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).

• Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches.

  PMID 19860898 · PMC2773781 · BMC microbiology · 2009 · 7 claims · 5 setups

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  VLU infections are polymicrobial with no single bacterium colonizing the wounds

  individual pooled second btefap quantitative bulk

• Predictive genomics of cardioembolic stroke.

  PMID 19064790 · PMC2752697 · Stroke · 2009 · 8 claims · 4 setups

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  A Bayesian network multivariate model achieves 86% predictive accuracy (AUC) for cardioembolic stroke on fitted values

  blood-derived gasros same custom bayesian roc

• Increased constraints on MC4R during primate and human evolution.

  PMID 19011902 · PMC9947067 · Human genetics · 2009 · 6 claims · 7 setups

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  There is a significant paucity of genetic diversity at MC4R in humans but not in chimpanzees.

  hgdp-ceph germans central additional dhplc direct coding

• Sequence determinants of human microsatellite variability.

  PMID 20015383 · PMC2806349 · BMC genomics · 2009 · 6 claims · 4 setups

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  Mean and maximum number of repeats across individuals are positively correlated with heterozygosity

  hgdp-ceph genome calibrated microsatellite blastn sequence

• Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans.

  PMID 16478714 · PMC1368655 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  SNP-MaP allele frequency estimates from pooled DNA on the 100K microarray set correlate strongly with allele frequencies from individual genotyping

  pooled single same caucasian snp individual quantification

• Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans.

  PMID 19860882 · PMC2775748 · BMC genetics · 2009 · 8 claims · 8 setups

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  A set of 47 SNPs selected via the 4gen pairwise F_ST approach serves as an ASM panel distinguishing four continental groups (African, Eurasian, Asian/Oceanian, Native American)

  ycc individuals hgdp-ceph asm snp structure pairwise

• Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

  PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

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  HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

  genomic genotype 293t pcr-amplified pcr haplotype cell-cell

• 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

• Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

  PMID 37853325 · PMC10583454 · Genetics, selection, evolution : GSE · 2023 · 8 claims · 6 setups

  Has reproduction

  Selective linkage disequilibrium pruning (SLDP) refines whole-genome SNP sets using GWAS prior information to improve genomic prediction accuracy.

  duroc 1000-individual real low-coverage genome-wide genomic

• Evolutionarily conserved human targets of adenosine to inosine RNA editing.

  PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

  panel brain chicken flna comparative rt-pcr homology

• An efficient method for multi-locus molecular haplotyping.

  PMID 17158153 · PMC1802573 · Nucleic acids research · 2007 · 7 claims · 6 setups

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  A novel molecular haplotyping method using limiting dilution, aliquot pre-screening, and tiling reconstruction can resolve haplotypes spanning many loci over long distances from a single individual's DNA.

  single agarose-embedded genotyping multiplexed monoplex primer-extension

• Completing the map of human genetic variation.

  PMID 17495918 · PMC2685471 · Nature · 2007 · 8 claims · 5 setups

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  A community resource initiative will sequence fosmid and BAC clone libraries from 62 HapMap individuals to systematically discover and resolve structural genetic variants at nucleotide resolution

  genomic fosmid full hapmap paired targeted genotyping

• Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

  PMID 20037582 · PMC2951730 · Nature biotechnology · 2010 · 8 claims · 7 setups

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  A standardized, non-redundant library of 1,889 breakpoint-resolved SVs was assembled from eight published surveys

  personal genomic pcr-validated unrelated short-read pcr sanger

• An attenuated phenotype of Costello syndrome in three unrelated individuals with a HRAS c.179G>A (p.Gly60Asp) mutation correlates with uncommon functional consequences.

  PMID 25914166 · PMC4830354 · American journal of medical genetics. Part A · 2015 · 7 claims · 8 setups

  Has reproduction

  HRAS c.179G>A (p.Gly60Asp) causes an attenuated Costello syndrome phenotype without severe failure-to-thrive, intellectual disability, or cancer predisposition

  cos-7 transiently patients parental ras co-immunoprecipitation immunoblotting

• DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project.

  PMID 15550986 · PMC529316 · PLoS biology · 2004 · 8 claims · 3 setups

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  The human MHC methylation profile is strongly bimodal, with the vast majority of analysed regions being either hypo- (≤30%) or hypermethylated (≥70%)

  mhc subset heterogeneously bisulphite maldi-ms sub-cloning

• Human genetics branches out in Barcelona.

  PMID 18710599 · PMC2575509 · Genome biology · 2008 · 8 claims · 8 setups

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  A meta-analysis of three GWAS scans (DIAGRAM) identifies new type 2 diabetes susceptibility loci (JAZF1, CDC123/CAMK1D, ADAMTS9, THADA) with modest individual effect

  patients families lymphoblastoid genome genome-wide gwas genetic

• Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

  PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups

  Has reproduction · 98

  Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)

  clinical dnaa isogenic h37rv genome-wide structural deep-sequencing

• GABRG1 and GABRA2 as independent predictors for alcoholism in two populations.

  PMID 18818659 · PMC2656604 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2009 · 8 claims · 8 setups

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  GABRG1 SNPs and haplotypes are significantly associated with alcohol use disorder (AUD) in both Finnish Caucasians and Plains American Indians

  finnish plains population hapmap snp haplotype ancestry

• Identification of new ETV6 modulators through a high-throughput functional screening.

  PMID 35198911 · PMC8851229 · iScience · 2022 · 7 claims · 8 setups

  Has reproduction · 68

  A genome-wide shRNA screen in an engineered ETV6-dependent Blasticidin-sensitive pre-B ALL cell line can identify modulators of ETV6 repressive transcriptional activity

  reh genome-wide qrt-pcr chip-seq

• Ovarian cancer biomarkers: current options and future promise.

  PMID 18926090 · PMC3381792 · Journal of the National Comprehensive Cancer Network : JNCCN · 2008 · 8 claims · 8 setups

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  CA125 lacks the sensitivity and specificity needed for reliable early-stage ovarian cancer detection, since only ~50% of stage I/II cases show elevated levels

  serum plasma preoperative advanced serum plasma elisa