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).

• TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity.

  PMID 25391375 · PMC4315292 · Genome research · 2015 · 8 claims · 8 setups

  Has reproduction · 80

  TP53 binding events fall into three distinct categories defined by the local chromatin environment: TSS (H3K4me3+), enhancer (H3K4me1+/H3K4me3-), and distal (H3K4me1-/H3K4me3-) peaks.

  imr90 hct116 chip-seq rna-seq atac-seq

• CTCF/cohesin-binding sites are susceptible to replication-associated DNA damage and genomic instability in cancer cells.

  PMID 41630911 · PMC12860730 · iScience · 2026 · 8 claims · 8 setups

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  CTCF and cohesin (RAD21) remain co-bound to DNA throughout interphase, including during the S (replication) phase, in HeLa cells

  hela tumors flow chromatin frap

• Improved chromosome-level genome assembly of the American cockroach, Periplaneta americana.

  PMID 41123565 · PMC12774602 · G3 (Bethesda, Md.) · 2026 · 8 claims · 7 setups

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  Produced the first chromosome-level genome assembly of P. americana, scaffolded into 17 chromosome-scale scaffolds consistent with karyotype

  leg midgut assembled blattodea pacbio hi-c bulk

• Early feature extraction drives model performance in high-resolution chromatin accessibility prediction.

  PMID 41526189 · PMC12951969 · Genome research · 2026 · 8 claims · 6 setups

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  Early feature extraction (via ConvNeXt V2 blocks), rather than downstream architecture type, is the primary determinant of prediction accuracy in high-resolution chromatin accessibility prediction.

  lines cancer sets gm12878 atac-seq peak input-shift

• Boosting the detection of enhancer-promoter loops via normalization methods for chromatin interaction data.

  PMID 41633996 · PMC12976324 · Nature communications · 2026 · 8 claims · 8 setups

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  ICE and KR matrix balancing normalization methods over-correct and attenuate low-frequency enhancer-promoter loop signals despite preserving structural (CTCF-mediated) loops

  gm12878 embryonic mescs hi-c chip-seq chia-pet

• Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation.

  PMID 41690937 · PMC13018191 · Nature communications · 2026 · 8 claims · 8 setups

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  Fountains are a distinct class of Hi-C chromatin feature, different from TADs/stripes/compartments, that emerge as the earliest hallmark of chromosome organization shortly after ZGA in zebrafish

  danio zebrafish medaka xenopus hi-c chip-seq atac-seq

• Epigenetic regulation of serine biosynthesis by PHF8 during neurogenesis.

  PMID 41714361 · PMC13022353 · EMBO reports · 2026 · 8 claims · 8 setups

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  PHF8 is required for neural stem cell (NSC) proliferation in vitro

  developing nscs embryonic single-cell shrna growth

• 3D-super-enhancers are condensate-associated cis-regulatory communities.

  PMID 41797539 · PMC12968393 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  BOUQUET integrates genome topology, chromatin occupancy, and graph theory (label propagation) to assign CREs and transcription protein machinery to target genes and identify protein-rich 'communities' associated with condensates.

  embryonic mesc thymocytes chip-seq hichip single-cell

• Protease-mediated PRC1 dissociation promotes H2AK119ub remodeling during stress responses.

  PMID 41813846 · PMC13083880 · The EMBO journal · 2026 · 8 claims · 8 setups

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  CAPN3 promotes rapid dissociation of PRC1 complexes from chromatin in response to stress

  hepatocytes liver doxycycline-inducible capn3 chip-seq cut&tag western

• Putting proteins in one place.

  PMID 12790144 · PMC1316915 · Environmental health perspectives · 2003 · 8 claims · 7 setups

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  Rapamycin inhibits TOR, causing the silencing protein Sir3 to detach from chromatin at stress-response genes, triggering a coordinated multigene stress response that halts cancer cell proliferation

  saccharomyces yeast vascular skin chemical chromatin microarray

• The rates of adult neurogenesis and oligodendrogenesis are linked to cell cycle regulation through p27-dependent gene repression of SOX2.

  PMID 36627412 · PMC9832098 · Cellular and molecular life sciences : CMLS · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  p27 restricts residual CDK activity after mitogen withdrawal to antagonize cell cycling, but is not essential for cell cycle exit per se

  sez-derived computational nsc npc atac-seq bulk lisa

• Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters.

  PMID 36869353 · PMC9983196 · Genome biology · 2023 · 8 claims · 5 setups

  Has reproduction · 64

  HiCFlow, a new bioinformatic pipeline, performs de novo haplotype assembly, phasing, and visualization of allele-specific (parental) chromatin conformation directly from Hi-C data without requiring pre-phased haplotypes.

  1-7hb2 gm12878 imr-90 lines region hi-c genome-wide

• Prediction of condition-specific regulatory genes using machine learning.

  PMID 32329779 · PMC7293043 · Nucleic acids research · 2020 · 8 claims · 6 setups

  Has reproduction · 85

  ConSReg integrates expression, DAP-seq TF-DNA binding, and ATAC-seq open chromatin data into machine learning models to predict condition-specific regulatory genes

  arabidopsis zea bulk dap-seq atac-seq

• An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.

  PMID 14519204 · PMC328458 · Genome biology · 2003 · 8 claims · 6 setups

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  The Myc Target Gene database integrates literature evidence to prioritize candidate Myc-responsive genes and cluster them into functional groups

  p493 rodent types quantitative chromatin northern

• From linear genome sequence to three-dimensional organization of the cell nucleus.

  PMID 12620101 · PMC153456 · Genome biology · 2003 · 8 claims · 8 setups

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  Chromosome conformation capture (3C) can quantify in vivo physical interaction frequencies between genomic loci by crosslinking, digestion, and intramolecular ligation followed by PCR

  saccharomyces mitotic nucleoplasm hela chromosome translocation stretched

• TFBScluster web server for the identification of mammalian composite regulatory elements.

  PMID 16845063 · PMC1538905 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  TFBScluster is a web server that identifies genome-wide clusters of TFBSs conserved in multiple mammalian species using human or mouse as the reference genome.

  imr90 tissues dog transgenic microarray-based gene

• Transcription dynamics.

  PMID 19782025 · PMC6326382 · Molecular cell · 2009 · 8 claims · 8 setups

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  Transcription factors locate their sparse specific binding sites via a 3D scanning mechanism combining rapid nuclear diffusion with frequent, very transient (seconds-scale) nonspecific chromatin interactions.

  living linker lac glucocorticoid frap single-molecule nucleosome

• Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer.

  PMID 39018396 · PMC466953 · Science advances · 2024 · 8 claims · 8 setups

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  Primate-specific ERVs are a rich source of enhancers displaying cancer-specific activity across multiple tumor types

  cancer hct116 tcga colorectal atac-seq chip-seq bulk

• Multiomics Analysis of Arboviral Capsid Targets in Mosquitoes Reveals a Proviral Function of the Chromatin-Remodeling Brahma Complex.

  PMID 41565204 · PMC12927048 · Molecular & cellular proteomics : MCP · 2026 · 7 claims · 8 setups

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  Capsids from 11 pathogenic arboviruses spanning 3 genera (Orthoflavivirus, Orthobunyavirus, Alphavirus) interact with distinct sets of Aedes aegypti host proteins, forming a multimodal PPI atlas.

  aag2 aag2-c3 ap-ms dsrna co-immunoprecipitation

• Single-nucleus multiome analysis in the human prefrontal cortex identifies gene expression and cis-regulatory elements associated with aging.

  PMID 41832957 · PMC13137218 · Cell reports · 2026 · 8 claims · 8 setups

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  Generated a single-nucleus multiome (snATAC + gene expression) dataset from 357 human dorsolateral prefrontal cortex samples (ages 15-100, European and African admixed ancestry), yielding over 1.5 million cells as a public resource.

  postmortem million+ pfc each single-nucleus umap pseudobulk