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).
-
Full-text index only
Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.
PMID 18618001 · PMC2442223 · PLoS genetics · 2008 · 8 claims · 6 setups
Zebrafish whole-adult-organism chemogenomics generates robust prediction models that discriminate P(H)AHs from ECs across independent experiments
-
Has reproduction · 81
Macrophages on the run: Exercise balances macrophage polarization for improved health.
PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups
Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.
-
Has reproduction · 42
CanCellCap: robust cancer cell capture across tissue types on single-cell RNA-seq data by multi-domain learning.
PMID 40739511 · PMC12312500 · BMC biology · 2025 · 8 claims · 8 setups
CanCellCap, a multi-domain learning framework integrating domain adversarial learning and Mixture of Experts, identifies cancer cells across all tissues, cancers, and sequencing platforms by extracting tissue-common and tissue-specific gene expression patterns.
-
Full-text index only
SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.
PMID 18366708 · PMC2289803 · BMC medical genetics · 2008 · 7 claims · 6 setups
Illumina validation/design scores above 0.6 are not strongly correlated with actual SNP genotyping performance (Gentrain score)
-
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.
-
Has reproduction · 83
Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients.
PMID 38650649 · PMC11034498 · PeerJ · 2024 · 8 claims · 8 setups
188 differentially expressed genes (DEGs) between IS and control blood samples were identified and enriched in immune-related biological pathways
-
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
-
Has reproduction · 80
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.
PMID 30951143 · PMC6450036 · Database : the journal of biological databases and curation · 2019 · 7 claims · 7 setups
PanglaoDB is a web server providing pre-processed and pre-computed analyses of >1054 single-cell experiments (>4 million cells) from mouse and human across many tissues and platforms.
-
Has reproduction · 91
A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles.
PMID 32111252 · PMC7049190 · Genome medicine · 2020 · 8 claims · 8 setups
DeClust is a reference profile-free deconvolution method that simultaneously deconvolves bulk tumor expression into cancer, immune, and stromal compartments and clusters samples into cancer cell-intrinsic molecular subtypes, outputting subtype-specific reference profiles for the cohort rather than for individuals.
-
Has reproduction · 89
miRge 2.0 for comprehensive analysis of microRNA sequencing data.
PMID 30153801 · PMC6112139 · BMC bioinformatics · 2018 · 8 claims · 6 setups
miRge 2.0 introduces a novel SVM-based miRNA detection method using both hairpin structure and isomiR composition, yielding higher specificity for miRNA identification
-
Has reproduction · 84
An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis.
PMID 36352408 · PMC9648005 · BMC biology · 2022 · 7 claims · 5 setups
A signal transduction/gene regulatory network model of the articular chondrocyte was built combining knowledge-based curation and data-driven (machine learning) network inference
-
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.
-
Has reproduction · 71
Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.
PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 7 claims · 8 setups
Two distinct RNA modification patterns exist among BCa samples with radically different clinical outcomes and biological characteristics.
-
Has reproduction · 78
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
A comprehensive genome-wide gene regulatory network resource for A. fumigatus (GRAsp) was constructed from 18 RNA-seq datasets using MERLIN-P-TFA.
-
Has reproduction · 84
DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.
PMID 34261540 · PMC8281595 · Genome medicine · 2021 · 6 claims · 7 setups
DeepProg, an ensemble of deep-learning and machine-learning models, robustly predicts patient survival subtypes from multi-omics data and explicitly models survival as the objective while predicting new patient risks
-
Has reproduction · 85
COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis.
PMID 35870428 · PMC9297827 · EBioMedicine · 2022 · 8 claims · 8 setups
COVID-19 lung disease resembles IPF at a fundamental level, recapitulating ViP/IPF gene expression patterns, an IL15-centric cytokine storm, and AT2 cytopathic changes (injury, DNA damage, transient progenitor-state arrest, senescence/SASP).
-
Has reproduction · 75
Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods.
PMID 34143800 · PMC8213194 · PloS one · 2021 · 7 claims · 6 setups
306 overlapping DEGs (265 up-regulated, 41 down-regulated) were identified across three independent GEO datasets in EOC vs normal ovarian tissue.
-
Has reproduction · 68
Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.
PMID 35012625 · PMC8743438 · Genome biology · 2022 · 7 claims · 8 setups
GENEVA is a semi-automated, study-design-agnostic framework that mines large-scale public RNA-seq data to identify conditions modulating a gene of interest's expression
-
Has reproduction · 91
Exploring the key genetic association between chronic pancreatitis and pancreatic ductal adenocarcinoma through integrated bioinformatics.
PMID 37501719 · PMC10369079 · Frontiers in genetics · 2023 · 6 claims · 7 setups
CEL (carboxyl ester lipase) is the real hub gene shared between CP and PDAC and is markedly downregulated in PDAC
-
Has reproduction · 75
Cross-species comparative hippocampal transcriptomics in Alzheimer's disease.
PMID 38292167 · PMC10824791 · iScience · 2024 · 8 claims · 7 setups
All three mouse models (hAβ-KI, 5xFAD, APP/PS1) share more differentially expressed genes, GO biological processes, and KEGG pathways with LOAD than with EOAD patients.