Genomics Papers

G2DR: A Genotype-First Framework for Genetics-Informed Target Prioritization and Drug Repurposing Muhammad Muneeb, David B. Ascher arxiv.org/abs/2603.20346 [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙻𝙶]

CERN: Correcting Errors in Raw Nanopore Signals Using Hidden Markov Models Simon Ambrozak, Ulysse McConnell, Bhargav Srinivasan, Burak Ozkan, Can Firtina arxiv.org/abs/2603.20420 [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙻𝙶 𝚚-𝚋𝚒𝚘.𝚀𝙼]

A harmonized benchmarking framework for implementation-aware evaluation of 46 polygenic risk score tools across binary and continuous phenotypes Muhammad Muneeb, David B. Ascher arxiv.org/abs/2603.21201 [𝚚-𝚋𝚒𝚘.𝙶𝙽]

TPMM: Three-component Posterior Mixture Model Enables Robust Inverton Detection in Low-Depth Metagenomes and Suggests Potential Viral Invertons Yi Lu, Jiaojiao Guan, Yang Shen, Jiayu Shang, Yanni Sun arxiv.org/abs/2603.16194 [𝚚-𝚋𝚒𝚘.𝙶𝙽]

Cross-Species Antimicrobial Resistance Prediction from Genomic Foundation Models Huilin Tai arxiv.org/abs/2603.11141 [𝚚-𝚋𝚒𝚘.𝙶𝙽]

A Standardized Framework For Evaluating Gene Expression Generative Models Andrea Rubbi, Andrea Giuseppe Di Francesco, Mohammad Lotfollahi, Pietro Liò arxiv.org/abs/2603.11244 [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙻𝙶]

ELISA: An Interpretable Hybrid Generative AI Agent for Expression-Grounded Discovery in Single-Cell Genomics Omar Coser arxiv.org/abs/2603.11872 [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙰𝙸]

Omics Data Discovery Agents Alexandre Hutton, Jesse G. Meyer arxiv.org/abs/2603.10161 [𝚚-𝚋𝚒𝚘.𝙶𝙽]

Benchmarking 80 binary phenotypes from the openSNP dataset using deep learning algorithms and polygenic risk score tools Muhammad Muneeb, David B. Ascher, YooChan Myung, Samuel F. Feng, Andreas Henschel arxiv.org/abs/2603.06768 [𝚚-𝚋𝚒𝚘.𝙶𝙽]

Identifying genes associated with phenotypes using machine and deep learning Muhammad Muneeb, David B. Ascher, YooChan Myung arxiv.org/abs/2603.06804 [𝚚-𝚋𝚒𝚘.𝙶𝙽]

How Private Are DNA Embeddings? Inverting Foundation Model Representations of Genomic Sequences Sofiane Ouaari, Jules Kreuer, Nico Pfeifer arxiv.org/abs/2603.06950 [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙰𝙸 𝚌𝚜.𝙻𝙶]

Machine Learning for analysis of Multiple Sclerosis cross-tissue bulk and single-cell transcriptomics data Francesco Massafra, Samuele Punzo, Silvia Giulia Galfré, Alessandro Maglione, Simone Pernice, Stefano Forti, … arxiv.org/abs/2603.05572 [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙻𝙶]

SeekRBP: Leveraging Sequence-Structure Integration with Reinforcement Learning for Receptor-Binding Protein Identification Xiling Luo, Le Ou-Yang, Yang Shen, Jiaojiao Guan, Dehan Cai, Jun Zhang, Rui Zhang, Yanni Sun, Jiayu Shang arxiv.org/abs/2603.04748 [𝚚-𝚋𝚒𝚘.𝙶𝙽]

GPU-accelerated single-cell analysis at scale with rapids-singlecell Severin Dicks, Lukas Heumos, Lilly May, Sara Jimenez, Philipp Angerer, Ilan Gold, Isaac Virshup, Felix Fischer, Michelle Gill, Melanie Boerries, Corey J Nolet, … arxiv.org/abs/2603.02402 [𝚚-𝚋𝚒𝚘.𝙶𝙽]

Sparse autoencoders reveal organized biological knowledge but minimal regulatory logic in single-cell foundation models: a comparative atlas of Geneformer and scGPT Ihor Kendiukhov arxiv.org/abs/2603.02952 [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙻𝙶 𝚚-𝚋𝚒𝚘.𝙲𝙱]

Graph-Based Multi-Omics Integration Improves Subtype Recovery and Survival Prediction Over Classical Integration Strategies in TCGA-BRCA Taha Ahmad arxiv.org/abs/2603.00212 [𝚚-𝚋𝚒𝚘.𝙶𝙽]

CrossLLM-Mamba: Multimodal State Space Fusion of LLMs for RNA Interaction Prediction Rabeya Tus Sadia, Qiang Ye, Qiang Cheng arxiv.org/abs/2602.22236 [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙲𝚅 𝚌𝚜.𝙻𝙶]

Multi-Dimensional Spectral Geometry of Biological Knowledge in Single-Cell Transformer Representations Ihor Kendiukhov arxiv.org/abs/2602.22247 [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙰𝙸 𝚌𝚜.𝙻𝙶]

BEDCrypt: Privacy-preserving interval analytics with homomorphic encryption Kimon Antonios Provatas, Ilias Georgakopoulos-Soares arxiv.org/abs/2602.21994 [𝚚-𝚋𝚒𝚘.𝙶𝙽]

AgriVariant: Variant Effect Prediction using DeepChem-Variant for Precision Breeding in Rice Ankita Vaishnobi Bisoi, Bharath Ramsundar arxiv.org/abs/2602.17747 [𝚚-𝚋𝚒𝚘.𝙶𝙽 𝚌𝚜.𝙻𝙶]