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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

  31. Deep and Probabilistic Models for Gene Regulatory Network Inference

    Jul 17, 2026Claudia Skok GibbsGene Regulatory Network InferenceGenomics

    Center for Data Science New York University

  32. LATTICE: Graph Self-Supervised Learning for Multimodal Spatial Omics Integration

    Jul 15, 2026Jagan Mohan Reddy Dwarampudi, Veena Kochat, Suresh Satpati +2Spatial TranscriptomicsGraph SSL

    University of Houston · MD Anderson Cancer Center

  33. Screening of Biosecurity Features in Metagenomic Data with Evo 2 Probes

    Jul 15, 2026Jeremy Guntoro, Alexander Dack, Dylan Danno +3Representation ProbingGenomics

    John Innes Centre · AIxBio Hackathon contestant · Department of Bioengineering, Imperial College London +1

  34. CoDiffGRN: Rethinking Gene Regulatory Network Inference via the BEELINE-KGC Benchmark and Co-evolutionary Discrete Diffusion

    Jul 14, 2026Jiaze Song, Runhao Zhao, Minghao Xu +2Link PredictionGene Regulatory Network Inference

    Peking University · National University of Defense Technology

  35. Data-Driven Soft Labeling Scales DNA Read Classification to Whole-Body Cell-Type Deconvolution

    Jul 6, 2026Dmytro Rizdvanetskyi, Nathan Roos, Pavlo LutsikSoft-Label LearningGenomics

    Department of Oncology KU Leuven Leuven, Belgium

  36. Causal ASCEND: Scalable Two-tier Causal Discovery on High Dimensional Multi-omics Data

    Jul 5, 2026Stephen Asiedu, David WatsonCausal DiscoveryGene Regulatory Network Inference

    Department of Informatics, King’s College London, Bush House, 30 Aldwych, WC2B 4BG, London, United Kingdom

  37. SHIFT: Survival Prediction from Incomplete and Heterogeneous Genomic Data

    Jul 4, 2026Muhammet Sami Yavuz, Ayhan Can Erdur, Sabri Mustafa Kahya +2Cancer GenomicsCancer Survival Prediction

    AI for Image-Guided Diagnosis and Therapy, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany · Munich Center for Machine Learning (MCML) · Department of Radiation Oncology, TUM University Hospital +4

  38. DNA Language Models: An Assessment of Pre-Training for Fine-Tuning Tasks

    Jun 29, 2026Romain Karpinsky, Julien Mozziconacci, Mickaël DelceyLanguage Model PretrainingFine-Tuning

    CNRS, LORIA · Nancy, 54000, France · CNRS +1

  39. GRAFT: Biological Graph and Hypergraph Benchmarks for Linked Gene Expression and Phenotypic Trait Prediction in Arabidopsis thaliana

    Jun 25, 2026Manuel Serna-Aguilera, Vanshika Jindal, Fiona L. Goggin +5Multimodal Graph LearningGenomics

    Department of Electrical Engineering and Computer Science, University of Arkansas, AR · CVIU Lab, University of Arkansas, AR · Department of Entomology and Plant Pathology, University of Arkansas, AR +3

  40. KG-TRACE: A Neuro-Symbolic Framework for Mechanistic Grounding in Antimicrobial Resistance Prediction

    Jun 24, 2026Naman Garg, Sarika Jain, Sourav Yadav +4GenomicsNeurosymbolic Learning

    National Institute of Technology Kurukshetra, Kurukshetra, India · Indian Institute of Information Technology Manipur, Manipur, India · Purdue University, West Lafayette, IN, USA +1

  41. JASPR: Joint Spatial Representation learning of histology and spatial genomics for improved virtual genomic screening and clinical prognostication

    Jun 24, 2026Marija Pizurica, Eric Zimmermann, Neil Tenenholtz +5Cancer GenomicsComputational Pathology

    Microsoft Research, Cambridge, MA, United States · Stanford University, CA, United States

  42. DeepBD: A Grounded Agentic Workflow for Variant Prioritization and Diagnosis of Genetic Birth Defects

    Jun 23, 2026Shiyu Li, Ziqi Yan, Zhihao Wu +7Rare Disease DiagnosisLLM Agents

    College of Computer Science and Technology, Zhejiang University, Hangzhou, China

  43. Stable-Shift: Biologically Structured Prediction of Transcriptional Responses to Unseen Gene Perturbations

    Jun 22, 2026Sajib Acharjee Dip, Liqing ZhangSingle-Cell Perturbation ModelingGenomics

    Department of Computer Science, Virginia Tech Blacksburg, VA, USA · Fralin Biomedical Research Institute, Virginia Tech Roanoke, VA, USA · FBRI Cancer Research Center Washington, DC, USA

  44. A Bayesian Boolean Matrix Factorization with Application to Copy Number Analysis in Cancer

    Jun 16, 2026Adolphus Wagala, Mehmet Samur, Giovanni ParmigianiCancer GenomicsBayesian Inference

    Department of Data Science, Dana-Farber Cancer Institute · Department of Biostatistics, Harvard T.H. Chan School of Public Health

  45. EpiBench: Verifiable Evaluation of AI Agents on Epigenomics Analysis

    Jun 11, 2026Harihara Muralidharan, Reema Baskar, Soo Hee Lee +2AI Agents for Scientific DiscoveryAI Agent Evaluation

    LatchBio, San Francisco, CA, USA

  46. CisTransCell: Single-Cell Perturbation Prediction via Gene Function, Regulatory Control, and Cellular Context

    Jun 10, 2026Wei Zhang, Xun Jiang, Yuesi Xi +1Single-Cell Perturbation ModelingGenomics

    1L3S Research Center, Leibniz Universität Hannover, Germany · School of Clinical Medicine & Laboratory Medicine, Jiangsu University, China · Institute for Information Processing (tnt), Leibniz Universität Hannover, Germany.

  47. Integrating gene regulatory priors into Transformer attention with scTransformer for interpretable scRNA-seq analysis

    Jun 8, 2026Mikele Milia, Louis Fabrice Tshimanga, Henning Mueller +2Transformer InterpretabilityTransformer Attention

    Department of Information Engineering, University of Padova, Padova, Italy · Department of Neuroscience, University of Padova, Padova, Italy · Padova Neuroscience Center, Padova, Italy +3

  48. The Dark Regulome: Disentangling Predictability from Regulation in Genomic Foundation Models

    Jun 5, 2026Chahat Baranwal, Aaditya Baranwal, Lakshya Nitin TandonGenomicsMolecular Representation Learning

    IIT Jodhpur · University of Central Florida · Northeastern University

  49. pp-adic Bi-Filtrations for Topological Machine Learning on Genomic Sequences

    Jun 4, 2026Tirtharaj Dash, Gunja SachdevaGenomicsPersistent Homology

    Department of CS & IS, BITS Pilani, K K Birla Goa Campus, Zuarinagar, Goa 403726, India. · Department of Mathematics, BITS Pilani, K K Birla Goa Campus, Zuarinagar, Goa 403726, India.

  50. LDARNet: DNA Adaptive Representation Network with Learnable Tokenization for Genomic Modeling

    Jun 3, 2026Daria Ledneva, Denis KuznetsovHierarchical Representation LearningGenomics

    Moscow Independent Research Institute of Artificial Intelligence, Moscow, Russia.

  51. GENEB: Why Genomic Models Are Hard to Compare

    Jun 3, 2026Daria Ledneva, Mikhail Nuridinov, Denis KuznetsovBenchmark DesignGenomics

    Moscow Independent Research Institute of Artificial Intelligence, Moscow, Russia · Moscow State Institute of Steel and Alloys, Moscow, Russia

  52. Prior-Guided Multi-Omic Transformers for Single-Cell Gene Regulatory Network Inference

    May 30, 2026Tianyang Xu, Tianci Liu, Niraj Rayamajhi +4TransformerGene Regulatory Network Inference

    Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, USA · Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA · School of Biological Sciences, Illinois State University, Normal, IL, USA

  53. Annotation-Informed Block-Sparse Bayesian Modeling for cis-Expression Prediction

    May 30, 2026Lei Huang, Hui Shen, Kuan-Jui Su +9Bayesian InferenceGenomics

    School of Computing Sciences and Computer Engineering, University of Southern Mississippi, Hattiesburg, MS, USA · Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA · Texas Tech University Health Sciences Center, School of Medicine, Texas Tech University

  54. Agentic Authoring of Interactive Multiview Visualizations in Genomics

    May 29, 2026Astrid van den Brandt, Kiroong Choe, Sehi L'Yi +2Scientific VisualizationData Visualization

    Harvard Medical School · Boston College

  55. Position: Genomic Model Research Must Move Beyond Anecdotal Evaluation of Interpretability Methods

    May 29, 2026Shasha Zhou, Mingyu Huang, Ke LiInterpretable MLGenomics

    Department of Computer Science, University of Exeter, Exeter, UK.

  56. Influence-Guided Symbolic Regression: Scientific Discovery via LLM-Driven Equation Search with Granular Feedback

    May 27, 2026Evgeny S. Saveliev, Samuel Holt, Nabeel Seedat +3GenomicsLarge Language Model-Guided Scientific Discovery

    University of Cambridge · Thomson Reuters Foundational Research · U. Colorado, Anschutz Medical Campus +1

  57. Geometry-First Generative Spatial Single-Cell Reconstruction

    May 27, 2026Ehtesamul Azim, Muhtasim Noor Alif, Tae Hyun Hwang +2Spatial TranscriptomicsGenomics

    University of Central Florida Orlando, Florida, USA · Vanderbilt University Medical Center Nashville, Tennessee, USA · Arizona State University Tempe, Arizona, USA

  58. ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks

    May 25, 2026Dongxin Ye, Fang Hu, Han Hu +6Distribution ShiftBenchmark Design

    Shanghai Innovation Institute Shanghai, China · University of Electronic Science and Technology of China Chengdu, China · Fudan University Shanghai, China +7

  59. AnnotateMissense: a genome-wide annotation and benchmarking framework for missense pathogenicity prediction

    May 23, 2026Muhammad Muneeb, David B. AscherGenomics

    School of Chemistry and Molecular Biology, The University of Queensland, Queen Street, 4067, Queensland, Australia · 2Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Commercial Road, 3004, Victoria, Australia

  60. WTKO-CNN: Deep Learning Reveals Sequence Motifs Distinguishing Wild-Type and Knockout ATAC-seq Peaks

    May 21, 2026Lopamudra DeyGenomicsSequence Modeling