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 20

System / cell line: disease ✕ Assay: common ✕ Clear

Analysis of protein sequence and interaction data for candidate disease gene prediction.

PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups

Full-text index only

Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold

ophid biocarta kegg pfam-annotated common benchmarking multiple-interval
Genome Wide Association Studies: identifying the genes that determine the risk of abdominal aortic aneurysm.

PMID 18621558 · PMC2697027 · European journal of vascular and endovascular surgery : the official journal of the European Society for Vascular Surgery · 2008 · 8 claims · 3 setups

Full-text index only

AAA has a strong genetic component, with up to ten-fold increased risk in first-degree relatives of affected individuals

aaa cases candidate genome-wide
Shotgun proteomics and biomarker discovery.

PMID 12364816 · PMC3851423 · Disease markers · 2002 · 8 claims · 7 setups

Full-text index only

Shotgun (LC/LC-MS/MS, e.g. MudPIT) proteomic approaches show advantages over gel-based techniques in speed, sensitivity, scope of analysis, and dynamic range.

urine yeast cysteine-containing hemoglobin 2d-ge lc-ms imac
Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups

Has reproduction · 88

COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.

peripheral leukocytes plasma degs bulk single-cell plasma
Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.

PMID 36254682 · PMC9612871 · Disease models & mechanisms · 2022 · 8 claims · 8 setups

Has reproduction · 100

iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action

ipsc-derived products microglia post-mortem single-cell ca2+ protein-protein
Metatranscriptomics of the human oral microbiome during health and disease.

PMID 24692635 · PMC3977359 · mBio · 2014 · 8 claims · 8 setups

Has reproduction · 62

Disease-associated periodontal communities display conserved community-level metabolic gene expression profiles between patients, whereas the metabolic gene expression of individual species is highly variable between patients.

patient-matched subset health rna-seq rrna comparison metatranscriptomics
Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

PMID 37471455 · PMC10393163 · PLoS computational biology · 2023 · 8 claims · 8 setups

Has reproduction · 100

A network-based meta-analysis across studies identifies a common 45-gene signature specific to active TB disease that accounts for cohort/population heterogeneity

n×m common independent viral blood gene random
Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.

PMID 37666859 · PMC10477296 · Scientific reports · 2023 · 8 claims · 8 setups

Has reproduction · 20

AM and RPR (Huangqi-Chishao decoction) alleviate bleomycin-induced pathological lung fibrotic damage in rats

ipf common key rats microarray network protein-protein
Social and ethical implications of genomics, race, ethnicity, and health inequities.

PMID 19000599 · PMC2892396 · Seminars in oncology nursing · 2008 · 8 claims · 5 setups

Full-text index only

Race and ethnicity are increasingly viewed as genetic surrogates for predicting disease risk and treatment response, though directly assessing genomic and environmental factors is more accurate.

population prostate non-small-cell breast genome-wide gene somatic
Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases.

PMID 34601390 · PMC8483812 · Computers in biology and medicine · 2021 · 8 claims · 8 setups

Has reproduction · 69

COVID-19 and neurological diseases (NDs) share pathophysiological connections that influence disease progression and severity

peripheral hippocampal spinal peritumoral microarray protein-protein
Mitochondrial D-loop mutations and deletion profiles of cancerous and noncancerous liver tissue in hepatitis B virus-infected liver.

PMID 15785740 · PMC2361973 · British journal of cancer · 2005 · 8 claims · 2 setups

Full-text index only

D-loop mutation frequency is significantly higher in both noncancerous and tumour liver tissue of HCC/HBV patients than in normal control liver

liver pcr
Integrative analysis reveals chemokines CCL2 and CXCL5 mediated shear stress-induced aortic dissection formation.

PMID 38163105 · PMC10757018 · Heliyon · 2024 · 7 claims · 8 setups

Has reproduction · 75

Chemokines CCL2 and CXCL5 mediate a shear stress-induced 'Endothelial-Monocyte-Neutrophil' axis that contributes to aortic dissection development.

ascending aortic clinical bulk bulk single-cell western
Integrated multi-level quality control for proteomic profiling studies using mass spectrometry.

PMID 19055809 · PMC2657802 · BMC bioinformatics · 2008 · 7 claims · 5 setups

Full-text index only

QC processes for identifying and removing low-quality spectra are often overlooked in proteomic profiling studies

serum pooled duplicate full seldi-tof principal technical
Sequence and structure signatures of cancer mutation hotspots in protein kinases.

PMID 19834613 · PMC2759519 · PloS one · 2009 · 8 claims · 6 setups

Full-text index only

Developed CKMD (Composite Kinase Mutation Database), an integrated bioinformatics resource mapping genetic variation in protein kinase genes to sequence, structural, and functional data

kinase common egfr autoinhibited database-driven structure-informed evolutionary
Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method.

PMID 16026601 · PMC1637030 · BMC bioinformatics · 2005 · 8 claims · 2 setups

Full-text index only

DF-SNPs, a novel adaptation of the Decision Forest method, can classify esophageal cancer cases vs. controls based on SNP genotype data with high concordance, sensitivity, and specificity.

genomic snp high-throughput decision
Human metapneumovirus, Australia, 2001-2004.

PMID 16965711 · PMC3291208 · Emerging infectious diseases · 2006 · 8 claims · 5 setups

Full-text index only

HMPV had a 7.1% average annual incidence among 10,025 respiratory samples tested over 4 years

nasopharyngeal npa hmpv-positive reverse direct multiplex
Size matters: just how big is BIG?: Quantifying realistic sample size requirements for human genome epidemiology.

PMID 18676414 · PMC2639365 · International journal of epidemiology · 2009 · 7 claims · 2 setups

Full-text index only

Conventional power calculations for case-control studies disregard analytic complexity (e.g. clinical assessment errors, unmeasured aetiological determinants) and can seriously underestimate true sample size requirements

simulated simulation-based simulated
The UCSC Genome Browser Database: 2008 update.

PMID 18086701 · PMC2238835 · Nucleic acids research · 2008 · 8 claims · 8 setups

Full-text index only

The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes.

zebrafish yale vertebrate non-human sage expression snp
Glycomic analysis: an array of technologies.

PMID 19728746 · PMC3443568 · ACS chemical biology · 2009 · 8 claims · 8 setups

Full-text index only

Glycosylation is the most prevalent protein post-translational modification, occurring on at least 50% of all proteins

sera t-cells serum glycoproteins lectin hydrazide bioorthogonal
BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.

PMID 18234728 · PMC2564862 · Journal of medical genetics · 2008 · 8 claims · 7 setups

Full-text index only

BHD germline mutation detection rate was 88% (51/58 families) using direct DNA sequencing

peripheral blood-derived folliculin chest direct subcloning sequence

Experiments

Analysis of protein sequence and interaction data for candidate disease gene prediction.

Genome Wide Association Studies: identifying the genes that determine the risk of abdominal aortic aneurysm.

Shotgun proteomics and biomarker discovery.

Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.

Metatranscriptomics of the human oral microbiome during health and disease.

Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.

Social and ethical implications of genomics, race, ethnicity, and health inequities.

Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases.

Mitochondrial D-loop mutations and deletion profiles of cancerous and noncancerous liver tissue in hepatitis B virus-infected liver.

Integrative analysis reveals chemokines CCL2 and CXCL5 mediated shear stress-induced aortic dissection formation.

Integrated multi-level quality control for proteomic profiling studies using mass spectrometry.

Sequence and structure signatures of cancer mutation hotspots in protein kinases.

Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method.

Human metapneumovirus, Australia, 2001-2004.

Size matters: just how big is BIG?: Quantifying realistic sample size requirements for human genome epidemiology.

The UCSC Genome Browser Database: 2008 update.

Glycomic analysis: an array of technologies.

BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.