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
Genome-wide estimation of transcript concentrations from spotted cDNA microarray data.
PMID 16204447 · PMC1243803 · Nucleic acids research · 2005 · 8 claims · 3 setups
A Bayesian model incorporating experimental covariates (array, pen, probe, dye, scanning) can estimate absolute transcript concentrations from spotted microarray intensities without needing calibration of each sample or gene individually
-
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
A proteomic strategy to identify novel serum biomarkers for liver cirrhosis and hepatocellular cancer in individuals with fatty liver disease.
PMID 19656391 · PMC2729079 · BMC cancer · 2009 · 8 claims · 4 setups
2D gel proteomic profiling of immunodepleted serum reveals protein spot patterns that differentiate pre-cirrhotic NAFLD, cirrhotic NAFLD, and cirrhotic NAFLD with HCC
-
Full-text index only
Overlapping gene mutations of hepatitis B virus in a chronic hepatitis B patient with hepatitis B surface antigen loss during lamivudine therapy.
PMID 15953865 · PMC2782199 · Journal of Korean medical science · 2005 · 7 claims · 5 setups
Serum HBsAg became negative after 36 months of lamivudine therapy while HBeAg and HBV DNA remained positive
-
Full-text index only
Preclinical and post-treatment changes in the HCC-associated serum proteome.
PMID 17060939 · PMC2360589 · British journal of cancer · 2006 · 7 claims · 6 setups
SELDI proteomic profiling of serum reveals consistent, statistically significant changes associated with the development of HCC in hepatitis C patients
-
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.
-
Full-text index only
Proposed methods for testing and selecting the ERCC external RNA controls.
PMID 16266432 · PMC1325234 · BMC genomics · 2005 · 8 claims · 5 setups
A consortium-developed, standardized set of external RNA control transcripts can be used to assess technical performance in gene expression assays (microarray and QRT-PCR)
-
Has reproduction · 68
Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress.
PMID 33170850 · PMC7654773 · PloS one · 2020 · 8 claims · 4 setups
Yeast cells activate a rapid transcriptional reprogramming process following acute lethal ethanol stress that is likely adaptive for post-stress survival.
-
Full-text index only
Serum protein profile in systemic-onset juvenile idiopathic arthritis differentiates response versus nonresponse to therapy.
PMID 15987476 · PMC1175022 · Arthritis research & therapy · 2005 · 8 claims · 8 setups
SELDI-TOF MS can differentiate serum protein profiles of active versus well-controlled SJIA
-
Has reproduction · 63
Contrasting nutrient retention in alpine soils: the role of soil microbiome in phosphorus and nitrogen mobility in scree and meadow environments.
PMID 41632073 · PMC12883989 · FEMS microbiology ecology · 2026 · 6 claims · 8 setups
Scree soils have high mobile nitrate and phosphate, low phosphate sorption ability, and significantly greater phosphorus leaching despite lower organic matter and microbial biomass
-
Has reproduction · 77
Sequential structure probing of cotranscriptional RNA folding intermediates.
PMID 40450030 · PMC12126503 · Nature communications · 2025 · 8 claims · 6 setups
TECprobe-LM (linked-multipoint Transcription Elongation Complex RNA structure probing) directly measures cotranscriptional rearrangement of RNA structures by sequentially arresting RNAP at two or more template positions and chemically probing nascent RNA at each point
-
Full-text index only
Proteomic-based identification of haptoglobin-1 precursor as a novel circulating biomarker of ovarian cancer.
PMID 15199385 · PMC2364749 · British journal of cancer · 2004 · 7 claims · 7 setups
Six serum protein spots (~40 kDa, pI 5.9–6.6) significantly overexpressed in grade 1, 2 and 3 ovarian cancer patients were identified by MALDI-TOFMS and n-ESIQ(q)TOFMS as isoforms of haptoglobin-1 precursor (HAP1)
-
Full-text index only
Synaptic proteins linked to HIV-1 infection and immunoproteasome induction: proteomic analysis of human synaptosomes.
PMID 19693676 · PMC2824116 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2010 · 8 claims · 7 setups
Proteomic screening of human synaptosomes identifies a set of proteins differentially expressed in HIV/AIDS brain
-
Has reproduction · 86
The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection.
PMID 37027361 · PMC10081788 · PloS one · 2023 · 7 claims · 7 setups
Obtaining an accurate species-level microbial profile using current direct-read metagenomics profiling software is still a challenging task.