrada Bravo, Gabriele Scalia, Aviv Regev, Graham Heimberg |
| 2025 | Learning a CoNCISE Language for Small-Molecule Binding. Mert Erden, Kapil Devkota, Lia Varghese, Lenore Cowen, Rohit Singh |
| 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 | OMKar: Optical Map Based Automated Karyotyping of Genomes to Identify Constitutional Disorders. Siavash Raeisi Dehkordi, Zhaoyang Jia, Joey Estabrook, Jen Hauenstein, Neil Miller, Naz Güleray-Lafci, Jürgen Neesen, Alex Hastie, Andy Wing Chun Pang, Paul Dremsek, Vineet Bafna |
| 2025 | Old Dog, New Tricks: Exact Seeding Strategy Improves RNA Design Performances. Théo 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 |
| 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 | 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 | Prokrustean Graph: A Substring Index for Rapid K-Mer Size Analysis. Adam Park, David Koslicki |
| 2025 | Rag2Mol: Structure-Based Drug Design Based on Retrieval Augmented Generation. Peidong Zhang, Xingang Peng, Rong Han, Ting Chen, Jianzhu Ma |
| 2025 | Research in Computational Molecular Biology - 29th International Conference, RECOMB 2025, Seoul, South Korea, April 26-29, 2025, Proceedings Sriram Sankararaman |
| 2025 | Rewiring Protein Sequence and Structure Generative Models to Enhance Protein Stability Prediction. Ziang Li, Yunan Luo |
| 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 | ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads. Rashid Al-Abri, Gamze Gürsoy |
| 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 | 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 | Steamboat: Attention-Based Multiscale Delineation of Cellular Interactions in Tissues. Shaoheng Liang, Junjie Tang, Guanghan Wang, Jian Ma |
| 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 | TX-Phase: Secure Phasing of Private Genomes in a Trusted Execution Environment. Natnatee Dokmai, Kaiyuan Zhu, S. Cenk Sahinalp, Hyunghoon Cho |
| 2025 | TarDis: Achieving Robust and Structured Disentanglement of Multiple Covariates. Kemal Inecik, Aleyna Kara, Antony Rose, Muzlifah Haniffa, Fabian J. Theis |
| 2025 | The Tree Labeling Polytope: A Unified Approach to Ancestral Reconstruction Problems. Henri Schmidt, Benjamin J. Raphael |
| 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 | 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 | Unified Integration of Spatial Transcriptomics Across Platforms. Ellie Haber, Ajinkya Deshpande, Jian Ma, Spencer Krieger |
| 2025 | Untying Rates of Gene Gain and Loss Leads to a New Phylogenetic Approach. Yoav Dvir, Sagi Snir |
| 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 | 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 | ralphi: A Deep Reinforcement Learning Framework for Haplotype Assembly. Enzo Battistella, Anant Maheshwari, Baris Ekim, Bonnie Berger, Victoria Popic |