Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• CaHoT-GRN: context-aware high-order topology learning for robust single-cell gene regulatory network inference.

  PMID 42059479 · PMC13130071 · Briefings in bioinformatics · 2026 · 7 claims · 5 setups

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  CaHoT-GRN integrates pretrained biological language model embeddings (DNABERT for DNA, ESM for protein) with scRNA-seq expression data to improve GRN inference

  embryonic gene dataset-specific same scrna-seq-based sequence protein-protein

• TDAGENE: Inference of Gene Regulatory Network Based on Topological Data Analysis and Graph Attention Network for Single-Cell RNA Sequencing Data.

  PMID 42093817 · PMC13139726 · Computational and structural biotechnology journal · 2026 · 7 claims · 5 setups

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  TDAGENE combines TDA features with a multilayer GAT via gate-controlled fusion to improve GRN inference accuracy

  scrna-seq gene string chip-seq grn persistent prior

• GRNFormer: accurate gene regulatory network inference using graph transformer.

  PMID 41883144 · PMC13069479 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  GRNFormer is a generalizable graph transformer framework for GRN inference from single-cell or bulk transcriptomics data across species, cell types, and platforms without cell-type annotations or prior regulatory information

  hematopoietic embryonic dendritic hepatocytes scrna-seq chip-seq string

• AutoGERN: single-cell RNA-seq gene regulatory network inference via explicit link modeling and adaptive architectures.

  PMID 41871930 · PMC13064981 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 3 setups

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  AutoGERN explicitly models regulatory information in the message-passing space via learned link (edge) embeddings, which are scored by a lightweight MLP to infer TF–target interactions.

  seven same scrna-seq-based chip-seq cold-start

• CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

  PMID 41498638 · PMC12948241 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  CellPolaris is a unified computational framework performing TF-centered GRN construction, master TF identification, and TF perturbation simulation

  bulk previously round paired transfer-learning cross-species

• PSGRN: Gene regulatory network inference from single-cell perturbational data through self-training with synthetic gold standards.

  PMID 42054465 · PMC13127566 · Science advances · 2026 · 8 claims · 4 setups

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  PSGRN infers GRNs by generating pseudoannotations from gene-gene correlations and iteratively refining them via a self-training classifier using pre/post-intervention expression features.

  k562 rpe1 processed single-cell computational biological

• Identification of Cell Subpopulation-Specific Driver Genes Reveals Ideal Candidates for Renal Cell Carcinoma Immunotherapy.

  PMID 42074110 · PMC13115843 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

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  25 immune-related candidate driver genes were identified from tumor, myeloid, and lymphoid cell gene regulatory networks (GRNs) using SCENIC and topological Q statistics.

  kidney lymphoid rcc tcga-kirc single-cell scenic genome-wide

• Identification of Key Differentially Expressed Genes in Arabidopsis thaliana Under Short- and Long-Term High Light Stress.

  PMID 40869111 · PMC12386182 · International journal of molecular sciences · 2025 · 8 claims · 6 setups

  Has reproduction · 75

  Meta-analysis of 21 experiments covering 58 HL conditions yielded ~218,000 DEG instances corresponding to ~19,000 unique A. thaliana genes

  arabidopsis bulk hierarchical gene

• Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

  PMID 41865369 · PMC13207208 · Cell reports · 2026 · 8 claims · 6 setups

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  Memory CD4+ T cells show enhanced chromatin accessibility proximal to rapid-recall genes compared to naive cells

  blood-derived computational pseudobulk cd4+ single-nuclei maxatac grn

• An AI-Enabled Single-Cell Transcriptomic Analysis Pipeline for Gene Signature Discovery in Natural Killer Cells Linked to Remission Outcomes in Chronic Myeloid Leukemia.

  PMID 41972591 · PMC13072394 · Biology · 2026 · 8 claims · 7 setups

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  GAFA integrates latent-space representation, pseudotime trajectory modeling, GRN inference, and machine learning-based gene panel discovery into a single coherent pipeline, unlike existing workflows that treat these steps independently.

  peripheral subset immune assigned scrna-seq latent-space automated

• Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.

  PMID 41369820 · PMC12799884 · Discover oncology · 2025 · 8 claims · 8 setups

  Has reproduction · 59

  Key genes AR, AKT1, UBC, CDH1, SMAD3, ROR1, and ROR2 are associated with chemotherapy resistance and poor prognosis in metastatic breast cancer

  breast tcga-brca geo gse40622 gene pan-cancer differential

• BMP and NODAL paracrine signalling regulate the totipotent-like cell state in embryonic stem cells.

  PMID 41660012 · PMC12876259 · Frontiers in cell and developmental biology · 2025 · 7 claims · 8 setups

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  BMP and NODAL (TGF-β) paracrine signalling are key routes of intercellular communication that respectively enhance or diminish the totipotent-like cell (TLC) state in mouse ESCs

  escs esc scrna-seq cellchat differential

• A multi-omic single-cell landscape of perinatal mouse skin maps lineage specification and reveals shared dynamics in human fetal skin.

  PMID 41998142 · PMC13144478 · Experimental & molecular medicine · 2026 · 7 claims · 8 setups

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  Integrated scATAC/scRNA multi-omics analysis of developing mouse skin identifies gene network axes underlying skin lineage specification

  dorsal scrna-seq skin fibroblast scatac-seq scrna-seq spatial