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).

• Chromatin architecture reprogramming reveals novel epigenetic dependencies in breast cancer.

  PMID 41412800 · PMC12849445 · Genes & development · 2026 · 7 claims · 7 setups

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  H3K9 methylation and the demethylase KDM4C, through association with SWI/SNF, drive proliferation of cells fated to become endocrine-resistant via a nongenomic estrogen-mediated mechanism

  parental t47d esr1 scrna-seq hi-c atac-seq

• iAODE for benchmarking and continuum modeling of single-cell chromatin accessibility.

  PMID 41775921 · PMC13066597 · Communications biology · 2026 · 8 claims · 5 setups

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  iAODE combines a ZINB-likelihood VAE, a latent Neural ODE, low-weight KL regularization, and an interpretable reconstruction (irecon) bottleneck to learn generative, temporally continuous latent spaces for scATAC-seq.

  simulated real small simulated scatac-seq

• Partially shared multi-modal embedding learns holistic representation of cell state.

  PMID 41741805 · PMC13021527 · Nature computational science · 2026 · 8 claims · 5 setups

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  APOLLO automatically learns partial information sharing between multiple data modalities using an autoencoder with a partially overlapping latent space trained via latent optimization.

  simulated paired single simulation scrna-seq multiplexed

• Accurate chromatin marks peak calling with Omnipeak.

  PMID 41521664 · PMC12784980 · Nucleic acids research · 2026 · 8 claims · 6 setups

  Has reproduction · 77

  Omnipeak is a universal unsupervised peak-calling algorithm based on a constrained three-state hidden Markov model (zero, noise, signal states)

  gm12878 roadmap abf immgen chip-seq ultra-low-input atac-seq

• Transcriptional landscape of repetitive elements in normal and cancer human cells.

  PMID 25012247 · PMC4122776 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 76

  RepEnrich, a computational method that uses all mapping reads (uniquely mapping plus multi-mapping reads assigned to repetitive element subfamily assemblies/pseudogenomes), quantifies genome-wide repetitive element enrichment

  chromosomes lines imr-90 prostate simulated pol chip-seq

• From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture.

  PMID 41507775 · PMC12870729 · BMC bioinformatics · 2026 · 8 claims · 3 setups

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  The 4DGBWorkflow and 4D Genome Browser (4DGB) are a containerized, cross-platform (macOS/Linux/Windows) toolkit that transforms Hi-C data into 3D chromosome reconstructions and provides comparative visualization

  a549 mus computationally hi-c molecular

• Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding.

  PMID 41639407 · PMC12900649 · Nature genetics · 2026 · 8 claims · 8 setups

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  Acute HDAC inhibition (TSA pulse) induces genome-wide H3K27 hyperacetylation and reorganizes the histone modification landscape, shifting more of the genome to an active state.

  e14 simulated mescs calibrated atac-seq bulk

• 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

• Uncertainty-aware genomic deep learning with knowledge distillation.

  PMID 41523993 · PMC12779563 · NPJ artificial intelligence · 2026 · 7 claims · 6 setups

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  DEGU distills an ensemble of teacher DNNs into a single student model by jointly predicting the ensemble mean and the variability (epistemic uncertainty) across ensemble predictions.

  drosophila k562 deepstarr starr-seq starr-seq-derived lentimpra base-resolution

• Discovery of key regulators in classical monocyte phenotypes linked to COVID-19 severity using single-cell multi-omics sequencing.

  PMID 41732268 · PMC12925236 · iScience · 2026 · 8 claims · 8 setups

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  Two severity-associated classical monocyte (cMono) subtypes, IL7R+ and CD163+, exist with distinct transcriptional and epigenetic landscapes.

  pbmcs pbmc classical cmono single-nucleus differential multimodal