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. Mining Negative Sequential Patterns to Improve Viral Genomic Feature Representation and Classification

    Apr 28, 2026Wenxi Zhu, Wensheng Gan, Zhenlian QiGenomicsSequence Modeling

  2. MIMIC: A Generative Multimodal Foundation Model for Biomolecules

    Apr 27, 2026Siavash Golkar, Jake Kovalic, Irina Espejo Morales +28Molecular GenerationGenomics

  3. StackFeat RL: Reinforcement Learning over Iterative Dual Criterion Feature Selection for Stable Biomarker Discovery

    Apr 24, 2026A. Yermekov, D. A. Herrera-MartíScientific DiscoveryFeature Selection

  4. Evaluating Post-hoc Explanations of the Transformer-based Genome Language Model DNABERT-2

    Apr 23, 2026Isabel Kurth, Paulo Yanez Sarmiento, Bernhard Y. RenardTransformer InterpretabilityAttention Mechanisms

  5. Interpretable DNA Sequence Classification via Dynamic Feature Generation in Decision Trees

    Apr 13, 2026Nicolas Huynh, Krzysztof Kacprzyk, Ryan Sheridan +2Interpretable MLDecision Tree Learning

  6. Towards Autonomous Mechanistic Reasoning in Virtual Cells

    Apr 13, 2026Yunhui Jang, Lu Zhu, Jake Fawkes +3Scientific Reasoning in Language ModelsMulti-Agent Reasoning

  7. EvoLen: Evolution-Guided Tokenization for DNA Language Model

    Apr 9, 2026Nan Huang, Xiaoxiao Zhou, Junxia Cui +4Language ModelingSequence Modeling

  8. PhageBench: Can LLMs Understand Raw Bacteriophage Genomes?

    Apr 7, 2026Yusen Hou, Weicai Long, Haitao Hu +3GenomicsLLM Evaluation

  9. GenomeQA: Benchmarking General Large Language Models for Genome Sequence Understanding

    Apr 7, 2026Weicai Long, Yusen Hou, Junning Feng +4LLM EvaluationGenomics

  10. Entropy, Disagreement, and the Limits of Foundation Models in Genomics

    Apr 5, 2026Maxime Rochkoulets, Lovro Vrček, Mile ŠikićGenomic Foundation ModelsGenomics

  11. An Imbalanced Dataset with Multiple Feature Representations for Studying Quality Control of Next-Generation Sequencing

    Apr 4, 2026Philipp Röchner, Clarissa Krämer, Johannes U Mayer +3Genomics

  12. Perturb-and-Restore: Simulation-driven Structural Augmentation Framework for Imbalance Chromosomal Anomaly Detection

    Apr 1, 2026Yilan Zhang, Hanbiao Chen, Changchun Yang +10Medical Image Anomaly DetectionSynthetic Anomaly Generation

  13. GenoBERT: A Language Model for Accurate Genotype Imputation

    Mar 31, 2026Lei Huang, Chuan Qiu, Kuan-Jui Su +13GenomicsTransformer

  14. A Boltzmann-machine-enhanced Transformer For DNA Sequence Classification

    Mar 27, 2026Zhixuan Cao, Yishu Xu, Xuang WUTransformerTransformer Attention

  15. CRANE: Correcting Errors in Raw Nanopore Signals Using Hidden Markov Models

    Mar 20, 2026Simon Ambrozak, Ulysse McConnell, Bhargav Srinivasan +3Genomics

  16. G2DR: A Genotype-First Framework for Genetics-Informed Target Prioritization and Drug Repurposing

    Mar 20, 2026Muhammad Muneeb, David B. AscherDrug DiscoveryScientific Hypothesis Generation

  17. SNPgen: Phenotype-Supervised Genotype Representation and Synthetic Data Generation via Latent Diffusion

    Mar 11, 2026Andrea Lampis, Michela Carlotta Massi, Nicola Pirastu +3Synthetic Data GenerationGenomics

  18. Adversarial Domain Adaptation Enables Knowledge Transfer Across Heterogeneous RNA-Seq Datasets

    Mar 9, 2026Kevin Dradjat, Massinissa Hamidi, Blaise HanczarCancer Subtype ClassificationDomain Adaptation

  19. Contact-Guided 3D Genome Structure Generation of E. coli via Diffusion Transformers

    Mar 8, 2026Mingxin Zhang, Xiaofeng Dai, Yu Yao +1GenomicsConditional Diffusion Models

  20. How Private Are DNA Embeddings? Inverting Foundation Model Representations of Genomic Sequences

    Mar 6, 2026Sofiane Ouaari, Jules Kreuer, Nico PfeiferGenomic Foundation ModelsModel Inversion Attacks

  21. Machine Learning for analysis of Multiple Sclerosis cross-tissue bulk and single-cell transcriptomics data

    Mar 5, 2026Francesco Massafra, Samuele Punzo, Silvia Giulia Galfré +8Medical DiagnosisGenomics

  22. Partial Causal Structure Learning for Valid Selective Conformal Inference under Interventions

    Mar 2, 2026Amir Asiaee, Kavey Aryan, James P. LongSelective InferenceCausal Structure Learning

  23. D3LM: A Discrete DNA Diffusion Language Model for Bidirectional DNA Understanding and Generation

    Mar 2, 2026Zhao Yang, Hengchang Liu, Chuan Cao +1Molecular Foundation ModelsGenomic Foundation Models

  24. Graph Attention Based Prioritization of Disease Responsible Genes from Multimodal Alzheimer's Network

    Mar 1, 2026Binon Teji, Subhajit Bandyopadhyay, Swarup RoyGenomicsMultimodal Graph Learning

  25. ResGene-T: A Tensor-Based Residual Network Approach for Genomic Prediction

    Feb 28, 2026Kuldeep Pathak, Kapil Ahuja, Eric de SturlerGenomicsConvolutional Neural Networks

  26. MEDNA-DFM: A Dual-View FiLM-MoE Model for Explainable DNA Methylation Prediction

    Feb 26, 2026Yi He, Yina Cao, Jixiu Zhai +3GenomicsSequence Modeling

  27. Extending Sequence Length is Not All You Need: Effective Integration of Multimodal Signals for Gene Expression Prediction

    Feb 25, 2026Zhao Yang, Yi Duan, Jiwei Zhu +3GenomicsMultimodal Learning

  28. AgriVariant: Variant Effect Prediction using DeepChem-Variant for Precision Breeding in Rice

    Feb 19, 2026Ankita Vaishnobi Bisoi, Bharath RamsundarGenomics