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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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.
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Full-text index only
KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.
PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups
KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.
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Has reproduction · 86
Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.
PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 6 claims · 4 setups
A training gene set of 719 unique upregulated DEGs (subtype-specific) can be used to build ML models that classify TNBC into BLIA, BLIS, MES, and LAR subtypes.
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DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists.
PMID 17576678 · PMC1933169 · Nucleic acids research · 2007 · 8 claims · 4 setups
The DAVID Gene Concept uses a single-linkage method to agglomerate tens of millions of gene/protein identifiers from NCBI, PIR, UniProt and other resources into unified DAVID genes.
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Has reproduction · 67
Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines.
PMID 34745063 · PMC8564382 · Frontiers in microbiology · 2021 · 7 claims · 7 setups
Tn-seq using the TnSC189 mariner transposon identified 329 essential genes in V. anguillarum NB10Sm from a library of 52,662 insertion mutants.
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Has reproduction · 61
Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.
PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups
Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.
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The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.
PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups
The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.
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Has reproduction · 65
Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids.
PMID 29983891 · PMC6033374 · Oncotarget · 2018 · 8 claims · 6 setups
UC patient-derived epithelial organoids histologically phenocopy primary UC tissue, while non-IBD organoids resemble healthy colonic epithelium.
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Has reproduction · 35
Transcriptional firing represses bactericidal activity in cystic fibrosis airway neutrophils.
PMID 33948572 · PMC8080108 · Cell reports. Medicine · 2021 · 8 claims · 8 setups
Neutrophils recruited to CF airways undergo rapid, broad transcriptional firing that upregulates anabolic genes and downregulates antimicrobial genes