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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Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.
PMID 16912992 · PMC1538848 · Nucleic acids research · 2006 · 7 claims · 8 setups
PANTHER HMMs built from family/subfamily multiple sequence alignments can classify novel protein sequences into functional groups based on statistically significant HMM match scores
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Has reproduction · 90
A2TEA: Identifying trait-specific evolutionary adaptations.
PMID 37224329 · PMC10186066 · F1000Research · 2022 · 8 claims · 7 setups
A2TEA integrates gene family expansion analysis with differential expression data across species to identify genes that were targets of evolutionary adaptation to a given stress/treatment
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Gene-disease relationship discovery based on model-driven data integration and database view definition.
PMID 19042916 · PMC2639000 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 4 setups
Explicit gene–disease relationships can be formulated as candidate gene definitions (e.g., co-localization, dysregulation, functional similarity) that may include intermediary orthologous or interacting genes
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Sequencing the regulatory genome.
PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups
Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)