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).
-
Full-text index only
Usefulness of cancer-testis antigens as biomarkers for the diagnosis and treatment of hepatocellular carcinoma.
PMID 17244360 · PMC1797003 · Journal of translational medicine · 2007 · 8 claims · 8 setups
HCC is a highly heterogeneous, non-linear disease driven by complex, multi-stage genetic and environmental alterations
-
Has reproduction · 81
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
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.
-
Has reproduction · 78
Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring.
PMID 42038409 · PMC13107125 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups
Long-read shotgun metagenomic sequencing of eDNA can simultaneously detect and quantify organismal DNA from viruses to mammals in a single assay
-
Full-text index only
Magnetically assisted DNA assays: high selectivity using conjugated polymers for amplified fluorescent transduction.
PMID 15905472 · PMC1131937 · Nucleic acids research · 2005 · 8 claims · 8 setups
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.
-
Full-text index only
Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry.
PMID 17166507 · PMC7094463 · Journal of chromatography. A · 2007 · 8 claims · 8 setups
Standardizing sample preparation procedures for serum/plasma profiling is critical for obtaining reliable biomarkers, since slight procedural changes can produce very different protein profiles.
-
Full-text index only
Proteomic analysis of aqueous humor from patients with myopia.
PMID 18334949 · PMC2268849 · Molecular vision · 2008 · 7 claims · 6 setups
Total protein concentration in AH is significantly greater in high myopia patients than in non-myopic controls
-
Has reproduction · 65
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses.
PMID 33932985 · PMC8088074 · BMC bioinformatics · 2021 · 8 claims · 5 setups
SPEAQeasy is a portable, easy-to-install, Nextflow-powered RNA-seq processing pipeline that lowers the computational entry barrier for biologists/clinicians
-
Full-text index only
Autoantibody profiling for the study and treatment of autoimmune disease.
PMID 12223102 · PMC128938 · Arthritis research · 2002 · 8 claims · 8 setups
Custom-fabricated antigen microarrays (spotted on poly-L-lysine-coated glass slides) enable multiplex profiling of autoantibody responses in autoimmune disease sera.
-
Full-text index only
Identification of novel markers for liver fibrosis in HIV/hepatitis C virus coinfected individuals using genomics-based approach.
PMID 18614866 · PMC2654216 · AIDS (London, England) · 2008 · 8 claims · 6 setups
An 8-marker model combining six serum markers, age, and ART experience predicts liver fibrosis stage with an AUROC of 0.904.
-
Has reproduction · 87
A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.
PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups
A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.
-
Full-text index only
Proteomics as a method for early detection of cancer: a review of proteomics, exhaled breath condensate, and lung cancer screening.
PMID 18095050 · PMC2150625 · Journal of general internal medicine · 2008 · 8 claims · 7 setups
Protein expression is closely aligned with cellular activity, unlike genomic changes which may have no functional significance
-
Full-text index only
Mining novel biomarkers for prognosis of gastric cancer with serum proteomics.
PMID 19740432 · PMC2753349 · Journal of experimental & clinical cancer research : CR · 2009 · 7 claims · 4 setups
A 5-peak prognosis pattern (4474, 4542, 6443/6643, 4988, 6685 Da) predicts poor vs good prognosis in GC with higher sensitivity/specificity than CEA and TNM stage
-
Has reproduction · 65
High-throughput sequencing SELEX for the determination of DNA-binding protein specificities in vitro.
PMID 35776646 · PMC9243297 · STAR protocols · 2022 · 8 claims · 8 setups
HT-SELEX enables unbiased, in vitro determination of preferred DNA target motifs for DNA-binding proteins by iterative selection and PCR amplification of bound oligonucleotides
-
Has reproduction
Comprehensive analysis of m(6)A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing.
PMID 38510975 · PMC10950754 · Computational and structural biotechnology journal · 2024 · 8 claims · 6 setups
m6A site number and m6A levels are significantly lower in post-treatment complete remission (CR) bone marrow than in pre-treatment AML bone marrow
-
Full-text index only
Detection of YMDD motif mutants by oligonucleotide chips in lamivudine-untreated patients with chronic hepatitis B virus infection.
PMID 15308845 · PMC2816888 · Journal of Korean medical science · 2004 · 6 claims · 5 setups
An oligonucleotide chip was developed using probes for wild-type YMDD, M552V, and three M552I probe variants to detect HBV polymerase YMDD motif mutations
-
Full-text index only
Elevated serum levels of interferon-regulated chemokines are biomarkers for active human systemic lupus erythematosus.
PMID 17177599 · PMC1702557 · PLoS medicine · 2006 · 8 claims · 4 setups
30 of 160 measured serum analytes (cytokines, chemokines, growth factors, soluble receptors) are dysregulated in SLE serum
-
Full-text index only
Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.
PMID 17610740 · PMC1925094 · BMC genomics · 2007 · 8 claims · 5 setups
SNP-MaP can be effectively applied to the Affymetrix 500K GeneChip, providing a cost-effective, reliable and valid initial genomewide screen
-
Full-text index only
Detection of venous thromboembolism by proteomic serum biomarkers.
PMID 17579716 · PMC1891085 · PloS one · 2007 · 5 claims · 8 setups
A neural network-based classifier built from direct MALDI-TOF MS serum protein expression profiles can diagnose VTE with sensitivity/specificity that exceeds D-dimer assays
-
Full-text index only
Validation of reverse phase protein array for practical screening of potential biomarkers in serum and plasma: accurate detection of CA19-9 levels in pancreatic cancer.
PMID 18615426 · PMC2992687 · Proteomics · 2008 · 8 claims · 6 setups
RPPA-measured CA19-9 levels correlate strongly with ELISA-measured levels in the same patient samples
-
Full-text index only
Rapid preparation of nuclei-depleted detergent-resistant membrane fractions suitable for proteomics analysis.
PMID 18534013 · PMC2440737 · BMC cell biology · 2008 · 6 claims · 4 setups
A modified differential detergent extraction method (pelleting nuclei/intact cells at low speed before detergent solubilization) yields DRM fractions with markedly reduced nuclear protein contamination compared to the conventional method.