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).

• A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen.

  PMID 41505094 · PMC12781895 · Nucleic acids research · 2026 · 8 claims · 5 setups

  Has reproduction · 78

  A comprehensive genome-wide gene regulatory network resource for A. fumigatus (GRAsp) was constructed from 18 RNA-seq datasets using MERLIN-P-TFA.

  aspergillus fumigatus bulk computational chip-seq-based

• Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.

  PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups

  Has reproduction · 96

  An integrated 50K mouse and 24K human mammary epithelial cell atlas (scRNA-seq) captures mammary epithelium reorganization across most lifetime stages.

  surgically mammary menopaused integrated single-cell scrna-seq mammary

• Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.

  PMID 41122970 · PMC12581678 · JCI insight · 2025 · 8 claims · 7 setups

  Has reproduction · 75

  CLAD harbors disease-specific cellular subsets including Fibro.AT2 cells, exhausted CD8+ T cells, and superactivated macrophages

  clad covid-19 ffpe end-stage single-cell single-nucleus integrative

• Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.

  PMID 41898210 · PMC13024220 · Biomedicines · 2026 · 8 claims · 8 setups

  Has reproduction · 71

  Liver metastatic potential in RCC is marked by stem-like tumor states, metabolic plasticity, and microenvironmental remodeling.

  right-sided single integrated malignant single-cell copy dimensionality

• Transcriptomics, regulatory syntax, and enhancer identification in mesoderm-induced ESCs at single-cell resolution.

  PMID 35977485 · PMC9644345 · Cell reports · 2022 · 8 claims · 8 setups

  Has reproduction · 63

  Bmp4 treatment instructs ESCs to downregulate pluripotency genes and upregulate genes associated with formative pluripotency and fate specification

  escs naive facs-isolated freshly bulk atac-seq chip-seq

• Core transcriptional signatures of phase change in the migratory locust.

  PMID 31292921 · PMC6881432 · Protein & cell · 2019 · 8 claims · 7 setups

  Has reproduction · 60

  PhaseCore genes defined by AC-PCA contribution to phase differentiation predict phase status with >87.5% accuracy

  locusta integrated bulk rnai computational

• Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

  PMID 38254989 · PMC10815467 · Genes · 2024 · 8 claims · 8 setups

  Has reproduction · 85

  Combining scRNA-seq and spatial transcriptomics enables inference of malignant cells at the invasive front of the ER+ breast cancer TME and dissection of events at the tumor infiltration forefront

  normal er+ epithelial malignant single-cell spatial copy

• Toward a Consensus in the Repertoire of Hemocytes Identified in Drosophila.

  PMID 33748138 · PMC7969988 · Frontiers in cell and developmental biology · 2021 · 8 claims · 8 setups

  Has reproduction · 74

  Comparative analysis of three scRNAseq studies identifies eight common, robust hemocyte subgroups associated with distinct functions (proliferation, immune response, phagocytosis, secretion)

  wandering feeding stage type single scenic immunolabeling

• Neuronal Small RNAs Control Behavior Transgenerationally.

  PMID 31178120 · PMC6579485 · Cell · 2019 · 8 claims · 8 setups

  Has reproduction · 49

  Neuron-specific synthesis of RDE-4-dependent small RNAs regulates germline amplified endogenous siRNAs and germline gene expression for multiple generations

  elegans prab-3 dissected worms small sequencing facs

• FRMD8 inhibits tumor metastasis in BRCA1-associated TNBC by negatively regulating tmTNF-α.

  PMID 40619383 · PMC12229025 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  Low FRMD8 expression in BRCA1-mutant breast cancer cells significantly enhances metastatic potential to various organs

  tnbc geo breast frmd8 bulk meta-analysis single-cell

• Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.

  PMID 38358352 · PMC10903300 · Cancer research communications · 2024 · 8 claims · 7 setups

  Has reproduction · 64

  Two main neutrophil subtypes exist in primary tumors: an activated subtype sharing transcriptomic signatures with healthy neutrophils, and a tumor-specific subtype.

  colorectal sorted integrated neutrophil scrna-seq bulk immunohistochemistry

• Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.

  PMID 40993300 · PMC12460824 · NPJ digital medicine · 2025 · 8 claims · 7 setups

  Has reproduction

  A ResNet classifier built on a 10-gene metabolic signature distinguishes all thyroid cancer differentiation states with ~92.7% average accuracy.

  fuscc epithelial aggregated untargeted whole-exome bulk

• A global database for modeling tumor-immune cell communication.

  PMID 37438390 · PMC10338499 · Scientific data · 2023 · 7 claims · 6 setups

  Has reproduction · 66

  TICCom integrates 739 experimentally-validated or manually-curated TIC interactions collected from more than 3,000 literatures

  pubmed scrna-seq tcga basal manual scrna-seq bulk

• L-Arabinose Alters the E. coli Transcriptome to Favor Biofilm Growth and Enhances Survival During Fluoroquinolone Stress.

  PMID 40732174 · PMC12299780 · Microorganisms · 2025 · 8 claims · 6 setups

  Has reproduction · 74

  L-arabinose increases planktonic growth rate but reduces total growth of E. coli at both 28°C and 37°C

  coli growth crystal colony