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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A statistical approach for array CGH data analysis.
PMID 15705208 · PMC549559 · BMC bioinformatics · 2005 · 8 claims · 4 setups
Existing model-selection criteria (AIC, BIC, and prior ad hoc penalties) are not well adapted to estimating the number of segments in array CGH data
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Mathematical models in mammalian cell biology.
PMID 18638360 · PMC2530880 · Genome biology · 2008 · 8 claims · 8 setups
A point mutation in the circadian Per2 gene causes familial advanced sleep phase syndrome (FASPS) via a phosphorylation defect that alters PER2 stability and subcellular localization.
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Is replication the gold standard for validating genome-wide association findings?
PMID 19112512 · PMC2605260 · PloS one · 2008 · 8 claims · 4 setups
The probability of replicating a specific GWA-identified variant decreases as the number of independent GWA/replication studies increases, when individual study power is less than 100%.
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Splicing bioinformatics to biology.
PMID 16732900 · PMC1779529 · Genome biology · 2006 · 8 claims · 8 setups
Mutually exclusive selection of Dscam exon 6 variants is governed by base pairing between a conserved intronic docking site and selector sequences adjacent to each alternative exon.
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Bayesian coestimation of phylogeny and sequence alignment.
PMID 15804354 · PMC1087833 · BMC bioinformatics · 2005 · 7 claims · 3 setups
Alignment and phylogenetic inference are mutually dependent, and treating them as separate sequential steps (align then infer tree) is fundamentally flawed and produces biased, overconfident estimates.
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Has reproduction · 50
Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.
PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 5 setups
A 186-gene signature derived from six GEO transcriptomic datasets predicts nCRT response in LARC with AUC 0.80 in cross-validation
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Assessing the gene space in draft genomes.
PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups
The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.
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Solving structures of protein complexes by molecular replacement with Phaser.
PMID 17164524 · PMC2483468 · Acta crystallographica. Section D, Biological crystallography · 2007 · 7 claims · 4 setups
Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components using a 'tree search with pruning' approach implemented in Phaser's automated MR mode.
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Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.
PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups
High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb
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Metabolic syndrome: from epidemiology to systems biology.
PMID 18852695 · PMC2829312 · Nature reviews. Genetics · 2008 · 8 claims · 8 setups
MetSyn component traits (obesity, insulin resistance, dyslipidaemia, hypertension) exhibit causal interactions and common etiologies rather than being independent conditions
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Has reproduction · 95
Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.
PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups
Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature
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Population history and natural selection shape patterns of genetic variation in 132 genes.
PMID 15361935 · PMC515367 · PLoS biology · 2004 · 7 claims · 5 setups
Developed a rigorous computational approach that corrects for multiple hypothesis testing and models population demographic history to test for natural selection
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Of mice and men: comparative proteomics of bronchoalveolar fluid.
PMID 20032019 · PMC3049194 · The European respiratory journal · 2010 · 8 claims · 8 setups
Comparative shotgun proteomics of human and mouse BALF identifies conserved pathways (immunity, defence response, protease activity) alongside species-specific divergent pathways.
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Ontological Discovery Environment: a system for integrating gene-phenotype associations.
PMID 19733230 · PMC2783409 · Genomics · 2009 · 8 claims · 8 setups
ODE is a web-based system for storing, sharing, retrieving and analyzing phenotype-centered genomic data sets across species and experimental systems
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Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.
PMID 19889231 · PMC2779197 · BMC genomics · 2009 · 8 claims · 6 setups
A novel, plant-specific family of longin-related proteins, the 'Phytolongins', was identified in land plant genomes.
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Has reproduction · 58
Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.
PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups
Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.