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 · 86
Multi-INTACT: integrative analysis of the genome, transcriptome, and proteome identifies causal mechanisms of complex traits.
PMID 39901160 · PMC11789355 · Genome biology · 2025 · 8 claims · 2 setups
Multi-INTACT achieves higher power than existing single-gene-product methods while maintaining calibrated false discovery rates in simulations.
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Has reproduction · 40
Machine learning developed an intratumor heterogeneity signature for predicting clinical outcome and immunotherapy benefit in bladder cancer.
PMID 39100839 · PMC11291408 · Translational andrology and urology · 2024 · 8 claims · 8 setups
An integrative machine learning procedure (10 methods, 101 algorithm combinations) identified an Enet (alpha=0.2)-based intratumor heterogeneity-related signature (IRS) with the highest average C-index (0.69) across TCGA and GEO cohorts
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Has reproduction · 51
A platelet-related signature for predicting the prognosis and immunotherapy benefit in bladder cancer based on machine learning combinations.
PMID 39280688 · PMC11399026 · Translational andrology and urology · 2024 · 8 claims · 8 setups
An Enet (alpha=0.4) machine-learning algorithm built from 10 platelet-related genes yields the optimal platelet-related signature (PRS) for bladder cancer prognosis, with average C-index 0.73
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JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.
PMID 16925843 · PMC1810558 · Genome biology · 2006 · 8 claims · 4 setups
Adding model states for specific biological features (signal peptides, CpG islands, etc.) to non-comparative GHMM gene finders did little or nothing to enhance predictive accuracy, sometimes reducing it.
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Human chromosome 7: DNA sequence and biology.
PMID 12690205 · PMC2882961 · Science (New York, N.Y.) · 2003 · 6 claims · 2 setups
Presents the DNA sequence and annotation of the entire human chromosome 7
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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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In silico meets in vivo.
PMID 18304380 · PMC2374716 · Genome biology · 2008 · 8 claims · 8 setups
About 10% of positions in multiple sequence alignments of the human genome with other vertebrate genomes are likely incorrect.
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Biocomputing enters its adolescence.
PMID 15960815 · PMC1175967 · Genome biology · 2005 · 8 claims · 8 setups
A 'match augmentation' algorithm efficiently matches structural motifs by prioritizing functionally significant residues, enabling function prediction between evolutionarily unrelated proteins
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Has reproduction · 69
Genomic insights into the diversity, virulence, and antimicrobial resistance of group B Streptococcus clinical isolates from Saudi Arabia.
PMID 38711928 · PMC11070470 · Frontiers in cellular and infection microbiology · 2024 · 8 claims · 8 setups
Sequenced GBS isolates from Saudi Arabia show high genetic diversity, with 28 sequence types and nine distinct serotypes including uncommon serotypes VII and VIII