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).

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

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

  Full-text index only

  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

• Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet.

  PMID 41786602 · PMC13138013 · Genome research · 2026 · 7 claims · 5 setups

  Full-text index only

  NNet uses PCA embedding followed by local KNN regression in PC space to construct cell-specific coexpression networks (CSNs), improving computational efficiency and estimate stability versus pairwise approaches.

  pbmc thp-1 lin small scrna-seq perturb-seq

• Identification of Radiation-Induced Injury Pathways and Hub Genes from RNA-Seq Data Based on Integrative Bioinformatics Approach.

  PMID 42074497 · PMC13116960 · Genes · 2026 · 8 claims · 6 setups

  Full-text index only

  Ionizing radiation induces extensive transcriptome reprogramming in mouse bone marrow HSCs 3 days after whole-body irradiation.

  bone deg transcriptome deg-encoded rna-seq gene kegg

• 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

  Full-text index only

  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