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).
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Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction.
PMID 20003400 · PMC2806376 · BMC genetics · 2009 · 7 claims · 4 setups
Pooled genotyping on the Affymetrix 500k platform using PPC yields highly accurate allele frequency estimates (correlation 0.988) comparable to or better than the 10k/100k platforms.
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Has reproduction · 50
The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.
PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 7 claims · 7 setups
Most published adult/other-cohort sepsis gene signatures have limited utility for infant sepsis; only 2 of 7 achieved >80% accuracy in infants
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Has reproduction · 66
Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.
PMID 37583471 · PMC10423927 · Neurobiology of stress · 2023 · 7 claims · 5 setups
Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.
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Molecular tumor profiling: translating genomic insights into clinical advances.
PMID 15287965 · PMC507868 · Genome biology · 2004 · 8 claims · 8 setups
Gene-expression profiling can distinguish BRCA1- and BRCA2-linked breast tumors from sporadic breast tumors with similar hormone-receptor status
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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
AAA has a strong genetic component, with up to ten-fold increased risk in first-degree relatives of affected individuals
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Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs.
PMID 15811185 · PMC1079828 · BMC genomics · 2005 · 8 claims · 4 setups
Relative Allele Signal (RAS) values from SNP microarrays provide a quantitative index of allele frequencies in pooled DNA
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A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples.
PMID 18194558 · PMC2248205 · BMC genetics · 2008 · 8 claims · 5 setups
A hierarchical/modular approach integrating quality control, LD, physical distance, and gene ontology identifies authentic associations among those found by statistical tests in pooled DNA GWAS
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Has reproduction · 67
Reverse Engineering of the Pediatric Sepsis Regulatory Network and Identification of Master Regulators.
PMID 34680414 · PMC8533457 · Biomedicines · 2021 · 7 claims · 8 setups
A set of 15 TFs was identified as sepsis-specific master regulators of pediatric sepsis, dividing into two non-overlapping clusters.
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Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.
PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups
Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.
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Genetics and proteomics: deciphering gene association studies in critical illness.
PMID 16934133 · PMC1750993 · Critical care (London, England) · 2006 · 8 claims · 8 setups
Most critical illnesses are complex traits (multifactorial), unlike single-gene Mendelian diseases.
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Has reproduction · 23
Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals.
PMID 39418301 · PMC11521246 · PLoS computational biology · 2024 · 7 claims · 4 setups
COPD GWAS loci are more spatially clustered across the genome than expected by chance, with significant enrichment on chromosome 4q.
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Current and future directions in genomics of amyotrophic lateral sclerosis.
PMID 18625410 · PMC3524513 · Physical medicine and rehabilitation clinics of North America · 2008 · 8 claims · 8 setups
Familial ALS (FALS, 5-10% of cases) follows Mendelian autosomal dominant inheritance, with 20% caused by SOD1 mutations and 80% by unknown mutations
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Calibrating the performance of SNP arrays for whole-genome association studies.
PMID 18584036 · PMC2432039 · PLoS genetics · 2008 · 8 claims · 7 setups
Previous SNP array genetic coverage estimates are inflated due to SNP overfitting and sample overfitting, since they were evaluated on the same HapMap SNPs/individuals used to design the arrays.
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The UCSC Genome Browser Database: 2008 update.
PMID 18086701 · PMC2238835 · Nucleic acids research · 2008 · 8 claims · 8 setups
The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes.