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 1.6k

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Multi-omics reveal vitamin D regulation of immune-gut microbiome interactions and tolerogenic pathways in inflammatory bowel disease.

PMID 41895287 · PMC13130636 · Cell reports. Medicine · 2026 · 8 claims · 7 setups

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12 weeks of vitamin D treatment decreases disease activity scores and inflammatory markers (fecal calprotectin) and improves quality of life in IBD patients

stool peripheral iga-bound ibd iga-seq igg-seq blood
ZFP148 is a transcriptional repressor of cytolytic effector CD8(+) T cell differentiation.

PMID 41896465 · PMC13043298 · Nature immunology · 2026 · 8 claims · 8 setups

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ZFP148 is enriched in CD8+ T progenitor (T PRO) cells and its expression declines during differentiation into effector (T EFF) and exhausted (T EX) cells

p14 splenic cd8+ b16-gp scrna-seq flow tcr
Single-Cell Multi-Tissue T Cell Clonal Dynamics Reveal Distinct Immune Coercion Landscapes in MSI and MSS Colorectal Cancer.

PMID 41898550 · PMC13027115 · International journal of molecular sciences · 2026 · 8 claims · 5 setups

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Immunotherapy response in CRC is better explained by TCR clonal dynamics (expansion, migration, functional transitions) than by MSI status alone

crc single high-quality cd4+ scrna-seq tcr pseudotime
A tissue-resolved, network-based transcriptomic framework for abiotic stress responses in sorghum.

PMID 41904985 · PMC13033392 · The Plant journal : for cell and molecular biology · 2026 · 8 claims · 8 setups

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Tissue specificity is the dominant determinant of abiotic stress-induced gene reprogramming across drought, heat, and salinity stress in sorghum

sorghum rna-seq qrt-pcr wgcna
Therapeutic manipulation and spatial quantification of the tumor microenvironment in colorectal cancer.

PMID 41907400 · PMC13018967 · iScience · 2026 · 8 claims · 8 setups

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Colorectal cancer fibroblast heterogeneity can be distilled into two overarching, transcriptomically distinct CAF populations marked by PDGFRA+ and ACTA2+ expression

crc colonic gemm scrna-seq multiplex bulk
Single-cell transcriptomic analysis reveals intra-tumoral heterogeneity and immunotherapy strategies in high-grade serous ovarian cancer.

PMID 41907410 · PMC13018870 · iScience · 2026 · 8 claims · 8 setups

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scRNA-seq of 17 HGSOC tissue samples reveals seven major cell types and extensive intra-tumoral heterogeneity

hgsoc epithelial tcga gse165897 single-cell copy kegg
KRT15 identified by scRNA-Seq and machine learning as stemness regulator and prognostic biomarker in ESCC.

PMID 41907411 · PMC13018899 · iScience · 2026 · 8 claims · 8 setups

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A malignant epithelial subpopulation (Cluster 0) with the highest CytoTRACE stemness potential and highest EMT activity exists in ESCC scRNA-seq data

escc degs eca109 kyse180 scrna-seq machine immunohistochemistry
Dissecting host stress responses for predictable heterologous gene expression in E. coli.

PMID 41909945 · PMC13034041 · Nucleic acids research · 2026 · 8 claims · 6 setups

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Excessive heterologous mRNA triggers a cold shock response that controls mRNA stability (cspA–I, deaD)

coli combined rna-seq independent flow
Boolean logic links chromatin accessibility states to gene expression variability across cell types.

PMID 41909952 · PMC13148175 · Nucleic acids research · 2026 · 7 claims · 4 setups

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ocrRBBR infers interpretable Boolean rules from combinations of accessible OCRs that explain gene expression variability across cell types

immune genes atac-seq bulk hi-c
Cell neighborhood topology directs rare cell population identification.

PMID 41912521 · PMC13199379 · Nature communications · 2026 · 8 claims · 8 setups

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RareQ is a framework that quantifies neighborhood connectivity (Q), a cell-specific measure of kNN-graph cliquishness, to detect rare cell populations from single-cell and spatial omics data

downsampled pbmc brain simulated scrna-seq cite-seq single-cell
Quemliclustat and chemotherapy with or without zimberelimab in metastatic pancreatic adenocarcinoma: a randomized phase 1 trial.

PMID 41912809 · PMC13099643 · Nature medicine · 2026 · 7 claims · 8 setups

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Quemliclustat combined with gemcitabine/nab-paclitaxel (G/nP) with or without zimberelimab has a safety profile consistent with G/nP alone across dose-escalation and dose-expansion phases

mia hct-116 patients randomized rna-seq rt-pcr phase
Genomic Landscape Analysis of Canine Pulmonary Adenocarcinoma Reveals Candidate Targetable Gene Fusions.

PMID 41914575 · PMC13161739 · Veterinary and comparative oncology · 2026 · 8 claims · 7 setups

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STAR-Fusion identified 26 gene fusions in 19 of 36 (53%) cPAC tumours with RNA-seq data

cpac matched sdc4 rna-seq whole-genome whole-exome
scDenorm: a denormalization tool for integrating single-cell transcriptomics data.

PMID 41915012 · PMC13142155 · GigaScience · 2026 · 8 claims · 7 setups

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Inconsistent delta-method normalization across datasets introduces biases (e.g., B-cell separation) that persist even after integration with Harmony, scanorama, or BBKNN.

10x brain ucsc datasets scrna-seq integration snrna-seq
Compact and informative representation learning for scRNA-seq data clustering with masked information bottleneck.

PMID 41917934 · PMC13162528 · BMC biology · 2026 · 6 claims · 4 setups

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scMIB achieves state-of-the-art and more stable clustering performance across diverse scRNA-seq datasets compared with ten baseline methods

real same splatter-simulated scrna-seq clustering denoising
An end-to-end generalizable deep learning framework to comprehensively analyze transcriptional regulation.

PMID 41922356 · PMC13212934 · Nature communications · 2026 · 8 claims · 7 setups

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BioSeq2Seq is a transformer-based deep learning framework that predicts genome-wide transcriptional regulatory profiles at 128-bp resolution by jointly using RO-seq data and DNA sequence as tri-modal input

k562 gm12878 imr-90 ro-seq chip-seq functional
MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy.

PMID 41922875 · PMC13095666 · Nature structural & molecular biology · 2026 · 8 claims · 6 setups

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MitoPerturb-Seq combines pooled CRISPR–Cas9 screening (CROP-seq) with 10x Genomics multiome (scATAC-seq + scRNA-seq) to simultaneously profile mtDNA sequence/copy number/heteroplasmy and the nuclear transcriptome/chromatin accessibility in single heteroplasmic cells

cas9-expressing heteroplasmic tfam-ko pooled tap-seq hybridization-capture-based
Aging-dependent microglial heterogeneity worsens outcomes in models of traumatic brain injury.

PMID 41926211 · PMC13262727 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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Aged TBI brains predominantly harbor proinflammatory NLRP3+ microglia, whereas young TBI brains harbor neuroprotective Lysozyme+ microglia

injured sorted facs-purified cas9-gfp scrna-seq atac-seq untargeted
PMEPA1 modulates YAP1 nuclear translocation to disrupt EMT subtypes and promote metastasis in Biliary tract cancer.

PMID 41932868 · PMC13172513 · Cell death & disease · 2026 · 8 claims · 8 setups

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PMEPA1 is a pivotal EMT regulator in BTC; its high expression correlates with adverse prognosis and distant metastasis

btc tcga hucct1 scrna-seq cnmf bulk
Single-Cell Computational Frameworks for Quantifying BET Bromodomain Inhibitor Resistance and Screening Re-Sensitizer Drugs in Triple-Negative Breast Cancer.

PMID 41933924 · PMC13205605 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

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Ferroptosis inhibition, marked by upregulation of suppressors (e.g., FTH1, GPX4) and downregulation of drivers, underlies the evolution of JQ1 resistance in TNBC cells

sum159 sum149 six lincs scrna-seq bulk cck8
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

Multi-omics reveal vitamin D regulation of immune-gut microbiome interactions and tolerogenic pathways in inflammatory bowel disease.

ZFP148 is a transcriptional repressor of cytolytic effector CD8(+) T cell differentiation.

Single-Cell Multi-Tissue T Cell Clonal Dynamics Reveal Distinct Immune Coercion Landscapes in MSI and MSS Colorectal Cancer.

A tissue-resolved, network-based transcriptomic framework for abiotic stress responses in sorghum.

Therapeutic manipulation and spatial quantification of the tumor microenvironment in colorectal cancer.

Single-cell transcriptomic analysis reveals intra-tumoral heterogeneity and immunotherapy strategies in high-grade serous ovarian cancer.

KRT15 identified by scRNA-Seq and machine learning as stemness regulator and prognostic biomarker in ESCC.

Dissecting host stress responses for predictable heterologous gene expression in E. coli.

Boolean logic links chromatin accessibility states to gene expression variability across cell types.

Cell neighborhood topology directs rare cell population identification.

Quemliclustat and chemotherapy with or without zimberelimab in metastatic pancreatic adenocarcinoma: a randomized phase 1 trial.

Genomic Landscape Analysis of Canine Pulmonary Adenocarcinoma Reveals Candidate Targetable Gene Fusions.

scDenorm: a denormalization tool for integrating single-cell transcriptomics data.

Compact and informative representation learning for scRNA-seq data clustering with masked information bottleneck.

An end-to-end generalizable deep learning framework to comprehensively analyze transcriptional regulation.

MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy.

Aging-dependent microglial heterogeneity worsens outcomes in models of traumatic brain injury.

PMEPA1 modulates YAP1 nuclear translocation to disrupt EMT subtypes and promote metastasis in Biliary tract cancer.

Single-Cell Computational Frameworks for Quantifying BET Bromodomain Inhibitor Resistance and Screening Re-Sensitizer Drugs in Triple-Negative Breast Cancer.

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