Regulatory Networks

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1 paper in the last four weeks, against 1 the four weeks before. 0.0% of all new papers.

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  1. Towards a knowledge-enhanced single-cell foundation model

    Sep 14, 2026Hanqing Zhang, Jie Bao, Mei Ma +7Regulatory NetworksPretraining

    College of Animal Science and Technology, China Agricultural University, Beijing 100193, China · College of Information and Electrical Engineering, China Agricultural University, Beijing 100193, China

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

    Aug 27, 2026Jose A. BirdRegulatory NetworksRegulation

    Independent Researcher, Bird AI Solutions

  3. Control-Anchored Residual Flow Matching Conditioned on Gene Geometry for Virtual Cell Perturbation Modeling

    Aug 7, 2026Quanquan Li, Yihe Chi, Liuyang Song +10Single-Cell Perturbation PredictionTranscriptomics

    1East China Normal University · 2Peking University · University of Science and Technology of China +2

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

    Aug 5, 2026Jose A. BirdTranscriptomicsRegulatory Networks

    Independent Researcher

  5. Continuous surrogates versus threshold Boolean networks for modeling Arabidopsis ISR gene regulation

    Jul 25, 2026Gonzalo A. RuzRegulatory NetworksSurrogate Models

    Facultad de Ingenier´ıa y Ciencias, Universidad Adolfo Ib´a˜nez · Millennium Nucleus for Social Data Science (SODAS) · Millennium Nucleus in Data Science for Plant Resilience (PhytoLearning) +1

  6. Amortized Bayesian Causal Discovery of Extended Factor Graphs

    Jul 24, 2026Yichen Gu, Yuxuan Song, Weizhou Qian +2Causal GraphRegulatory Networks

    Department of Electrical and Computer Engineering University of Michigan Ann Arbor, MI 48109, USA · Department of Computational Medicine and Bioinformatics University of Michigan, Ann Arbor Ann Arbor, MI 48109, USA · Department of Statistics University of Michigan, Ann Arbor Ann Arbor, MI 48109, USA +1

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

    Jul 21, 2026Maryam Rahimimovassagh, Clayton Thomas Barham, Ivan Garibay +1Regulatory NetworksRegulation

    University of Central Florida

  8. Deep and Probabilistic Models for Gene Regulatory Network Inference

    Jul 17, 2026Claudia Skok GibbsRegulatory NetworksGenome-Wide Association Study

    Center for Data Science New York University

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

    Jul 14, 2026Jiaze Song, Runhao Zhao, Minghao Xu +2Regulatory NetworksTranscriptomics

    Peking University · National University of Defense Technology

  10. Deep Gaussian Processes on Directed Acyclic Graphs

    Jul 10, 2026Federico L. Perlino, Oliver Hamelijnck, Adam M. Johansen +1Directed Acyclic GraphGaussian Process

    Department of Statistics, University of Warwick · 2AI Team, Unilink Software Ltd · Department of Computer Science, University of Warwick

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

    Jul 5, 2026Stephen Asiedu, David WatsonCausal Discovery MethodsRegulatory Networks

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

  12. Recovering Candidate Circadian Regulators of Arrhythmic Pituitary Hormone Genes Using Reliability-Weighted Magnetic Laplacian with rwMagLap

    Jul 3, 2026Shabnam Sodagari, Nick JaspersonPeriodicRegulatory Networks

  13. 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 +5PhenotypesRegulatory Networks

    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

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

    Jun 22, 2026Sajib Acharjee Dip, Liqing ZhangTranscriptomicsRegulatory Networks

    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

  15. Biological Reasoning-Informed Regression for Interpretable Regulatory DNA Activity Prediction

    Jun 6, 2026Yi Duan, Zhao Yang, Jiwei Zhu +3Regulatory NetworksBiological

    Gaoling School of Artificial Intelligence · Renmin University of China · Beijing, China +1

  16. BRIDGE: Biological Evidence Refinement and Heterogeneous Dynamic Gating for Gene Regulatory Networks

    Jun 2, 2026Ziyang Dong, Shanwen Tan, Hengchuang Yin +5Regulatory NetworksSingle-Cell Rna

    College of Computer Science, Sichuan University, Chengdu, 610065, China · Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, China · School of Mathematics, Sichuan University, Chengdu, 610065, China +2

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

    May 30, 2026Tianyang Xu, Tianci Liu, Niraj Rayamajhi +4Regulatory NetworksMultiplex Graph Transformers

    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

  18. Applications of temporal graph learning for predicting the dynamics of biological systems

    May 27, 2026Manuel Dileo, Andrea SottorivaRegulatory NetworksTemporal Graph Neural Networks

    Center for Computational Biology, Human Technopole Foundation, Milan, Italy

  19. Evolving Causal Regulatory Networks (ECR-Net)

    May 24, 2026Govind Vallabhasseri Binish, Abdhul Ahadh, Rano Roy Kavanal +1Causal Discovery MethodsRegulatory Networks

  20. SCOPE: Siamese Contrastive Operon Pair Embeddings for Functional Sequence Representation and Classification

    May 10, 2026Akarsh Gupta, Kenneth Rodrigues, Sagnik ChatterjeeRegulatory Networks

  21. When Does Gene Regulatory Network Inference Break? A Controlled Diagnostic Study of Causal and Correlational Methods on Single-Cell Data

    May 6, 2026Miguel Fernandez-de-Retana, Ruben Sanchez-Corcuera, Unai Zulaika +2Regulatory NetworksSingle-Cell Rna

    Faculty of Engineering University of Deusto Bilbao, Spain

  22. Partially Observed Structural Causal Models

    May 5, 2026Turan Orujlu, Jordan Matelsky, Martin V. Butz +2Causal Discovery MethodsRegulatory Networks

    University of Tübingen · MPI for Biological Cybernetics · University of Pennsylvania +1

  23. Towards Universal Gene Regulatory Network Inference: Unlocking Generalizable Regulatory Knowledge in Single-cell Foundation Models

    May 1, 2026Jiaxin Qi, Hang Li, Yan Cui +2Regulatory NetworksGraph Foundation Model

    Computer Network Information Center, Chinese Academy of Sciences, Beijing, China · Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China · University of Chinese Academy of Sciences, Beijing, China

  24. Learning biophysical models of gene regulation with probability flow matching

    Apr 27, 2026Suryanarayana Maddu, Victor Chardès, Michael J. ShelleyRegulatory NetworksProbability

    Center for Computational Biology, Flatiron Institute, New York, NY, USA, 10010 · Molecular & Cellular Biology Department, Harvard University, Cambridge, MA 02138 · Courant Institute of Mathematical Sciences, New York University, New York, NY, USA, 10012

  25. Central Dogma Transformer II: An AI Microscope for Understanding Cellular Regulatory Mechanisms

    Feb 9, 2026Nobuyuki OtaRegulatory NetworksRegulation

    Independent Researcher, Burlingame, CA, USA