Genomics

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7 papers in the last four weeks, up 40% on the four weeks before. 0.1% of all new papers.

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  1. GeneICL: A Tabular Foundation Model for Bulk Transcriptomics

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

    ETH Zurich · Max Planck Institute for Intelligent Systems · Swiss Institute of Bioinformatics +1

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

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

    Applied AI Architecture, NVIDIA, Israel. · Worldwide Field Ops, NVIDIA, Israel. · Developer Programs, NVIDIA, Israel. +3

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

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

    Department of Computer Science and Engineering, Indian Institute of Technology Patna, Bihta, 801106, Bihar, India · Prasannadeb Women’s College, India

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

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

    Old Dominion University, Norfolk, VA, USA · Florida International University, USA · AI Motion Labs, Melbourne, Australia +7

  5. 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

    Shanghai Artificial Intelligence Laboratory · Yazhouwan National Laboratory · Shanghai Innovation Institute +2

  6. 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

    Department of Computer Engineering, College of Computing and Informatics University of Sharjah, Sharjah, United Arab Emirates · Department of Medicine I, University Medical Center Schleswig-Holstein, University of Lubeck, Lübeck, Germany · Department of Computer Science, College of Computing and Informatics University of Sharjah, Sharjah, United Arab Emirates +1

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

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

    Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK · The Francis Crick Institute, London, UK · UK Dementia Research Institute at King’s College London, London, UK +1

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

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

    AI and Computational Biomedicine Unit, Department of Medical Sciences, University of Torino, Torino, Italy · Department of Physics, University of Padova, Padova, Italy · Max Planck Institute for the Physics of Complex Systems, Dresden, Germany

  9. 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

    1*Centre for Artificial Intelligence in Public Health Research (ZKI-PH),2026 Robert Koch Institute, Nordufer 20, Berlin, 13353, Germany. · 2Directorate-General for Health and Food Safety, European Commission, Rue de Loi 200, Brussels, B-1049, Belgium.Aug · Department of Natural Sciences, School of Science and Technology, Deree-The American College of Greece, Gravias 6, Athens, 15342,31 Greece. +5

  10. Orchestra: Corroboration-Based Regulatory Candidate Discovery via Composed Bioinformatics MCP Agents

    Aug 27, 2026Jose A. BirdCancer GenomicsMulti-Agent Orchestration

    Independent Researcher, Bird AI Solutions

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

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

    Department of Computer Science, American International University-Bangladesh, 408/1, Kuratoli, Khilkhet, 1229, Dhaka, Bangladesh.

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

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

    DEIB - Dipartimento Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy

  13. Uncertainty-Aware Deep Learning for Genomics Applications: Insights from an Empirical Study

    Aug 11, 2026Sepideh Saran, Mahsa Ghanbari, Uwe OhlerBayesian Neural NetworksUncertainty Quantification

    The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Germany · Department of Electrical Engineering and Computer Science, Technical University of Berlin, Germany · Department of Biology, Humboldt University of Berlin, Germany +1

  14. bioMoR: Biology-Guided Mixture-of-Recursions for Effective Genomic Learning

    Aug 7, 2026Koushik Howlader, Tirtho Roy, Md Tauhidul Islam +1Recurrent TransformersGenomics

    1Iowa State University, Iowa, USA · 2Stanford University, CA, USA

  15. BioM-JEPA: joint-embedding prediction of graph-connected gene blocks in single cells

    Aug 6, 2026Yuhao Wang, Zelin Zang, Yuxuan Liu +2Joint-Embedding Predictive ArchitecturePredictive Representation Learning

    Westlake University, Hangzhou, Zhejiang, China · Centre for Artificial Intelligence and Robotics (CAIR), Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences (HKISI-CAS), Hong Kong SAR, China · State Key Laboratory of Multimodal Artificial Intelligence Systems (MAIS), Institute of Automation, Chinese Academy of Sciences (CASIA), Beijing, China +1

  16. CASCADE: An Agentic Regulatory Network Framework for Patient-Data-Validated Downstream Perturbation Prediction

    Aug 5, 2026Jose A. BirdCancer GenomicsGenomics

    Independent Researcher

  17. CLARA: Clarification of Language Ambiguity through Result Analysis for Natural-Language Cancer Genomics Queries

    Aug 3, 2026Pratyush Kumar Shukla, Manveer Singh Tib, Siddhant GargCancer GenomicsClarification Question Generation

    Independent Researchers

  18. Beyond Gene Reconstruction: Learning Cell Representations through Complementary Transcriptomic Views

    Aug 2, 2026Jiaqi Xiong, Yuntao hu, Yu Zheng +3Contrastive LearningRepresentation Learning

    University of Oxford, Oxford, United Kingdom · Tongji University, Shanghai, China · Hunan University, Changsha, China +2

  19. Gene Ontology-Guided Hierarchical Spatial Gene Expression Prediction from Histopathology Images

    Aug 1, 2026Zhiwen Xu, Xiaoming Yan, Chengkun Wu +3Computational PathologySpatial Transcriptomics

    National University of Defense Technology Changsha, China

  20. Can We Trust In-Distribution Success? Locked Evaluation Reveals Transfer Failure and Sampling-Depth Entanglement in CRISPRi Perturbation Prediction

    Jul 31, 2026Mehrdad Shoeibi, Niloofar YousefiOOD GeneralizationSingle-Cell Perturbation Modeling

    University of Central Florida

  21. LLMBDC: Language Model for Biological Domains Oriented Clustering of Gene Ontology

    Jul 30, 2026Ximing Ran, Jie Xu, Peng Jin +3ClusteringGenomics

    Emory University Atlanta, GA, USA

  22. VESTIGE: A Knowledge-Guided Masking Strategy for Corruption-Aware Fine-Tuning of Genomic Transformers, Validated on Ancient DNA Reconstruction

    Jul 30, 2026Angshuman Chakravertty, Rahul MaheshwariMasked Language ModelingLanguage Modeling

    School of Technology Management & Engineering, SVKM’s Narsee Monjee Institute of Management Studies (NMIMS) Deemed-to-be-University, Jadcherla, Hyderabad 509301, Telangana, India, Hyderabad, India · School of Pharmacy and Technology Management, SVKM's Narsee Monjee Institute of Management Studies (NMIMS) Deemed-to-be-University, Hyderabad, Jadcheral-509301, Telangana, India · School of Pharmacy and Technology Management, SVKM's Narsee Monjee Institute of Management Studies (NMIMS) Deemed-to-University, Hyderabad, Jadcheral-509301, Telangana, India

  23. PlantBGC: Transformer for Plant BGC Discovery via Label-Free Domain Adaptation and Weak Supervision

    Jul 29, 2026Yuhan Zhao, Nidhi Grover, Zhishan Guo +1Genomics

    North Carolina State University Department of Computer Science Raleigh, North Carolina, USA · North Carolina State University Department of Molecular and Structural Biochemistry Raleigh, North Carolina, USA

  24. MOSAIC-FL, a micro-service based privacy-preserving framework with application to genomics

    Jul 27, 2026Paul Largillier, Karl Paygambar, Cédric Gouy-Pailler +3Privacy-Preserving MLGenomics

    Université Paris-Saclay, CEA, LIST, France · Université Paris-Saclay, CEA, CNRGH, France

  25. HistoGPA: A Context-Conditioned Gene-Prior Attention Framework for Histology-Based Spatial Gene Expression Prediction

    Jul 27, 2026Ziang Liu, Xinhai Chen, Yigui Feng +3Computational PathologySpatial Transcriptomics

    Laboratory of Digitizing Software for Frontier Equipment, National University of Defense Technology · National Key Laboratory of Parallel and Distributed Computing, National University of Defense Technology · College of Computer Science and Technology, National University of Defense Technology, Changsha 410073, China

  26. Foundation-model-guided radiogenomic discovery linking cancer genomes to cancer scans

    Jul 22, 2026Frederik Hauke, Jeremias Krause, Patrick Wienholt +6Cancer GenomicsOncology

    Department of Diagnostic and Interventional Radiology, University Hospital RWTH Aachen, Aachen, Germany · Center for Human Genetics and Genomic Medicine, University Hospital RWTH Aachen, Aachen, Germany · Department of Nephrology, Rheumatology and Immunology (Medical Clinic II), University Hospital RWTH Aachen, Aachen, Germany +3

  27. Causal dictionary learning reveals and validates transcription-factor binding features in genomic language models

    Jul 21, 2026Sarwan AliLLM InterpretabilityGenomics

    Columbia University Irving Medical Center, New York, USA

  28. BioSecBench-Surveillance: A Verifiable Benchmark for AI Agents in Pathogen Genomic Surveillance

    Jul 21, 2026Harmon Bhasin, Kevin Flyangolts, Dianzhuo Wang +9AI Agent EvaluationAI Agent Benchmarks

    LatchBio, San Francisco, CA · Aclid, New York, NY

  29. BRIDGE: Bottleneck-Aware Regulator-Set Inference and Diagnosis for Cooperative Gene Regulatory Recovery

    Jul 21, 2026Maryam Rahimimovassagh, Clayton Thomas Barham, Ivan Garibay +1Feature Interaction ModelingGene Regulatory Network Inference

    University of Central Florida

  30. GeneSpeak-FP: Target and Compound Retrieval from Observed Cell-Level Perturbation Signatures

    Jul 20, 2026Kseniia Vaniushkina, Jeongmin Lim, Jinyong ParkSingle-Cell Perturbation ModelingInformation Retrieval

    AIFFEL Research, Modulabs, Republic of Korea