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 65

System / cell line: cell-type-specific ✕ Assay: single-cell ✕ Clear

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
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
A cell atlas of the adult female Aedes aegypti midgut revealed by single-cell RNA sequencing.

PMID 38839790 · PMC11153528 · Scientific data · 2024 · 8 claims · 4 setups

Has reproduction · 95

Established a protocol for isolating single cells from Ae. aegypti midgut and performing scRNA-seq (dissociation, density-gradient purification, viability QC, 10x Genomics library prep and sequencing).

dissociated scrna-seq merged single-cell viability computational
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
Differentiation in the human urothelia is defined by distinct alternative polyadenylation.

PMID 41533515 · PMC12937501 · Cell reports · 2026 · 8 claims · 8 setups

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APA introduces a major layer of transcriptomic diversity during urothelial differentiation, largely independent of changes in mRNA levels

urothelial urothelial-specific ureter hek293t single-cell poly fluorescence
Epigenetic context defines the transcriptional activity of canonical and noncanonical NF-κB signaling in pancreatic cancer.

PMID 41844578 · PMC13039881 · Cell death discovery · 2026 · 8 claims · 8 setups

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TNFα is the primary activator of canonical NF-κB signaling via RELA in PDAC

pdac patient-derived aspc-1 l3.6pl single-cell bulk multiplex
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
Deep single-cell decoding of human pancreatic islets reveals T2D β-cell gene expression defects.

PMID 41986506 · PMC13226668 · The EMBO journal · 2026 · 8 claims · 6 setups

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Single-cell transcriptome profiling of 245,878 islet cells from 48 donors (ND/PD/T2D) identifies 14 distinct, robust islet cell types detected in every donor

pancreatic aggregated endoc-βh3 subset droplet-based pseudobulk unsupervised
CellMap: precision mapping of cellular landscape in spatial transcriptomics.

PMID 41505103 · PMC12781899 · Nucleic acids research · 2026 · 7 claims · 3 setups

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CellMap combines co-linearity of seed genes, a random forest model, and the linear assignment algorithm to achieve optimal assignment of single cells to spatial spots

platforms single-cell expression computational scrna-seq spatial
Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo.

PMID 35784648 · PMC9243631 · Cell reports methods · 2022 · 8 claims · 7 setups

Has reproduction · 66

A purification-free hyperTRIBE method (FMR1-ADARcd-V5) can identify stress granule RNAs in bulk and single Drosophila S2 cells and in Drosophila neurons

fmr1-adarcd-v5 single bioinformatic drosophila immunofluorescence western bulk
FEM: mining biological meaning from cell level in single-cell RNA sequencing data.

PMID 34909283 · PMC8641482 · PeerJ · 2021 · 8 claims · 5 setups

Has reproduction · 75

The FEM algorithm converts a single-cell gene expression matrix into a functional expression matrix using multi-module gene set enrichment analysis, utilizing information from all expressed genes rather than discarding filtered genes.

pbmc pancreas liver scrna-seq single-cell fisher's dimensionality
Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.

PMID 36254682 · PMC9612871 · Disease models & mechanisms · 2022 · 8 claims · 8 setups

Has reproduction · 100

iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action

ipsc-derived products microglia post-mortem single-cell ca2+ protein-protein
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
Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

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TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental
Single-Cell RNA-Seq Profiling of Transposable Element Expression in Human Peripheral Blood Cells During Viral Infections.

PMID 41683713 · PMC12898442 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

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TE expression is significantly higher in PBMCs from viral infection cohorts (and recovered individuals) compared to healthy controls

pbmcs pbmc cd8+ single-cell cell-type expression
Single-cell mapping of cholesterol metabolism reveals FDPS as a therapeutic vulnerability in hepatocellular carcinoma.

PMID 41706364 · PMC12916967 · Cellular oncology (Dordrecht, Netherlands) · 2026 · 7 claims · 8 setups

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Cholesterol metabolic activity is markedly elevated in HCC tumors and in immune checkpoint blockade (ICB) non-responders, with pronounced intratumoral heterogeneity across malignant cell subpopulations

hcc tcga-lihc malignant hepa1-6 scrna-seq bulk hdwgcna
Comprehensive analysis for the role of macrophage-driven genes in abdominal aortic aneurysm.

PMID 41815567 · PMC12973086 · Cardiovascular diagnosis and therapy · 2026 · 8 claims · 8 setups

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SMU1 is identified as a novel macrophage-related gene associated with AAA development, serving as a potential diagnostic biomarker and therapeutic target

aaa macrophage-related merged gwas single-cell bulk rt-qpcr
A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer.

PMID 41844817 · PMC13111741 · Discover oncology · 2026 · 8 claims · 8 setups

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MTRNR2L8 is markedly upregulated in RCRC tumor cells and is associated with poorer patient survival

crc epithelial rcrc tcga-read scrna-seq copy gene
Opioid-induced transcriptional reprogramming of cerebrospinal fluid immune cells is associated with neuroinflammatory signaling in antiretroviral treated SIV-infected rhesus macaques.

PMID 42010620 · PMC13227897 · Journal of neuroinflammation · 2026 · 8 claims · 5 setups

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Morphine-dependent macaques show increased CD4+ TCM and Treg cell proportions and decreased CD8+ TEM cell proportions in CSF at the pre-infection timepoint compared to saline controls

csf scrna-seq necropsy single-cell flow cell-cell
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

Experiments

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

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

A cell atlas of the adult female Aedes aegypti midgut revealed by single-cell RNA sequencing.

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

Differentiation in the human urothelia is defined by distinct alternative polyadenylation.

Epigenetic context defines the transcriptional activity of canonical and noncanonical NF-κB signaling in pancreatic cancer.

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

Deep single-cell decoding of human pancreatic islets reveals T2D β-cell gene expression defects.

CellMap: precision mapping of cellular landscape in spatial transcriptomics.

Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo.

FEM: mining biological meaning from cell level in single-cell RNA sequencing data.

Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.

Multiomics and deep learning dissect regulatory syntax in human development.

Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

Single-Cell RNA-Seq Profiling of Transposable Element Expression in Human Peripheral Blood Cells During Viral Infections.

Single-cell mapping of cholesterol metabolism reveals FDPS as a therapeutic vulnerability in hepatocellular carcinoma.

Comprehensive analysis for the role of macrophage-driven genes in abdominal aortic aneurysm.

A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer.

Opioid-induced transcriptional reprogramming of cerebrospinal fluid immune cells is associated with neuroinflammatory signaling in antiretroviral treated SIV-infected rhesus macaques.

pmid-42054465