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 18

System / cell line: gene ✕ Assay: spectral ✕ Clear

Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups

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A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.

liver simulated conserved nearly gene simulation kolmogorov-smirnov
Brain-specific proteins decline in the cerebrospinal fluid of humans with Huntington disease.

PMID 18984577 · PMC2649809 · Molecular & cellular proteomics : MCP · 2009 · 8 claims · 6 setups

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Brain-specific proteins are 1.8 times more likely to be observed in CSF than in plasma

csf brain normal 2d-dige label-free isotopic
Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases.

PMID 18842138 · PMC2760875 · Genome biology · 2008 · 8 claims · 6 setups

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AD-related genes (APOE, A2M, PON2, MAP4) and CVD-associated genes (COMT, CBS, WNK1) congregate in a single co-expression module, linking AD and CVD at the transcriptional level

entorhinal subjects expression differentially microarray significance principal
Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families.

PMID 16895434 · PMC1534073 · PLoS computational biology · 2006 · 8 claims · 7 setups

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The density of transmembrane gene duplicates positively correlates with the estimated maximum number of cell types of common ancestors

transmembrane simulated age duplicate maximum kernel monte
Blood and tissue correlates of steroid non-response in checkpoint inhibition-induced immune-related adverse events.

PMID 41254329 · PMC12627558 · Communications medicine · 2025 · 7 claims · 6 setups

Has reproduction · 71

An enhanced type 1/type 17 (Th1/Th17, TC1/TC17) immune response in blood and tissue is associated with steroid non-response in irAEs

pbmcs pre-steroids extended snap-frozen spectral pd-1 ici-bound
Metatranscriptomics-based investigation of bacterial community dynamics across a dissolved organic matter gradient in southern Lake Michigan.

PMID 41860215 · PMC13101498 · Applied and environmental microbiology · 2026 · 7 claims · 6 setups

Has reproduction · 81

DOM composition changes significantly across the nearshore-to-offshore transect, with more terrestrially derived and high-molecular-weight DOM nearshore, despite only minor reductions in DOC and similar inorganic N and P levels.

free-living bacterioplankton 0.2-µm lake metatranscriptomics metagenomics dissolved
G-quadruplexes in promoters throughout the human genome.

PMID 17169996 · PMC1802602 · Nucleic acids research · 2007 · 8 claims · 6 setups

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Promoter regions (1 kb upstream of TSS) are significantly enriched in quadruplex motifs (PQS) relative to the rest of the genome

genome quiescent gene synthetic computational nuclease gene
High-resolution metagenomic reconstruction of the freshwater spring bloom.

PMID 36698172 · PMC9878933 · Microbiome · 2023 · 8 claims · 8 setups

Has reproduction · 69

High-frequency metagenomic sampling (57 samples, 3 filter sizes, 2 depths, 37 days) recovers thousands of prokaryotic, eukaryotic, and viral genomes tracking spring bloom succession in fine detail

freshwater phytoplankton heterotrophic reservoir 16s 18s shotgun
Comparative proteomic analysis of the PhoP regulon in Salmonella enterica serovar Typhi versus Typhimurium.

PMID 19746165 · PMC2736619 · PloS one · 2009 · 7 claims · 4 setups

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Comparative HPLC-MS/MS proteomic analysis, using phoP-/Q- mutants as controls, identifies PhoP-regulated proteins in S. Typhimurium LT2, S. Typhi CT18, and S. Typhi Ty2

typhimurium typhi genomic hplc-ms phon microarray
Genomics meets nanoscience: probing genes and the cell nucleus at 10-9 meters.

PMID 11897022 · PMC139022 · Genome biology · 2002 · 8 claims · 8 setups

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Trans-splicing generates cell-specific protocadherin mRNAs in human neurons

individual cancer pre-b saccharomyces reverse-transcriptase karyotypic spectral
A proteomic approach for plasma biomarker discovery with iTRAQ labelling and OFFGEL fractionation.

PMID 19888438 · PMC2771280 · Journal of biomedicine & biotechnology · 2010 · 6 claims · 6 setups

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iTRAQ labelling combined with OFFGEL fractionation improves proteome coverage of human plasma compared to iTRAQ alone or no iTRAQ

pooled plasma prefractionated immunodepleted itraq 1-dimensional fluorescence-based
Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.

PMID 19763266 · PMC2740864 · PloS one · 2009 · 8 claims · 8 setups

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Androgen treatment alters the whole-cell proteome of LNCaP prostate cancer cells

lncap androgen prostate itraq mudpit immunoblot
Expression Patterns of Immune Genes Reveal Heterogeneous Subtypes of High-Risk Neuroblastoma.

PMID 32629858 · PMC7408437 · Cancers · 2020 · 8 claims · 8 setups

Has reproduction · 73

Unsupervised biclustering of 283 NB-specific immune genes stratifies HR-NB into two reproducible subtypes: ultra-high-risk (UHR-NB) and (revised) HR-NB.

pediatric target cohorts neuroblastoma bulk spectral kaplan-meier
Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures.

PMID 36527260 · PMC10952672 · Glia · 2023 · 6 claims · 3 setups

Has reproduction · 26

The bulk microglial and monocyte transcriptomic program is highly contingent on the disease environment, challenging the notion of a universal microglial disease signature

acutely microglia c57bl meta-analysis integration spectral
Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.

PMID 29335641 · PMC5864184 · The ISME journal · 2018 · 7 claims · 6 setups

Has reproduction

Increasing salinity to >=43 ppt inhibits Trichodesmium growth/increases mortality while stimulating growth of associated Alteromonas, shifting community dominance to the heterotroph

alteromonas co-culture trichodesmium differential bulk whole-genome
Magnetically assisted DNA assays: high selectivity using conjugated polymers for amplified fluorescent transduction.

PMID 15905472 · PMC1131937 · Nucleic acids research · 2005 · 8 claims · 8 setups

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Introducing streptavidin-coated magnetic microparticles (MMPs) into a sandwich-type CP-based DNA sensor significantly improves selectivity against non-cognate DNA compared with previously reported CP-amplified sensors.

cell-free synthetic brca1-related artificial fluorescence magnetically salt-stringency
A mouse plasma peptide atlas as a resource for disease proteomics.

PMID 18522751 · PMC2481425 · Genome biology · 2008 · 8 claims · 6 setups

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A publicly available, high-quality mouse plasma peptide/protein repository (mouse PeptideAtlas) was built from 568 LC-MS/MS runs on four reference plasma pools.

plasma peptides fully tissues lc-ms anion database
Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

PMID 18510725 · PMC2481497 · Breast cancer research : BCR · 2008 · 7 claims · 7 setups

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Unsupervised hierarchical clustering of 130 SELDI-TOF peaks yielded six peak clusters and five distinct groups of breast cancer patients.

lysates breast microarrays imac-preseparated seldi-tof pilot immunohistochemistry

Experiments

Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

Brain-specific proteins decline in the cerebrospinal fluid of humans with Huntington disease.

Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases.

Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families.

Blood and tissue correlates of steroid non-response in checkpoint inhibition-induced immune-related adverse events.

Metatranscriptomics-based investigation of bacterial community dynamics across a dissolved organic matter gradient in southern Lake Michigan.

G-quadruplexes in promoters throughout the human genome.

High-resolution metagenomic reconstruction of the freshwater spring bloom.

Comparative proteomic analysis of the PhoP regulon in Salmonella enterica serovar Typhi versus Typhimurium.

Genomics meets nanoscience: probing genes and the cell nucleus at 10-9 meters.

A proteomic approach for plasma biomarker discovery with iTRAQ labelling and OFFGEL fractionation.

Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.

Expression Patterns of Immune Genes Reveal Heterogeneous Subtypes of High-Risk Neuroblastoma.

Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures.

Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.

Magnetically assisted DNA assays: high selectivity using conjugated polymers for amplified fluorescent transduction.

A mouse plasma peptide atlas as a resource for disease proteomics.

Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.