Overview

Genomics studies how genomes are organized, inherited, regulated, and changed, and how those changes relate to cell function, traits, and disease. Researchers use statistical genetics, sequence-based neural networks and foundation models, and graph or multimodal methods that combine DNA with expression, chromatin, protein, or clinical data. Applications include variant interpretation, gene-expression and regulatory-network prediction, perturbation analysis, genome annotation, and crop breeding, with evaluation spanning sequence benchmarks, single-cell experiments, and population or clinical datasets. A central challenge is turning predictive performance into reliable biological insight: models must generalize across populations, species, and assays, while explanations, causal claims, privacy, and clinical usefulness require independent validation.

Latest papers

CardsList

126 papers10 papers in the last four weeks, down 23% on the four weeks before. 0.1% of all new papers.

  1. HELICS: Biobank-scale Conditional Synthetic Genome Generation via Latent Flow Matching

    Oct 26, 2026Ahmad Abdel-Azim, Xihong LinSynthetic Data GenerationGenomics

  2. Clustering of High-Dimensional Human Gene Score Data for Target Cell Classification

    Oct 24, 2026S. Das, V. Madala, P. Majumder +1ClusteringGenomics

  3. HyperTaxa: Multiscale Genome Representations for Generalized Microbial Taxonomic Inference

    Oct 19, 2026Akash Rao, Sushim Gupta, Vishalini Ramnath +2BioinformaticsRepresentation Learning

  4. CloneOT: predicting clone-specific perturbation responses with lineage-supervised neural inverse optimal transport

    Oct 12, 2026Yanshuo Chen, Wei Chen, Heng HuangSingle-Cell Perturbation ModelingInverse Optimal Transport

  5. What DNA Foundation Models Learn Beyond Sequence Composition

    Oct 11, 2026Vincenzo Yuto Civale, Andrew David Bagdanov, Alberto MagiGenomic Foundation ModelsMolecular Foundation Models

  6. Unlocking the Regulatory Genome by ARGUS: An Evidence-Constrained Agentic Framework for Interpreting Single Nucleotide Variants

    Oct 8, 2026Pratik Dutta, Matthew B. Obusan, Max Chao +3GenomicsLarge Language Model-Guided Scientific Discovery

  7. RAGenome: Scaling Retrieval-Based Genomic Language Models to Long Contexts

    Oct 8, 2026Frederikke Isa Marin, Panagiotis Antoniadis, Dionysia Danai Brilli +5GenomicsBioinformatics

  8. GeneICL: A Tabular Foundation Model for Bulk Transcriptomics

    Oct 6, 2026Michael Bohl, Alexander Theus, David Wissel +1Tabular Foundation ModelsClinical Outcome Prediction

  9. SoftGene: Protein Language Model-Enhanced Soft Prompting for Interpretable Gene Set Annotation

    Oct 2, 2026Drew Ross, Arya Hadizadeh Moghaddam, Dongjie Wang +2LLM-Assisted AnnotationGenomics

  10. VANDAM: Viewing a nucleotide sequence with DNA molecular priors

    Sep 30, 2026Jeremy Levy, Ariel Larey, Yury Nahshan +18Self-Supervised Pre-TrainingGenomic Foundation Models

  11. GenoMorph: Pathway-Grounded Genomic Disease Reasoning via Adaptive Latent Computation

    Sep 28, 2026Tanmoy Kanti Halder, Akash Ghosh, Arijit Roy +1LLM Reasoning with GraphsGenomics

  12. GenomeOcean Anywhere: Private WebGPU Inference for Genome MoEs

    Sep 27, 2026Guang Yang, Fengchen LiuGenomic Foundation ModelsDistributed Inference

  13. GenoTrace: Inheritable Watermarks for Genome Foundation Model Distillation

    Sep 27, 2026Guang Yang, Fengchen LiuRobust WatermarkingGenomics

  14. Evaluating Single and Multi-Omics Based Explainable Artificial Intelligence (MOXAI) for Molecular Subclass Classification of Adult-Type Diffuse Gliomas

    Sep 26, 2026Md Zahangir Alom, Quynh T. Tran, Breuer Alexandar +1Multi-Omics Data IntegrationBrain Tumor Classification

  15. BaseCamp --- An Agentic AI Framework for Automating DNA Sequencing Data Pipelines

    Sep 23, 2026Eranga Bandara, Xueping Liang, Asanga Gunaratna +19Multi-Agent OrchestrationGenomics

  16. Tool-Augmented On-Policy Distillation for LLM Domain Adaptation in Sequence-Based Omics Tasks

    Sep 20, 2026Jie Ying, Zhefan Wang, Zihong Chen +11LLM EvaluationOn-Policy Distillation

  17. Semi-Supervised Learning-Based Genetic Biomarkers Dataset for Multiple-Stage Hepatocellular Carcinoma Prediction

    Sep 15, 2026Ahmed Ammar Kubba, Manar Abu Talib, Jibran Sualeh Muhammad +4Cancer GenomicsGenomics

  18. Potential of Artificial Intelligence Algorithms for Identification of Relevant Diagnostic and Prognostic Biomarkers of Early-Stage Liver Cancer

    Sep 14, 2026Ali Bou Nassif, Darko Castven, Manar Abu Talib +4Cancer GenomicsMedical Diagnosis

  19. SeqMaestro: From nucleotide sequences to biological hypotheses through interpretable machine learning

    Sep 14, 2026Evgeny S. Saveliev, Krzysztof Kacprzyk, Charlotte Capitanchik +7Interpretable MLGenomics

  20. Human mutation field reveals an equilibrium-like structure with irreversible circulation

    Sep 7, 2026Isabella Caranzano, Daniel Maria Busiello, Stefano Priorelli +2Hodge DecompositionGenomics

  21. When Genomic Masking Priors Fail to Transfer: Strong Variant Prediction, Weak Functional Generation

    Sep 4, 2026Susu Hu, Preetam Gattogi, Jens Lehmann +3Masked Diffusion ModelsGenomic Foundation Models

  22. A Semantic Model of Genetic Evidence: A Step Toward Bridging the Basic-Science-Clinic Gap

    Sep 3, 2026Michael Bouzinier, Dmitry EtinKnowledge RepresentationGenomics

  23. Responsible Integration of AI in Cancer Genomics: Barriers, Risks, and Pathways to Trustworthy Clinical Translation

    Aug 31, 2026Bahar İlgen, Yiannos Tolias, Denise Kühnert +5Cancer GenomicsOncology

  24. Correlation-Guided Flow Matching with Annealed Masking for Spatial Transcriptomics Generation

    Aug 28, 2026Yupei Zhang, Hao Chen, Li Pan +2Spatial Gene Expression PredictionGene Expression Prediction from Histopathology Images

  25. Homo-RAG: Homology-Guided Retrieval-Augmented Generation for Cross-Species Gene Function Prediction

    Aug 26, 2026Azrin SultanaRetrieval-Augmented GenerationLLM-Assisted Annotation

  26. HiFiC-G: Adapting HiFiC for Hi-C Contact Matrices

    Aug 19, 2026Andre Antonio StratonNeural Network CompressionGenomics

  27. GenEx: A Graph-Based Representational Paradigm for SARS-CoV-2 Variant Detection via Codon Co-occurrence Networks

    Aug 18, 2026Arefin Amin, Labiba Faiza Karim, M. Monir UddinGenomicsGraph Representation Learning

  28. Novel Knowledge-Guided Generative Methods for Synthetic Transcriptomic Data

    Aug 13, 2026Francesca Pia Panaccione, Sofia Mongardi, Marco Masseroli +1Graph Neural NetworksSynthetic Data Generation