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. 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

  2. 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

  3. Deep and Probabilistic Models for Gene Regulatory Network Inference

    Jul 17, 2026Claudia Skok GibbsGene Regulatory Network InferenceGenomics

    Center for Data Science New York University

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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

  20. 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

  21. 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.

  22. 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.

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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.

  28. 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

  29. 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

  30. 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