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 · 85
Optimisation of the core subset for the APY approximation of genomic relationships.
PMID 36418945 · PMC9682752 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 3 setups
APY approximates the full genomic relationship matrix by splitting genotyped animals into a core subset (fully dependent, direct inverse) and a non-core subset (conditionally independent given core), reducing inversion cost.
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Has reproduction · 83
Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of Arabidopsis Under Cold Stress.
PMID 30258841 · PMC6143811 · Frontiers in bioengineering and biotechnology · 2018 · 7 claims · 4 setups
A metabolite-centric reporter pathway analysis (RPAm) can infer cold-stress-associated metabolites and pathways in Arabidopsis directly from transcriptome data without metabolome data
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Has reproduction · 71
Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.
PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups
TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.
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Has reproduction · 94
Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.
PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups
HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)
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Has reproduction · 70
Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential.
PMID 36450752 · PMC9712620 · Nature communications · 2022 · 8 claims · 8 setups
AR enhancer/chromatin binding usage is highly heterogeneous between primary prostate tumors, with <5% of all AR binding sites shared by half of tumors analyzed.
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Has reproduction · 87
ddRAD-seq reveals the genetic structure and detects signals of selection in Italian brown trout.
PMID 35100964 · PMC8805291 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 8 setups
Italian brown trout populations are genetically differentiated but show strong admixture introduced by stocking, especially with the Atlantic lineage.
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Has reproduction · 84
Strong population differentiation in lingcod (Ophiodon elongatus) is driven by a small portion of the genome.
PMID 33294007 · PMC7691466 · Evolutionary applications · 2020 · 7 claims · 8 setups
Lingcod comprise two distinct genetic clusters separated latitudinally at a break near Point Reyes off Northern California, with a high frequency of admixed individuals near the break.
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Has reproduction · 64
Candidates for Balancing Selection in Leishmania donovani Complex Parasites.
PMID 34865011 · PMC8717319 · Genome biology and evolution · 2021 · 7 claims · 8 setups
Five genetically distinct, well-sampled populations exist within the L. donovani complex: EA1, EA2 (East Africa), ISC1, ISC2 (Indian subcontinent), and BM (Brazil-Mediterranean)