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: types ✕ Assay: umap ✕ Clear

T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups

Has reproduction · 78

Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification

kidney scrna-seq microarray meblack microarray single-cell scissor
Comprehensive comparison of gene expression diversity among a variety of human stem cells.

PMID 36458020 · PMC9706419 · NAR genomics and bioinformatics · 2022 · 8 claims · 8 setups

Has reproduction · 71

Tissue origin has a stronger influence on gene expression in iPSCs than in other stem cell types

escs stem batch-corrected degs bulk batch dimensionality
Single-nucleus multiome analysis in the human prefrontal cortex identifies gene expression and cis-regulatory elements associated with aging.

PMID 41832957 · PMC13137218 · Cell reports · 2026 · 8 claims · 8 setups

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Generated a single-nucleus multiome (snATAC + gene expression) dataset from 357 human dorsolateral prefrontal cortex samples (ages 15-100, European and African admixed ancestry), yielding over 1.5 million cells as a public resource.

postmortem million+ pfc each single-nucleus umap pseudobulk
Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer.

PMID 38066424 · PMC10709847 · BMC bioinformatics · 2023 · 8 claims · 8 setups

Has reproduction · 83

CHCT, a two-tier hierarchical classification tool built from methylation data, accurately classifies primary cancer type across 30 cancer types.

tumor clinical methylation clustered methylation unsupervised anova
scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

PMID 41507436 · PMC12859067 · Communications biology · 2026 · 7 claims · 7 setups

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scXDR outperforms seven methods that transfer drug response information from bulk RNA-seq to single-cell data, across all four evaluated scenarios

single-cell scrna-seq scxdr gse117872 heterogeneous benchmarking type
Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.

PMID 41029822 · PMC12486589 · Journal of translational medicine · 2025 · 8 claims · 6 setups

Has reproduction · 67

The negative binomial distribution best fits fRNA-seq transcript counts, with little evidence supporting zero-inflated extensions

compendium ffpe simulated frna-seq statistical bulk integrity
Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.

PMID 41438041 · PMC12719757 · iScience · 2025 · 8 claims · 8 setups

Has reproduction · 78

INVADE-seq (single-cell RNA-seq combined with 16S rRNA targeting) detects a sparse but widespread bacterial presence across diverse testicular cell types

testis young testicular invade-seq histology sperm
Inferring a spatial code of cell-cell interactions across a whole animal body.

PMID 36395331 · PMC9714814 · PLoS computational biology · 2022 · 8 claims · 6 setups

Has reproduction · 90

cell2cell computes cell-cell interaction (CCI) potential using a novel modified Bray-Curtis score based on complementary coexpression of ligand-receptor pairs between cells

elegans computational single-cell random genetic
TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution.

PMID 41296555 · PMC12807651 · Nucleic acids research · 2026 · 8 claims · 8 setups

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TE-SCALE is a comprehensive single-cell database integrating TE expression across 20 human cancer types and 12 tissue origins

tumor quality-controlled scrna-seq metacells scrna-seq subfamily automated
Excitatory GABA receptors shape locomotor circuit organization in C. elegans.

PMID 41703147 · PMC13003095 · Scientific reports · 2026 · 8 claims · 5 setups

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lgc genes are broadly and preferentially enriched in C. elegans locomotion motor neurons compared to other neuron types/subgroups

elegans cys-loop single-cell ucell multi-species
Human-scATAC-Corpus: a comprehensive database of scATAC-seq data.

PMID 41296545 · PMC12807747 · Nucleic acids research · 2026 · 8 claims · 6 setups

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Human-scATAC-Corpus is a comprehensive database of human scATAC-seq data comprising 5,407,621 cells from 35 datasets across 37 tissues or cell lines

tissues scatac-seq five subset scatac-seq genome unified
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
Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models.

PMID 41543530 · PMC12811152 · Microbial genomics · 2026 · 8 claims · 8 setups

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HBV splicing efficiency (coSI) correlates more strongly with disease progression than the overall proportion of spliced HBV RNA.

hbv same host bulk splicing splicebert
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
Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data.

PMID 41714655 · PMC13039149 · NPJ systems biology and applications · 2026 · 8 claims · 8 setups

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scRNA-seq and spatial transcriptomics data provide a rich, underused source of information for calibrating tissue-scale PDE models of ligand dynamics.

skin combined annotated scrna-seq single-cell spatial cell2location
Epigenetic loss of heterogeneity from low to high grade localized prostate tumours.

PMID 34911933 · PMC8674326 · Nature communications · 2021 · 8 claims · 7 setups

Has reproduction · 79

Low-grade (Gleason pattern 3) prostate cancer cells share chromatin accessibility features that are lost in high-grade (Gleason pattern 4) tumours

flash-frozen tcga single differentially single-cell bulk topic
Identification and validation of prognostic genes related to glycolysis and M2 macrophage in hepatocellular carcinoma: an integrated analysis of bulk RNA sequencing and single-cell RNA sequencing.

PMID 41766871 · PMC12935947 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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52 candidate genes were identified at the intersection of glycolysis-related genes (GRGs), M2 macrophage-related genes (MRGs), and HCC-vs-control DEGs (DEGs2).

tcga-lihc gse149614 key hcc bulk immune cox
PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells.

PMID 41565684 · PMC12881479 · Nature communications · 2026 · 8 claims · 8 setups

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PURE-seq integrates FACS sorting directly into PIP-seq barcoding reaction tubes, minimizing manual handling and cell loss for rare-cell single-cell sequencing.

hek293t pbmcs melanoma bone single-cell infercnv gene
Identification and validation of lymphangiogenesis-related genes for predicting acute myeloid leukemia prognosis: insights from bulk RNA sequencing and single-cell RNA sequencing analyses.

PMID 41772327 · PMC12979290 · Clinical and experimental medicine · 2026 · 7 claims · 8 setups

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A 6-LYMRG risk model (ANGPT1, HGF, MAPK8, PCNA, TBL1XR1, TLR4) is the optimal prognostic signature for AML

gse142698 tcga-laml tcga-laml1 gse116256 differential univariate kaplan-meier

Experiments

T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

Comprehensive comparison of gene expression diversity among a variety of human stem cells.

Single-nucleus multiome analysis in the human prefrontal cortex identifies gene expression and cis-regulatory elements associated with aging.

Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer.

scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.

Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.

Inferring a spatial code of cell-cell interactions across a whole animal body.

TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution.

Excitatory GABA receptors shape locomotor circuit organization in C. elegans.

Human-scATAC-Corpus: a comprehensive database of scATAC-seq data.

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

Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models.

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

Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data.

Epigenetic loss of heterogeneity from low to high grade localized prostate tumours.

Identification and validation of prognostic genes related to glycolysis and M2 macrophage in hepatocellular carcinoma: an integrated analysis of bulk RNA sequencing and single-cell RNA sequencing.

PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells.

Identification and validation of lymphangiogenesis-related genes for predicting acute myeloid leukemia prognosis: insights from bulk RNA sequencing and single-cell RNA sequencing analyses.