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).

• Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders.

  PMID 33958982 · PMC8093778 · Frontiers in neuroscience · 2021 · 7 claims · 8 setups

  Has reproduction · 59

  Fourteen gene modules were consistently associated with ReHo across three independent fMRI datasets.

  healthy six ahba neurons resting-state microarray wgcna

• Cell type- and species-specific regulation of hepatic lncRNAs by TCDD-activated aryl hydrocarbon receptor.

  PMID 41136526 · PMC12552753 · Scientific reports · 2025 · 7 claims · 7 setups

  Has reproduction · 71

  TCDD elicits dose-dependent AHR-mediated differential expression of hepatic lncRNAs in both mouse and rat liver, with more DE lncRNAs in mice than rats and a subset conserved across species.

  c57bl sprague-dawley liver mm39 bulk single-nuclei ahr

• Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.

  PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 5 claims · 6 setups

  Has reproduction · 78

  CIBERSORTx can combine scRNA-seq-derived signatures with bulk HCC transcriptomes to estimate proportions of 11 TIL subsets and infer cell-type-specific gene expression.

  hcc tcga geo single-cell bulk microarray

• Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.

  PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups

  Has reproduction · 78

  Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely

  gene racipe clinical tcga racipe influence principal

• Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer.

  PMID 33584715 · PMC7873865 · Frontiers in immunology · 2020 · 8 claims · 7 setups

  Has reproduction · 45

  Eight distinct T cell populations are identifiable in CRC tumor tissue and seven in peripheral blood by unsupervised clustering of scRNA-seq data.

  tumor peripheral cd4+ eight single-cell unsupervised ligand-receptor

• Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans.

  PMID 15361934 · PMC515368 · PLoS biology · 2004 · 7 claims · 8 setups

  Full-text index only

  The HIF-1/VHL-1/EGL-9 hydroxylase pathway is tightly conserved in C. elegans

  elegans whole-genome rnase pharmacological

• PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

  PMID 30951143 · PMC6450036 · Database : the journal of biological databases and curation · 2019 · 7 claims · 7 setups

  Has reproduction · 80

  PanglaoDB is a web server providing pre-processed and pre-computed analyses of >1054 single-cell experiments (>4 million cells) from mouse and human across many tissues and platforms.

  grch38 homogeneous per single single-cell clustering cell-type

• RummaGEO: Automatic mining of human and mouse gene sets from GEO.

  PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups

  Has reproduction · 63

  RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO

  genes rummageo rummageo-derived leiden bulk gene leiden

• Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.

  PMID 41029822 · PMC12486589 · Journal of translational medicine · 2025 · 8 claims · 5 setups

  Has reproduction · 67

  fRNA-seq transcript counts are best fit by the negative binomial distribution, with little evidence supporting zero-inflated extensions

  compendium frna-seq nb-generated breast ffpe distribution synthetic

• Celline: a flexible tool for one-step retrieval and integrative analysis of public single-cell RNA sequencing data.

  PMID 41458999 · PMC12738925 · Frontiers in bioinformatics · 2025 · 8 claims · 7 setups

  Has reproduction · 64

  Celline is a Python package executing an entire scRNA-seq workflow (retrieval, preprocessing, integration, analysis) using single-line commands per step

  mus brain integrated homo droplet-based scrna-seq cell-type

• huSA: a comprehensive database for multi-dimensional resolution of bulk, single cell and spatial transcription profiles in skin diseases.

  PMID 41719583 · PMC12923168 · Database : the journal of biological databases and curation · 2026 · 7 claims · 8 setups

  Has reproduction · 50

  huSA is a publicly accessible database integrating data from 17 skin diseases and 63 independent datasets, including 1434 scRNA-seq, 63 spatial transcriptomics, and 1502 bulk RNA-seq samples

  skin scrna-seq single prurigo scrna-seq bulk spatial

• Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

  PMID 16522644 · PMC1390679 · Nucleic acids research · 2006 · 7 claims · 6 setups

  Full-text index only

  Align-GVGD predicts loss of transactivation activity with high specificity (~88%) but lower sensitivity (67.9-71.2%) for neutral mutants

  p53 tp53 yeast-based sequence align-gvgd

• Characterisation of the genetic diversity of Brucella by multilocus sequencing.

  PMID 17448232 · PMC1877810 · BMC microbiology · 2007 · 8 claims · 5 setups

  Full-text index only

  Brucella isolates show low overall genetic diversity (1.5%) across nine sequenced loci, confirming the genus is genetically conserved.

  brucella sequenced concatenated allelic multilocus ratio neighbour-joining

• Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

  PMID 18282289 · PMC2270265 · BMC genomics · 2008 · 8 claims · 6 setups

  Full-text index only

  The sheep TRG1 and TRG2 loci evolved through a series of duplication events involving either entire V-J-J-C recombinational cassettes or single V genes

  sheep bac dot tandem

• CoINcIDE: A framework for discovery of patient subtypes across multiple datasets.

  PMID 26961683 · PMC4784276 · Genome medicine · 2016 · 8 claims · 6 setups

  Has reproduction · 87

  CoINcIDE is a methodological framework that discovers replicable patient subtypes (meta-clusters) across multiple datasets by finding consensus across dataset-specific clusterings, requiring no between-dataset transformations.

  breast ovarian simulated gene semi-supervised novo

• The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.

  PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 7 claims · 7 setups

  Has reproduction · 50

  Most published adult/other-cohort sepsis gene signatures have limited utility for infant sepsis; only 2 of 7 achieved >80% accuracy in infants

  infant merged individual pairwise whole-blood coconut gene-signature

• Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.

  PMID 37320872 · PMC10277597 · Translational oncology · 2023 · 8 claims · 9 setups

  Has reproduction · 50

  Seven distinct CAF subsets exist in HNSCC, identified via integration of scRNA-seq, bulk transcriptomic, and spatial transcriptomic data.

  hnscc tcga-hnscc caf fibroblast single-cell bulk spatial

• Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

  PMID 15608239 · PMC539999 · Nucleic acids research · 2005 · 8 claims · 8 setups

  Full-text index only

  GALA is now a set of interlinked relational databases covering five vertebrate species: human, chimpanzee, mouse, rat and chicken.

  chromosome genomic comparative phylohmmcons conserved

• Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

  PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

  Full-text index only

  Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

  disease mammalian compiled literature minigene computational

• nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs.

  PMID 36694127 · PMC9875403 · BMC bioinformatics · 2023 · 8 claims · 4 setups

  Has reproduction · 76

  Existing circRNA workflows are limited: none delineate circRNA-miRNA interactions and only one performs differential expression analysis, requiring users to supplement missing analysis types with in-house expertise

  paired-end rna-seq mature circrna read circrna mirna