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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Characterizing natural variation using next-generation sequencing technologies.
PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups
Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.
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Analysis of pooled DNA samples on high density arrays without prior knowledge of differential hybridization rates.
PMID 16627870 · PMC1440945 · Nucleic acids research · 2006 · 7 claims · 3 setups
A GLMM-based test statistic that models the nested structure of array replicate/strand/probe measurements achieves correct type I error, unlike naive or t-test based statistics.
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Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans.
PMID 16478714 · PMC1368655 · Nucleic acids research · 2006 · 7 claims · 6 setups
SNP-MaP allele frequency estimates from pooled DNA on the 100K microarray set correlate strongly with allele frequencies from individual genotyping
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Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.
PMID 17610740 · PMC1925094 · BMC genomics · 2007 · 8 claims · 5 setups
SNP-MaP can be effectively applied to the Affymetrix 500K GeneChip, providing a cost-effective, reliable and valid initial genomewide screen
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Allelotyping of pooled DNA with 250 K SNP microarrays.
PMID 17367522 · PMC1839100 · BMC genomics · 2007 · 8 claims · 5 setups
The polynomial based probe specific correction (PPC) algorithm is the most accurate method for estimating allele frequency from pooled DNA.
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NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region.
PMID 16998187 · PMC1636422 · Nucleic acids research · 2006 · 8 claims · 8 setups
The major BCL2 promoter G-quadruplex (bcl2Mid) is a well-defined, mixed parallel/antiparallel-stranded intramolecular structure with three G-tetrads, two lateral loops, one side loop, and four grooves of different widths
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Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.
PMID 19115125 · PMC2947716 · Journal of neurovirology · 2009 · 7 claims · 5 setups
HIV-1 isolates from CI patients induce a distinct macrophage proteome signature compared to isolates from NC patients and SF162
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Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.
PMID 18784189 · PMC2577347 · Nucleic acids research · 2008 · 8 claims · 6 setups
Genomic waves are present in both Illumina and Affymetrix SNP genotyping arrays, confirming they are not platform-specific
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Proteomic analysis identifies MMP-9, DJ-1 and A1BG as overexpressed proteins in pancreatic juice from pancreatic ductal adenocarcinoma patients.
PMID 18706098 · PMC2528014 · BMC cancer · 2008 · 7 claims · 6 setups
MMP-9, DJ-1 and A1BG are overexpressed in pancreatic juice and tissue from PDAC patients compared with cancer-free/normal controls
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Proteomic analysis of Alzheimer's disease cerebrospinal fluid from neuropathologically diagnosed subjects.
PMID 19689240 · PMC2832860 · Current Alzheimer research · 2009 · 8 claims · 6 setups
2D DIGE analysis of postmortem V-CSF pools identified 21-22 protein spots that significantly differ among neuropathologically-diagnosed AD, non-demented controls (NDC), and non-AD dementia (non-ADD) groups
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Increasing the number of SNP loci does not necessarily improve prediction power at least in the comparison of MTHFR SNP and haplotypes.
PMID 19075497 · PMC4771609 · Journal of epidemiology · 2008 · 7 claims · 6 setups
Increasing the number of typed SNP loci does not necessarily improve prediction power, at least for the MTHFR gene
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One-pot shotgun quantitative mass spectrometry characterization of histones.
PMID 19764812 · PMC2798817 · Journal of proteome research · 2009 · 8 claims · 8 setups
One-pot propionylation and trypsin digestion of unfractionated bulk histones enables quantitative Bottom Up MS characterization of histone PTMs without prior off-line HPLC or SDS-PAGE purification
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Quantitative analysis of SMN1 gene and estimation of SMN1 deletion carrier frequency in Korean population based on real-time PCR.
PMID 15608400 · PMC2816285 · Journal of Korean medical science · 2004 · 7 claims · 6 setups
Developed a reliable quantitative real-time PCR assay using SMN1-specific primers, SYBR Green I dye, and the comparative Ct (ΔΔCt) method, normalized to albumin, to determine SMN1 copy number
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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.