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).

• Illuminating cell states by a comprehensive and interpretable single cell foundation model.

  PMID 41839876 · PMC13139411 · Nature communications · 2026 · 6 claims · 6 setups

  Full-text index only

  CellVQ, incorporating a Single-Cell Discretization (SCD) module that converts cell embeddings into a discrete 'cell code' via a unified codebook, mitigates data heterogeneity and batch effects while improving interpretability

  pancreas sampled bulk lines scrna-seq type property

• CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing.

  PMID 30744683 · PMC6371477 · Genome biology · 2019 · 8 claims · 5 setups

  Has reproduction · 97

  CellFishing.jl achieves accuracy comparable to state-of-the-art software (scmap-cell) but is markedly faster

  scrna-seq shekhar2016 svd lsh hamming

• 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

• A latent activated olfactory stem cell state revealed by single-cell transcriptomic and epigenomic profiling.

  PMID 41512864 · PMC12903091 · Stem cell reports · 2026 · 7 claims · 8 setups

  Full-text index only

  HBC-derived regeneration proceeds via three distinct lineages (rHBC, Sus, mOSN) marked by sequential, lineage-specific transcription factor (TF) expression cascades.

  lineage-traced hbcs* icam1+ scrna-seq trajectory-based seurat

• Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals the transcriptome profile of Microtus fortis immune cells during the early phase of infection with Schistosoma japonicum.

  PMID 41675929 · PMC12886473 · Frontiers in cellular and infection microbiology · 2025 · 8 claims · 2 setups

  Full-text index only

  Both innate and adaptive immune responses were activated in M. fortis peripheral blood at 10 dpi, while activation was not obvious in Kunming mice at the same time point

  pbmcs single-cell qpcr

• bayesReact: expression-coupled regulatory motif analysis detects microRNA activity across cancers, tissues, and at the single-cell level.

  PMID 41657247 · PMC12884093 · Nucleic acids research · 2026 · 8 claims · 6 setups

  Full-text index only

  bayesReact is a novel fully Bayesian generative model for inferring regulatory motif (e.g., miRNA) activity from bulk or single-cell expression data

  tcga gtex stem embryonic paired semi-synthetic single-cell