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).

• Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.

  PMID 17540169 · PMC4647864 · Cell · 2007 · 8 claims · 13 setups

  Full-text index only

  DAPK1 promoter is epigenetically silenced by DNA methylation in almost all sporadic CLL cases

  cd19+ leukemia raji jurkat quantitative cobra chromatin

• Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

  PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups

  Full-text index only

  A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome

  genome vertebrate multi-species whole-genome conservation non-synonymous

• Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.

  PMID 17480121 · PMC1865561 · PLoS genetics · 2007 · 7 claims · 8 setups

  Full-text index only

  KLF14 is a novel imprinted gene showing monoallelic maternal expression in embryonic and extra-embryonic tissues of both human and mouse

  embryonic fetal monochromosomal fibroblasts allele-specific rt-pcr chromatin

• Heteropolymeric triplex-based genomic assay to detect pathogens or single-nucleotide polymorphisms in human genomic samples.

  PMID 17375191 · PMC1810429 · PloS one · 2007 · 7 claims · 6 setups

  Full-text index only

  The Genomic Assay can detect 100 copies of Bacillus globigii genomic dsDNA, including in the presence of human genomic dsDNA background, without PCR amplification

  bacillus drosophila genomic triplex

• Resequencing of genes for transforming growth factor beta1 (TGFB1) type 1 and 2 receptors (TGFBR1, TGFBR2), and association analysis of variants with diabetic nephropathy.

  PMID 17319955 · PMC1808054 · BMC medical genetics · 2007 · 7 claims · 7 setups

  Full-text index only

  TGFβ1 is a crucial mediator in the pathogenesis of diabetic nephropathy, promoting renal hypertrophy and extracellular matrix accumulation.

  genomic healthy irish case mutation direct taqman

• Evolutionary toggling of the MAPT 17q21.31 inversion region.

  PMID 19165922 · PMC2684794 · Nature genetics · 2008 · 8 claims · 6 setups

  Full-text index only

  The H2 (inverted) orientation is the most likely ancestral great ape/human configuration at 17q21.31

  chimpanzee lymphoblastoid donor whole-genome reciprocal bac

• Is replication the gold standard for validating genome-wide association findings?

  PMID 19112512 · PMC2605260 · PloS one · 2008 · 8 claims · 4 setups

  Full-text index only

  The probability of replicating a specific GWA-identified variant decreases as the number of independent GWA/replication studies increases, when individual study power is less than 100%.

  simulated diallelic hypothetical four statistical marker bayesian

• Prostate cancer genomics: towards a new understanding.

  PMID 19104501 · PMC2721916 · Nature reviews. Genetics · 2009 · 8 claims · 8 setups

  Full-text index only

  Multiple GWAS have identified over a dozen replicated germline SNPs each associated with a modest increase in prostate cancer risk

  germline families african-american combined genome-wide linkage admixture

• Identification of genomic regions contributing to etoposide-induced cytotoxicity.

  PMID 19089452 · PMC2714550 · Human genetics · 2009 · 7 claims · 6 setups

  Full-text index only

  Etoposide-induced cytotoxicity in CEPH lymphoblastoid cell lines is heritable, with genetics explaining 17-25% of variation

  ceph subset hapmap simulated growth heritability non-parametric

• Gene Prospector: an evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases.

  PMID 19063745 · PMC2613935 · BMC bioinformatics · 2008 · 8 claims · 5 setups

  Full-text index only

  Gene Prospector is a Web-based application that selects and prioritizes potential disease-related genes using a curated, updated literature database of genetic association studies

  huge pdgene snps3d dbsnp curated comparative snp

• Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1.

  PMID 18992264 · PMC2682550 · Mutation research · 2009 · 8 claims · 8 setups

  Full-text index only

  A combined functional assay, bioinformatics prediction, and structural modeling approach can classify BRCA1 variants of uncertain significance

  saccharomyces cerevisiae hek-293t yeast yeast β-galactosidase dual

• Searching for genes underlying behavior: lessons from circadian rhythms.

  PMID 18988844 · PMC3744585 · Science (New York, N.Y.) · 2008 · 8 claims · 5 setups

  Full-text index only

  Forward genetic mutagenesis screens successfully identified the molecular components of the circadian clock across Drosophila, Neurospora, cyanobacteria, Arabidopsis, and mouse.

  c57bl genomic automated contextual psychostimulant-induced

• Accurate whole human genome sequencing using reversible terminator chemistry.

  PMID 18987734 · PMC2581791 · Nature · 2008 · 8 claims · 7 setups

  Full-text index only

  A novel sequencing platform using fluorescent reversible terminator nucleotides on clonally amplified single-molecule DNA clusters generates several billion bases of accurate sequence per experiment at low cost.

  bac flow-sorted same yoruba reversible snp targeted

• An optimized procedure for the design and evaluation of Ecotilling assays.

  PMID 18973671 · PMC2586031 · BMC genomics · 2008 · 8 claims · 7 setups

  Full-text index only

  An optimized procedure integrating Vector NTI, Ensembl, Genomatix Suite, GelBuddy, and sequencing/functional-prediction tools streamlines the design, evaluation and interpretation of human Ecotilling assays

  genomic gene pcr cdna ecotilling sequence sanger

• MODBASE, a database of annotated comparative protein structure models and associated resources.

  PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

  Full-text index only

  MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

  sequences chains template chain comparative pairwise ligand

• Analysis of Nigerians with apparently sporadic Parkinson disease for mutations in LRRK2, PRKN and ATXN3.

  PMID 18927607 · PMC2559870 · PloS one · 2008 · 8 claims · 5 setups

  Full-text index only

  No pathogenic mutations were found in LRRK2, PRKN, or ATXN3 in a Nigerian cohort of apparently sporadic PD patients.

  nigerian same novel sanger targeted repeat

• An analysis of human microRNA and disease associations.

  PMID 18923704 · PMC2559869 · PloS one · 2008 · 8 claims · 8 setups

  Full-text index only

  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.

  literature-derived diseases mirnas mirna literature bipartite mirna

• Metabolic syndrome: from epidemiology to systems biology.

  PMID 18852695 · PMC2829312 · Nature reviews. Genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  MetSyn component traits (obesity, insulin resistance, dyslipidaemia, hypertension) exhibit causal interactions and common etiologies rather than being independent conditions

  populations rats adipose four genome-wide linkage gene

• Malaria research in the post-genomic era.

  PMID 18843360 · PMC2705782 · Nature · 2008 · 8 claims · 7 setups

  Full-text index only

  Genome-dependent methods can partially substitute for forward genetic approaches that are unavailable or limited in malaria parasites.

  falciparum plasmodium malaria hela comparative two-hybrid proteomics

• Genes on bovine chromosome 18 associated with bilateral convergent strabismus with exophthalmos in German Brown cattle.

  PMID 18836565 · PMC2556974 · Molecular vision · 2008 · 8 claims · 5 setups

  Full-text index only

  Haplotype association analysis refines the BCSE-linked region on BTA18 to a 6.82 Mb interval spanning 56.05–62.87 Mb

  eye genomic tnnt1 cdna genomic snp