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 28

System / cell line: types ✕ Assay: regulatory ✕ Clear

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
Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci.

PMID 41807385 · PMC12979833 · Nature communications · 2026 · 8 claims · 8 setups

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Integration of CAD GWAS summary statistics with epigenetic data from 45 cell types identifies 1580 candidate CAD genes

cad-associated disease-relevant types cad variant epigenetic tf-snv
Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

PMID 38254989 · PMC10815467 · Genes · 2024 · 7 claims · 8 setups

Has reproduction · 85

High expression of transcription factors FOXA1 and EZH2 in malignant cells at the invasive front plays a key role in driving tumor progression

breast er+ epithelial malignant scrna-seq spatial copy
Dissecting gene regulatory networks governing human cortical cell fate.

PMID 41565813 · PMC12999477 · Nature · 2026 · 8 claims · 6 setups

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ZNF219, a previously uncharacterized transcription factor, represses neural differentiation in human cortical radial glia

cortical rhesus single-cell scrna-seq immunocytochemistry
A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity.

PMID 37963558 · PMC10645512 · Journal of the Royal Society, Interface · 2023 · 8 claims · 7 setups

Has reproduction · 95

RKIP and BACH1 are negatively correlated with each other across most cancer types in TCGA

tcga er+ ccle computational spearman correlation gene
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
CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

PMID 41498638 · PMC12948241 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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CellPolaris is a unified computational framework performing TF-centered GRN construction, master TF identification, and TF perturbation simulation

bulk previously round paired transfer-learning cross-species
Identification of novel DNA sequence motifs that modulate transcription in T cells.

PMID 41514212 · PMC12879379 · BMC genomics · 2026 · 8 claims · 8 setups

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Identified 2,036 novel DNA motifs enriched in regulatory regions of T-cell-specific genes

t-cell non-t-cell cd4+ sequences rna-seq dnase-seq h3k27ac
Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

PMID 41547351 · PMC13069856 · Cell genomics · 2026 · 8 claims · 8 setups

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Otari, an attention-based graph neural network trained on long-read transcriptomes across 30 tissues/brain regions, predicts tissue-specific differential isoform abundance

tissues genomic gtex hgmd long-read variant splice
The evolution of gene regulation in mammalian cerebellum development.

PMID 41610256 · PMC7618896 · Science (New York, N.Y.) · 2026 · 8 claims · 8 setups

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Combined single-nucleus RNA-seq and ATAC-seq atlases of cerebellum development were generated/integrated across six mammals (human, bonobo, macaque, marmoset, mouse, opossum)

developing opossum marmoset cultures single-nucleus bulk gene
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
RMzyme: regulations of RNA-modifying enzymes in humans.

PMID 41672979 · PMC12895048 · Signal transduction and targeted therapy · 2026 · 8 claims · 7 setups

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RMzyme is a comprehensive multiomics knowledgebase covering 179 human RNA-modifying proteins across 18 major RNA modification types and 63 human tissues

nomo1 molm13 tissues cptac merip-seq bulk single-cell
ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.

PMID 41592570 · PMC13069865 · Cell genomics · 2026 · 8 claims · 7 setups

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ChromBERT is pre-trained via masked reconstruction on the Cistrome-Human-6K dataset (6,391 cistromes, 991 transcription regulators) to learn genome-wide interaction syntax of transcription regulators

lines chromosome embryonic transcription chip-seq chromhmm hi-c
Architectural and evolutionary features of TE-derived TSSs shape tissue-specific promoter activity in the human genome.

PMID 41620470 · PMC12963367 · Nature communications · 2026 · 8 claims · 8 setups

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A three-step RAMPAGE-based pipeline can systematically identify TE-derived transcription start sites (TSSs) genome-wide, distinguishing them from autonomous TE transcription and background noise.

biosamples same k562 genomic rampage rna-seq h3k4me3
Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs.

PMID 41735611 · PMC13095655 · Nature structural & molecular biology · 2026 · 6 claims · 7 setups

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TADs and large-scale chromatin structures remain largely unchanged during sex determination, suggesting a preformed configuration

facs-sorted same integrated fgf9 hi-c chip-seq metaloci
Epigenetics and phenotypic variation in mammals.

PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

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Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

mammalian mhc chromosomes embryonic methylation high-throughput chip
Differential neuronal survival defines a novel axis of sexual dimorphism in the Drosophila brain.

PMID 41529688 · PMC7618834 · Cell genomics · 2026 · 8 claims · 7 setups

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Sex differences in the Drosophila central brain do not result from large-scale transcriptional reprogramming, but from selective modifications within shared developmental lineages mediated by dsx and fru.

drosophila central dsx+ dsx-gal4>mcd8 single-cell differential scenic
To Explore the Key Subgroup and Their Immune Microenvironment During the Formation of Coronary Plaque With scRNA-seq.

PMID 40454289 · PMC12126265 · Cardiology research and practice · 2025 · 6 claims · 8 setups

Has reproduction · 33

C1 RACK1+ NK cells are a crucial subgroup for understanding coronary plaque formation, exhibiting the highest cell stemness/differentiation potential and positioned at the start of the pseudotime trajectory

coronary scrna-seq five type single-cell doublet copy
Large-scale discovery and validation of functional elements in the human genome.

PMID 15774039 · PMC1088940 · Genome biology · 2005 · 8 claims · 8 setups

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Genome-wide tiling microarray hybridization reveals large, diverse sets of transcripts, many of which lack existing gene annotations

liver genome yeast lines tiling computational dnase
Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

PMID 18831773 · PMC3226104 · BMC genomics · 2008 · 8 claims · 8 setups

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Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare

mcf7 arabidopsis specified different chip-seq microarray array-based

Experiments

Multiomics and deep learning dissect regulatory syntax in human development.

Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci.

Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

Dissecting gene regulatory networks governing human cortical cell fate.

A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity.

Prediction of condition-specific regulatory genes using machine learning.

CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

Identification of novel DNA sequence motifs that modulate transcription in T cells.

Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

The evolution of gene regulation in mammalian cerebellum development.

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

RMzyme: regulations of RNA-modifying enzymes in humans.

ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.

Architectural and evolutionary features of TE-derived TSSs shape tissue-specific promoter activity in the human genome.

Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs.

Epigenetics and phenotypic variation in mammals.

Differential neuronal survival defines a novel axis of sexual dimorphism in the Drosophila brain.

To Explore the Key Subgroup and Their Immune Microenvironment During the Formation of Coronary Plaque With scRNA-seq.

Large-scale discovery and validation of functional elements in the human genome.

Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.