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).

• BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies.

  PMID 41896736 · PMC13147680 · BMC microbiology · 2026 · 7 claims · 8 setups

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  BaGPipe is an automated, reproducible Nextflow pipeline that integrates pre-processing, Pyseer-based association analysis, and downstream visualisation into a unified bacterial GWAS workflow

  streptococcus staphylococcus aureus pneumoniae bacterial read amr

• Tracing human genetic histories and natural selection with precise local ancestry inference.

  PMID 40379651 · PMC12084304 · Nature communications · 2025 · 7 claims · 7 setups

  Has reproduction · 76

  Orchestra, a two-stage LAI method combining a recombination-distance base layer with a deep learning (convolutional + attention) smoothing module, outperforms RFmix, FLARE and Gnomix in precision and recall across simulated admixture generations.

  1kgp-16pops independent simulated 1kgp simulated population-level local

• Application of qualifying variants for genomic analysis.

  PMID 41570118 · PMC12926777 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 4 setups

  Full-text index only

  QVs should be treated as dynamic, multifaceted elements permeating the entire analysis workflow, not as a single static filtering step

  in-house hapmap3 genome framework exome gwas wgs

• Tractor workflow: a scalable Nextflow framework for local ancestry-aware genome-wide association studies.

  PMID 41838407 · PMC13197121 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 6 setups

  Full-text index only

  Developed a scalable Nextflow workflow that automates phasing, local ancestry inference (LAI), and Tractor GWAS into a reproducible end-to-end pipeline

  biobank phased two-way simulated haplotype local gwas

• Statistical framework for calling allelic imbalance in high-throughput sequencing data.

  PMID 39966391 · PMC11836314 · Nature communications · 2025 · 8 claims · 6 setups

  Has reproduction · 89

  MIXALIME is a versatile computational framework for calling allele-specific variants (ASVs) from diverse high-throughput omics data

  wa01 left heart chip-seq rna-seq cage-seq