Single-Cell RNA Sequencing

Also known as scRNA-seq

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

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  1. Finsler Flow Matching: Dynamics-Aware Geodesic Interpolation for Single-Snapshot Trajectory Inference

    Oct 8, 2026Niklas Canova, Jonas Simon FleckFlow-Based Generative ModelingSingle-Cell Transcriptomics

    Institute of Human Biology (IHB), Roche, Basel, Switzerland

  2. CellMSA: Context Modeling for Single-Cell Representation Learning

    Sep 30, 2026Suyuan Zhao, Minghao Liu, Yizhen Luo +1Representation LearningSingle-Cell Transcriptomics

    Institute for AI Industry Research (AIR), Tsinghua University · Department of Computer Science and Technology, Tsinghua University · Tsinghua Institute of Multidisciplinary Biomedical Research (TIMBR), Tsinghua University +2

  3. scTrilemma: Balancing Identity, Invariance, and Fidelity in Single-Cell Representation Learning

    Sep 30, 2026Yunhak Oh, Yoonho Lee, Junseok Lee +9Variational AutoencodersRepresentation Learning

    KAIST · Work done during an internship at HITS · HITS

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

    Sep 14, 2026Hanqing Zhang, Jie Bao, Mei Ma +7Language Model PretrainingSingle-Cell Transcriptomics

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

  5. PopPert: Population-level Joint-Distribution Modeling for Single-Cell Perturbation Prediction

    Sep 1, 2026Handong Wang, Jiaxin Qi, Haochen Feng +1Single-Cell Perturbation ModelingSingle-Cell RNA Sequencing

    Computer Network Information Center, Chinese Academy of Sciences · University of Chinese Academy of Sciences

  6. Improving scDiffusion with Sparsity-Biased Classifier-Free Guidance

    Jul 31, 2026Yu Song, Hao Sun, Ikuko Nishikawa +1Classifier-Free GuidanceDiffusion Sampling

    College of Information Science and Engineering, Ritsumeikan University, Osaka, Japan

  7. PerturbMap: Cross-Context Transfer of Single-Cell Perturbation Responses

    Jul 30, 2026Panpan Cui, Yiqi Liu, Wenhao SunSingle-Cell Perturbation ModelingCross-Domain Transfer Learning

    School of Advanced Interdisciplinary Sciences, University of Chinese Academy of Sciences · Institute of Computing Technology, CAS; University of Chinese Academy of Sciences · 3Hong Kong University of Science and Technology

  8. When Does Deep Representation Learning Help Single-Cell Clustering? A Sensitivity-Aware Diagnostic Benchmark for Biomedical AI Pipelines

    Jul 28, 2026Nguyen Thanh Phong, Truong Viet Vu, Nguyen Ha Thu +4Representation LearningClustering

    Faculty of Information Technology, Van Lang School of Technology, Van Lang University, Ho Chi Minh City, Vietnam · Faculty of Law, Van Lang University, Ho Chi Minh City, Vietnam

  9. SCTA: An Agentic Framework for Stable and Interpretable Target Gene Discovery from Single-Cell RNA Sequencing

    Jul 26, 2026Shuyu Chen, Chen Zhu, Ye Zhang +3AI Agents for Scientific DiscoveryScientific Workflow Automation

    Siebel School of Computing and Data Science University of Illinois Urbana-Champaign Champaign, IL, USA · School of Information Sciences University of Illinois Urbana-Champaign Champaign, IL, USA · Novartis Biomedical Research Biomedical Research Cambridge, MA, USA +1

  10. Score Distributions, Not Cells: Evaluating Single-Cell Perturbations Under Class Overlap

    Jul 6, 2026Youssef Marrakchi, Davide D'Ascenzo, Sebastiano Cultrera di MontesanoSingle-Cell Perturbation ModelingClassification

    Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA. · Department of Computer Science, University of Milan, Milan, Italy. · Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy. +1

  11. Modeling Cell-Cycle-Aware Single-Cell Drug Perturbation Responses

    Jun 29, 2026Dingping Zhao, Jie Lin, Feng Xu +1Single-Cell Perturbation ModelingSingle-Cell RNA Sequencing

    Division of Pharmacognosy, School of Pharmaceutical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China · Department of Computer Science at School of Informatics, Xiamen University, Xiamen, China · Peking University Health Science Center, Peking University, Beijing, China

  12. scKDGM: KAN-guided Dynamic Graph Masked Learning for Single-Cell RNA-seq Clustering

    Jun 26, 2026Jun Tang, Pengwei Hu, Sicong Gao +3Graph SSLClustering

    College of Computer and Information Science, Southwest University, Chongqing, China · Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, China

  13. scGTN: Deep Siamese Graph Transformer Network for Single-cell RNA Sequencing Clustering

    Jun 17, 2026Jinke Wu, Yifan Wang, Siyu Yi +5Graph SSLClustering

    Sichuan University · University of International Business and Economics · Great Bay University +1

  14. scLLM-DSC: LLM-Knowledge Enhanced Cross-Modal Deep Structural Clustering for Single-Cell RNA Sequencing

    Jun 11, 2026Ping Xu, Pengjiang Li, Tian Du +6ClusteringUnsupervised Clustering

    Computer Network Information Center, Chinese Academy of Sciences, Beijing, China · University of Chinese Academy of Sciences, Beijing, China · School of Computing and Information Technology, Great Bay University, Dongguan, China +2

  15. 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

  16. scCBGM: Interpretable Single-Cell Counterfactual Editing

    Jun 5, 2026Alma Andersson, Aya Abdelsalam Ismail, Edward De Brouwer +6Concept Bottleneck ModelsCausal Counterfactual Generation

    Genentech · Guide Labs · Department of Computer Science, New York University +1

  17. Single-Cell Cross-Modal Transfer by Adversarial Fine-Tuning of Foundation Models

    Jun 4, 2026Joseph Boyd, Matthew Lyon, Martino Mansoldo +2Spatial TranscriptomicsFine-Tuning

    GSK.ai, GlaxoSmithKline, London, United Kingdom.

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

    Jun 2, 2026Ziyang Dong, Shanwen Tan, Hengchuang Yin +5Heterogeneous GNNsGraph SSL

    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

  19. CellBRIDGE: Learning Cellular Trajectories via Interaction-Aware Alignment

    May 28, 2026Silas Ruhrberg Estévez, Nicolas Huynh, Tennison Liu +4Single-Cell TranscriptomicsOptimal Transport

    DAMTP, University of Cambridge · Francis Crick Institute · University of Colorado Anschutz Medical Campus

  20. 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

  21. Learning Latent Dynamical Causal Processes for Single-Cell Perturbation Prediction

    May 25, 2026Wenkang Jiang, Yuhang Liu, Erdun Gao +3Causal Representation LearningLatent Dynamics Modeling

  22. scHelix: Asymmetric Dual-Stream Integration via Explicit Gene-Level Disentanglement

    May 18, 2026Xichen Yan, Zelin Zang, Changxi Chi +8Representation DisentanglementMulti-Scale Feature Fusion

    Jinan University · Westlake University · HKISI +1

  23. scShapeBench: Discovering geometry from high dimensional scRNAseq data

    May 12, 2026Andrew J Steindl, João Felipe Rocha, Brian Tshilengi Di Bassinga +13Single-Cell RNA SequencingTopological Data Analysis

    Yale University · Mila / Université de Montréal · Garvan Institute of Medical Research +2

  24. Prototype Guided Post-pretraining for Single-Cell Representation Learning

    May 8, 2026Sachini Weerasekara, Natasha Darras, Sagar Kamarthi +2Representation LearningContinued Pretraining

    Sachini Weerasekara∗ · Natasha Darras · Sagar Kamarthi +2

  25. GATHER: Convergence-Centric Hyper-Entity Retrieval for Zero-Shot Cell-Type Annotation

    May 7, 2026Zhonghui Zhang, Feng Jiang, Shaowei Qin +2Zero-Shot LearningGraph Retrieval-Augmented Generation

    Artificial Intelligence Research Institute, Shenzhen University of Advanced Technology Shenzhen, China · Software College, Northeastern University Shenyang, China

  26. 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 +2Causal DiscoveryGene Regulatory Network Inference

    Faculty of Engineering University of Deusto Bilbao, Spain

  27. Donor-Aware scRNA-seq Benchmarks for IBD Classification

    May 5, 2026Jonathan MuhireMedical DiagnosisSingle-Cell RNA Sequencing

    Department of Computer Science, Oklahoma Christian University

  28. CellxPert: Inference-Time MCMC Steering of a Multi-Omics Single-Cell Foundation Model for In-Silico Perturbation

    Apr 30, 2026Andac Demir, Erik W. Anderson, Jeremy L. Jenkins +1Single-Cell Perturbation ModelingGenomics

    Novartis Biomedical Research

  29. Transcriptomic Models for Immunotherapy Response Prediction Show Limited Cross-cohort Generalisability

    Apr 7, 2026Yuheng Liang, Lucy Chhuo, Ahmadreza Argha +8Clinical Outcome PredictionOncology

    UNSW BioMedical Machine Learning Lab (BML), School of Biomedical Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia · Garvan Institute of Meidical Research, Sydney, NSW, 2000, Australia · School of Biomedical Engineering, UNSW, Sydney, NSW, 2052, Australia +7