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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LMPD: LIPID MAPS proteome database.
PMID 16381922 · PMC1347484 · Nucleic acids research · 2006 · 8 claims · 5 setups
LMPD is an object-relational database of lipid-associated protein sequences and annotations, publicly available from the LIPID MAPS Consortium website.
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Has reproduction · 51
Polyploidy and the petal transcriptome of Gossypium.
PMID 24393201 · PMC3890615 · BMC plant biology · 2014 · 8 claims · 8 setups
Most homoeologous gene pairs in polyploid cotton petals are expressed at equal levels, indicating a surprising level of expression homeostasis; only ~20% of expressed genes show significant genome bias.
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From genomics to chemical genomics: new developments in KEGG.
PMID 16381885 · PMC1347464 · Nucleic acids research · 2006 · 8 claims · 5 setups
KEGG BRITE has been formally added as a fourth main KEGG database to establish a logical foundation for functional interpretation and pathway reconstruction.
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The Edinburgh human metabolic network reconstruction and its functional analysis.
PMID 17882155 · PMC2013923 · Molecular systems biology · 2007 · 8 claims · 7 setups
EHMN is a high-quality, manually curated human metabolic network combining genome-based and literature-based (EMP) reconstruction, containing nearly 3000 reactions and over 2000 metabolic genes.
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Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.
PMID 19907644 · PMC2770834 · PloS one · 2009 · 8 claims · 6 setups
Existing pathway databases and tools do not satisfy all requirements for a generic, comprehensive pathway browser (integrated maps, data access, mapping/editing, export, installation-free availability).
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Columba: an integrated database of proteins, structures, and annotations.
PMID 15801979 · PMC1087474 · BMC bioinformatics · 2005 · 8 claims · 6 setups
COLUMBA physically integrates data from twelve protein structure-related databases (PDB, KEGG, Swiss-Prot, CATH, SCOP, Gene Ontology, ENZYME, etc.) into a single PostgreSQL data warehouse.
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Reconstruction of pathways associated with amino acid metabolism in human mitochondria.
PMID 18267298 · PMC5054205 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 5 setups
Out of 20 amino acids, the metabolic pathways of 17 utilize mitochondrial enzymes, and dysfunction of these enzymes causes over 40 known human mitochondrial diseases/disorders
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Has reproduction · 78
Transcriptomic and physiological analysis of atractylodes chinensis in response to drought stress reveals the putative genes related to sesquiterpenoid biosynthesis.
PMID 38317086 · PMC10845750 · BMC plant biology · 2024 · 8 claims · 6 setups
Drought stress significantly increases MDA, proline, soluble sugar, and crude protein content and antioxidative enzyme (SOD, POD, CAT) activity in A. chinensis seedlings
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Has reproduction · 68
Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs.
PMID 30542296 · PMC6277807 · Frontiers in physiology · 2018 · 8 claims · 8 setups
The complete genome of L. plantarum ZLP001 comprises a single 3,164,369 bp circular chromosome (GC 44.65%) plus seven plasmids (A–G), encoding 3,264 protein-coding sequences.