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).

• Investigating epigenetic biomarkers of age, sex, and disease in captive South African cheetahs (Acinonyx jubatus jubatus).

  PMID 41528985 · PMC12798976 · PloS one · 2026 · 8 claims · 7 setups

  Has reproduction · 58

  A cheetah-specific epigenetic age clock using 52 CpG sites predicts chronological age across blood and liver with r=0.97 and MAE=0.86 years

  cheetah lion genes methylation epigenome-wide differential

• Genome-scale approaches to the epigenetics of common human disease.

  PMID 19844740 · PMC3107986 · Virchows Archiv : an international journal of pathology · 2010 · 7 claims · 8 setups

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  DNA methylation is a stable, mitotically heritable epigenetic mark faithfully propagated by DNMT1 acting on hemimethylated DNA during replication

  autopsy colorectal colon genomic charm quantitative bisulfite

• Post-translational modifications of histones H3 and H4 associated with the histone methyltransferases Suv39h1 and G9a.

  PMID 18096052 · PMC2246272 · Genome biology · 2007 · 6 claims · 4 setups

  Full-text index only

  Suv39h1 and G9a associate with previously reported methylation states (Suv39h1 with H3K9me3; G9a with H3K9me/me2)

  crude hela-suv39h1 suv39h1 normal propionylation-based double maldi-tof

• 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

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  The human MHC methylation profile is strongly bimodal, with the vast majority of analysed regions being either hypo- (≤30%) or hypermethylated (≥70%)

  mhc subset heterogeneously bisulphite maldi-ms sub-cloning

• Nucleosome deposition and DNA methylation at coding region boundaries.

  PMID 19723310 · PMC2768978 · Genome biology · 2009 · 8 claims · 8 setups

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  Nucleosomes and DNA methylation form distinct peaks just downstream of the start codon and just upstream of the stop codon, marking both ends of protein coding units genome-wide.

  yeast drosophila resting naive nucleosome methylation pol

• RADAR: differential analysis of MeRIP-seq data with a random effect model.

  PMID 31870409 · PMC6927177 · Genome biology · 2019 · 8 claims · 6 setups

  Has reproduction · 10

  RADAR is a novel analytical tool for differential methylation analysis of MeRIP-seq data combining gene-level INPUT normalization with a Poisson random effect model.

  simulated fallopian pancreatic liver merip-seq m6a-merip-seq pca

• Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

  PMID 30010758 · PMC6065499 · GigaScience · 2018 · 6 claims · 7 setups

  Has reproduction · 91

  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.

  yeonsan tissues ogye_1.1 locus whole-genome sequencing reduced

• Predicting enhancers in mammalian genomes using supervised hidden Markov models.

  PMID 30917778 · PMC6437899 · BMC bioinformatics · 2019 · 8 claims · 8 setups

  Has reproduction · 70

  eHMM predicts enhancers with high precision and recall comparable to state-of-the-art methods and consistently outperforms them in accuracy and resolution

  esc atac-seq chip-seq cage

• Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx.

  PMID 34254998 · PMC8575036 · Briefings in bioinformatics · 2021 · 6 claims · 4 setups

  Has reproduction · 79

  ParProx implements overlapping and non-overlapping (latent) group lasso regression for time-to-event (Cox) and classification (logistic) analysis with variables grouped by biological priors.

  tcga breast liver synthetic somatic gene methylation-based

• Candidate target genes for loss of heterozygosity on human chromosome 17q21.

  PMID 15187990 · PMC2409524 · British journal of cancer · 2004 · 8 claims · 5 setups

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  JUP (plakoglobin) is the only identified gene physically located between the D17S746 and D17S846 markers that define the smallest common region of LOH on chromosome 17q21

  genomic normal breast p1-phage nucleotide rt-pcr cold

• pwrEWAS: a user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS).

  PMID 31035919 · PMC6489300 · BMC bioinformatics · 2019 · 7 claims · 8 setups

  Has reproduction · 88

  pwrEWAS is a user-friendly tool (R package and Shiny web interface) for comprehensive power estimation in two-group EWAS using Illumina HumanMethylation BeadChip technology.

  saliva blood cord-blood pbmc illumina simulation

• The impact of new research technologies on our understanding of environmental causes of disease: the concept of clinical vulnerability.

  PMID 19948053 · PMC2793242 · Environmental health : a global access science source · 2009 · 8 claims · 8 setups

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  GWAS-identified genetic variants confer only modest relative risks (1.15-1.5), comparable in magnitude to weak/contested environmental exposures

  polish cohort nonsmokers low genome-wide biomarker epidemiological

• Loss of heterozygosity at 2q37 in sporadic Wilms' tumor: putative role for miR-562.

  PMID 19789318 · PMC2756455 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

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  2q37 harbors a tumor suppressor gene important in Wilms tumor pathogenesis

  sporadic wilms fetal 293t loh multiplex genome-wide