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).

• 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

• Rise of the machines.

  PMID 18670625 · PMC2467494 · PLoS genetics · 2008 · 8 claims · 4 setups

  Full-text index only

  New short-read sequencing platforms (Illumina Genome Analyzer, 454 FLX, ABI SOLiD) enable rapid, scalable whole-genome resequencing that was previously restricted to dedicated sequencing centers using Sanger methods.

  bacillus independent subtilis whole-genome read

• MoGAAAP: a modular Snakemake workflow for automated genome assembly and annotation with quality assessment.

  PMID 41585413 · PMC12824462 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups

  Full-text index only

  MoGAAAP is a modular Snakemake pipeline that automates assembly, provisional annotation, and quality assessment (QA) for any diploid eukaryotic organism

  arabidopsis grapevine pangenome invertebrate genome novo gene

• Genomic approaches used to investigate an atypical outbreak of Salmonella Adjame.

  PMID 30648934 · PMC6412060 · Microbial genomics · 2019 · 8 claims · 7 setups

  Has reproduction · 100

  WGS typing of the S. Adjame outbreak showed marked sub-clustering and genetic heterogeneity atypical of a point-source Salmonella outbreak

  adjame first outbreak food genome snp-based core

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome

• Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance.

  PMID 39009986 · PMC11247842 · Genetics, selection, evolution : GSE · 2024 · 5 claims · 8 setups

  Has reproduction · 69

  Meta-analysis of GWAS across six dairy cattle breeds identifies 58 lead markers associated with clinical mastitis and somatic cell score

  six combined per-breed genome-wide sequence-based trans-ethnic fixed-effect

• Performance of mitochondrial DNA mutations detecting early stage cancer.

  PMID 18834532 · PMC2572633 · BMC cancer · 2008 · 8 claims · 6 setups

  Full-text index only

  The Affymetrix MitoChip resequencing array is a high-throughput, higher-resolution alternative to capillary sequencing for detecting mtDNA point mutations and heteroplasmy in clinical specimens.

  matched blood mtdna low-quantity mitochondrial capillary str

• Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies.

  PMID 18654633 · PMC2464715 · PLoS genetics · 2008 · 8 claims · 5 setups

  Full-text index only

  A Bayesian-inspired penalised maximum likelihood stochastic search method can simultaneously analyse all SNPs (up to 500K) from a GWA study in a few hours on a desktop workstation

  fregene-simulated 80k-snp 480k 192k simulated null whole-genome

• FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors.

  PMID 42102720 · PMC13201080 · GigaScience · 2026 · 8 claims · 6 setups

  Full-text index only

  A pipeline combining IDF transformation, sparse random projection (SRP), and NNDescent (the FEDRANN strategy) enables accurate overlap detection across diverse long-read datasets

  real same chromosome genome overlap exact simulated