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 411

System / cell line: healthy ✕ Clear

Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.

PMID 42098796 · PMC13154700 · Microbiome · 2026 · 8 claims · 5 setups

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Poly(A)-enriched mRNA-seq can reliably reconstruct microbiome composition, validated against a quantitative mock community standard and metagenomic analysis

zymobiomics vls-vscc vulvar subset mrna-seq rna-seq poly
TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.

PMID 42277027 · PMC13260335 · Nature communications · 2026 · 8 claims · 5 setups

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TOFU-MAaPO yields significantly more high-quality MAGs than metaFun, nf-core/mag, and ATLAS due to integration of multiple complementary binning tools with unified MAGScoT refinement

gut same uniquely metagenome quality assembly-free
Integrated transcriptomic landscape of medulloblastoma and ependymoma reveals novel tumor subtype-specific biology.

PMID 41159380 · PMC12979040 · Neuro-oncology · 2026 · 8 claims · 8 setups

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A unified UMAP-based transcriptomic landscape built from 888 medulloblastoma and 370 ependymoma tumors reveals distinct clusters corresponding to known and novel molecular subtypes.

medulloblastoma ependymoma healthy shh bulk fusion copy
Single-Nucleus Multi-Omics Reveals Hypoxia-Driven Angiogenic Programs and Their Epigenetic Control in Sinonasal Squamous Cell Carcinoma.

PMID 41498635 · PMC12948189 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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Five distinct malignant cell populations exist in SNSCC, with hypoxic (TC1) and proliferative (TC2) subtypes associated with adverse clinical outcomes.

snscc bulk single-nucleus bulk single-nucleus methylation
A cellular epigenetic classification system for glioblastoma.

PMID 41499453 · PMC13128495 · Neuro-oncology · 2026 · 8 claims · 8 setups

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ITHresolveGBM, a hierarchical two-step NMF method, deconvolutes bulk GBM DNA methylation profiles into three non-malignant (immune, glial, neuronal) and three malignant components

gbm healthy pseudo-bulk tcga illumina single-cell deconvolution
Single-cell and spatial transcriptomic profiling of cardiac fibroblasts following myocardial infarction.

PMID 41526391 · PMC12890913 · Scientific data · 2026 · 7 claims · 6 setups

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Cthrc1+ Reparative Cardiac Fibroblasts (RCFs) are the primary driver of the cardiac healing process after myocardial infarction

col1α1-gfp+ heart frozen bulk single-cell spatial
Exploring phenotype-related single-cells through attention-enhanced representation learning.

PMID 41566378 · PMC12906058 · Genome medicine · 2026 · 6 claims · 5 setups

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scPhase, an attention-based multiple instance learning (AMIL) framework with Mixture-of-Experts aggregation, predicts sample-level clinical phenotypes from raw scRNA-seq data and generalizes across patient cohorts

pbmcs brain tumor scrna-seq
Single-immunocyte transcriptomics reveal the role of natural killer cell-dependent exogenous antigen presentation in ankylosing spondylitis severity.

PMID 41593306 · PMC12868835 · Experimental & molecular medicine · 2026 · 8 claims · 8 setups

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Innate antibacterial defense functions are generally enhanced in most cell types at AS onset and are negatively associated with AS severity

pbmcs gwas pbmc-derived cd4+ single-cell bulk mendelian
Integrative miRNA-mRNA Network and Molecular Dynamics-Based Identification of Therapeutic Candidates for Paroxysmal Nocturnal Hemoglobinuria.

PMID 41599741 · PMC12845513 · Pharmaceuticals (Basel, Switzerland) · 2026 · 8 claims · 8 setups

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A PIGA-knockout (PIGA-KO) THP-1 cell model was successfully established using CRISPR/Cas9 RNP technology as a PNH model

thp-1 literature-validated pnh cxcl8 crispr rt-qpcr bulk
Tumour-brain crosstalk restrains cancer immunity via a sensory-sympathetic axis.

PMID 41639447 · PMC12935554 · Nature · 2026 · 8 claims · 8 setups

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Lung adenocarcinoma (LUAD) induces increased innervation and functional/transcriptional engagement of vagal sensory neurons (VSNs)

kras-g12d tumour-bearing vagal npy2r-ires-cre whole-mount aav neurite
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
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
PAH-former: Transfer learning for efficient discovery of pulmonary arterial hypertension-associated genes.

PMID 41790620 · PMC12965534 · PloS one · 2026 · 7 claims · 7 setups

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PAH-former, a Geneformer model fine-tuned on public PAH scRNA-seq data, can perform in silico perturbation to identify and rank candidate PAH disease-associated genes

pah scrna-seq pah-former candidate scrna-seq transfer perturbation
Integrative CSF profiling identifies disease-specific immune responses in leptomeningeal disease.

PMID 41794040 · PMC13006398 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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CSF exhibits distinct, disease-specific immune landscapes across CNSL, BrMs, and GB-associated LMD

csf peripheral brain cell-free single-cell deep spatial
Design of a targeted blood transcriptional panel for monitoring immunological changes accompanying pregnancy.

PMID 38352867 · PMC10861739 · Frontiers in immunology · 2024 · 6 claims · 3 setups

Has reproduction · 73

A targeted panel of 176 transcripts plus 8 housekeeping genes was identified for monitoring immunological changes during pregnancy

blood bulk microarray bloodgen3
pyrpipe: a Python package for RNA-Seq workflows.

PMID 34085037 · PMC8168212 · NAR genomics and bioinformatics · 2021 · 8 claims · 3 setups

Has reproduction · 79

pyrpipe enables development of flexible, reproducible, and easy-to-debug RNA-Seq computational pipelines purely in Python, in an object-oriented manner

circulating zea bulk novo
Discrimination of three mutational events that result in a disruption of the R122 primary autolysis site of the human cationic trypsinogen (PRSS1) by denaturing high performance liquid chromatography.

PMID 11734061 · PMC60523 · BMC genetics · 2001 · 7 claims · 3 setups

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DHPLC can readily discriminate the two known mutational events (c.365G>A and c.365~366GC>AT) that both cause the R122H mutation

genomic pcr independently pcr denaturing direct
Systematic mutation analysis of KIAA0767 and KIAA1646 in chromosome 22q-linked periodic catatonia.

PMID 16225677 · PMC1274336 · BMC psychiatry · 2005 · 8 claims · 3 setups

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Systematic mutation screening of KIAA0767 and KIAA1646 was performed in chromosome 22q-linked periodic catatonia pedigrees

genomic unrelated systematic case-control
Adequate use of allele frequencies in Hispanics--a problem elucidated in nephrotic syndrome.

PMID 19876656 · PMC2899680 · Pediatric nephrology (Berlin, Germany) · 2010 · 7 claims · 3 setups

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Self-identified Hispanic SRNS patients in the USA are genetically heterogeneous, being of either Caucasian or Mesoamerican (Native-American) descent

genomic same healthy direct genome-wide
Aryl Hydrocarbon Receptor (AhR) Activation by 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) Dose-Dependently Shifts the Gut Microbiome Consistent with the Progression of Non-Alcoholic Fatty Liver Disease.

PMID 34830313 · PMC8625315 · International journal of molecular sciences · 2021 · 8 claims · 2 setups

Has reproduction · 79

TCDD dose-dependently enriches Lactobacillus species, particularly L. reuteri, in the mouse cecum microbiome

cecum fecal shotgun humann

Experiments

Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.

TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.

Integrated transcriptomic landscape of medulloblastoma and ependymoma reveals novel tumor subtype-specific biology.

Single-Nucleus Multi-Omics Reveals Hypoxia-Driven Angiogenic Programs and Their Epigenetic Control in Sinonasal Squamous Cell Carcinoma.

A cellular epigenetic classification system for glioblastoma.

Single-cell and spatial transcriptomic profiling of cardiac fibroblasts following myocardial infarction.

Exploring phenotype-related single-cells through attention-enhanced representation learning.

Single-immunocyte transcriptomics reveal the role of natural killer cell-dependent exogenous antigen presentation in ankylosing spondylitis severity.

Integrative miRNA-mRNA Network and Molecular Dynamics-Based Identification of Therapeutic Candidates for Paroxysmal Nocturnal Hemoglobinuria.

Tumour-brain crosstalk restrains cancer immunity via a sensory-sympathetic axis.

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

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

PAH-former: Transfer learning for efficient discovery of pulmonary arterial hypertension-associated genes.

Integrative CSF profiling identifies disease-specific immune responses in leptomeningeal disease.

Design of a targeted blood transcriptional panel for monitoring immunological changes accompanying pregnancy.

pyrpipe: a Python package for RNA-Seq workflows.

Discrimination of three mutational events that result in a disruption of the R122 primary autolysis site of the human cationic trypsinogen (PRSS1) by denaturing high performance liquid chromatography.

Systematic mutation analysis of KIAA0767 and KIAA1646 in chromosome 22q-linked periodic catatonia.

Adequate use of allele frequencies in Hispanics--a problem elucidated in nephrotic syndrome.

Aryl Hydrocarbon Receptor (AhR) Activation by 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) Dose-Dependently Shifts the Gut Microbiome Consistent with the Progression of Non-Alcoholic Fatty Liver Disease.