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).

• High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

  PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

  Full-text index only

  Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

  embryonic neural t-cells mm8 chip-seq chip-chip pwm

• Epigenetic loss of heterogeneity from low to high grade localized prostate tumours.

  PMID 34911933 · PMC8674326 · Nature communications · 2021 · 7 claims · 4 setups

  Has reproduction · 79

  Shared chromatin accessibility features among low-grade (Gleason pattern 3) prostate cancer cells are lost in high-grade (Gleason pattern 4) tumours.

  flash-frozen prostate ffpe single-cell bulk cyclic

• Single-Cell Hi-C Technologies and Computational Data Analysis.

  PMID 39887949 · PMC11884588 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025 · 8 claims · 12 setups

  Has reproduction · 80

  Thirteen scHi-C protocols currently exist—eight capturing chromatin interactions exclusively and five combining scHi-C with other assays for multi-omics data.

  mm9 mm10 hg19 hg38 schi-c snhi-c sci-hi-c

• 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

  Has reproduction · 77

  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.

  mcf10a t47d gm12878 mcf7 hi-c chip-seq atac-seq

• Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets.

  PMID 35672799 · PMC9175345 · Genome biology · 2022 · 8 claims · 6 setups

  Has reproduction

  CD4 T cells and B cells independently mediate MS GWAS genetic signals through their open chromatin regions, beyond shared regulatory landscapes.

  flow-sorted cd4 gwas bulk ldsc

• 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

  Has reproduction · 80

  BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules

  lncap sonicated adaptor-modified native bischip-seq chromatin chip-qpcr

• Genome-wide prediction of DNase I hypersensitivity using gene expression.

  PMID 29051481 · PMC5715040 · Nature communications · 2017 · 6 claims · 3 setups

  Has reproduction · 79

  Gene expression substantially predicts genome-wide DNase I hypersensitivity (DH), demonstrating transcriptome-based prediction as a feasible approach for regulome mapping

  distinct encode dnase-seq exon computational

• iceDP: identifying inter-chromatin engagement via density peaks clustering algorithm.

  PMID 41499218 · PMC12777978 · Briefings in bioinformatics · 2026 · 7 claims · 8 setups

  Has reproduction · 53

  iceDP is a tool that uses the Density Peaks clustering algorithm plus a distribution test and fold-change filter to identify non-homologous inter-chromatin contacts (NHCCs) from Hi-C data

  olfactory mosn hesc type in-situ h3k27ac micro-c

• RNA structure maps across mammalian cellular compartments.

  PMID 30886404 · PMC6640855 · Nature structural & molecular biology · 2019 · 8 claims · 6 setups

  Has reproduction · 45

  icSHAPE-based cytotopic RNA structuromes across chromatin, nucleoplasm and cytoplasm in human and mouse cells substantially expand the scope of RNA structural information beyond whole-cell data.

  v6.5 mes icshape rt-qpcr western

• Lineage commitment of dermal fibroblast progenitors is controlled by Kdm6b-mediated chromatin demethylation.

  PMID 37602956 · PMC10548174 · The EMBO journal · 2023 · 6 claims · 5 setups

  Has reproduction · 91

  E14.5 DFPs have a repressed transcriptional profile marked by high H3K27me3 and inaccessible chromatin at lineage-specific genes

  skin dermal single-cell chamber chip-seq

• DNA Methylation Directs Polycomb-Dependent 3D Genome Re-organization in Naive Pluripotency.

  PMID 31722211 · PMC6856714 · Cell reports · 2019 · 7 claims · 6 setups

  Has reproduction · 50

  The altered 3D genome of 2i-cultured ESCs (chromatin decompaction and loss of polycomb interactions at polycomb targets) is due to redistribution of polycomb away from its targets.

  ring1b− e3.5 e14 3b3l fluorescence fish situ

• Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.

  PMID 18084025 · PMC2241897 · Nucleic acids research · 2008 · 5 claims · 7 setups

  Full-text index only

  QUMA (quantitative real-time PCR) and AUMA (fingerprinting PCR) methods can quantify and individually identify unmethylated Alu elements on a genomic scale using the methylation-sensitive SmaI site as a surrogate marker

  paired colorectal genome normal quma auma bioinformatic

• Given the complexity of the human genome, can 'personalised medicine' or 'individualised drug therapy' ever be achieved?

  PMID 19706359 · PMC3525196 · Human genomics · 2009 · 7 claims · 3 setups

  Full-text index only

  The human genome is far too complex, given current understanding, for personalised medicine or individualised drug therapy to be realised in the near term

  populations genome genome-wide genome

• Involvement of HTLV-I Tax and CREB in aneuploidy: a bioinformatics approach.

  PMID 16822311 · PMC1553470 · Retrovirology · 2006 · 8 claims · 6 setups

  Full-text index only

  CTLL cells stably expressing wild-type Tax (CTLL/WT) show higher aneuploidy than a CREB-transactivation-deficient Tax clone (CTLL/703)

  ctll gene promoter metaphase microarray bioinformatics

• Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation.

  PMID 35953471 · PMC9372134 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 83

  ATX1, ATX2, and ATXR7 redundantly mediate H3K4 monomethylation genome-wide

  arabidopsis chip-seq western random

• Nucleosome regulatory dynamics in response to TGFβ.

  PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 59

  SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.

  hepatocellular hepg2 130-bp mnase strand-specific taqman

• Differentiating Drosophila female germ cells initiate Polycomb silencing by regulating PRC2-interacting proteins.

  PMID 32773039 · PMC7438113 · eLife · 2020 · 7 claims · 3 setups

  Has reproduction · 87

  Drosophila female germline stem cells lack canonical Polycomb silencing and have a non-canonical H3K27me3 distribution resembling early embryos.

  drosophila facs-purified hsgfp germline-specific chipseq

• Fluent genomics with  plyranges and  tximeta.

  PMID 32528659 · PMC7243206 · F1000Research · 2020 · 6 claims · 2 setups

  Has reproduction · 69

  A simple three-step workflow (import, model, integrate) using R/Bioconductor enables fluent, reproducible genomics data analysis integrating RNA-seq and ATAC-seq.

  ipsc-derived bulk atac-seq

• Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor.

  PMID 30576656 · PMC6310685 · Molecular cell · 2018 · 8 claims · 8 setups

  Has reproduction

  Depletion of Rap1 induces divergent noncoding transcription at a large fraction of Rap1-regulated gene promoters

  cerevisiae rap1-aid northern western poly

• Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading.

  PMID 35260568 · PMC8904849 · Nature communications · 2022 · 7 claims · 8 setups

  Has reproduction · 55

  RBV, a WD40 repeat protein, is required for global microRNA biogenesis in Arabidopsis

  amir-sul col 14-day-old arabidopsis small rna-seq gel