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).

• Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

  PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

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  Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

  genome h-invdb gene sets genome transcript-to-genome coding

• Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan.

  PMID 16055919 · PMC1182175 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  MDA genotyping call rates and accuracy are only marginally lower than for genomic DNA

  genomic same monozygotic subset genome-wide genome

• Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping.

  PMID 20021669 · PMC2803178 · BMC genetics · 2009 · 8 claims · 8 setups

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  WGA DNA from archived serum samples produced low genotyping call rates and is unsuitable for high-resolution genotyping on SNP 6.0 arrays

  wga non-amplified archived serum-derived snp purification whole-genome

• Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples.

  PMID 18793462 · PMC2537568 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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  Batch size affects genotype calling results (call rate and concordance) and the resulting lists of significantly associated SNPs.

  hapmap genotype genotype raw case-control

• 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

• 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

• A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

  PMID 18940863 · PMC2602776 · Nucleic acids research · 2008 · 7 claims · 4 setups

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  A novel Invader assay-based procedure can accurately determine SNP genotypes in trisomic genomic DNA samples in a simple, cost-effective manner

  genomic same synthetic invader pyrosequencing hplc

• Silhouette scores for assessment of SNP genotype clusters.

  PMID 15760469 · PMC555759 · BMC genomics · 2005 · 7 claims · 5 setups

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  Silhouette scores provide a relevant, objective numeric measure of SNP genotype cluster quality, condensing tightness and separation into a single value from -1.0 to 1.0.

  genomic blood extended hybridized single genomic multiplex

• Combinatorial Mismatch Scan (CMS) for loci associated with dementia in the Amish.

  PMID 16515697 · PMC1448207 · BMC medical genetics · 2006 · 8 claims · 7 setups

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  CMS compares IBS allele/genotype sharing between distantly related (beyond grandparental) affected and unaffected individuals from founder populations to detect disease loci while reducing confounding from population stratification and genetic heterogeneity.

  amish unrelated same overall microsatellite combinatorial permutation

• Allelotyping of pooled DNA with 250 K SNP microarrays.

  PMID 17367522 · PMC1839100 · BMC genomics · 2007 · 8 claims · 5 setups

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  The polynomial based probe specific correction (PPC) algorithm is the most accurate method for estimating allele frequency from pooled DNA.

  pool nspi individual snp individual call

• The specificity of the FOXL2 c.402C>G somatic mutation: a survey of solid tumors.

  PMID 19956657 · PMC2777318 · PloS one · 2009 · 6 claims · 4 setups

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  The FOXL2 c.402C>G mutation is not commonly found in a wide variety of other cancers and is likely pathognomonic for A-GCTs and closely related tumors.

  tumor ovarian kgn high sanger taqman

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

  PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 74

  ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

  small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot

• A computational pipeline to visualize DNA-protein binding states using dSMF data.

  PMID 35463472 · PMC9026571 · STAR protocols · 2022 · 8 claims · 2 setups

  Has reproduction · 89

  The pipeline maps states of protein-binding DNA in vivo using dSMF data and identifies binding states at an enhancer in Drosophila S2 cells

  drosophila dual-enzyme starr-seq

• Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals.

  PMID 18803882 · PMC2566316 · BMC genomics · 2008 · 8 claims · 5 setups

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  About 20% of the 909,622 SNPs on the SNP Array 6.0 are monomorphic in the Japanese population

  genomic japanese reference snp concentration agarose

• Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

  PMID 23284297 · PMC3527207 · PLoS genetics · 2012 · 8 claims · 8 setups

  Has reproduction · 93

  Wolbachia infection status can be accurately predicted in silico from whole-genome shotgun sequence of individual host strains, showing 99% concordance with diagnostic PCR.

  melanogaster dgrp complete wolbachia-infected whole-genome diagnostic coverage-based

• Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

  PMID 15601538 · PMC3525068 · Human genomics · 2004 · 8 claims · 8 setups

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  An integrated system combining Ensembl, ACeDB, Gbrowse and custom relational databases provides a scalable genome informatics and workflow infrastructure for complex disease gene discovery.

  pcr candidate embl clinical snp manual homology

• Molecular haplotyping by linking emulsion PCR: analysis of paraoxonase 1 haplotypes and phenotypes.

  PMID 15886392 · PMC1092276 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  LE-PCR (linking PCR combined with emulsion PCR) enables molecular determination of haplotypes at two linked polymorphic loci without specialized instrumentation beyond real-time PCR

  leukocyte capped genomic plasma linking quantitative emulsion

• SNP identification in unamplified human genomic DNA with gold nanoparticle probes.

  PMID 15659576 · PMC548375 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  A microarray-based method allows multiplex SNP genotyping in total human genomic DNA without target amplification or complexity reduction

  unamplified genomic fragmented factor multiplex sequencing poly

• Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.

  PMID 18842124 · PMC2569949 · BMC genomics · 2008 · 7 claims · 7 setups

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  GS-FLX pyrosequencing of pooled amplicons detects sequence variants with high specificity (99.95%) and no false negatives at ≥30× coverage

  pools pcr genomic gs-flx massively sanger pcr

• Characterizing natural variation using next-generation sequencing technologies.

  PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups

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  Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.

  pichia individuals saccharomyces individual whole-genome partial comparative