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).

• Anti-CSF-1R therapy with combined immuno-chemotherapy coordinate an adaptive immune response to eliminate macrophage enriched triple negative breast cancers.

  PMID 41484081 · PMC12858953 · Nature communications · 2026 · 8 claims · 8 setups

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  Combined low-dose CTX + anti-CSF-1R (SNDX-ms6352) is highly effective against aggressive metastatic Trp53-null TNBC models with high macrophage infiltration, producing complete tumor regression in claudin-low models.

  trp53-null complete t12 cell-deficient imaging survival tumor

• Immune profiling in a living human recipient of a gene-edited pig kidney.

  PMID 41507576 · PMC12823403 · Nature medicine · 2026 · 8 claims · 8 setups

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  Xenograft experienced early T cell-mediated rejection (Banff grade 2A) within 1 week post-transplant despite profound circulating T cell depletion, likely driven by subtherapeutic immunosuppression and residual CD8+ T cells in lymph nodes.

  xenotransplant recipient kidney integrative single-cell flow

• PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells.

  PMID 41565684 · PMC12881479 · Nature communications · 2026 · 8 claims · 8 setups

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  PURE-seq integrates FACS sorting directly into PIP-seq barcoding reaction tubes, minimizing manual handling and cell loss for rare-cell single-cell sequencing.

  hek293t pbmcs melanoma bone single-cell infercnv gene

• Genetics and environment distinctively shape the human immune cell epigenome.

  PMID 41593234 · PMC12900638 · Nature genetics · 2026 · 8 claims · 6 setups

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  Exposure-associated differentially methylated regions (eDMRs) and genotype-associated DMRs (gDMRs) show distinct genomic distributions: eDMRs are enriched at enhancers/regulatory regions, while gDMRs are predominantly found in gene bodies.

  pbmcs pbmc edmrs differentially single-nucleus fluorescence-activated motif

• Protocadherin 20 Is a POU Class 2 Homeobox 3 Target Gene Required for Proper Tuft Cell Microvillus Organization.

  PMID 41619969 · PMC13051935 · Cellular and molecular gastroenterology and hepatology · 2026 · 8 claims · 8 setups

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  POU2F3 ChIP-seq in isolated murine tuft cells identifies high-confidence POU2F3 binding sites/target genes enriched at gene promoters and the POU consensus motif

  facs-isolated pou2f3 duodenal non-small-cell chip-seq novo bulk

• FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models.

  PMID 41644528 · PMC12982622 · Nature communications · 2026 · 8 claims · 6 setups

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  FLASH-MM produces LMM parameter estimates identical to lmer (lme4) up to the sixth decimal place while being 50- to 140-fold faster as sample size increases from 20,000 to 120,000 cells

  simulated same healthy female-biased simulated comparative single-cell

• Genomic biomarkers of immunotherapy plus chemotherapy in patients with advanced NSCLC: Insights from the phase 3 ORIENT-11 study.

  PMID 41660271 · PMC12876322 · iScience · 2026 · 8 claims · 8 setups

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  A 9-gene Immune-Chemotherapy Prediction Score (ICPscore), derived from ORIENT-11 via WGCNA and LASSO Cox regression, predicts survival benefit from ICI plus chemotherapy in advanced NSCLC

  orient-11 hub nsclc oak bulk pd-l1 wgcna

• A muscle-centered hierarchical breakdown underlies flight loss during silkworm domestication.

  PMID 41716997 · PMC12915254 · iScience · 2026 · 8 claims · 8 setups

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  Flight loss in B. mori results from a muscle-centered collapse of a three-tiered hierarchical genetic module comprising mitochondrial energy production (COX3/ND1), wing vein patterning (Dally/CtBP), and flight muscle specification (Yki)

  wing wings flight mandarina single-cell spatial velocity

• Multi-cohort and single-cell profiling of aging genes reveals prognostic and therapeutic targets in breast cancer.

  PMID 41732271 · PMC12924738 · iScience · 2026 · 8 claims · 7 setups

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  The eight-gene MLAG signature outperforms 100 previously published prognostic models across 12 independent breast cancer cohorts

  tcga-brca senescent normal single-cell machine univariate gene

• Vγ1 γδ T cells steer airway macrophages toward a profibrotic response in an autochthonous lung cancer mouse model.

  PMID 41779856 · PMC12959402 · Science advances · 2026 · 7 claims · 6 setups

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  Lung tumors drive expansion of both CD27+ and CD27- pulmonary γδ T cells, which acquire distinct spatial and phenotypic changes in the tumor microenvironment

  spc-cre+ microdissected sorted merged flow confocal single-cell

• Unique phenotypic and T cell receptor characteristics of CD8(+) T cells accumulated in the brains of Alzheimer's disease mice.

  PMID 41794902 · PMC13087195 · Scientific reports · 2026 · 8 claims · 5 setups

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  Brain CD8+ T cells segregate into two major, mutually exclusive Trm populations: a CXCR6-related immunosuppressive cluster (cd8_c0) present in both aged non-Tg and 5xFAD_WT mice, and an AD-associated stem-like cluster (cd8_c1) present only in 5xFAD mice.

  brain-derived brain cd8+ clonally scrna-seq paired cellchat

• scComm: a contrastive learning framework for deciphering cell-cell communications at single-cell resolution.

  PMID 41877186 · PMC13134144 · Genome biology · 2026 · 8 claims · 7 setups

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  scComm infers cell-cell communications at single-cell resolution using a data-adaptive L-R weighting module and supervised contrastive learning (SupCon loss) to distinguish significant CCC events from background noise

  simulated spatial liver single-cell simulated spatial scrna-seq

• Lymphodepleting preconditioning impairs host antitumor immunity induced by adoptive T cell therapy in mouse models.

  PMID 41912536 · PMC13172322 · Nature communications · 2026 · 8 claims · 8 setups

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  ACT with TCR-transgenic (OTI) CD8+ T cells eradicates established B16F10-OTI tumors and expands host CD8+ T cells with tumor-reactive (PD-1+GzmB-/PD-1+GzmB+, Tpex/Tex) and tissue-resident phenotypes

  b16f10-oti draining ragko c57bl flow tumor antibody

• Robust transcriptomic hallmarks targeting intratumor heterogeneity in intrahepatic cholangiocarcinoma.

  PMID 41916296 · PMC13130669 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  Immune and stromal heterogeneity, rather than genetic variation, are primary drivers of gene expression ITH in iCCA

  multi-region icca four lihv bulk hallmark single-cell

• PD-1 antibody-bound progenitor-exhausted CD8(+) T cells in lymph nodes boost PD-1-blockade anti-tumor immunity in gastrointestinal cancer.

  PMID 41951588 · PMC13237225 · Nature communications · 2026 · 8 claims · 6 setups

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  Progenitor-exhausted CD8+ T cells (CD8-Tpex, TCF7+PDCD1+) are enriched in proximal lymph nodes and proliferate at a high rate after ICI treatment

  esophagogastric cancer surgically tcga scrna-seq scrna reanalysis

• Benchmarking tools for deciphering cellular crosstalk in spatially-resolved transcriptomics.

  PMID 41952215 · PMC13174004 · Genome biology · 2026 · 8 claims · 5 setups

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  No prior systematic, quantitative benchmark exists for CCI inference methods specifically developed for spatial transcriptomics across multiple platforms

  synthetic real simulated simulation spot-purity real-data

• Charting spatial ligand-target activity using Renoir.

  PMID 42086556 · PMC13144314 · Nature communications · 2026 · 8 claims · 8 setups

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  Renoir computes a neighborhood activity score for curated ligand-target pairs at each spatial spot/cell by integrating cell type abundance, cell type-specific mRNA abundance, receptor expression, gene entropy, and mutual information between ligand and target genes.

  intestine triple-negative dorsolateral dlpfc semi-synthetic spatial single-cell

• GAMMI: graph-guided contrastive and adversarial integration of single-cell and spatial multi-omics data.

  PMID 42108634 · PMC13158126 · Briefings in bioinformatics · 2026 · 6 claims · 5 setups

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  GAMMI consistently outperforms state-of-the-art integration methods (GLUE, Harmony, MIDAS, scMoMaT) in biological conservation and batch correction across five mosaic single-cell multi-omics benchmarks

  pbmc postmortem gse138852 gammi-derived multi-omics scrna-seq differential

• Systems biology: where it's at in 2005.

  PMID 16086862 · PMC1273629 · Genome biology · 2005 · 8 claims · 8 setups

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  High-throughput genetic-interaction and physical-interaction maps show only minimal overlap with each other, whereas literature-derived genetic and physical interaction maps share a much greater fraction of edges

  saccharomyces drosophila environmental literature systematic genome-wide

• Toxicoproteomics: a parallel approach to identifying biomarkers.

  PMID 12940285 · PMC1241639 · Environmental health perspectives · 2003 · 8 claims · 8 setups

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  Combining parallel DNA microarray and proteomic analyses on the same tissues merges microarray's gene discovery power with proteomics' ability to exploit post-translational modifications for biomarker identification.

  liver serum peptide digested two-dimensional seldi maldi