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).

• An OMICs-based meta-analysis to support infection state stratification.

  PMID 33560295 · PMC8388022 · Bioinformatics (Oxford, England) · 2021 · 7 claims · 6 setups

  Has reproduction · 44

  Multi-class machine learning models built from cross-platform microarray meta-analysis can distinguish bacterial, viral and no-infection states with high accuracy (best model: 93% bacterial, 89% viral correct).

  blood merged affymetrix-optimized gene feature out-of-sample

• Delineation of a gene network underlying the pulmonary response to oxidative stress in asthma.

  PMID 19730131 · PMC3328512 · Journal of investigative medicine : the official publication of the American Federation for Clinical Research · 2009 · 8 claims · 6 setups

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  Integration of multiple public microarray datasets via a four-way Venn diagram identifies genes commonly expressed in asthma- and cigarette smoke-exposed lung

  respiratory lung a549 gene affymetrix network

• Genomic studies of mood disorders -- the brain as a muscle?

  PMID 15833130 · PMC1088952 · Genome biology · 2005 · 7 claims · 5 setups

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  FGF family members and receptors (notably FGF1, FGF2, FGFR2, FGFR3) are down-regulated in postmortem prefrontal cortex of subjects with major depressive disorder but not in bipolar or control subjects.

  postmortem brain rodent hippocampus affymetrix quantification gene

• Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals.

  PMID 18803882 · PMC2566316 · BMC genomics · 2008 · 8 claims · 5 setups

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  About 20% of the 909,622 SNPs on the SNP Array 6.0 are monomorphic in the Japanese population

  genomic japanese reference snp concentration agarose

• Calibrating the performance of SNP arrays for whole-genome association studies.

  PMID 18584036 · PMC2432039 · PLoS genetics · 2008 · 8 claims · 7 setups

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  Previous SNP array genetic coverage estimates are inflated due to SNP overfitting and sample overfitting, since they were evaluated on the same HapMap SNPs/individuals used to design the arrays.

  american liver simulated hapmap snp gene simulation-based

• Reconstructing Indian population history.

  PMID 19779445 · PMC2842210 · Nature · 2009 · 8 claims · 8 setups

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  Most Indian populations descend from a mixture of two ancient, genetically divergent populations: ANI (close to Middle Easterners, Central Asians, Europeans) and ASI (as distinct from ANI and East Asians as those are from each other).

  indian pairs gujarati genome-wide principal fst-based

• A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability.

  PMID 19941644 · PMC2789744 · BMC bioinformatics · 2009 · 7 claims · 4 setups

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  Feature variability strongly influences breast cancer signature composition even when array platform and patient stratification are identical.

  breast preprocessed microarray two-color perturbation

• 6th annual meeting of the Complex Trait Consortium.

  PMID 17906895 · PMC2042027 · Mammalian genome : official journal of the International Mammalian Genome Society · 2007 · 8 claims · 7 setups

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  The NIEHS Perlegen/resequencing project has generated over 8.5 million SNPs from 15 inbred mouse strains but shows a high false-negative discovery rate, with an estimated 45 million SNPs actually present.

  inbred recombinant yeast gallstone genome affymetrix microarray

• Macrophages on the run: Exercise balances macrophage polarization for improved health.

  PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups

  Has reproduction · 81

  Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.

  gene affymetrix pooled muscle meta-analysis stepminer gene