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).

• GermVarX: A Robust Workflow for Joint Germline Variant Exploration in whole-exome sequencing cohorts.

  PMID 41926483 · PMC13046259 · PloS one · 2026 · 8 claims · 8 setups

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  GermVarX is a fully automated, modular Nextflow DSL2 workflow for joint germline variant discovery and exploration in WES cohort studies

  ashkenazim paired-end consensus multi-sample joint germline consensus

• Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.

  PMID 36611079 · PMC9825621 · NPJ precision oncology · 2023 · 8 claims · 8 setups

  Has reproduction

  Tree-based (XGBoost, LightGBM) and deep-learning (TabNet) tabular ML classifiers achieve state-of-the-art somatic vs germline classification in tumor-only WES samples, outperforming PureCN.

  tcga same metastatic tumor-only whole-exome wes copy-number

• Metapipeline-DNA: A comprehensive germline and somatic genomics Nextflow pipeline.

  PMID 41850291 · PMC13030954 · Cell reports methods · 2026 · 8 claims · 7 setups

  Full-text index only

  Metapipeline-DNA automates germline and somatic DNA sequencing analysis end-to-end, from raw reads through preprocessing, feature detection, QC, and visualization.

  pcawg giab pcawg-5 tumor-normal whole-genome germline somatic

• TOSCA: an automated Tumor Only Somatic CAlling workflow for somatic mutation detection without matched normal samples.

  PMID 36699358 · PMC9710689 · Bioinformatics advances · 2022 · 6 claims · 4 setups

  Has reproduction · 50

  TOSCA is the first automated, modular open-source tumor-only somatic calling workflow for whole-exome and targeted panel sequencing, covering raw reads through variant classification.

  t-cell hcc1395 clinical targeted whole-exome

• HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.

  PMID 17117180 · PMC2360759 · British journal of cancer · 2006 · 6 claims · 5 setups

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  Common genetic variation (tSNPs and haplotypes) across the 400-kb 17q21 ERBB2 amplicon is not associated with breast cancer risk in British women.

  white same hapmap snp haplotype tagging

• Accurate detection of somatic single-nucleotide variants from bulk RNA-seq data using RNA-MosaicHunter.

  PMID 41505106 · PMC12781890 · Nucleic acids research · 2026 · 6 claims · 8 setups

  Full-text index only

  RNA-MosaicHunter accurately detects sSNVs from bulk RNA-seq with high precision (94.7% in TCGA, 99.3% in cell-line mixture) in default mode

  tcga cell-line same gtex bulk whole-exome whole-genome

• Cancer genome standards for long-read sequencing using cancer cell line mixtures.

  PMID 41934171 · PMC13137868 · GigaScience · 2026 · 8 claims · 6 setups

  Full-text index only

  Long-read variant calling tools achieve recall rates comparable to short-read gold standards

  colo829 same whole-genome short-read 5mc

• Multi-omics profiling reveals microenvironmental remodeling as a key driver of house dust mite-induced lung cancer progression.

  PMID 41610471 · PMC12874334 · Neoplasia (New York, N.Y.) · 2026 · 8 claims · 7 setups

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  Chronic HDM exposure accelerates lung tumor growth through non-mutagenic, immune-mediated mechanisms

  orthotopic lung beas-2b tumor bioluminescence h&e viability