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 19

System / cell line: stem ✕ Assay: score ✕ Clear

Molecular interactome of HNRNPU reveals regulatory networks in neuronal differentiation and DNA methylation.

PMID 41674383 · PMC12895067 · Nucleic acids research · 2026 · 7 claims · 8 setups

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HNRNPU forms extensive protein networks including an association with the mammalian SWI/SNF chromatin-remodeling complex

ipsc-derived computational neocortical ip-ms formaldehyde alphapulldown expression-weighted
A comparative analysis of blastoid models through single-cell transcriptomics.

PMID 39524369 · PMC11543915 · iScience · 2024 · 8 claims · 7 setups

Has reproduction · 60

EPSC-derived blastoids are transcriptomically distinct from nPSC-derived blastoids, with nPSC-blastoids clustering closer to natural blastocysts.

blastoid natural combined integrated scrnaseq lineage kolmogorov-smirnov
Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.

PMID 40699865 · PMC12191508 · Current issues in molecular biology · 2025 · 8 claims · 8 setups

Has reproduction

The coronavirus pathogenesis pathway is activated in SARS-CoV-2-infected iPSC-derived cardiac cells and in SARS-CoV/SARS-CoV-2-infected LUAD cells

ace2-transfected calu-3 luad ipsc-derived ipa sequencing convolutional
High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

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Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

embryonic neural t-cells mm8 chip-seq chip-chip pwm
CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

PMID 19922652 · PMC3091324 · Genome biology · 2009 · 8 claims · 8 setups

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CTCF binding sites can be classified into three occupancy-based classes (LowOc, MedOc, HighOc) based on similarity to the CTCF PWM motif

cd4+ hela imr90 embryonic chip-seq computational gene
Dissecting the contribution of transposable elements to interphase chromosome structure.

PMID 41559820 · PMC12903442 · Genome biology · 2026 · 8 claims · 5 setups

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TE sequences are responsible for 3D genome structure in interphase nuclei

pluripotent mesoderm hpsc hi-c chip-seq te-subset
iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes.

PMID 18974167 · PMC2639305 · Bioinformatics (Oxford, England) · 2008 · 6 claims · 3 setups

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iMapper is a web application for automated analysis and mapping of insertional mutagenesis sequence data against vertebrate and invertebrate Ensembl genomes (human, mouse, rat, zebrafish, Drosophila, S. cerevisiae).

piggybac splinkerette-pcr-derived sequence splinkerette genome throughput
Differential Infiltration of Key Immune T-Cell Populations Across Malignancies Varying by Immunogenic Potential and the Likelihood of Response to Immunotherapy.

PMID 39682743 · PMC11640164 · Cells · 2024 · 8 claims · 5 setups

Has reproduction

Estimated T-cell infiltration differs significantly across melanoma, bladder, ovarian, and pancreatic cancers, tracking known immunogenic potential.

tumor melanoma orien bulk gene kaplan-meier
Distinguishing benign from pathogenic duplications involving GPR101 and VGLL1-adjacent enhancers in the clinical setting with the bioinformatic tool POSTRE.

PMID 41540017 · PMC12890961 · NPJ genomic medicine · 2026 · 6 claims · 7 setups

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POSTRE correctly classified all 34 GPR101-associated duplications (27 pathogenic X-LAG, 7 non-pathogenic) as pathogenic or benign

anterior embryonic patient-derived genome h3k27ac atac-seq rna-seq
Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.

PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups

Has reproduction · 96

Integration of five mouse scRNAseq datasets reveals a trifurcating lineage trajectory originating from embryonic mammary stem cells (MaSCs) that differentiates into three epithelial lineages (Basal, L-Alv, L-Hor) via unipotent progenitor clusters

mammary surgically normal single-cell whole-mount integration
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
A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.

PMID 37277355 · PMC10241789 · Nature communications · 2023 · 8 claims · 8 setups

Has reproduction · 94

2232 genome-wide putative super-enhancers (SEs) were identified in mouse cranial neural crest cell (CNCC) subpopulations

e10.5 embryonic pa2 h3k27ac promoter hi-c
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

PMID 16381984 · PMC1347458 · Nucleic acids research · 2006 · 8 claims · 5 setups

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MPromDb is a novel database integrating experimentally supported gene promoters, TSS annotation, cis-regulatory elements, CpG islands, and ChIP-chip data with an integrated visualization interface.

chip-chip sequence genbank
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

PMID 16381831 · PMC1347497 · Nucleic acids research · 2006 · 6 claims · 6 setups

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miRNAMap integrates known miRNA genes from miRBase, literature-curated validated targets, and computationally predicted miRNA genes and targets for human, mouse, rat and dog.

conserved putative mirna-target normal comparative machine mirna
The chromosome-scale genome assembly, annotation of Bischofia polycarpa (H. Lév.) Airy Shaw, Phyllanthaceae.

PMID 41765919 · PMC13066037 · Scientific data · 2026 · 8 claims · 8 setups

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B. polycarpa genome was assembled de novo using PacBio HiFi reads and Hi-C data to a size of 585.68 Mb with contig N50 of 12.62 Mb

polycarpa illumina pacbio hi-c
Learning collective multicellular dynamics with an interacting mean field neural SDE model.

PMID 41564117 · PMC12854464 · PLoS computational biology · 2026 · 7 claims · 5 setups

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scIMF models multicellular dynamics as interacting diffusion processes using a McKean-Vlasov SDE solved via Neural SDE, with a Transformer-based cell-wise attention mechanism approximating the distribution-dependent drift term

zebrafish embryonic pancreatic temporal umap cell-wise
bayesReact: expression-coupled regulatory motif analysis detects microRNA activity across cancers, tissues, and at the single-cell level.

PMID 41657247 · PMC12884093 · Nucleic acids research · 2026 · 8 claims · 6 setups

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bayesReact is a novel fully Bayesian generative model for inferring regulatory motif (e.g., miRNA) activity from bulk or single-cell expression data

tcga gtex stem embryonic paired semi-synthetic single-cell
Distinct radial glia subtypes regulate midbrain dopaminergic neuron development.

PMID 41699318 · PMC13061605 · Nature neuroscience · 2026 · 8 claims · 8 setups

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Rgl1 is the progenitor of the mesDA neuronal lineage

embryonic developing wa09 bulk scrna-seq ligand-receptor
Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups

Has reproduction · 50

A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.

erwinia intergenic candidate wounded small northern race

Experiments

Molecular interactome of HNRNPU reveals regulatory networks in neuronal differentiation and DNA methylation.

A comparative analysis of blastoid models through single-cell transcriptomics.

Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.

High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

Dissecting the contribution of transposable elements to interphase chromosome structure.

iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes.

Differential Infiltration of Key Immune T-Cell Populations Across Malignancies Varying by Immunogenic Potential and the Likelihood of Response to Immunotherapy.

Distinguishing benign from pathogenic duplications involving GPR101 and VGLL1-adjacent enhancers in the clinical setting with the bioinformatic tool POSTRE.

Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.

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

A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.

MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

The chromosome-scale genome assembly, annotation of Bischofia polycarpa (H. Lév.) Airy Shaw, Phyllanthaceae.

Learning collective multicellular dynamics with an interacting mean field neural SDE model.

bayesReact: expression-coupled regulatory motif analysis detects microRNA activity across cancers, tissues, and at the single-cell level.

Distinct radial glia subtypes regulate midbrain dopaminergic neuron development.

Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.