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 14

System / cell line: cell-type-specific ✕ Assay: chip-seq ✕ Clear

Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell-like cells.

PMID 41371963 · PMC12758400 · Genome research · 2026 · 8 claims · 6 setups

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GSC-like and CySC-like cells isolated from upd tumor testes are transcriptionally comparable to wild-type GSC/early-spermatogonia and CySC clusters, respectively

upd gsc-like wild-type scrna-seq differential gene
GRNFormer: accurate gene regulatory network inference using graph transformer.

PMID 41883144 · PMC13069479 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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GRNFormer is a generalizable graph transformer framework for GRN inference from single-cell or bulk transcriptomics data across species, cell types, and platforms without cell-type annotations or prior regulatory information

hematopoietic embryonic dendritic hepatocytes scrna-seq chip-seq string
pmid-42054465

PMID 42054465 · PMC13127566 · 8 claims · 4 setups

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PSGRN infers GRNs by generating pseudoannotations from gene-gene correlations and iteratively refining them via a self-training classifier using pre/post-intervention expression features.

k562 rpe1 processed single-cell computational biological
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
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
EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.

PMID 41527854 · PMC12796812 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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EpiXFormer achieves high accuracy (mean AUROC ~0.99) predicting binding sites of both TFs and non-sequence-specific DBPs across 199 DBP-cell type pairs

dbps tfs common ctcf deep comparative feature-ablation
Cell type- and species-specific regulation of hepatic lncRNAs by TCDD-activated aryl hydrocarbon receptor.

PMID 41136526 · PMC12552753 · Scientific reports · 2025 · 8 claims · 6 setups

Has reproduction · 71

AHR-mediated lncRNA dysregulation may be a contributing mechanism in TCDD-elicited progression of steatosis to steatohepatitis with fibrosis

liver mm39 bulk single-nuclei ahr
Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

PMID 41528844 · PMC12971065 · Cell reports · 2026 · 8 claims · 8 setups

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Generated a single-cell gene expression and chromatin accessibility (multiome) atlas of human RPE and choroid from control and AMD eyes

rpe-choroid rpe arpe-19 scatac-seq joint h3k27ac activity-by-contact
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
Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

PMID 41865369 · PMC13207208 · Cell reports · 2026 · 8 claims · 6 setups

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Memory CD4+ T cells show enhanced chromatin accessibility proximal to rapid-recall genes compared to naive cells

blood-derived computational pseudobulk cd4+ single-nuclei maxatac grn
AutoGERN: single-cell RNA-seq gene regulatory network inference via explicit link modeling and adaptive architectures.

PMID 41871930 · PMC13064981 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 3 setups

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AutoGERN explicitly models regulatory information in the message-passing space via learned link (edge) embeddings, which are scored by a lightweight MLP to infer TF–target interactions.

seven same scrna-seq-based chip-seq cold-start
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
EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles.

PMID 41832145 · PMC13133354 · Nature communications · 2026 · 8 claims · 7 setups

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EPInformer outperforms existing gene expression prediction models (Xpresso, CREaTor, Seq-GraphReg, Enformer, Borzoi) in rigorous 12-fold cross-chromosome validation for both RNA-seq and CAGE expression prediction

k562 lines likely cell-type-specific rna-seq cage abc
An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease.

PMID 41937210 · PMC13067603 · Genome biology · 2026 · 8 claims · 8 setups

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Constructed an integrated multiomic atlas of the human left ventricle combining ~2.3M snRNA-seq nuclei from 299 donors and ~690K snATAC-seq nuclei from 106 donors

left heart cardiac snrna-seq snatac-seq bulk

Experiments

Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell-like cells.

GRNFormer: accurate gene regulatory network inference using graph transformer.

pmid-42054465

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

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

EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.

Cell type- and species-specific regulation of hepatic lncRNAs by TCDD-activated aryl hydrocarbon receptor.

Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

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

Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

AutoGERN: single-cell RNA-seq gene regulatory network inference via explicit link modeling and adaptive architectures.

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

EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles.

An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease.