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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Pooled DNA genotyping on Affymetrix SNP genotyping arrays.
PMID 16480507 · PMC1382214 · BMC genomics · 2006 · 7 claims · 4 setups
Pooled genotyping on Affymetrix 10K arrays estimates allele frequency differences between pools with accuracy comparable to lower-throughput pooling platforms.
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Has reproduction · 83
Analyzing biomarker discovery: Estimating the reproducibility of biomarker sets.
PMID 35901020 · PMC9333302 · PloS one · 2022 · 7 claims · 3 setups
A Reproducibility Score, RS(D,BD), defined as the average Jaccard overlap between biomarker sets found by the same discovery process on comparable datasets from the same distribution, quantifies biomarker reproducibility on a 0-1 scale
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Next-generation high-density self-assembling functional protein arrays.
PMID 18469824 · PMC3070491 · Nature methods · 2008 · 8 claims · 7 setups
A next-generation NAPPA method produces high-density protein microarrays displaying over 1500 unique proteins with >90% expression success
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Development of proteomic patterns for detecting lung cancer.
PMID 14757945 · PMC3851077 · Disease markers · 2003 · 8 claims · 3 setups
A decision tree classification algorithm built on three serum protein mass peaks (8122Da, 1452Da, 1610Da) can discriminate lung cancer patients from healthy controls
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Expression profiling of drug response--from genes to pathways.
PMID 17117610 · PMC3181826 · Dialogues in clinical neuroscience · 2006 · 8 claims · 8 setups
Understanding individual response to a drug (efficacy/tolerability) is the major bottleneck in current drug development and clinical trials.
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CLEAN: CLustering Enrichment ANalysis.
PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups
The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).
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Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.
PMID 17406619 · PMC2688820 · Nature protocols · 2007 · 8 claims · 7 setups
Combining three human-optimized DOP-PCR primers before a secondary amino-labeled PCR increases array hybridization sensitivity and reproducibility sixfold compared to the standard 6MW DOP-PCR primer
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Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning.
PMID 18163913 · PMC2242801 · BMC cancer · 2007 · 8 claims · 8 setups
SELDI-TOF-MS serum proteomic patterns analyzed by decision tree classification (Biomarker Pattern Software) can discriminate DLBCL patients from healthy controls with high sensitivity and specificity.
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A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.
PMID 16423292 · PMC1382217 · BMC genomics · 2006 · 7 claims · 6 setups
Expression context is largely conserved between orthologs across four eukaryote species.
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Localized-statistical quantification of human serum proteome associated with type 2 diabetes.
PMID 18795103 · PMC2529402 · PloS one · 2008 · 8 claims · 5 setups
Developed LSPAD (localized statistics of protein abundance distribution) to calculate statistical significance of protein-abundance bias between two serum cohorts using a local Fisher's exact test window
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Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.
PMID 18482458 · PMC2408589 · BMC microbiology · 2008 · 8 claims · 6 setups
CGS combined with targeted DDT sequencing and whole genome fingerprinting (WGF) can accurately determine a treponemal genome sequence using only three arrays, at accuracy comparable to or better than finished DDT sequencing
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Proteomics analysis of human skeletal muscle reveals novel abnormalities in obesity and type 2 diabetes.
PMID 19833877 · PMC2797941 · Diabetes · 2010 · 7 claims · 5 setups
Mitochondrial protein abundance is decreased in insulin-resistant (obese and type 2 diabetic) skeletal muscle
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High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.
PMID 18786630 · PMC2659594 · Genomics · 2008 · 8 claims · 7 setups
WGA product performs well on the Affymetrix 250K SNP array compared to genomic DNA, especially with the BRLMM calling algorithm.
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Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.
PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups
A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.
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An analysis of human microRNA and disease associations.
PMID 18923704 · PMC2559869 · PloS one · 2008 · 8 claims · 8 setups
MicroRNAs tend to show similar dysfunctional evidence (both up- or both down-regulated) for diseases within the same disease cluster, and different dysfunctional evidence between different disease clusters.
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Proposed methods for testing and selecting the ERCC external RNA controls.
PMID 16266432 · PMC1325234 · BMC genomics · 2005 · 8 claims · 5 setups
A consortium-developed, standardized set of external RNA control transcripts can be used to assess technical performance in gene expression assays (microarray and QRT-PCR)