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).

• Expression in human prostate of drug- and carcinogen-metabolizing enzymes: association with prostate cancer risk.

  PMID 9823980 · PMC2063181 · British journal of cancer · 1998 · 7 claims · 5 setups

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  CYP2D6, CYP3A, and an N-acetyltransferase enzyme activity are functionally expressed in human prostate tissue

  peripheral prostate genomic allele-specific enzymatic determination

• Multiplexed genetic analysis using an expanded genetic alphabet.

  PMID 15319316 · PMC1592527 · Clinical chemistry · 2004 · 7 claims · 6 setups

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  MultiCode PLx is a three-step platform (PCR, target-specific extension, liquid chip decoding) performed in a single reaction vessel and completed in ~3 h

  genomic synthetic subset newborn multicode eracode automated

• Ensembl 2013.

  PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

  genome species supported variants evidence-based rna-seq chip-seq

• Method for determination of (-102C>T) single nucleotide polymorphism in the human manganese superoxide dismutase promoter.

  PMID 15598343 · PMC544190 · BMC genetics · 2004 · 6 claims · 4 setups

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  A novel TaqMan allelic discrimination assay can reliably genotype the MnSOD -102C>T SNP from diverse DNA sources including blood, buccal swabs, frozen tissue, and paraffin blocks.

  genomic paraffin-embedded taqman pcr-restriction automated

• PAX6 gene variations associated with aniridia in south India.

  PMID 15086958 · PMC419353 · BMC medical genetics · 2004 · 7 claims · 5 setups

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  Mutations in PAX6 cause the aniridia phenotype via haploinsufficiency (loss-of-function/null alleles)

  genomic pcr aniridia sscp automated allele-specific

• siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P3-mTOR signaling pathway as a primary regulator of transferrin uptake.

  PMID 17640392 · PMC2323231 · Genome biology · 2007 · 8 claims · 8 setups

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  The PtdIns(3,4,5)P3-mTOR signaling pathway is a primary positive regulator of transferrin uptake.

  hela sirna secondary synthetic

• BRCA1 and BRCA2 mutations in Turkish breast/ovarian families and young breast cancer patients.

  PMID 10952777 · PMC2363542 · British journal of cancer · 2000 · 7 claims · 4 setups

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  11 mutations (9 BRCA1, 2 BRCA2) were identified across 105 Turkish patients using combined PTT, sequencing, and heteroduplex analysis.

  peripheral genomic truncation direct heteroduplex

• oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

  PMID 22973536 · PMC3429929 · G3 (Bethesda, Md.) · 2012 · 8 claims · 6 setups

  Has reproduction · 49

  oPOSSUM-3 is a web-accessible system that identifies over-represented TFBS and TFBS families in DNA sequences of co-expressed genes or in sequences from high-throughput methods such as ChIP-Seq.

  hg19 large-scale gene-based jaspar tfbs sequence-based anchored

• Human stool contains a previously unrecognized diversity of novel astroviruses.

  PMID 19814825 · PMC2765957 · Virology journal · 2009 · 8 claims · 8 setups

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  Human stool contains a previously unrecognized diversity of astroviruses beyond the classic 8 serotypes and AstV-MLB1/AstV-VA1

  stool consensus-pcr-positive negative one consensus specific sanger

• The UCSC Genome Browser Database: update 2006.

  PMID 16381938 · PMC1347506 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data, with web tools (Genome Browser, Table Browser, Proteome Browser, Gene Sorter, BLAT, In Silico PCR) for visualizing and querying genomes of about a dozen vertebrate species and several model organisms.

  dog vertebrate encode genome comparative automated cross-species

• Familial Wolfram syndrome due to compound heterozygosity for two novel WFS1 mutations.

  PMID 18660851 · PMC2483297 · Molecular vision · 2008 · 8 claims · 6 setups

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  The four affected siblings are compound heterozygotes for two novel WFS1 mutations, one from each parent, causing Wolfram syndrome.

  genomic affected microsatellite pcr allele-specific

• Analysis of the p53 gene by PCR-SSCP in ten cases of Wilms' tumor.

  PMID 10772697 · PMC11166235 · Sao Paulo medical journal = Revista paulista de medicina · 2000 · 7 claims · 3 setups

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  Point mutations of the p53 gene (exons 5-9) were not detected in any of the 10 Wilms' tumor samples studied

  extracted pcr-amplified pcr pcr pcr-sscp automated

• Structural evolution of the protein kinase-like superfamily.

  PMID 16244704 · PMC1261164 · PLoS computational biology · 2005 · 8 claims · 5 setups

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  All kinases in the superfamily share a 'universal core' domain consisting only of the regions required for ATP binding and the phosphotransfer reaction.

  bank representative same kinase comparative manual structure-annotated

• Chips to hits.

  PMID 11983055 · PMC139346 · Genome biology · 2002 · 8 claims · 8 setups

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  Illumina's fiber-optic bead array technology allows ~2,000 oligonucleotide-based assays per bead array for high-throughput genotyping

  individual yeast pools lncap cell-based affymetrix automated

• DNA sequencing: bench to bedside and beyond.

  PMID 17855400 · PMC2094077 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  DNA sequencing methods derived from Sanger's 1977 dideoxy method have dominated sequencing for 30 years despite being only incrementally refined.

  bacteriophage double-stranded single-stranded cloned plus maxam-gilbert dideoxy

• GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments.

  PMID 15790402 · PMC1274265 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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  GeneKeyDB is a lightweight, gene-centric relational database that supports data mining and integration with computational analysis tools.

  genekeydb database gene automated

• Familial hypercholesterolemia in St-Petersburg: the known and novel mutations found in the low density lipoprotein receptor gene in Russia.

  PMID 15701167 · PMC551615 · BMC medical genetics · 2005 · 8 claims · 6 setups

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  21 rare sequence variations of the LDL receptor gene were identified in St.-Petersburg FH patients, 19 of which are probably pathogenic and 2 (P518P, T705I) neutral.

  genomic pcr proband restriction sscp automated

• High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

  PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

  genomic ecotilling non-synonymous ecotilling sanger universal-primer

• A global view of protein expression in human cells, tissues, and organs.

  PMID 20029370 · PMC2824494 · Molecular systems biology · 2009 · 7 claims · 6 setups

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  A high fraction (>65%) of proteins is expressed in most human cells and tissues, while very few proteins (<2%) are detected in any single cell type.

  normal computational hepatocytes same immunohistochemistry immunofluorescence unsupervised

• Histochemical and molecular genetic study of MELAS and MERRF in Korean patients.

  PMID 11850598 · PMC3054831 · Journal of Korean medical science · 2002 · 7 claims · 5 setups

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  MELAS muscle shows strongly SDH-positive blood vessels (SSVs) and many COX-positive ragged-red fibers, while MERRF muscle shows neither SSVs nor COX-positive RRFs, giving distinct histochemical staining patterns between the two diseases.

  frozen muscle extracted pcr-amplified histochemical electron pcr-rflp