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).

• Histone methyl-transferase G9a inhibition boosts the efficacy of immune checkpoint inhibitors in experimental hepatocellular carcinoma.

  PMID 41923620 · PMC13130624 · Cell reports. Medicine · 2026 · 7 claims · 8 setups

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  G9a expression inversely correlates with gene signatures predictive of favorable ICI response across multiple HCC patient cohorts

  tcga advanced nm53 plc bulk single-cell rt-qpcr

• Dissecting host stress responses for predictable heterologous gene expression in E. coli.

  PMID 41909945 · PMC13034041 · Nucleic acids research · 2026 · 8 claims · 6 setups

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  Excessive heterologous mRNA triggers a cold shock response that controls mRNA stability (cspA–I, deaD)

  coli combined rna-seq independent flow

• Precise modulation of BRG1 levels reveals features of mSWI/SNF dosage sensitivity.

  PMID 40846763 · PMC12425804 · Nature genetics · 2025 · 8 claims · 8 setups

  Has reproduction · 75

  BRG1 binding to chromatin exhibits a linear, dose-dependent response to BRG1 protein levels, independent of TF or histone-modification co-occupancy

  brg1-fkbp12-f36v brg1-knock-in mes snf2h-fkbp12-f36v western cut&run atac-seq

• Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs.

  PMID 17542650 · PMC1885280 · PLoS genetics · 2007 · 8 claims · 7 setups

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  H3me3K9 and H3me3K27 mark largely mutually exclusive, distinct classes of transcription factor genes: H3me3K9 at ZNF genes, H3me3K27 at homeobox genes

  ntera2 fibroblasts chip-chip chip-pcr expression

• 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 epigenomic investigation of atrial fibrillation in a matched left and right atrial human cohort.

  PMID 41906156 · PMC13045105 · Clinical epigenetics · 2026 · 8 claims · 6 setups

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  H3K27ac epigenomic profiles differ more strongly by anatomical side (left vs right atrium) than by disease status (AF vs SR)

  left independent paired ipsc-derived h3k27ac bulk rt-qpcr

• TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells.

  PMID 23233547 · PMC3589534 · Genome research · 2013 · 8 claims · 8 setups

  Has reproduction · 78

  TRIM28 repression of ERVs protects cellular gene expression in early embryos from perturbation by cis-acting activators contained within these retroelements.

  embryonic trim28 mrna-seq trim28 h3k9me3

• Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.

  PMID 18366677 · PMC2324081 · BMC medical genetics · 2008 · 8 claims · 7 setups

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  Distinct sets of dysregulated genes are found in peripheral blood during the relapse phase versus the remission phase of RRMS

  peripheral blood pooled trio gene quantitative promoter

• Predicting enhancer-gene links from single-cell multi-omics data by integrating prior Hi-C information.

  PMID 42100854 · PMC13229940 · Nucleic acids research · 2026 · 8 claims · 6 setups

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  SCEG-HiC, a weighted graphical lasso (wglasso) method, predicts enhancer-gene links from single-cell multi-omics data by integrating bulk average Hi-C as a prior penalty matrix

  specified covid-19 scatac scatac-seq bulk