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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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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A distinct epigenetic signature at targets of a leukemia protein.
PMID 17266773 · PMC1796549 · BMC genomics · 2007 · 7 claims · 7 setups
Combining gene expression microarray analysis with bioinformatic search for AML1-consensus sequences identifies direct AML1 targets that expression analysis alone cannot resolve
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Has reproduction · 95
Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.
PMID 23999385 · PMC6505400 · Scientific reports · 2013 · 8 claims · 8 setups
Four epigenetic modifications (DNA methylation, H3K4me2, H3K4me3, H3K27me3) in mouse CGIs undergo combinatorial variation (co-variation) across ESCs, NPCs and adult brain during neuron differentiation.
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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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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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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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Application of OMICS technologies in occupational and environmental health research; current status and projections.
PMID 19933307 · PMC2910417 · Occupational and environmental medicine · 2010 · 8 claims · 6 setups
Five OMICS technologies are well established: genotyping, transcriptomics, epigenomics, proteomics, and metabolomics
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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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Bases and spaces: resources on the web for accessing the draft human genome.
PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups
By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.