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).

• Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

  PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

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  Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

  embryonic high-quality unique m15e est sequence comparative

• Defective DNA repair and increased genomic instability in Artemis-deficient murine cells.

  PMID 12615897 · PMC2193825 · The Journal of experimental medicine · 2003 · 8 claims · 8 setups

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  Artemis-deficient ES cells are severely impaired in VDJ coding joining but retain relatively normal RS (signal) joining

  recombined southern rt-pcr colony

• Gene duplication: the genomic trade in spare parts.

  PMID 15252449 · PMC449868 · PLoS biology · 2004 · 8 claims · 7 setups

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  Gene duplication relaxes selective constraint on one copy, allowing exploration of evolutionary space that is otherwise forbidden in single-copy genes, making duplication the major opportunity for new gene function evolution.

  great genome recently yeast genome-wide molecular comparative

• A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish.

  PMID 16271140 · PMC1309616 · BMC genomics · 2005 · 8 claims · 4 setups

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  149 putative MHC gene loci and their paralogues were identified in the zebrafish genome using sequence similarity searches against the Zv4 draft assembly.

  zebrafish sequence comparative cross-validation

• SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data.

  PMID 16262895 · PMC1280925 · BMC genomics · 2005 · 8 claims · 5 setups

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  Poorly performing SNPs (NoCall rate ≥25%) fail primarily due to inadequate training/localization of the MPAM statistical model call zone, not detection filter failure

  genomic genotype genotyped chromosomal snp clustering mendelian

• Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

  PMID 15790398 · PMC1082905 · BMC genomics · 2005 · 8 claims · 6 setups

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  Twenty-three chemokine genes and 14 chemokine receptor genes were identified in the chicken genome, including 12 new chemokines and 7 new receptors beyond prior reports.

  chicken comparative amino phylogenetic

• Independent component analysis reveals new and biologically significant structures in micro array data.

  PMID 16762055 · PMC1557674 · BMC bioinformatics · 2006 · 7 claims · 8 setups

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  ICA applied to three microarray datasets reveals many biologically significant components, including low-ranking ones not obvious by rank alone

  acute serum-stimulated head aml microarray clust term

• Comparative genomics of the syndecans defines an ancestral genomic context associated with matrilins in vertebrates.

  PMID 16620374 · PMC1464127 · BMC genomics · 2006 · 8 claims · 6 setups

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  Syndecan-encoding sequences are present in Cnidaria and throughout the Bilateria, showing deep conservation of the family.

  invertebrate syndecan full-length chicken wu-blastp clustalw tcoffee

• BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH).

  PMID 16439806 · PMC1356528 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  oaCGH, not BAC CGH arrays, is the platform that will prevail in the future

  genomic lung genetics bt474 array exon

• Personalized genomic medicine with a patchwork, partially owned genome.

  PMID 18449389 · PMC2347364 · The Yale journal of biology and medicine · 2007 · 8 claims · 6 setups

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  Structural variants (CNVs) cover as much as 20 percent of the human genome length and are present in phenotypically normal individuals without apparent negative consequences.

  phenotypically single genome chimpanzee molecular diploid encode

• Nutrigenomics: the genome--food interface.

  PMID 18087577 · PMC2137135 · Environmental health perspectives · 2007 · 8 claims · 8 setups

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  Nutrigenomics integrates genomic science with nutrition to study how dietary components affect gene expression, the proteome, and the metabolome.

  general humans lymphocytes healthy snp controlled micronucleus

• Previously described sequence variant in CDK5RAP2 gene in a Pakistani family with autosomal recessive primary microcephaly.

  PMID 17764569 · PMC2072945 · BMC medical genetics · 2007 · 7 claims · 4 setups

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  A nonsense mutation in CDK5RAP2 exon 4, correctly designated 246T>A (Y82X), was identified in all four affected individuals of a Pakistani family linked to MCPH3

  pakistani affected unrelated one microsatellite sanger mutation

• Genomic expression during human myelopoiesis.

  PMID 17683550 · PMC2045681 · BMC genomics · 2007 · 8 claims · 5 setups

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  An integrated myelopoiesis expression dataset of 9,425 genes, each mapped to a unique genomic position, was generated from 24 microarray experiments across 8 myeloid cell types.

  myeloid same cd34+ gene microarray unsupervised sam

• Effects of DNA-targeted ionizing radiation produced by 5-[125I]iodo-2'-deoxyuridine on global gene expression in primary human cells.

  PMID 17594496 · PMC1934370 · BMC genomics · 2007 · 8 claims · 7 setups

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  125I-IUdR-induced DNA damage alters expression of only a limited subset of genes in primary human cells

  ag09319 gm05388 nhfk whole-genome quantitative dna-associated

• FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

  PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

  user-supplied gene predicted interactome gene kegg transcription

• Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates.

  PMID 17408487 · PMC1853099 · BMC microbiology · 2007 · 8 claims · 8 setups

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  Arginase activity varies more than 100-fold among H. pylori clinical isolates and laboratory-adapted strains

  minimally-passaged pylori coli arginase urease heterologous

• QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.

  PMID 17341461 · PMC1874617 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  QuantiSNP (OB-HMM) provides probabilistic quantification of copy number states and significantly improves accuracy of segmental aneuploidy identification and breakpoint mapping relative to existing tools (BeadStudio/Illumina)

  genomic same pseudo-normal artificially snp fish molecular

• Genome screen to detect linkage to common susceptibility genes for intracranial and aortic aneurysms.

  PMID 18948608 · PMC2629798 · Stroke · 2009 · 8 claims · 4 setups

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  Genomewide linkage analysis in 26 multiplex IA families with AA-affected members identified LOD peaks on chromosome 11 (LOD=3.0) and chromosome 6 (LOD=2.3) using a broad IA/AA-combined phenotype

  multiplex individuals fia subjects genomewide snp medical

• Systems genetics of alcoholism.

  PMID 23584748 · PMC3860445 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2008 · 8 claims · 8 setups

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  Alcoholism is a multifactorial disease driven by interacting genetic, social, and environmental factors, with genetics accounting for 50-60% of risk.

  families drosophila mice han linkage metabolic gene

• Oncogenic mutations in GNAQ occur early in uveal melanoma.

  PMID 18719078 · PMC2634606 · Investigative ophthalmology & visual science · 2008 · 8 claims · 7 setups

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  Activating GNAQ mutations at codon 209 occur in 33/67 (49%) of primary uveal melanomas, making it the most common known oncogenic mutation in UM

  uveal peripheral normal well-characterized pcr sequencing array-based