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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Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.
PMID 15258335 · PMC3851082 · Disease markers · 2003 · 8 claims · 8 setups
Proteomic pattern analysis of serum mass spectra, without identifying the underlying proteins, can distinguish cancer patients from healthy controls with high sensitivity and specificity.
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An initial characterization of the serum phosphoproteome.
PMID 19824718 · PMC2789176 · Journal of proteome research · 2009 · 8 claims · 8 setups
A TiO2-based phosphopeptide enrichment method coupled with LC-MS/MS (LTQ-Orbitrap CID and LTQ-ETD) was developed and applied to characterize the serum phosphoproteome
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Has reproduction · 86
Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.
PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 6 claims · 4 setups
A training gene set of 719 unique upregulated DEGs (subtype-specific) can be used to build ML models that classify TNBC into BLIA, BLIS, MES, and LAR subtypes.
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Inferring combinatorial regulation of transcription in silico.
PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups
Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets
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Has reproduction · 89
Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.
PMID 36046020 · PMC9421002 · Frontiers in microbiology · 2022 · 7 claims · 8 setups
Milk serves as a reservoir for both human- and animal-derived S. aureus strains in sub-Saharan Africa
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Shotgun proteomics and biomarker discovery.
PMID 12364816 · PMC3851423 · Disease markers · 2002 · 8 claims · 7 setups
Shotgun (LC/LC-MS/MS, e.g. MudPIT) proteomic approaches show advantages over gel-based techniques in speed, sensitivity, scope of analysis, and dynamic range.
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Two committees tackle toxicogenomics.
PMID 12501852 · PMC1241123 · Environmental health perspectives · 2002 · 8 claims · 8 setups
NIEHS funded a $37 million, five-year Toxicogenomics Research Consortium (TRC) linking the NIEHS Microarray Center with five academic institutions (UNC, Duke, Fred Hutchinson/UW, MIT, OHSU) to coordinate gene-expression research on environmental health effects.
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Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.
PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups
The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.
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Has reproduction · 82
Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.
PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups
An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.