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).

Publications 1.3k Datasets 392.5k Experiments 18

System / cell line: chromatin ✕ Assay: profile ✕ Clear

Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5.

PMID 41547832 · PMC12914055 · Nature communications · 2026 · 8 claims · 8 setups

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Af-CUT&Tag eliminates dependence on conventional target antibodies by using CRISPR-integrated HiBiT/ALFA-tags recognized by LgBiT/NbALFA-Tn5 fusion proteins

recombinant sw480 lysates genomic bio-layer chemiluminescent co-immunoprecipitation
Gene Regulatory Interactions at Lamina-Associated Domains.

PMID 36833261 · PMC9957430 · Genes · 2023 · 8 claims · 8 setups

Has reproduction · 31

Active genes in constitutive LADs (cLADs) reside in euchromatic regions with low LMNB1 and LMNA/C enrichment, i.e., are locally detached from the nuclear lamina

adipose ascs mesenchymal chip-seq rna-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
The AICL-KLRF1 axis supports CD4-CD8 T cell communication and cytokine competence in pre-exhausted CD8(+) T cells.

PMID 41851343 · PMC13121605 · EMBO reports · 2026 · 8 claims · 8 setups

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Progressive expression of KLRB1, KLRG1, GPR56, and KLRF1 tracks CD8+ T cell differentiation stages (TN, TCM, TEM, TEMRA), mirroring the pattern previously shown in CD4+ T cells

unstimulated cd3+-enriched enriched cd8+ flow sorting-based spatial
Hi-Compass: a depth-aware deep learning framework for predicting cell-type-specific 3D genome organization from single-cell to spatial resolution.

PMID 41980945 · PMC13250166 · Nature communications · 2026 · 8 claims · 8 setups

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Hi-Compass predicts cell-type-specific Hi-C contact maps using only ATAC-seq as cell-type-specific input, plus DNA sequence and a generalized CTCF binding profile

gm12878 curated bulk training hi-c ctcf matched
Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups

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A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning

genomic raji monocyte-derived rj2.2.5 computational chip-on-chip chromatin
The integrated world of functional genomics.

PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups

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Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.

cerevisiae sequenced elegans drosophila chromatin integration comparative
Feed-forward loops by NR5A2 ensure robust gene activation during pre-implantation development.

PMID 41355514 · PMC12848575 · Development (Cambridge, England) · 2026 · 8 claims · 8 setups

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NR5A2 chromatin binding is dynamic, changing genome-wide from the 2-cell to the morula stage, with peak numbers and target regions (e.g. SINE B1/Alu) shifting over developmental time

2-cell embryonic 8-cell zygotes cut&tag chip-seq h3k27ac
Modeling nascent transcription from chromatin landscape and structure with CLASTER.

PMID 41691282 · PMC13011747 · Genome biology · 2026 · 7 claims · 8 setups

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CLASTER, a deep neural network combining chromatin landscape tracks and 3D contact maps, accurately predicts kilobasepair-resolution nascent RNA (EU-seq) profiles in a DNA-sequence-agnostic manner

embryonic mescs chromatin k562 eu-seq chip-seq micro-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 · 6 claims · 8 setups

Has reproduction · 77

PredTAD, a Gradient Boosting Machine model using epigenomic and genomic ChIP-seq-derived features plus neighboring-bin information, classifies 10 kb genomic bins as TAD boundary or non-boundary

mcf10a t47d mcf7 tcga hi-c chip-seq atac-seq
Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.

PMID 18786246 · PMC2556353 · BMC genomics · 2008 · 6 claims · 6 setups

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PLP, Sox10, SOD3, and Ptn are direct regulatory targets of Sox10, confirmed by chromatin immunoprecipitation binding to conserved cis-elements

rt4d6 gst-sox10 microarray comparative real
Multiomics and deep learning dissect regulatory syntax in human development.

PMID 41951735 · PMC13216069 · Nature · 2026 · 8 claims · 8 setups

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The Human Development Multiomic Atlas (HDMA) is a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types

fetal annotated embryo chrombpnet share-seq chromvar activity-by-contact
Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis.

PMID 32155147 · PMC7138332 · PLoS biology · 2020 · 8 claims · 7 setups

Has reproduction · 90

Replacing Scc1 with Rec8 in mitosis impairs sister chromosome cohesion, advances the timing of genome replication, and reduces reproductive fitness by 45%

saccharomyces cerevisiae competitive live-cell flow
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
Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing sarcoma.

PMID 41792463 · PMC13084053 · EMBO molecular medicine · 2026 · 7 claims · 8 setups

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Combining cfDNA methylome (EwingSign) and fragmentome analysis detects all clinically confirmed relapse events in EwS/CIC patients

plasma cfdna t7-mbd-seq ichorcna fragment
Nonsense-mediated mRNA decay orchestrates neuronal migration and cortical lamination while modulating Reelin and ciliary gene regulatory networks.

PMID 41746809 · PMC13042203 · Cell reports · 2026 · 8 claims · 8 setups

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UPF2-mediated NMD is required for proper cortical lamination; conditional Upf2 deletion in radial glia disrupts layering of TBR1+/SATB2+ and CTIP2+/CUX1+ neurons.

cortex embryonic cortical neural immunofluorescence utero co-electroporation
Single cell multiomics revealed fibrotic trajectories of endometrial cells and interaction with the pro-fibrotic macrophages in intrauterine adhesion.

PMID 41947225 · PMC13188631 · Genome medicine · 2026 · 8 claims · 8 setups

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Human IUA endometrium contains a novel ACTA2+KRT8+ myofibrotic-epithelial subpopulation and an ACTA2+CD31+ myofibrotic-endothelial subpopulation, in addition to myofibroblasts

endometrial iua scrna-seq snatac-seq spatial
Patient-derived orthotopic xenograft models recapitulate the peritoneal dissemination of pancreatic cancer and delineate its transcriptional and regulatory programs.

PMID 41673768 · PMC12998334 · Journal of experimental & clinical cancer research : CR · 2026 · 6 claims · 8 setups

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Organoids derived from malignant effusions of PDAC patients reproducibly generate peritoneal metastases after orthotopic implantation into the pancreas of immunodeficient mice

pdac organoids frozen pdox orthotopic single-nucleus single-cell

Experiments

Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5.

Gene Regulatory Interactions at Lamina-Associated Domains.

Uncertainty-aware genomic deep learning with knowledge distillation.

The AICL-KLRF1 axis supports CD4-CD8 T cell communication and cytokine competence in pre-exhausted CD8(+) T cells.

Hi-Compass: a depth-aware deep learning framework for predicting cell-type-specific 3D genome organization from single-cell to spatial resolution.

Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

The integrated world of functional genomics.

Feed-forward loops by NR5A2 ensure robust gene activation during pre-implantation development.

Modeling nascent transcription from chromatin landscape and structure with CLASTER.

PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.

Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.

Multiomics and deep learning dissect regulatory syntax in human development.

Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis.

Nucleosome regulatory dynamics in response to TGFβ.

Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing sarcoma.

Nonsense-mediated mRNA decay orchestrates neuronal migration and cortical lamination while modulating Reelin and ciliary gene regulatory networks.

Single cell multiomics revealed fibrotic trajectories of endometrial cells and interaction with the pro-fibrotic macrophages in intrauterine adhesion.

Patient-derived orthotopic xenograft models recapitulate the peritoneal dissemination of pancreatic cancer and delineate its transcriptional and regulatory programs.