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).

• Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method.

  PMID 16026601 · PMC1637030 · BMC bioinformatics · 2005 · 8 claims · 2 setups

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  DF-SNPs, a novel adaptation of the Decision Forest method, can classify esophageal cancer cases vs. controls based on SNP genotype data with high concordance, sensitivity, and specificity.

  genomic snp high-throughput decision

• Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing.

  PMID 36401180 · PMC9673297 · Genetics, selection, evolution : GSE · 2022 · 8 claims · 8 setups

  Has reproduction · 50

  BaseVar + STITCH at 1.0X sequencing depth with a sample size >300 achieves the highest genotyping accuracy among tested imputation strategies (genotype concordance >98.8%, genotype accuracy >0.97).

  angora domesticated candidate low-coverage multivariate principal

• QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data.

  PMID 36699347 · PMC9722223 · Bioinformatics advances · 2022 · 6 claims · 8 setups

  Has reproduction · 78

  QuasiFlow is a Nextflow pipeline that runs entirely locally via command-line tools and a local HIVdb database copy to analyze NGS-based HIV-1 drug resistance testing data.

  hiv-1 same paired-end reads ngs-based concordance read

• "Sequencing-grade" screening for BRCA1 variants by oligo-arrays.

  PMID 18973698 · PMC2583995 · Journal of translational medicine · 2008 · 7 claims · 6 setups

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  An oligo-array platform can detect BRCA1 SNPs, insertions, and deletions of known and unknown variants, including in heterozygous conditions, with accuracy comparable to direct sequencing

  genomic pcr mcf-10a brca1 oligo-nucleotide direct pcr

• 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

• The next epidemic.

  PMID 16737558 · PMC1779519 · Genome biology · 2006 · 8 claims · 1 setups

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  More than 75% of susceptibility to sporadic Alzheimer's disease may be due to genetic factors

  twins twin

• Addressing the obesity epidemic: a genomics perspective.

  PMID 17362622 · PMC1893129 · Preventing chronic disease · 2007 · 8 claims · 8 setups

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  Obesity is a multifactorial disorder reflecting complex interactions of genes, environment, and lifestyle

  identical fraternal children younger twin family longitudinal

• Genetics of bipolar disorder.

  PMID 18689285 · PMC3181866 · Dialogues in clinical neuroscience · 2008 · 8 claims · 6 setups

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  BP-I has a strong genetic component supported by segregation, adoption, and twin studies across populations

  multiplex pooled bp-affected monozygotic genome-wide genome candidate

• High-resolution, high-throughput HLA genotyping by next-generation sequencing.

  PMID 19845894 · PMC4205125 · Tissue antigens · 2009 · 7 claims · 5 setups

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  Clonal 454 sequencing reads (>250 nt) are long enough to span HLA exons and set phase of linked polymorphisms, resolving ambiguities inherent to Sanger-based heterozygote sequencing.

  cell-line mixtures blood genomic flx amplicon pcr

• Accurate sequence variant genotyping in cattle using variation-aware genome graphs.

  PMID 31092189 · PMC6521551 · Genetics, selection, evolution : GSE · 2019 · 8 claims · 7 setups

  Has reproduction · 45

  Graphtyper outperformed GATK and SAMtools in genotype concordance, non-reference sensitivity, and non-reference discrepancy compared to microarray genotypes

  original sire-son whole-genome multi-sample graph-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

• A SNP-centric database for the investigation of the human genome.

  PMID 15046636 · PMC395999 · BMC bioinformatics · 2004 · 8 claims · 3 setups

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  SNPper is a web-based, integrated SNP database combining dbSNP, the Human Genome sequence (Goldenpath), LocusLink, GeneOntology, and SWISS-PROT data with querying, visualization, and export tools.

  genome genes user-supplied database snp-gene user-submitted

• 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

• Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders.

  PMID 33958982 · PMC8093778 · Frontiers in neuroscience · 2021 · 7 claims · 8 setups

  Has reproduction · 59

  Fourteen gene modules were consistently associated with ReHo across three independent fMRI datasets.

  healthy six ahba neurons resting-state microarray wgcna

• Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.

  PMID 23326238 · PMC3542081 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 49

  B-cell non-Hodgkin lymphomas display striking intra-tumor (intra-sample) and inter-patient (inter-sample) cytosine methylation heterogeneity that increases progressively with disease aggressiveness (NBC<NGC<FL<GCB<ABC).

  dlbcl normal same lymphoma help errbs massarray

• Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation.

  PMID 17608949 · PMC1934372 · BMC genomics · 2007 · 7 claims · 5 setups

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  Developed a statistical model-fitting method to infer generalized (multi-allelic, copy-number-aware) genotypes from raw SNP microarray data

  individuals mother-father-child transcribed snp quantitative multiplex

• Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

  PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

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  A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

  coriell myeloma duplicate snp targeted genotyping machine

• Single-molecule sequencing of an individual human genome.

  PMID 19668243 · PMC4117198 · Nature biotechnology · 2009 · 8 claims · 7 setups

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  Single-molecule sequencing without cloning, amplification or ligation can sequence an individual human genome on one instrument by a single operator in four runs

  genome staphylococcus single-molecule snp sanger

• The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.

  PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 7 claims · 7 setups

  Has reproduction · 50

  Most published adult/other-cohort sepsis gene signatures have limited utility for infant sepsis; only 2 of 7 achieved >80% accuracy in infants

  infant merged individual pairwise whole-blood coconut gene-signature

• 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