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 69

Assay: spectral ✕ Clear

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
Measurement reproducibility in the early stages of biomarker development.

PMID 15665389 · PMC3839328 · Disease markers · 2004 · 6 claims · 3 setups

Full-text index only

Functional PCA can be used as the basis for gauge R&R (repeatability and reproducibility) assessment of mass spectra without prior identification of which spectral features are biomarkers

pooled same registered seldi-tof univariate functional
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
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

Offshore Lake Michigan bacterioplankton show higher expression of DOM, N, and P acquisition/transporter genes than nearshore bacterioplankton

bacterioplankton lake metatranscriptomics metagenomic nutrient
Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.

PMID 36457147 · PMC9721438 · RNA biology · 2022 · 8 claims · 7 setups

Has reproduction · 93

Long-read RNA-seq detected 53,863 transcript isoforms from 10,426 genes in HUVECs, of which 22,195 were novel

huvecs huvec long-read bottom-up offline
A colorimetric method for point mutation detection using high-fidelity DNA ligase.

PMID 16257979 · PMC1275593 · Nucleic acids research · 2005 · 8 claims · 8 setups

Full-text index only

High-fidelity Tth DNA ligase combined with allele-specific ligation-based gold nanoparticle assembly enables colorimetric single-base discrimination without precise temperature control

p3-modified nanoparticle synthetic ligated uv-vis colorimetric melting
G-quadruplexes in promoters throughout the human genome.

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

Full-text index only

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
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

Full-text index only

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
Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

PMID 16646984 · PMC1557991 · Genome biology · 2006 · 8 claims · 4 setups

Full-text index only

A six-frame genomic ORF translation used as an MS search database can detect novel peptides absent from standard protein databases, revealing incomplete genome annotation.

pooled genome est novel tandem whole-genome est
Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes.

PMID 17486137 · PMC2673710 · Molecular systems biology · 2007 · 8 claims · 7 setups

Full-text index only

Global MudPIT-based proteomic profiling across six mouse lung developmental time points (E13.5–P56) identifies thousands of proteins and captures developmental/cell-biological expression patterns.

lung analysis embryonic homologues shotgun microarray k-nearest
Proteomics of the lysosome.

PMID 18977398 · PMC2684028 · Biochimica et biophysica acta · 2009 · 8 claims · 8 setups

Full-text index only

The mammalian lysosome has been shown to contain ~60 soluble luminal proteins and ~25 transmembrane proteins

liver placenta brain conditioned lc-ms n-terminal man6-p
A mouse plasma peptide atlas as a resource for disease proteomics.

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

Full-text index only

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

Full-text index only

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
A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.

PMID 19997597 · PMC2781549 · PloS one · 2009 · 8 claims · 7 setups

Full-text index only

The majority of proteins expressed in growing and non-growing S. aureus cells can be identified and quantified by a metabolic labeling proteomic approach

aureus 2-d 1-d gelc-ms
Metabolomics applied to diabetes research: moving from information to knowledge.

PMID 19875619 · PMC2768174 · Diabetes · 2009 · 8 claims · 7 setups

Full-text index only

Metabolomics measures chemical phenotypes that are the net result of genomic, transcriptomic, and proteomic variability, providing the most integrated profile of biological status

ins-1-derived pancreatic liver stedman 13c targeted ms-based
Nucleotide oligomerization domain-2 interacts with 2'-5'-oligoadenylate synthetase type 2 and enhances RNase-L function in THP-1 cells.

PMID 19853919 · PMC2787966 · Molecular immunology · 2009 · 7 claims · 6 setups

Full-text index only

OAS2 is identified as a novel NOD2-binding partner in THP-1 cells by tandem affinity purification and mass spectrometry

thp-1 hek293 tandem co-immunoprecipitation oas2
Isoforms of U1-70k control subunit dynamics in the human spliceosomal U1 snRNP.

PMID 19784376 · PMC2747018 · PloS one · 2009 · 8 claims · 8 setups

Full-text index only

Native human U1 snRNP shows differential incorporation of four protein isoforms (U1-70k isoforms 1/2, Sm-B/B')

native snrna intact denatured proteomic denaturing nucleic
FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors.

PMID 42102720 · PMC13201080 · GigaScience · 2026 · 8 claims · 6 setups

Full-text index only

A pipeline combining IDF transformation, sparse random projection (SRP), and NNDescent (the FEDRANN strategy) enables accurate overlap detection across diverse long-read datasets

real same chromosome genome overlap exact simulated
Tumour-brain crosstalk restrains cancer immunity via a sensory-sympathetic axis.

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

Full-text index only

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
Pilot proteomic profile of differentially regulated proteins in right atrial appendage before and after cardiac surgery using cardioplegia and cardiopulmonary bypass.

PMID 18824761 · PMC2629397 · Circulation · 2008 · 8 claims · 3 setups

Full-text index only

CP/CPB causes multiple consistent, reproducible changes in the human myocardial (right atrial) protein profile

right excised 2-dimensional tandem sds-page

Experiments

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

Measurement reproducibility in the early stages of biomarker development.

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

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

Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.

A colorimetric method for point mutation detection using high-fidelity DNA ligase.

G-quadruplexes in promoters throughout the human genome.

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

Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes.

Proteomics of the lysosome.

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.

A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.

Metabolomics applied to diabetes research: moving from information to knowledge.

Nucleotide oligomerization domain-2 interacts with 2'-5'-oligoadenylate synthetase type 2 and enhances RNase-L function in THP-1 cells.

Isoforms of U1-70k control subunit dynamics in the human spliceosomal U1 snRNP.

FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors.

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

Pilot proteomic profile of differentially regulated proteins in right atrial appendage before and after cardiac surgery using cardioplegia and cardiopulmonary bypass.