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).

• Frequent and multiple mutations at minisatellite loci in sporadic human colorectal and gastric cancers--possible mechanistic differences from microsatellite instability in cancer cells.

  PMID 11985787 · PMC5927018 · Japanese journal of cancer research : Gann · 2002 · 6 claims · 3 setups

  Full-text index only

  MN mutations occur significantly more frequently in sporadic colorectal cancer (56%) than in gastric cancer (25%)

  sporadic same multilocus pcr-simple

• High frequency of mitochondrial genome instability in human endometrial carcinomas.

  PMID 12915881 · PMC2376924 · British journal of cancer · 2003 · 7 claims · 3 setups

  Full-text index only

  56% (28 out of 50) of endometrial carcinoma cases carry one or more somatic mtDNA changes (deletion, point mutation, or mtMSI) compared with matched normal tissue

  endometrial paraffin-embedded long-range pcr polyacrylamide

• Analysis of polymorphic TGFB1 codons 10, 25, and 263 in a German patient group with non-syndromic cleft lip, alveolus, and palate compared with healthy adults.

  PMID 15212689 · PMC441379 · BMC medical genetics · 2004 · 8 claims · 3 setups

  Full-text index only

  Arg25Pro heterozygous genotype is significantly less frequent in CLP patients (3.3%) than in healthy controls (16.7%)

  peripheral genomic platelet-poor real-time sanger enzyme-linked

• Randomised trial of a decision aid and its timing for women being tested for a BRCA1/2 mutation.

  PMID 14735173 · PMC2410151 · British journal of cancer · 2004 · 6 claims · 3 setups

  Full-text index only

  The DA had no impact on well-being (anxiety, depression, cancer-related distress, general health)

  women brca1 same randomised comparative validated

• An SVM-based system for predicting protein subnuclear localizations.

  PMID 16336650 · PMC1325059 · BMC bioinformatics · 2005 · 7 claims · 3 setups

  Full-text index only

  New kernels defined on k-peptide vectors mapped by BLOSUM62-based high-scored pair matrices (D1, D2, D3) improve SVM discrimination of protein subnuclear localization compared to conventional k-peptide encodings.

  single-localization multi-localization same svm sequence

• Systematic mutation analysis of KIAA0767 and KIAA1646 in chromosome 22q-linked periodic catatonia.

  PMID 16225677 · PMC1274336 · BMC psychiatry · 2005 · 8 claims · 3 setups

  Full-text index only

  Systematic mutation screening of KIAA0767 and KIAA1646 was performed in chromosome 22q-linked periodic catatonia pedigrees

  genomic unrelated systematic case-control

• Increased risk of breast cancer among female relatives of patients with ataxia-telangiectasia: a causal relationship?

  PMID 16222317 · PMC2361617 · British journal of cancer · 2005 · 6 claims · 3 setups

  Full-text index only

  Breast cancer risk is strongly and significantly elevated specifically among mothers of AT patients (SIR=7.14), consistent with Olsen et al's finding (SIR=6.7)

  blood same retrospective atm weighted

• Genome-wide estimation of transcript concentrations from spotted cDNA microarray data.

  PMID 16204447 · PMC1243803 · Nucleic acids research · 2005 · 8 claims · 3 setups

  Full-text index only

  A Bayesian model incorporating experimental covariates (array, pen, probe, dye, scanning) can estimate absolute transcript concentrations from spotted microarray intensities without needing calibration of each sample or gene individually

  cervix same spotted quantitative

• Bayesian coestimation of phylogeny and sequence alignment.

  PMID 15804354 · PMC1087833 · BMC bioinformatics · 2005 · 7 claims · 3 setups

  Full-text index only

  Alignment and phylogenetic inference are mutually dependent, and treating them as separate sequential steps (align then infer tree) is fundamentally flawed and produces biased, overconfident estimates.

  globin same four-sequence bayesian mcmc comparison

• Rare germline mutations in the BRCA2 gene are associated with early-onset prostate cancer.

  PMID 17700570 · PMC2360390 · British journal of cancer · 2007 · 8 claims · 3 setups

  Full-text index only

  Germline protein-truncating BRCA2 mutations confer an elevated relative risk (~7.8-fold) of early-onset prostate cancer in Caucasian men

  peripheral population-based same germline epidemiological genotype-phenotype

• Effective quantitative real-time polymerase chain reaction analysis of the parkin gene (PARK2) exon 1-12 dosage.

  PMID 17324265 · PMC1810516 · BMC medical genetics · 2007 · 8 claims · 3 setups

  Full-text index only

  Developed a real-time TaqMan PCR method that quantifies PARK2 exon 1-12 copy number by comparing amplification signal to the β-globin internal control gene

  genomic same real-time prior

• A novel, non-functional, COL1A1 polymorphism is not associated with lumbar disk disease in young male Greek subjects unlike that of the Sp1 site.

  PMID 18694864 · PMC3124709 · Hormones (Athens, Greece) · 2008 · 5 claims · 3 setups

  Full-text index only

  The COL1A1 3'UTR 4bp insertion polymorphism (A1/A2 alleles) is not associated with LDD in young male Greek subjects

  genomic subset genotype pcr-based sequencing chi-square

• Association of CFH, LOC387715, and HTRA1 polymorphisms with exudative age-related macular degeneration in a northern Chinese population.

  PMID 18682812 · PMC2493029 · Molecular vision · 2008 · 7 claims · 3 setups

  Full-text index only

  CFH Y402H (rs1061170) variant is not associated with exudative AMD in this northern Chinese cohort

  peripheral subset same pcr direct statistical

• Putting science over supposition in the arena of personalized genomics.

  PMID 18665132 · PMC2531214 · Nature genetics · 2008 · 6 claims · 3 setups

  Full-text index only

  There is a rapidly widening gap between gene-disease association discovery and research into the public health/clinical utility of that information.

  adults same tested baseline multiplex telephone-based

• Increase in endoplasmic reticulum stress-related proteins and genes in adipose tissue of obese, insulin-resistant individuals.

  PMID 18567819 · PMC2518495 · Diabetes · 2008 · 8 claims · 3 setups

  Full-text index only

  UPR/ER stress-related proteins (calreticulin, PDI A3, glutathione-S-transferase P) are upregulated in adipose tissue of obese versus lean humans

  subcutaneous same adipose two-dimensional western real-time

• Nicotinamide N-methyl transferase (NNMT) gene polymorphisms and risk for spina bifida.

  PMID 18553462 · PMC2630518 · Birth defects research. Part A, Clinical and molecular teratology · 2008 · 7 claims · 3 setups

  Full-text index only

  NNMT was identified in a genome-wide linkage scan (Souto et al., 2005) as an important regulator of plasma homocysteine concentration in a Spanish population.

  infants infant same snp case-control haplotype

• Mutation patterns of mtDNA: empirical inferences for the coding region.

  PMID 18518963 · PMC2438339 · BMC evolutionary biology · 2008 · 5 claims · 3 setups

  Full-text index only

  Heteroplasmy was detected in 6.5% (3/46) of Azorean families analyzed, all caused by new point mutations with no insertions/deletions.

  extended-family same direct electropherogram molecular

• BOAT: Basic Oligonucleotide Alignment Tool.

  PMID 19958483 · PMC2788372 · BMC genomics · 2009 · 7 claims · 3 setups

  Full-text index only

  BOAT can accurately and efficiently map sequencing reads to a reference genome while handling several substitutions and indels simultaneously

  same short-read snp

• The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus.

  PMID 19911046 · PMC2768904 · PLoS computational biology · 2009 · 8 claims · 3 setups

  Full-text index only

  The replication rate of the strain that initiates an infection has a strong effect on the fitness of the infection at the between-host level, even though the virus evolves rapidly within the host.

  computational same simulation stochastic parameter-sweep multivariate

• Risk of pancreatic cancer in families with Lynch syndrome.

  PMID 19861671 · PMC4091624 · JAMA · 2009 · 7 claims · 3 setups

  Full-text index only

  Families with germline MMR gene mutations (Lynch Syndrome) have an 8.6-fold increased risk of pancreatic cancer compared to the general U.S. population.

  individuals extracted same modified germline proportional