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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Tipping the balance in autoimmune disease.
PMID 18001485 · PMC2246277 · Genome biology · 2007 · 8 claims · 8 setups
Human autoimmune diseases are fundamentally diseases of immune dysfunction, evidenced by predisposing genes being immune-function genes, some shared and some unique across MS, T1D, SLE, CD and RA
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Has reproduction · 63
Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain.
PMID 24992200 · PMC4081786 · PLoS pathogens · 2014 · 8 claims · 8 setups
The CL-SL L. donovani isolate is severely attenuated for survival in visceral organs (liver, spleen) of BALB/c mice compared with the VL-SL isolate, while inducing transient footpad swelling that VL-SL does not.
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Supervised learning-based tagSNP selection for genome-wide disease classifications.
PMID 18366619 · PMC2386071 · BMC genomics · 2008 · 7 claims · 2 setups
SRFA (Supervised Recursive Feature Addition) is a novel feature selection method combining supervised learning and statistical redundancy measures for SNP selection
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Characterization of the linkage disequilibrium structure and identification of tagging-SNPs in five DNA repair genes.
PMID 16091150 · PMC1208870 · BMC cancer · 2005 · 7 claims · 5 setups
Three of the five DNA repair genes (MRE11A, RAD50, XRCC4) do not conform to a contiguous haplotype block structure; instead SNPs in high LD can be non-contiguous, fitting a more flexible LD group paradigm
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Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.
PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups
High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb
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The meso-genomic era.
PMID 11516332 · PMC139414 · Genome biology · 2001 · 8 claims · 8 setups
Linkage disequilibrium (LD) between SNPs extends much further in Northern European populations (~120 kb) than in a Nigerian population (<10 kb), reflecting differing population histories (bottlenecks vs. constant expansion).
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Optimal step length EM algorithm (OSLEM) for the estimation of haplotype frequency and its application in lipoprotein lipase genotyping.
PMID 12529185 · PMC149347 · BMC bioinformatics · 2003 · 5 claims · 4 setups
OSLEM (Optimal Step Length EM), which approximates an optimal step length via a fixed-point search (D_N = D_{N-1} + λ(D_preN - D_{N-1})), runs about twice as fast as standard EM while producing the same haplotype frequency estimates.
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An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer.
PMID 18676830 · PMC2680495 · Cancer research · 2008 · 8 claims · 5 setups
PIK3CA mutations are more common in hormone receptor-positive and HER2-positive tumors than in basal-like breast cancers
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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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A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.
PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups
A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl
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Has reproduction · 38
RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.
PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups
A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).
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BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.
PMID 19668202 · PMC3661775 · Nature methods · 2009 · 8 claims · 8 setups
BreakDancer (BreakDancerMax + BreakDancerMini) is a software package that predicts a wide variety of structural variants including deletions, insertions, inversions, and intra/inter-chromosomal translocations from paired-end short-insert sequencing reads.
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Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.
PMID 18588709 · PMC2464599 · BMC genetics · 2008 · 8 claims · 7 setups
Porcine PNAS-4 encodes a 194-amino-acid protein that localizes to the Golgi complex
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Twin peaks: the draft human genome sequence.
PMID 11276423 · PMC138909 · Genome biology · 2001 · 8 claims · 8 setups
The predicted number of human genes (~26,000-40,000) is far lower than the widely assumed ~100,000, though downstream RNA/protein complexity can still generate substantial biological complexity.
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G2Cdb: the Genes to Cognition database.
PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups
G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.