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 188

Assay: group ✕ Clear

Of mice and men: comparative proteomics of bronchoalveolar fluid.

PMID 20032019 · PMC3049194 · The European respiratory journal · 2010 · 8 claims · 8 setups

Full-text index only

Comparative shotgun proteomics of human and mouse BALF identifies conserved pathways (immunity, defence response, protease activity) alongside species-specific divergent pathways.

pooled oxidative unpooled balf shotgun functional protein-protein
Application of OMICS technologies in occupational and environmental health research; current status and projections.

PMID 19933307 · PMC2910417 · Occupational and environmental medicine · 2010 · 8 claims · 6 setups

Full-text index only

Five OMICS technologies are well established: genotyping, transcriptomics, epigenomics, proteomics, and metabolomics

population genomic blood genome array-based comparative gene
Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora.

PMID 19900279 · PMC3091320 · Genome biology · 2009 · 8 claims · 6 setups

Full-text index only

This is the first genetic linkage map constructed for any coral species or any non-Bilaterian animal

acropora millepora coral snp genetic segregation
Involvement of the modifier gene of a human Mendelian disorder in a negative selection process.

PMID 19888326 · PMC2765618 · PloS one · 2009 · 7 claims · 4 setups

Full-text index only

The frequency of SAA1 alpha/alpha homozygotes is much higher among Armenian FMF patients (24%) than Karabakhian FMF patients (4%)

genomic population simulated pcr pearson monte
Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

PMID 19883501 · PMC3091315 · Genome biology · 2009 · 8 claims · 7 setups

Full-text index only

ESEs and ESSs diverge especially fast shortly after gene duplication, correlating with time since duplication (Ks)

paralogous human-mouse duplicated comparative ortholog binomial
Sequence variations of GRM6 in patients with high myopia.

PMID 19862333 · PMC2765235 · Molecular vision · 2009 · 7 claims · 8 setups

Full-text index only

Three novel GRM6 variations with predicted functional consequences (c.67-82delCAGGCGGGCCTGGCGCinsT, c.858-5a>g, c.1537G>A) were found in high myopia patients but absent in 96 controls

genomic pcr mglur6 grm6 pcr heteroduplex pcr-restriction
Toward the use of genomics to study microevolutionary change in bacteria.

PMID 19855823 · PMC2756242 · PLoS genetics · 2009 · 7 claims · 5 setups

Full-text index only

The clonal population structure of bacteria, combined with occasional DNA import, provides a powerful context for identifying genetic bases of adaptive phenotypes via association studies.

neisseria campylobacter helicobacter sequence multilocus phylogeny-based
Point mutations in GLI3 lead to misregulation of its subcellular localization.

PMID 19829694 · PMC2758996 · PloS one · 2009 · 6 claims · 8 setups

Full-text index only

The MID1-α4-PP2A complex regulates the subcellular localization and transcriptional activity of GLI3.

hela immunofluorescence real-time luciferase
Reconstructing Indian population history.

PMID 19779445 · PMC2842210 · Nature · 2009 · 8 claims · 8 setups

Full-text index only

Most Indian populations descend from a mixture of two ancient, genetically divergent populations: ANI (close to Middle Easterners, Central Asians, Europeans) and ASI (as distinct from ANI and East Asians as those are from each other).

indian pairs gujarati genome-wide principal fst-based
MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

PMID 19758471 · PMC2745589 · BMC bioinformatics · 2009 · 8 claims · 5 setups

Full-text index only

MtSNPscore, a weighted scoring pipeline combining literature evidence, in silico predictions, and case/control frequency, can prioritize likely pathogenic mtDNA variations

sporadic mitochondrial reported ataxia mitochondrial functional compensatory
A statistical model to identify differentially expressed proteins in 2D PAGE gels.

PMID 19763172 · PMC2734266 · PLoS computational biology · 2009 · 7 claims · 5 setups

Full-text index only

A mixture likelihood model incorporating both detected and non-detected proteins has higher statistical power to detect differential expression than standard approaches like the Student's t-test.

plasma simulated page simulated
CLEAN: CLustering Enrichment ANalysis.

PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups

Full-text index only

The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).

four breast combined hierarchical cluster csimm-based
Tracing the early bacterial settlers in preterm and very-low birth-weight infants: first report of microbiota dynamics in South American neonates.

PMID 41563098 · PMC12890024 · Infection and immunity · 2026 · 7 claims · 7 setups

Full-text index only

Klebsiella pneumoniae species complex and Escherichia coli dominate the gut microbial composition of VLBW infants

stool 16s fecal full-length taxonomic alpha
pmid-41507436

PMID 41507436 · PMC12859067 · 7 claims · 7 setups

Full-text index only

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
pmid-41513659

PMID 41513659 · PMC12858858 · 7 claims · 6 setups

Full-text index only

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
Peeling off the layers: skin taping and a novel proteomics approach to study atopic dermatitis.

PMID 19748658 · PMC8648281 · The Journal of allergy and clinical immunology · 2009 · 8 claims · 3 setups

Full-text index only

Noninvasive D-Squame tape stripping coupled with MS proteomics can profile the AD skin proteome

skin extracted lesion skin lc-ms statistical
scPASU: A computational protocol for quantifying polyadenylation site usage and alternative polyadenylation from 3' scRNA-seq data.

PMID 42085187 · PMC13157062 · STAR protocols · 2026 · 8 claims · 6 setups

Full-text index only

scPASU is a Snakemake-based workflow that quantifies APA from standard 3′ scRNA-seq data without requiring specialized library preparation

ureter processed scrna-seq read poly
Method of regulatory network that can explore protein regulations for disease classification.

PMID 19962281 · PMC7126395 · Artificial intelligence in medicine · 2010 · 6 claims · 2 setups

Full-text index only

A regulatory network (RN) can be constructed as a hopfield-like network, with nodes as biomarkers and directed weighted connections as regulatory relationships, optimized by minimizing an energy function measuring input-output disagreement.

nasopharyngeal sars seldi-tof-ms
A novel peak detection approach with chemical noise removal using short-time FFT for prOTOF MS data.

PMID 19681055 · PMC2782493 · Proteomics · 2009 · 8 claims · 2 setups

Full-text index only

PDA_stFFT is a novel automatic peak detection method for prOTOF MS data that does not require a priori knowledge of protein masses

peptide serum maldi-tof
Changes in social contacts in England during the COVID-19 pandemic between March 2020 and March 2021 as measured by the CoMix survey: A repeated cross-sectional study.

PMID 35231023 · PMC8887739 · PLoS medicine · 2022 · 8 claims · 2 setups

Full-text index only

Recorded social contacts in England decreased dramatically compared to prepandemic levels measured by the POLYMOD study

general population comix polymod

Experiments

Of mice and men: comparative proteomics of bronchoalveolar fluid.

Application of OMICS technologies in occupational and environmental health research; current status and projections.

Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora.

Involvement of the modifier gene of a human Mendelian disorder in a negative selection process.

Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

Sequence variations of GRM6 in patients with high myopia.

Toward the use of genomics to study microevolutionary change in bacteria.

Point mutations in GLI3 lead to misregulation of its subcellular localization.

Reconstructing Indian population history.

MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

A statistical model to identify differentially expressed proteins in 2D PAGE gels.

CLEAN: CLustering Enrichment ANalysis.

Tracing the early bacterial settlers in preterm and very-low birth-weight infants: first report of microbiota dynamics in South American neonates.

pmid-41507436

pmid-41513659

Peeling off the layers: skin taping and a novel proteomics approach to study atopic dermatitis.

scPASU: A computational protocol for quantifying polyadenylation site usage and alternative polyadenylation from 3' scRNA-seq data.

Method of regulatory network that can explore protein regulations for disease classification.

A novel peak detection approach with chemical noise removal using short-time FFT for prOTOF MS data.

Changes in social contacts in England during the COVID-19 pandemic between March 2020 and March 2021 as measured by the CoMix survey: A repeated cross-sectional study.