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 · 69
Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.
PMID 34675242 · PMC8531356 · Scientific reports · 2021 · 8 claims · 8 setups
Only 8 of 20 previously published COVID-19 scRNA-seq findings were reproducible across all relevant datasets in a standardized meta-analysis
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Has reproduction · 50
Loss of mutual protection between human osteoclasts and chondrocytes in damaged joints initiates osteoclast-mediated cartilage degradation by MMPs.
PMID 34811438 · PMC8608887 · Scientific reports · 2021 · 6 claims · 8 setups
Human osteoclasts can differentiate on acellular cartilage, express osteoclast markers, and degrade cartilage matrix in a contact-dependent manner without forming F-actin rings or resorption pits.
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Has reproduction · 58
Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.
PMID 26333840 · PMC4632049 · G3 (Bethesda, Md.) · 2015 · 8 claims · 8 setups
Virulence attenuation in the longer-passaged Bd isolate (JEL427-P39) is associated with loss of chromosome copy number relative to the shorter-passaged, more virulent isolate (JEL427-P9)
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Has reproduction · 44
Population differentiation and epidemic tracking of Bursaphelenchus xylophilus in China based on chromosome-level assembly and whole-genome sequencing data.
PMID 34839581 · PMC9300093 · Pest management science · 2022 · 6 claims · 8 setups
Generated the first chromosome-level genome assembly (AH1) of B. xylophilus using PacBio, Illumina, BioNano, and Hi-C data
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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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Has reproduction · 73
Dioxin-elicited decrease in cobalamin redirects propionyl-CoA metabolism to the β-oxidation-like pathway resulting in acrylyl-CoA conjugate buildup.
PMID 35931118 · PMC9418907 · The Journal of biological chemistry · 2022 · 8 claims · 8 setups
TCDD dose-dependently decreases cobalamin (Cbl) levels, compromising MUT activity and redirecting propionyl-CoA metabolism from the canonical Cbl-dependent carboxylation pathway to the alternate Cbl-independent β-oxidation-like pathway.
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Has reproduction · 59
Global chromatin accessibility profiling analysis reveals a chronic activation state in aged muscle stem cells.
PMID 36093058 · PMC9459695 · iScience · 2022 · 8 claims · 8 setups
PFA-perfusion-based isolation preserves the true in vivo chromatin accessibility state, avoiding artifacts caused by tissue dissociation-induced activation
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Has reproduction · 65
β-Catenin activity induces an RNA biosynthesis program promoting therapy resistance in T-cell acute lymphoblastic leukemia.
PMID 36597789 · PMC9906382 · EMBO molecular medicine · 2023 · 8 claims · 8 setups
β-catenin binds directly to promoters of RNA processing, splicing, and ribosomal biogenesis genes in T-ALL cells
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Has reproduction
Unlocking the microbial studies through computational approaches: how far have we reached?
PMID 36920617 · PMC10016191 · Environmental science and pollution research international · 2023 · 8 claims · 8 setups
Metagenomics enables culture-independent study of microbial communities directly from their natural environments, bypassing the need for clonal isolation.
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Has reproduction · 80
Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.
PMID 36928603 · PMC10101853 · Nature genetics · 2023 · 8 claims · 6 setups
The WHO histopathological classification of MPM accounts for only up to ~10% of interpatient molecular differences
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Has reproduction · 78
Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.
PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups
A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors
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Has reproduction · 58
Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.
PMID 38529307 · PMC10962337 · PeerJ · 2024 · 8 claims · 8 setups
PPARA, PPARD and PPARG are more abnormally expressed in STAD samples and cell lines compared to most of 32 cancer types in TCGA
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Has reproduction · 70
MACanalyzeR scRNAseq analysis tool reveals PPARγ(HIGH)/GDF15(HIGH) lipid-associated macrophages facilitate thermogenic expansion in BAT.
PMID 40450001 · PMC12126529 · Nature communications · 2025 · 8 claims · 8 setups
MACanalyzeR is a novel computational scRNAseq framework (with FoamSpotteR, MacPolarizeR, and PathAnalyzeR modules) for comprehensive monocyte/macrophage metabolic and phenotypic profiling
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Has reproduction · 68
Identification of new ETV6 modulators through a high-throughput functional screening.
PMID 35198911 · PMC8851229 · iScience · 2022 · 7 claims · 8 setups
A genome-wide shRNA screen in an engineered ETV6-dependent Blasticidin-sensitive pre-B ALL cell line can identify modulators of ETV6 repressive transcriptional activity
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Full-text index only
Asthma investigators begin to reap the fruits of genomics.
PMID 14611649 · PMC329104 · Genome biology · 2003 · 7 claims · 8 setups
Microarray profiling of animal models of allergic asthma can identify novel differentially expressed candidate genes involved in inflammation and airway remodeling.
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Has reproduction · 80
Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.
PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups
BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules
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Has reproduction · 100
Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.
PMID 24131564 · PMC3875859 · Genome research · 2014 · 8 claims · 8 setups
TSscan, a computational pipeline integrating long- and short-read transcriptome sequencing from multiple hESC lines, can detect trans-splicing while minimizing false positives from experimental artifacts and genetic rearrangements.
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Has reproduction · 67
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.
PMID 24715956 · PMC3962008 · F1000Research · 2013 · 8 claims · 6 setups
Cyrface is a Cytoscape app/Java library providing a general interface from Cytoscape (Java) to any R function or package.
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A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.
PMID 17186946 · PMC1860054 · Molecular & cellular proteomics : MCP · 2007 · 8 claims · 8 setups
Three complementary membrane-enrichment proteomic methods (lectin affinity, biotin/NeutrAvidin affinity, free flow electrophoresis) combined with LC-MS/MS identify 136 transmembrane proteins in human platelets, including many novel ones.
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Selection of target sites for mobile DNA integration in the human genome.
PMID 17166054 · PMC1664696 · PLoS computational biology · 2006 · 8 claims · 8 setups
A comprehensive bioinformatic method was developed to annotate every base pair in the human genome for its likelihood of hosting integration by each of seven mobile DNA elements, using >200 genomic feature variables.