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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Indirect genomic effects on survival from gene expression data.
PMID 18358079 · PMC2397510 · Genome biology · 2008 · 7 claims · 6 setups
A novel methodology (dynamic path analysis combined with additive hazard survival regression) can detect and quantify indirect effects of gene expression on survival mediated through transcription factor target genes.
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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
Noninvasive D-Squame tape stripping coupled with MS proteomics can profile the AD skin proteome
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Two-dimensional electrophoretic comparison of metastatic and non-metastatic human breast tumors using in vitro cultured epithelial cells derived from the cancer tissues.
PMID 18416831 · PMC2377273 · BMC cancer · 2008 · 6 claims · 4 setups
Three protein spots were significantly altered in abundance between metastase-positive and metastase-negative breast cancer patient groups
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Has reproduction · 81
Transcriptome analysis reveals differential splicing events in IPF lung tissue.
PMID 24647608 · PMC3960165 · PloS one · 2014 · 8 claims · 6 setups
873 genes are differentially expressed in IPF lung tissue versus healthy controls at FDR<5%, with more up-regulated than down-regulated genes.
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Has reproduction · 100
Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility.
PMID 33707641 · PMC7970949 · Scientific reports · 2021 · 8 claims · 8 setups
WGCNA on control human cervical spinal cord RNA-seq identifies 13 co-expression modules (SC.M1-M13), each representing distinct biological processes or cell types.
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Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.
PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups
A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.
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A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.
PMID 18631455 · PMC2727981 · Immunity · 2008 · 7 claims · 8 setups
Transcriptional modules constructed from coordinately expressed genes across 8 diseases form stable, biologically coherent functional units
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Polymorphism screening and haplotype analysis of the tryptophan hydroxylase gene (TPH1) and association with bipolar affective disorder in Taiwan.
PMID 15799788 · PMC1079843 · BMC medical genetics · 2005 · 8 claims · 7 setups
Systematic screening of TPH1 exons and promoter region in Taiwanese Han identified five sequence variants: A-1067G, G-347T, T3804A, C27224T, A27237G.
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Has reproduction
Using random walks to identify cancer-associated modules in expression data.
PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups
Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.