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).

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

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

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  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

• Divergent clonal evolution and tumor microenvironment remodeling shape gastric cancer peritoneal metastasis.

  PMID 41882239 · PMC13181027 · Communications biology · 2026 · 8 claims · 7 setups

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  Substantial intra-patient heterogeneity exists between GCPM and primary tumors at both genetic and functional (transcriptomic) levels

  gastric wgs paired genes whole-genome whole-transcriptome mutational

• TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.

  PMID 42277027 · PMC13260335 · Nature communications · 2026 · 8 claims · 5 setups

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  TOFU-MAaPO yields significantly more high-quality MAGs than metaFun, nf-core/mag, and ATLAS due to integration of multiple complementary binning tools with unified MAGScoT refinement

  gut same uniquely metagenome quality assembly-free

• Leveraging the germ layer development patterns to predict prognosis and identify MEST as a novel therapeutic target in glioma.

  PMID 41501725 · PMC12870398 · Cancer cell international · 2026 · 7 claims · 8 setups

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  MEST is a key oncogenic GLD-related gene and a novel therapeutic target in glioma, identified via a machine learning feature selection framework

  bulk single-cell tcga glioma gsva aucell machine

• Multi-omics analyses related to unfolded protein response in prostate cancer implicate pro-tumor role of IFRD1.

  PMID 41694360 · PMC12894258 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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  Luminal prostate epithelial cells, especially the LE-KLK3 subpopulation, show elevated UPR activity compared to other cell types

  pca tcga-prad external scrna-seq bulk immune

• Robust and efficient annotation of cell states through gene signature scoring.

  PMID 41708334 · PMC12951948 · Genome research · 2026 · 8 claims · 8 setups

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  Established scoring methods (Seurat, SCANPY, UCell, JASMINE) fail to provide robust and comparable score distributions across diverse signatures and experimental conditions, precluding accurate unsupervised cell-state annotation.

  pbmc colorectal esophageal crc scrna-seq cross-implementation signature

• The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository.

  PMID 40926267 · PMC12421755 · Genome biology · 2025 · 8 claims · 3 setups

  Has reproduction · 99

  Across 253 manually curated studies (164,000+ samples), over 25% of critical metadata are omitted, with only 74.8% of relevant phenotypes available overall.

  randomly repositories geo manual automated

• Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics.

  PMID 31918046 · PMC6992905 · iScience · 2020 · 8 claims · 8 setups

  Has reproduction · 96

  Assembled the largest reference blood gene expression profiling (GEP) dataset for AML to date: 12,029 samples from 105 studies across three platforms.

  peripheral datasets hg-u133 disjoint bulk machine deep

• Improving melanoma classification by integrating genetic and morphologic features.

  PMID 18532874 · PMC2408611 · PLoS medicine · 2008 · 7 claims · 5 setups

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  BRAF-mutant melanomas show distinct morphological features (upward migration and nesting of intraepidermal melanocytes, epidermal thickening, sharper lateral demarcation, larger/rounder/more pigmented tumor cells) compared to non-mutant melanomas

  archival same subset patients histopathological mutation quantitative

• Metagenomic Comparison of Bat Colony Resistomes Across Anthropogenic and Pristine Habitats.

  PMID 41594088 · PMC12838372 · Antibiotics (Basel, Switzerland) · 2026 · 8 claims · 7 setups

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  Anthropogenic exposure enhances the diversity and evenness of resistance mechanisms within bat-associated microbiomes, increasing their potential as AMR reservoirs.

  bat mag-derived shotgun metagenome arg

• 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

• Protocol for single-cell optimization objective and trade-off inference.

  PMID 41790544 · PMC12992945 · STAR protocols · 2026 · 6 claims · 6 setups

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  SCOOTI is a computational framework that integrates bulk and single-cell omics data with genome-scale metabolic modeling to infer metabolic objectives and trade-offs

  mcf10a serum-starved contact-inhibited zygote bulk scrna-seq genome-scale