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).

• Spatial transcriptomics reveals the molecular signatures of prodromal and advanced α-synucleinopathy.

  PMID 41736854 · PMC12927100 · iScience · 2026 · 8 claims · 6 setups

  Has reproduction · 70

  Induction of aSyn pathology in rodent brainstem at the early/prodromal stage triggers upregulation of energy metabolism pathways (glycolysis, oxidative phosphorylation, fatty acid metabolism)

  m83+ brain spatial immunofluorescence cell-cell

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• Computational modeling demonstrates that glioblastoma cells can survive spatial environmental challenges through exploratory adaptation.

  PMID 31836713 · PMC6911112 · Nature communications · 2019 · 8 claims · 6 setups

  Has reproduction · 100

  Stochastic exploration of the gene-regulatory network structure confers enhanced adaptive capacity, enabling GBM cells to converge to new target phenotypes in novel environments.

  gbm glioma gbm-focused glioma-related transcriptomic differential gene-regulatory

• 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

• Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.

  PMID 28583124 · PMC5458481 · Environmental health : a global access science source · 2017 · 7 claims · 6 setups

  Has reproduction · 71

  Gestational PM2.5 exposure is associated with sex-specific gene expression changes in newborn cord blood, with major differences between boys and girls.

  cord maternal genes significant genome pm2.5 isolation

• Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.

  PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 5 setups

  Has reproduction · 50

  A 186-gene signature derived from six GEO transcriptomic datasets predicts nCRT response in LARC with AUC 0.80 in cross-validation

  pre-treatment domingo geo bulk bulk external spatial

• Optimisation of the core subset for the APY approximation of genomic relationships.

  PMID 36418945 · PMC9682752 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 3 setups

  Has reproduction · 85

  APY approximates the full genomic relationship matrix by splitting genotyped animals into a core subset (fully dependent, direct inverse) and a non-core subset (conditionally independent given core), reducing inversion cost.

  simulated real genotyped gblup population

• Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development.

  PMID 34643182 · PMC8555986 · eLife · 2021 · 8 claims · 8 setups

  Has reproduction · 84

  Tbx5 directly maintains Aldh1a2 expression in the foregut lateral plate mesoderm/pSHF via an evolutionarily conserved intronic enhancer.

  micro-dissected dissected e9.5 xenopus bulk rt-qpcr whole-mount

• Statistical challenges in preprocessing in microarray experiments in cancer.

  PMID 18829474 · PMC3529914 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 7 setups

  Full-text index only

  Choice of pre-processing method materially changes which features are found significantly associated with survival in the Beer et al. lung cancer microarray dataset

  lung beer individual outlier expression rank-covariance quality-control

• Protein co-evolution, co-adaptation and interactions.

  PMID 18818697 · PMC2556093 · The EMBO journal · 2008 · 8 claims · 6 setups

  Full-text index only

  The mirrortree method predicts protein-protein interactions by detecting pairs of protein families with similar phylogenetic trees (quantified as Pearson correlation of sequence similarity matrices).

  nuoe intra-protein coli interacting phylogenetic correlated domain-restricted

• The UCSC genome browser database: update 2007.

  PMID 17142222 · PMC1669757 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  The UCSC Genome Browser Database provides sequence and annotation data for 13 vertebrate and 19 invertebrate species as of September 2006.

  hg17 genome lines xenopus comparative snp linkage