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 · 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 · 32
Developing prognostic gene panel of survival time in lung adenocarcinoma patients using machine learning.
PMID 35117753 · PMC8799101 · Translational cancer research · 2020 · 7 claims · 4 setups
A panel of 22 genetic features with Naïve Bayes can predict whether lung adenocarcinoma patient survival time is >3 years (accuracy=75%, AUC=0.81).
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Has reproduction · 100
Differential Gene Expression and Methylation Analysis of Melanoma in TCGA Database to Further Study the Expression Pattern of KYNU in Melanoma.
PMID 35893303 · PMC9329910 · Journal of personalized medicine · 2022 · 8 claims · 8 setups
KYNU expression is decreased in melanoma despite a high KYNU mutation rate in the TCGA database
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Has reproduction · 93
Integrated bioinformatics analysis screened the key genes and pathways of idiopathic pulmonary fibrosis.
PMID 40280949 · PMC12032202 · Scientific reports · 2025 · 8 claims · 8 setups
5328 differentially expressed transcripts (4083 genes) were identified in GSE173355 by limma, with 4012 transcripts (3206 genes) confirmed by both limma and edgeR (logFC>1, FDR<0.05)
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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
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Has reproduction
DNA demethylation is associated with malignant progression of lower-grade gliomas.
PMID 30760837 · PMC6374451 · Scientific reports · 2019 · 8 claims · 8 setups
Nearly half of IDH-mutant glioblastomas that progressed from lower-grade gliomas show characteristic partial DNA demethylation in previously methylated (G-CIMP) genomic regions of their initial tumor.
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Has reproduction · 76
High DNA methylation age deceleration defines an aggressive phenotype with immunoexclusion environments in endometrial carcinoma.
PMID 37388735 · PMC10303802 · Frontiers in immunology · 2023 · 8 claims · 8 setups
Almost 90% of TCGA EC tumors exhibit DNA methylation age deceleration (DNAmad) relative to patient chronological age as assessed by the Horvath clock
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Has reproduction · 93
5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.
PMID 38277218 · PMC10911375 · Aging · 2024 · 8 claims · 8 setups
Most of the 17 m5C regulators are differentially expressed between AML and normal samples and correlate with AML prognosis.
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Has reproduction · 55
H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity.
PMID 40764058 · PMC12487818 · Genome research · 2025 · 8 claims · 8 setups
H3K9 and H3K27 methylation regulate CTCF binding at distinct genomic regions, and their simultaneous loss induces drastic changes in CTCF binding
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Full-text index only
Next-generation sequencing in aging research: emerging applications, problems, pitfalls and possible solutions.
PMID 19900591 · PMC2878865 · Ageing research reviews · 2010 · 8 claims · 8 setups
NGS platforms offer superior performance, specificity, and cost-effectiveness compared to traditional Sanger sequencing
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Has reproduction · 61
A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.
PMID 25392735 · PMC4228822 · 8 claims · 8 setups
T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.
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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.
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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 · 76
Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer.
PMID 33890574 · PMC8104967 · eLife · 2021 · 8 claims · 8 setups
FOXM1 and RHNO1 are head-to-head bidirectional genes co-amplified and co-expressed in HGSC, regulated by a shared bidirectional promoter (F/R-BDP).
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Has reproduction · 91
Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.
PMID 30010758 · PMC6065499 · GigaScience · 2018 · 6 claims · 7 setups
A hybrid de novo assembly combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X) produced the YO draft genome Ogye_1.1 with contig and scaffold NG50 of 362.3 Kbp and 16.8 Mbp.
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Has reproduction · 72
Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.
PMID 29041914 · PMC5644144 · BMC genomics · 2017 · 8 claims · 8 setups
A high-quality ~375 Mbp draft genome and transcriptome of Holacanthella duospinosa was assembled and annotated, providing a genomic resource for hexapod evolution.
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Has reproduction · 77
PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.
PMID 34093998 · PMC8142020 · Computational and structural biotechnology journal · 2021 · 7 claims · 8 setups
PredTAD, a Gradient Boosting Machine model using epigenomic and genomic features plus neighboring-bin information, classifies 10 kb genomic regions as TAD boundary or non-boundary across normal and breast cancer cell lines.
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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 · 68
Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.
PMID 41963303 · PMC13181133 · Cell death & disease · 2026 · 7 claims · 8 setups
The integrated stress response induces colorectal cancer cell plasticity, subclonal diversity, and tumor progression in stress-surviving cells
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Full-text index only
ENCODE whole-genome data in the UCSC Genome Browser.
PMID 19920125 · PMC2808953 · Nucleic acids research · 2010 · 7 claims · 8 setups
The UCSC ENCODE Data Coordination Center serves as the primary repository for ENCODE experimental results, providing access via Genome Browser, Table Browser, and FTP download.