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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Putting proteins in one place.
PMID 12790144 · PMC1316915 · Environmental health perspectives · 2003 · 8 claims · 7 setups
Rapamycin inhibits TOR, causing the silencing protein Sir3 to detach from chromatin at stress-response genes, triggering a coordinated multigene stress response that halts cancer cell proliferation
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Has reproduction · 71
Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii.
PMID 40153700 · PMC11975115 · PLoS genetics · 2025 · 8 claims · 6 setups
The vast majority of A. baumannii essential genes show significant chemical-gene interactions upon knockdown
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Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling.
PMID 19825513 · PMC2787914 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups
Multidimensional phenotypic profiling leverages information content from multiple parallel or multiplexed measurements of compound action on cells, unlike hierarchical screening which filters to few 'interesting' compounds.
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Chemical genomics: what will it take and who gets to play?
PMID 11423004 · PMC138939 · Genome biology · 2001 · 8 claims · 8 setups
Scaling chemical genetics to a genome-wide 'chemical genomics' requires large, well-funded, multidisciplinary centers that integrate compound libraries, protein resources, automation, and profiling technology, and freely distribute data and reagents.
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Genomics, proteomics and bioinformatics: all in the same boat.
PMID 12374575 · PMC244909 · Genome biology · 2002 · 8 claims · 8 setups
Microarray sensitivity has improved enough to analyze clinical samples as small as 10-50 nanograms, and many early microarray experiments may need to be repeated due to data quality issues
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FeatureScan: revealing property-dependent similarity of nucleotide sequences.
PMID 16845077 · PMC1538849 · Nucleic acids research · 2006 · 6 claims · 5 setups
FeatureScan transforms nucleotide sequences into numerical signals of physico-chemical/conformational properties and compares them via a convolution/correlation (Fourier transform) method rather than comparing letters
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Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.
PMID 18618001 · PMC2442223 · PLoS genetics · 2008 · 8 claims · 6 setups
Zebrafish whole-adult-organism chemogenomics generates robust prediction models that discriminate P(H)AHs from ECs across independent experiments
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Use of genomic data in risk assessment.
PMID 11983054 · PMC139345 · Genome biology · 2002 · 8 claims · 4 setups
New genomic technologies (CGH, SNP analysis, restriction landmark genome scanning, spectral karyotyping, transcript profiling) can be applied to improve risk assessment accuracy
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Malaria genomics meets drug-resistance phenotyping in the field.
PMID 19664295 · PMC2745762 · Genome biology · 2009 · 8 claims · 8 setups
Significantly longer parasite clearance times in Pailin (western Cambodia) versus Wang Pha (Thailand-Myanmar border) establish the presence of artemisinin resistance in western Cambodia.
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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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Toxicogenomics research consortium sails into uncharted waters.
PMID 12460811 · PMC1241122 · Environmental health perspectives · 2002 · 8 claims · 8 setups
The NIEHS-funded $37 million Toxicogenomics Research Consortium (TRC) combines the NIEHS Microarray Center with five academic institutions (UNC, Duke, Fred Hutchinson/UW, MIT, OHSU) to define genetic variability, set gene expression standards, and study environmental stress responses.
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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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Has reproduction · 50
RNA modifications detection by comparative Nanopore direct RNA sequencing.
PMID 34893601 · PMC8664944 · Nature communications · 2021 · 7 claims · 5 setups
Nanocompore is a model-free comparative method that uses a 2-component Gaussian mixture model (GMM) and univariate statistical tests on signal intensity/dwell time to detect RNA modifications in Nanopore direct RNA sequencing data without needing a training set
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Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring.
PMID 19121650 · PMC2706936 · Journal of proteomics · 2009 · 7 claims · 5 setups
A new MRM worksheet was implemented in The Global Proteome Machine database (GPMDB) that provides all information needed to design MRM transitions based solely on archived observations from previous experiments by other researchers.
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Translating genome sequences into biological understanding.
PMID 12801409 · PMC193614 · Genome biology · 2003 · 8 claims · 7 setups
Gene-trap insertional mutagenesis in mouse ES cells (BayGenomics) generates a large resource of cell lines and knockout mice for studying gene expression patterns and function.