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 · 95
MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data.
PMID 29901703 · PMC6025204 · GigaScience · 2018 · 6 claims · 7 setups
A two-step 'omni' RNA-seq pipeline (MetaMap) combining STAR human alignment with CLARK-S metagenomic classification can quantify archaeal, bacterial, and viral reads from the non-human read fraction of human RNA-seq data
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Has reproduction · 90
Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles.
PMID 37444556 · PMC10340377 · Cancers · 2023 · 7 claims · 4 setups
Different EV isolation methods vary in reproducibility for isolating small RNAs and have characteristic effects on small RNA composition, with differential ultracentrifugation showing the highest variability/lowest replicability.
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Applying proteomics to the diagnosis and treatment of ALS and related diseases.
PMID 19670321 · PMC2836583 · Muscle & nerve · 2009 · 8 claims · 8 setups
Protein-based biomarkers for ALS/MND require further verification and large-scale validation/qualification studies, including disease mimics, before clinical use
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Has reproduction · 44
An OMICs-based meta-analysis to support infection state stratification.
PMID 33560295 · PMC8388022 · Bioinformatics (Oxford, England) · 2021 · 7 claims · 6 setups
Multi-class machine learning models built from cross-platform microarray meta-analysis can distinguish bacterial, viral and no-infection states with high accuracy (best model: 93% bacterial, 89% viral correct).
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Has reproduction · 52
Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity.
PMID 31980607 · PMC6981202 · Nature communications · 2020 · 6 claims · 4 setups
A meta-analysis (MetaMEx) of 66 published human skeletal muscle datasets reveals pathways selectively activated by inactivity, aerobic versus resistance, and acute versus chronic exercise training.
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Has reproduction · 94
SOX10-regulated promoter use defines isoform-specific gene expression in Schwann cells.
PMID 32770939 · PMC7430845 · BMC genomics · 2020 · 8 claims · 5 setups
SOX10 binds preferentially at proximal promoter elements directly over TSSs in Schwann cells in vivo, identifying candidate SOX10-regulated promoters.
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Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.
PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups
Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function
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Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.
PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups
CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.
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Has reproduction · 53
Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.
PMID 34577617 · PMC8472593 · Pharmaceuticals (Basel, Switzerland) · 2021 · 7 claims · 5 setups
A computational framework integrating independently measured CNV (DNA sequencing) and single-cell RNA-seq from the same patients identifies recurrent concordant copy number gain and gene upregulation (CNG-UP) events and functional modules at the single-cell level.
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Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.
PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups
A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.
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Has reproduction · 75
Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.
PMID 41122970 · PMC12581678 · JCI insight · 2025 · 8 claims · 7 setups
CLAD harbors disease-specific cellular subsets including Fibro.AT2 cells, exhausted CD8+ T cells, and superactivated macrophages
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Variation resources at UC Santa Cruz.
PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups
The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.
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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 · 68
Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter.
PMID 38587191 · PMC11077057 · Nucleic acids research · 2024 · 6 claims · 8 setups
A dual fluorescence (GFP-mCherry) readthrough reporter with a PAS inserted between the two reporters enables measurement of 3' end processing efficiency in living cells.