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).

Publications 1.3k Datasets 392.5k Experiments 466

System / cell line: cohort ✕ Clear

NeoPrecis: enhancing immunotherapy response prediction through integration of qualified immunogenicity and clonality-aware neoantigen landscapes.

PMID 41577704 · PMC12932759 · Nature communications · 2026 · 8 claims · 8 setups

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NeoPrecis-Immuno, a T-cell recognition model incorporating MHC-binding motif enrichment into a cross-reactivity-distance framework, improves neoantigen immunogenicity prediction.

tcr-pmhc cedar cedar-derived nci cross-reactive t-cell immunogenicity
NGSTroubleFinder: a tool for detection and quantification of contamination and kinship across human NGS data.

PMID 41608734 · PMC12838523 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups

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NGSTroubleFinder detects cross-sample contamination, sample swaps, kinship, and sex mismatches from BAM/CRAM files without requiring additional variant-calling steps

genomes 1000gp internal whole-genome whole-transcriptome wgs
Gut microbiome signatures associated with depression and obesity.

PMID 41615149 · PMC13011431 · mSystems · 2026 · 8 claims · 4 setups

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Taxonomic gut microbiome profiles classify depressed vs non-depressed subjects with a balanced accuracy of 0.90 using machine learning

stool subjects shotgun alpha machine
TNF-⍺-mediated myeloid-instructed CD14(+)CD4(+) T cells are associated with poor survival in lung adenocarcinoma.

PMID 41666923 · PMC12923953 · Cell reports. Medicine · 2026 · 8 claims · 5 setups

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Tumors stratify into lymphoid-enriched, myeloid-enriched, and mixed immune-infiltrated subtypes independent of oncogenic driver status

resected luad cd4+ multiplex spatial image
From forest to farm: the impact of a broad spectrum of lifestyles on the porcine gut microbiota.

PMID 41810129 · PMC12969317 · Current research in microbial sciences · 2026 · 8 claims · 6 setups

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Dietary variables had the largest effect on microbiota composition among lifestyle factors tested

faecal 16s microbiota 16s volatile faecal
MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.

PMID 41918857 · PMC13034871 · PeerJ · 2026 · 7 claims · 6 setups

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MetaPepticon is a modular, end-to-end Snakemake pipeline that predicts ACP candidates directly from raw genomic, metagenomic, transcriptomic, metatranscriptomic reads, assembled contigs, or peptide sequences.

validated gut representative predicted acp shotgun genome
StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.

PMID 42097292 · PMC13188985 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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StrainMake is a Snakemake-based, Conda-managed workflow for de novo metagenomic analysis from short, long, or hybrid sequencing data.

cami high-quality recovered gut metagenome metagenomic mag
CLUES A Comprehensive Workflow for Integrating Geospatial Data in Biomedical Research.

PMID 42128886 · PMC13172076 · Nature communications · 2026 · 8 claims · 5 setups

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CLUES is an open-source, end-to-end workflow that automates selection, download, harmonization, and linkage of open-access geospatial environmental data to individual-level biomedical data without requiring geospatial expertise.

national copernicus digital norwegian large-scale download spatial
Tight junction-high and CDH17-positive cell population is the source of colorectal cancer liver metastases.

PMID 41484106 · PMC12881549 · Nature communications · 2026 · 8 claims · 8 setups

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Loss/inhibition of IKKα unexpectedly promotes, rather than suppresses, CRC liver metastasis in patient-derived organoid (PDO) xenograft models.

pdo5 pdo5-derived crc dld1 intrasplenic immunohistochemistry kaplan-meier
Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

PMID 41484196 · PMC12800305 · Scientific reports · 2026 · 8 claims · 8 setups

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A B cell subpopulation co-expressing HLA-DRB5, HLA-DQA2, HLA-DQB1, CD74, and ACTG1 is significantly associated with favorable nCRT response in rectal cancer

larc scrna-seq scissor+ single-cell bulk pseudotime
Single-cell resolution of an open chromatin signature in persister tumor cells.

PMID 41485222 · PMC12978573 · Cell reports · 2026 · 8 claims · 8 setups

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Single-nucleus multi-omic (snRNA-seq + snATAC-seq) profiling of fallopian tube, treatment-naive, and NACT-treated HGSOC tissue identifies a persister cell signature (PCS) defining the chemotherapy-tolerant state.

non-malignant same epithelial tumor single-nucleus mitochondrial copy-number
Advancing Prognosis Prediction and Immunotherapy Efficacy in Lung Adenocarcinoma Through Machine Learning: Novel Insights From Anoikis Regulator Patterns in Single-Cell Multiomics.

PMID 41488744 · PMC12764181 · International journal of genomics · 2026 · 8 claims · 8 setups

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Epithelial and endothelial cells show the highest anoikis-enriched scores among LUAD TME cell types, with AT2-like Epi being the most anoikis-related epithelial subpopulation.

luad pan-cancer tumor scrna-seq spatial bulk
Deep-learning prediction of gene expression from personal genomes.

PMID 41495833 · PMC12869966 · Genome biology · 2026 · 8 claims · 8 setups

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Fine-tuning Enformer on paired personal WGS and RNA-seq data (Variformer) corrects Enformer's failure to predict inter-individual gene expression differences across held-out people.

gtex rosmap same monocyte paired mutagenesis chromhmm
A machine learning-defined cellular senescence signature systematically enhances prognostication and guides immunotherapy strategies for the treatment of gliomas.

PMID 41501133 · PMC12886967 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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CSRGPS is a robust, machine-learning-derived prognostic signature that outperforms existing glioma prognostic models across multiple cohorts

tcga-gbm glioma meta consensus wgcna machine
Distinct phenotypes and repertoires of bronchoalveolar and airway mucosal T cells in health and allergic asthma.

PMID 41519381 · PMC12983186 · Mucosal immunology · 2026 · 8 claims · 6 setups

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BAL and endobronchial brush sampling capture phenotypically and clonally distinct T cell populations

sorted paired bal subjects single-cell fluorescence-activated methacholine
Hypoxia-driven remodeling of SELENOP(+) macrophages shapes T cell dynamics and promotes ovarian cancer metastasis.

PMID 41526347 · PMC12852879 · Nature communications · 2026 · 8 claims · 8 setups

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SELENOP+ macrophages co-occur and spatially co-localize with precursor exhausted (GZMH+) CD8+ T cells and activate these T cells via selenoprotein P in vitro and in vivo.

hgsoc million pseudo-bulk hgsoc-derived scrna-seq sctcr-seq spatial
scSNViz: visualization and analysis of cell-specific expressed SNVs.

PMID 41533688 · PMC12866635 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 7 setups

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scSNViz is an R package for exploration, quantification, and visualization of expressed SNVs from cell-barcoded scRNA-seq data, supporting VAF estimation, SNV clustering, and 2D/3D visualization.

prostate non-small cholangiocarcinoma neuroblastoma scrna-seq cell-level single-cell
PRDM1+ Malignant Cells Mediate an Immunosuppressive Landscape and Resistance to Neoadjuvant Chemoradiotherapy and Immunotherapy in Esophageal Squamous Cell Carcinoma.

PMID 41556358 · PMC13042517 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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A PRDM1+ malignant epithelial cell subcluster (Epi_C4) is enriched in NMPR patients and is associated with nICRT treatment resistance

locally escc pd-1 kyse-30 single-arm scrna-seq bulk
FAP expression as a marker of malignant transformation enabling in vivo characterization in peripheral nerve sheath tumors: a multimodal and translational study.

PMID 41591566 · PMC12847211 · Acta neuropathologica · 2026 · 8 claims · 7 setups

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FAP is consistently upregulated in MPNSTs compared to neurofibromas at the transcript level across independent bulk datasets

archival tcga peripheral nf-1-associated bulk spatial single-cell
pmid-41593306

PMID 41593306 · PMC12868835 · 8 claims · 8 setups

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Innate antibacterial defense functions are generally enhanced in most cell types at AS onset and are negatively associated with AS severity

pbmcs gwas pbmc-derived cd4+ single-cell bulk mendelian

Experiments

NeoPrecis: enhancing immunotherapy response prediction through integration of qualified immunogenicity and clonality-aware neoantigen landscapes.

NGSTroubleFinder: a tool for detection and quantification of contamination and kinship across human NGS data.

Gut microbiome signatures associated with depression and obesity.

TNF-⍺-mediated myeloid-instructed CD14(+)CD4(+) T cells are associated with poor survival in lung adenocarcinoma.

From forest to farm: the impact of a broad spectrum of lifestyles on the porcine gut microbiota.

MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.

StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.

CLUES A Comprehensive Workflow for Integrating Geospatial Data in Biomedical Research.

Tight junction-high and CDH17-positive cell population is the source of colorectal cancer liver metastases.

Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

Single-cell resolution of an open chromatin signature in persister tumor cells.

Advancing Prognosis Prediction and Immunotherapy Efficacy in Lung Adenocarcinoma Through Machine Learning: Novel Insights From Anoikis Regulator Patterns in Single-Cell Multiomics.

Deep-learning prediction of gene expression from personal genomes.

A machine learning-defined cellular senescence signature systematically enhances prognostication and guides immunotherapy strategies for the treatment of gliomas.

Distinct phenotypes and repertoires of bronchoalveolar and airway mucosal T cells in health and allergic asthma.

Hypoxia-driven remodeling of SELENOP(+) macrophages shapes T cell dynamics and promotes ovarian cancer metastasis.

scSNViz: visualization and analysis of cell-specific expressed SNVs.

PRDM1+ Malignant Cells Mediate an Immunosuppressive Landscape and Resistance to Neoadjuvant Chemoradiotherapy and Immunotherapy in Esophageal Squamous Cell Carcinoma.

FAP expression as a marker of malignant transformation enabling in vivo characterization in peripheral nerve sheath tumors: a multimodal and translational study.

pmid-41593306