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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DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight.
PMID 18628296 · PMC2504308 · Nucleic acids research · 2008 · 8 claims · 6 setups
Digital PCR compartmentalizes individual bisulfite-converted DNA template molecules into separate wells, enabling single-molecule DNA methylation analysis
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CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.
PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups
CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)
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Has reproduction · 99
Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.
PMID 34103501 · PMC8187371 · Nature communications · 2021 · 8 claims · 6 setups
Existing Nanopore methylation detection tools present a tradeoff between false positives and false negatives and show high dispersion relative to expected methylation frequency values.
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Human epigenome project--up and running.
PMID 14691553 · PMC300691 · PLoS biology · 2003 · 7 claims · 4 setups
Epigenetic modifications (e.g., DNA methylation) rather than DNA sequence differences explain phenotypic differences between genetically identical individuals, such as monozygotic twins or inbred mice.
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Has reproduction
Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.
PMID 35473573 · PMC9044877 · Genome biology · 2022 · 8 claims · 8 setups
Combining multiple enhancer-definition and enhancer-gene link data sources yields 1860 genome-wide EnTDefs covering >500 cell types
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Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.
PMID 18606010 · PMC2464579 · BMC medical genetics · 2008 · 6 claims · 4 setups
Methylation of the MHC2TA promoter pIV is not associated with MS susceptibility; no methylation was detected in any twin sample regardless of disease status
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Has reproduction
Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.
PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 7 claims · 7 setups
Differential DNA methylation occurs predominantly in intergenic regions and low methylated regions (LMRs), highlighting the role of distal regulatory elements in COVID-19 severity.
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Widely variable endogenous retroviral methylation levels in human placenta.
PMID 17617638 · PMC1950553 · Nucleic acids research · 2007 · 6 claims · 6 setups
Three HERV-E LTRs that function as alternative gene promoters (LTR-PTN, LTR-EBR, LTR-MID1) are unmethylated in placenta but heavily methylated in blood cells, where they are not active promoters
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The stem cell population of the human colon crypt: analysis via methylation patterns.
PMID 17335343 · PMC1808490 · PLoS computational biology · 2007 · 8 claims · 3 setups
A coalescent-based, full probabilistic model with MCMC Bayesian inference provides a more powerful alternative to prior forward-simulation approaches for analyzing methylation pattern data from crypts.
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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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Genetic and epigenetic alterations of Ras signalling pathway in colorectal neoplasia: analysis based on tumour clinicopathological features.
PMID 17923875 · PMC2360240 · British journal of cancer · 2007 · 8 claims · 4 setups
K-ras/BRAF mutations and RASSF2 methylation frequently co-occur in colorectal adenomas, suggesting synergistic cooperation
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Coexistence of two different pseudohypoparathyroidism subtypes (Ia and Ib) in the same kindred with independent Gs{alpha} coding mutations and GNAS imprinting defects.
PMID 19858129 · PMC3030964 · Journal of medical genetics · 2010 · 7 claims · 5 setups
Two unrelated PHP-I families each include at least one patient with a Gsα coding mutation (PHP-Ia) and another with GNAS imprinting defects (PHP-Ib)
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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 · GigaScience · 2014 · 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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pmid-34435438
PMID 34435438 · PMC9290141 · 6 claims · 6 setups
Bisulphite conversion of unmethylated cytosines to thymines violates strand-complementarity assumptions of SNP callers and confounds true C->T SNPs with unmethylated cytosines, complicating SNP calling from bisulphite sequencing data.
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DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project.
PMID 15550986 · PMC529316 · PLoS biology · 2004 · 8 claims · 3 setups
The human MHC methylation profile is strongly bimodal, with the vast majority of analysed regions being either hypo- (≤30%) or hypermethylated (≥70%)
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Has reproduction · 78
4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans.
PMID 33301041 · PMC7708080 · Nucleic acids research · 2020 · 7 claims · 8 setups
Inactivation of the orphan 4mC methyltransferase (LomA) causes complete abrogation of CTAG motif methylation genome-wide
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CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.
PMID 12556968 · PMC2376780 · British journal of cancer · 2003 · 8 claims · 4 setups
RB1 CpG island hypermethylation is a common epigenetic event associated with development of malignant nervous system tumours
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Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.
PMID 18413340 · PMC2425484 · Nucleic acids research · 2008 · 8 claims · 8 setups
CpG-rich regions (CpG islands) show low and similar methylation levels across individuals, but the sequential order of the few methylated CpGs among the many unmethylated ones varies randomly between individuals.
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Non-imprinted allele-specific DNA methylation on human autosomes.
PMID 19958531 · PMC2812945 · Genome biology · 2009 · 8 claims · 7 setups
SNPs within CpG islands are associated with allele-specific DNA methylation differences between alleles.
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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.