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).
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Has reproduction · 93
Single-nucleus mRNA-sequencing reveals dynamics of lipogenic and thermogenic adipocyte populations in murine brown adipose tissue in response to cold exposure.
PMID 40945691 · PMC12506565 · Molecular metabolism · 2025 · 8 claims · 8 setups
snRNA-seq of murine BAT identifies seven distinct brown adipocyte subtypes with distinct metabolic profiles, part of a 21-cell-type atlas.
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A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage.
PMID 20026476 · PMC2849709 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups
A SILAC-based 'spatial proteomics' method can quantitatively measure the relative subcellular distribution of thousands of proteins across cytoplasm, nucleus, and nucleolus.
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Has reproduction · 64
Spatial-reprogramming derived GPNMB(+) macrophages interact with COL6A3(+) fibroblasts to enhance vascular fibrosis in glioblastoma.
PMID 41174767 · PMC12577258 · Genome medicine · 2025 · 7 claims · 8 setups
A distinct subset of COL6A3+ tumor-associated fibroblasts (TAFs) with matrix-fibroblast characteristics exists in GBM and is significantly enriched in non-responders to neoadjuvant combination therapy.
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Has reproduction · 100
Computational modeling demonstrates that glioblastoma cells can survive spatial environmental challenges through exploratory adaptation.
PMID 31836713 · PMC6911112 · Nature communications · 2019 · 8 claims · 6 setups
Stochastic exploration of the gene-regulatory network structure confers enhanced adaptive capacity, enabling GBM cells to converge to new target phenotypes in novel environments.
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Has reproduction · 70
Spatial transcriptomics reveals the molecular signatures of prodromal and advanced α-synucleinopathy.
PMID 41736854 · PMC12927100 · iScience · 2026 · 8 claims · 6 setups
Induction of aSyn pathology in rodent brainstem at the early/prodromal stage triggers upregulation of energy metabolism pathways (glycolysis, oxidative phosphorylation, fatty acid metabolism)
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Has reproduction · 50
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
A 186-gene signature derived from six GEO transcriptomic datasets predicts nCRT response in LARC with AUC 0.80 in cross-validation
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Has reproduction · 90
Inferring a spatial code of cell-cell interactions across a whole animal body.
PMID 36395331 · PMC9714814 · PLoS computational biology · 2022 · 8 claims · 6 setups
cell2cell computes cell-cell interaction (CCI) potential using a novel modified Bray-Curtis score based on complementary coexpression of ligand-receptor pairs between cells
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Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.
PMID 16847467 · PMC3099416 · The pharmacogenomics journal · 2007 · 8 claims · 6 setups
NAT2 variants are homogeneously distributed across native populations of the American continent
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Has reproduction · 85
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
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
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A combined approach exploring gene function based on worm-human orthology.
PMID 15877817 · PMC1112593 · BMC genomics · 2005 · 8 claims · 6 setups
Strict phylogenetic criteria (concordant Neighbor Joining and Maximum Parsimony tree topology) can select single most-likely human orthologs for C. elegans genes despite the large phylogenetic distance between worm and human sequences.
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Has reproduction · 23
Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals.
PMID 39418301 · PMC11521246 · PLoS computational biology · 2024 · 7 claims · 4 setups
COPD GWAS loci are more spatially clustered across the genome than expected by chance, with significant enrichment on chromosome 4q.
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Has reproduction · 95
Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.
PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups
Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature
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Has reproduction · 85
An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.
PMID 42147490 · PMC13179517 · Cell press blue · 2026 · 8 claims · 8 setups
Fibroblasts act as central regulators of structural immunity in the human oral cavity, forming peri-epithelial hubs enriched in effector cytokines
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Has reproduction · 100
Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility.
PMID 33707641 · PMC7970949 · Scientific reports · 2021 · 8 claims · 8 setups
WGCNA on control human cervical spinal cord RNA-seq identifies 13 co-expression modules (SC.M1-M13), each representing distinct biological processes or cell types.
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Has reproduction · 68
Genome-wide DNA hypermethylation opposes healing in patients with chronic wounds by impairing epithelial-mesenchymal transition.
PMID 35819852 · PMC9433101 · The Journal of clinical investigation · 2022 · 8 claims · 8 setups
Chronic wound-edge tissue exhibits genome-wide DNA hypermethylation, with hypermethylation more prominent than hypomethylation across differentially methylated regions.
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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
The HIF-1/VHL-1/EGL-9 hydroxylase pathway is tightly conserved in C. elegans
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Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene.
PMID 17557180 · PMC1998882 · Mammalian genome : official journal of the International Mammalian Genome Society · 2007 · 7 claims · 7 setups
A BAC transgene containing Prop1 completely rescues the Prop1 mutant (dwarf) phenotype, showing all necessary regulatory elements lie within the BAC
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Systems analysis of bone.
PMID 20046860 · PMC2790199 · Wiley interdisciplinary reviews. Systems biology and medicine · 2009 · 8 claims · 7 setups
Fracture risk and skeletal traits are highly heritable, with over 350 QTLs mapped across the mouse genome and genes such as LRP5, Alox15, and Darc identified as regulators of bone mass.
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Protein co-evolution, co-adaptation and interactions.
PMID 18818697 · PMC2556093 · The EMBO journal · 2008 · 8 claims · 6 setups
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).
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Has reproduction · 49
Numb prevents a complete epithelial-mesenchymal transition by modulating Notch signalling.
PMID 29187638 · PMC5721160 · Journal of the Royal Society, Interface · 2017 · 7 claims · 8 setups
Numb (and Numbl) inhibits a full EMT by stabilizing a hybrid E/M phenotype, acting as a 'phenotypic stability factor'.