Spatial Transcriptomics

Ask about this field

Recent momentum

emerging

0 papers in the last 28 days · 0.0% of indexed attention

Twelve weeks of publication activity for this topic as it is defined today.

Weekly history

Recent digests

What was published in this field, kept on the site without email delivery.

Period ending 2026-09-21

4 new papers

A weekly snapshot of new work published in Spatial Transcriptomics.

Period ending 2026-09-14

3 new papers

A weekly snapshot of new work published in Spatial Transcriptomics.

Period ending 2026-09-07

1 new paper

A weekly snapshot of new work published in Spatial Transcriptomics.

Inside this field

Focused directions

176 papers

Latest in Spatial Transcriptomics

Open your feed →
CardsList

  1. ERCPMP-Gx: Endoscopic Image and Video Dataset for Morphological, Histopathological, and Genomic Characterization of Colorectal Polyposis

    Sep 17, 2026Zahra Ghaffari, Massih Bahar, Mojgan Forootan +2Colorectal CancerPolyp Segmentation

  2. Dynamic Generalized Gromov-Wasserstein Optimal Transport

    Sep 17, 2026Junda Ying, Zhiwei Zeng, Peijie Zhou +1Optimal TransportSpatial Transcriptomics

  3. HyCoSeq: Contextual Hyperbolic Representation Learning for Genomic Sequences

    Sep 15, 2026Chenhao Zeng, Zhibin Pu, Shufei GeHyperbolic LearningGenomics

  4. Hyperbolic Contrastive Learning with Entailment for Spatial Transcriptomics

    Sep 14, 2026Daniela Vega, Paula Cárdenas, Hannah Ceballos +2Spatial TranscriptomicsComputational Pathology

  5. Why Sample What You Can Enumerate? Exact Policy Optimization for Genomic Tool Selection

    Sep 9, 2026Haoyue Liu, Xiaoyu Ma, Ye Chen +2Group Relative Policy OptimizationExternal Reward Models

  6. A Transformer-Based Delta Expression Encoder for Psilocybin Transcriptional Response: Architecture, Representations, and Biological Validation

    Sep 8, 2026Sai JayakumarSpatial TranscriptomicsTransformer Encoder

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

    Sep 7, 2026Isabella Caranzano, Daniel Maria Busiello, Stefano Priorelli +2Cryptographically Authorized MutationGenomics

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

    Sep 1, 2026Handong Wang, Jiaxin Qi, Haochen Feng +1Single-Cell Perturbation PredictionSpatial Transcriptomics

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

    Aug 13, 2026Francesca Pia Panaccione, Sofia Mongardi, Marco Masseroli +1Spatial TranscriptomicsSynthetic Data

  10. Static analysis-guided agentic AI translation enables Rust as a full stack bioinformatics language

    Aug 13, 2026Johan HenrikssonSingle-Cell Rna Sequencing

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

    Aug 11, 2026Sepideh Saran, Mahsa Ghanbari, Uwe OhlerGenomicsBayesian Neural Networks

  12. CosMAP: Contrastive Manifold Approximation and Projection for Dimensionality Reduction of Omics and Genealogical Data

    Aug 11, 2026Fenosoa Randrianjatovo, Maya Saleh, Simon Girard +1Dimensionality ReductionSingle-Cell Rna Sequencing

  13. Idea Search: Guiding Tree Search with Ideas to Explore Diverse Scientific Methods

    Aug 9, 2026Xuefei Julie Wang, Hao Cui, Michael P. Brenner +1Tree SearchScientific Discovery

  14. Decoding Phenotypes: A Framework for Fusing Genomic Language Models and Neuroimaging

    Aug 9, 2026Tianli Tao, Ziyang Wang, Emma Robinson +2Neuroimaging ModelsGenomics

  15. VOICE: A Vision-Omics Foundation Model Integrating Direct and Retrieval-Based Prediction of In-situ Single-Cell Gene Expression

    Aug 8, 2026Xin Luo, Yicheng Tao, Haoxuan Zeng +6Spatial TranscriptomicsSingle-Cell Rna Sequencing

  16. 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 PredictionSpatial Transcriptomics

  17. CellWorld: From Gene-Level Reconstruction to Latent Cell Prediction in Spatial Transcriptomics Foundation Models

    Aug 7, 2026Haiping Liu, Qian Zhao, Lijing Lin +2Spatial TranscriptomicsLatent Bridge Matching

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

    Aug 6, 2026Yuhao Wang, Zelin Zang, Yuxuan Liu +2Single-Cell Rna SequencingJoint-Embedding Predictive Architectures

  19. CohortHijack: Robustness of Single Cell Annotation to Companion Cell Removal

    Aug 6, 2026Arash Vashagh, Yasmin VashaghSingle-Cell Rna SequencingHijacking

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

    Aug 5, 2026Jose A. BirdCancer Genome AtlasGene-Regulatory Networks

  21. MS-MLB: An Open Machine Learning Benchmark for Blood-Based MS Classification

    Aug 4, 2026Adam Simson, Ankush Dutta, Quang BuiMultiple SclerosisMle-Bench Lite

  22. Scaling an Autoregressive Transformer for Single-Cell Generation

    Aug 3, 2026Aleksandr Sharipov, Yusif Mukhtarov, Igor MolybogAutoregressive TransformersSingle-Cell Rna Sequencing

  23. LLM-Guided Retrieval for Prediction of Molecular Perturbation Responses

    Aug 3, 2026Betty Xiong, Jan-Christian Huetter, Gabriele Scalia +2Single-Cell Perturbation PredictionDrug Discovery

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

    Aug 2, 2026Jiaqi Xiong, Yuntao hu, Yu Zheng +3Single-Cell Rna SequencingSpatial Transcriptomics

  25. Zero-Cost Virtual RNA: Approximating Immunotherapy Signatures via Cross-Modal WSI Retrieval

    Aug 1, 2026Sigrid Vila-Bagaria, Mar Teixidó, Miquel Piñol +3Spatial TranscriptomicsMessenger Rna

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

    Aug 1, 2026Zhiwen Xu, Xiaoming Yan, Chengkun Wu +3Spatial TranscriptomicsComputational Pathology

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

    Jul 31, 2026Mehrdad Shoeibi, Niloofar YousefiSpatial TranscriptomicsResponse Magnitude

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

    Jul 31, 2026Yu Song, Hao Sun, Ikuko Nishikawa +1Single-Cell Rna Sequencing

  29. What Carries the Signal in Pathology Foundation-Model Atlases? A Patient-Level Controlled Benchmark in Breast Cancer

    Jul 31, 2026Chimdi Walter NdubuisiPathology Foundation ModelsSpatial Transcriptomics

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

    Jul 29, 2026Yuhan Zhao, Nidhi Grover, Zhishan Guo +1Genomics3D Plant Phenotyping

  31. A large-scale corpus of religious radio broadcast transcripts from webstream recordings in the United States

    Jul 28, 2026Samuel Bestvater, Athena Chapekis, Skyler Seets +3Dissipative MediaAccurate Transcription

  32. 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 +4Single-Cell Rna SequencingImage Clustering

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

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

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

    Jul 27, 2026Ziang Liu, Xinhai Chen, Yigui Feng +3Spatial TranscriptomicsCancer Genome Atlas

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

    Jul 26, 2026Shuyu Chen, Chen Zhu, Ye Zhang +3Single-Cell Rna Sequencing

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

    Jul 25, 2026Gonzalo A. RuzGene-Regulatory NetworksSurrogate Models

  37. Distributional Determinantal Point Process for Repulsive Clustering of Distributions

    Jul 23, 2026Khai Nguyen, Yang Ni, Elizabeth Juarez-Colunga +1Determinantal Point ProcessMixture Models

  38. M^3-Gen: Interpretable Multimodal Generation of Gene Expression Profiles Using Clinical and Imaging Data

    Jul 23, 2026Francesca Pia Panaccione, Carlo Sgaravatti, Marco VenereMultimodal Clinical DataCancer Genome Atlas

  39. HierarchicalDAEW: Domain-Aware Edge-Weighted Graph Convolution with Evidential Uncertainty for Multi-Section Spatial Gene Expression Prediction from H&E Histology

    Jul 23, 2026Kritanu Chattopadhyay, Soumya Chatterjee, Ondrej Krejcar +1Spatial TranscriptomicsComputational Pathology

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

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

  41. Local Causal Structure Learning in the Presence of Latent Variables and Selection Bias

    Jul 22, 2026Zheng Li, Hao Zhang, Ruxin Wang +3Causal Foundation ModelsCausal Reasoning

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

    Jul 21, 2026Sarwan AliSpatial TranscriptomicsUnsupervised Dictionary Learning

  43. Making Single-Cell Data Distillation Auditable: Traceable Real-Cell Coresets via Discrete Min--Max Selection

    Jul 20, 2026Yaodi Luo, Peize He, Lingbei Meng +4Single-Cell Rna SequencingGeometry-Aware Uncertainty Coresets

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

    Jul 20, 2026Kseniia Vaniushkina, Jeongmin Lim, Jinyong ParkSingle-Cell Perturbation PredictionSpatial Transcriptomics

  45. Deep and Probabilistic Models for Gene Regulatory Network Inference

    Jul 17, 2026Claudia Skok GibbsGene-Regulatory NetworksGenomics

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

    Jul 15, 2026Jagan Mohan Reddy Dwarampudi, Veena Kochat, Suresh Satpati +2Multi-Omic FrameworkSpatial Transcriptomics

  47. Gene Expression-Informed Jointly Controlled Generative Modeling for Precision Molecular Design

    Jul 13, 2026Hang Yuan, Chen Li, Wenjun Ma +2Molecular GenerationSpatial Transcriptomics

  48. NVAITC AI Scientist: A Governed End-to-End Research System -- A Hypertension GWAS Case Study

    Jul 13, 2026Eddie Huang, Ken Liao, Iven Fu +14Scientific WorkflowsArtificial Intelligence Scientists

  49. COAST: Context-Aware Differential Learning for Gene Expression Prediction in Spatial Transcriptomics

    Jul 10, 2026Keunho Byeon, Sunhong Park, Jeewoo Lim +1Spatial TranscriptomicsOcean

  50. SpaCellAgent: A Self-Evolving LLM-Based Multi-Agent Framework for Trajectory Analysis

    Jul 8, 2026Songhan Wang, Haoang Chi, He Li +6Single-Cell Rna SequencingTrajectory Prediction

  51. The Regularization Parameter: Sparse Precision Matrix Estimation

    Jul 7, 2026Aryan Eftekhari, Daniel Sergio Vega, Ernst-Jan Camiel Wit +1Maximum LikelihoodRegularization Techniques

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

    Jul 6, 2026Dmytro Rizdvanetskyi, Nathan Roos, Pavlo LutsikSingle-Cell Rna SequencingMulti-Label Classification

  53. DriftST: One-Step Generative Inference of Spatial Transcriptomics from H\&E Histology

    Jul 6, 2026Yuhang Yang, Yonggan Bu, Shengyuan Zhou +2Spatial TranscriptomicsGenomics

  54. Predicting Therapeutic Outcome via Aligning Patient-Specific Knowledge Graph and Gene-Level Perturbation Representations

    Jul 6, 2026Dongmin Bang, Sugyun An, Inyoung Sung +3Spatial TranscriptomicsBiomedical Knowledge Graph

  55. HASSL: Hierarchy-Aware Self-Supervised Learning Framework for Single Cell Microscopy

    Jul 5, 2026Julius Riel, Vishwa Mohan Singh, Sai Anirudh Aryasomayajula +10Single-Cell Rna SequencingSelf-Supervised

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

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

  57. EVOTS: Evolutionary Transformer Search for Time Series Forecasting

    Jun 30, 2026AbdElRahman ElSaid, Damir PulatovMultivariate Time Series ForecastingEvolutionary Search

  58. Resolving superposition in AI for interpretability and cross-modal alignment in patient-neuronal images

    Jun 30, 2026Jisung Park, Seohyeon Kang, Daeun Yoo +8Neuroimaging ModelsImplicit Neural Representations

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

    Jun 29, 2026Romain Karpinsky, Julien Mozziconacci, Mickaël DelceyGenerative Pretrained TransformersGenomics

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

    Jun 26, 2026Jun Tang, Pengwei Hu, Sicong Gao +3Single-Cell Rna SequencingGraph Representation Learning