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: using ✕ Assay: single ✕ Clear

Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.

PMID 16925841 · PMC1810556 · Genome biology · 2006 · 8 claims · 5 setups

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Exogean is a framework using directed acyclic coloured multigraphs (DACMs) to represent biological objects (mRNA, ESTs, protein alignments, exons) and iteratively combine them into complex protein-coding transcript models.

genome sequences automatic manual sequence
Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.

PMID 15640441 · PMC546178 · Nucleic acids research · 2005 · 8 claims · 7 setups

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NCL aggregation of DNA-modified gold nanoparticles shows extraordinary selectivity against terminal mismatches at the free ends of surface-bound duplexes

probe-modified probe-gnp synthetic four uv-vis ssdna pcr
Alternative splicing dynamics during human cardiac development in vivo and in vitro.

PMID 41483812 · PMC12925949 · Stem cell reports · 2026 · 8 claims · 8 setups

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iPSC-CMs globally resemble prenatal cardiac cells at both the transcriptional and splicing levels

ipsc-cms heart bulk ipsc-cm immunofluorescence single-cell bulk
Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.

PMID 37065499 · PMC10098459 · Frontiers in genetics · 2023 · 8 claims · 8 setups

Has reproduction · 63

Clustering of 31 CAFs genes across 868 HNSCC samples identifies two distinct molecular patterns (C1, C2) with different survival outcomes

hnscc combined gse164690 tcga-hnsc ssgsea unsupervised immune
Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

PMID 34519538 · PMC8546597 · mBio · 2021 · 8 claims · 8 setups

Has reproduction · 90

Eleven new genomes were added to the Tethybacterales order and a novel family (Polydorabacteraceae) was identified

tsitsikamma tethybacterales putative bin genome 16s multi-locus
Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.

PMID 41792309 · PMC13171632 · Nature microbiology · 2026 · 7 claims · 6 setups

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Enzymatic in situ polyadenylation increases bacterial RNA recovery in oligo(dT)-based spatial transcriptomics arrays by up to ~100-fold while preserving host gene capture

apc-deficient heart ileum fresh-frozen spatial high-resolution bulk
Chromosome-scale genome assembly and annotation of the two-spotted cricket Gryllus bimaculatus (Orthoptera: Gryllidae).

PMID 41678355 · PMC13042277 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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A chromosome-scale genome assembly of the white-eyed mutant G. bimaculatus strain was generated using ONT + PacBio HiFi long reads integrated with Hi-C data

bimaculatus nanopore pacbio hi-c
Putting proteins in one place.

PMID 12790144 · PMC1316915 · Environmental health perspectives · 2003 · 8 claims · 7 setups

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Rapamycin inhibits TOR, causing the silencing protein Sir3 to detach from chromatin at stress-response genes, triggering a coordinated multigene stress response that halts cancer cell proliferation

saccharomyces yeast vascular skin chemical chromatin microarray
scTWAS: a powerful statistical framework for single-cell transcriptome-wide association studies.

PMID 41820391 · PMC13121454 · Nature communications · 2026 · 8 claims · 5 setups

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scTWAS uses a latent-variable expression-measurement model combined with a moment-based regression to more accurately estimate genetic regulation of gene expression from single-cell data, improving GReX prediction across cell types and datasets

onek1k-derived onek1k-based immune brain simulated two-sample stage
Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models.

PMID 41540084 · PMC12894745 · NPJ systems biology and applications · 2026 · 8 claims · 8 setups

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The presence of immune cells in the environment significantly alters CLL cell activation

autologous monoculture non-adherent pbmc bulk flow deconvolution
sCellST predicts single-cell gene expression from H& E images.

PMID 41513659 · PMC12858858 · Nature communications · 2026 · 7 claims · 6 setups

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sCellST is a weakly supervised (Multiple Instance Learning) deep learning framework that predicts single-cell gene expression from H&E images alone, trained using paired spatial transcriptomics (Visium) and H&E slides

ovarian kidney prostate breast simulation spot-level nucleus
OTMODE: an optimal transport theory-based framework for identifying differential features in single-cell multi-omics data.

PMID 41335419 · PMC12766913 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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OTMODE, using an unbalanced Sinkhorn algorithm and Wald test, improves differential feature identification in single-cell multi-omics data

simulated classical degs naive simulated bulk real
Viral and host determinants of RNA virus vector replication and expression.

PMID 15734041 · PMC7115378 · Vaccine · 2005 · 7 claims · 4 setups

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BMV RNA replication occurs in a virus-induced, membrane-bounded compartment rather than in the open cytoplasm.

bmv saccharomyces wild-type immunogold genome-wide northern
An SVM-based system for predicting protein subnuclear localizations.

PMID 16336650 · PMC1325059 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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New kernels defined on k-peptide vectors mapped by BLOSUM62-based high-scored pair matrices (D1, D2, D3) improve SVM discrimination of protein subnuclear localization compared to conventional k-peptide encodings.

single-localization multi-localization same svm sequence
Imputation-based analysis of association studies: candidate regions and quantitative traits.

PMID 17676998 · PMC1934390 · PLoS genetics · 2007 · 8 claims · 2 setups

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Imputation-based Bayesian regression increases power to detect association compared with standard single-SNP tests, even when the causal variant is directly typed

study phenotyped genotype bayesian
Complex germline and somatic mutation processes at a haploid human minisatellite shown by single-molecule analysis.

PMID 18929582 · PMC2599865 · Mutation research · 2008 · 8 claims · 5 setups

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Overall MSY1 mutation frequencies in sperm (2.68%) and blood (1.88%) are not significantly different

sperm donor hgr1b3 single-molecule fluorescent radioactive
A chromosome-level reference genome and pangenome for barn swallow population genomics.

PMID 36662619 · PMC10044405 · Cell reports · 2023 · 8 claims · 8 setups

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A chromosome-level, karyotype-validated reference genome (bHirRus1) was assembled using the VGP pipeline combining PacBio CLR, 10x Linked-Reads, Bionano optical maps, and Hi-C data

single barn bhirrus1 rustica genome cytogenetic reference-free
Mutational analysis of BRCA1 gene in ovarian and breast-ovarian cancer families in Japan.

PMID 9197534 · PMC5921420 · Japanese journal of cancer research : Gann · 1997 · 5 claims · 2 setups

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Germline BRCA1 mutations were detected in 7 of 19 Japanese cancer families (4 breast-ovarian, 3 site-specific ovarian)

genomic tumor single-strand loss
Mutations in the ST7/RAY1/HELG locus rarely occur in primary colorectal, gastric, and hepatocellular carcinomas.

PMID 12799635 · PMC2741100 · British journal of cancer · 2003 · 7 claims · 4 setups

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ST7 gene mutations are rare in primary colorectal, gastric, and hepatocellular carcinomas

colorectal pcr same clinicopathological pcr-single-strand direct microsatellite
Comprehensive analysis of the causal risk factor from hypertension associated with prognosis and therapeutic response in renal cell carcinoma by multi-omics analysis and validation.

PMID 41680825 · PMC12998095 · Biology direct · 2026 · 8 claims · 8 setups

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A 48-gene cross-species hypertension (HTN) gene module identified from human and SHR rat scRNA-seq can classify ccRCC patients into two molecular subgroups with distinct survival and targeted therapy response

aortic spontaneously tcga icgc single-cell bulk summary-data-based

Experiments

Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.

Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.

Alternative splicing dynamics during human cardiac development in vivo and in vitro.

Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.

Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.

Chromosome-scale genome assembly and annotation of the two-spotted cricket Gryllus bimaculatus (Orthoptera: Gryllidae).

Putting proteins in one place.

scTWAS: a powerful statistical framework for single-cell transcriptome-wide association studies.

Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models.

sCellST predicts single-cell gene expression from H& E images.

OTMODE: an optimal transport theory-based framework for identifying differential features in single-cell multi-omics data.

Viral and host determinants of RNA virus vector replication and expression.

An SVM-based system for predicting protein subnuclear localizations.

Imputation-based analysis of association studies: candidate regions and quantitative traits.

Complex germline and somatic mutation processes at a haploid human minisatellite shown by single-molecule analysis.

A chromosome-level reference genome and pangenome for barn swallow population genomics.

Mutational analysis of BRCA1 gene in ovarian and breast-ovarian cancer families in Japan.

Mutations in the ST7/RAY1/HELG locus rarely occur in primary colorectal, gastric, and hepatocellular carcinomas.

Comprehensive analysis of the causal risk factor from hypertension associated with prognosis and therapeutic response in renal cell carcinoma by multi-omics analysis and validation.