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).

• Dissecting glioblastoma risk signatures in the tumor immune microenvironment based on multi-dimensional transcriptomics.

  PMID 41880523 · PMC13154832 · GigaScience · 2026 · 7 claims · 8 setups

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  Hallmarks of malignancy and cell cycle regulatory pathways are consistently enriched across single-cell, bulk, and spatial transcriptomic modalities, promoting tumor cell proliferation and progression.

  tumor gbm normal wild-type single-cell bulk microarray

• Transient tumor exposure induces persistent functional defects in memory CD8(+) T cells.

  PMID 42023146 · PMC13098610 · iScience · 2026 · 8 claims · 8 setups

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  Memory CD8+ T cells generated after transient tumor rejection (Tum-CD8+) display a distinct, partially exhausted phenotype compared to virus-induced memory cells (Vir-CD8+)

  cd45.1 single-cell memory ctv flow single-cell cytokine

• DAESC + : high-performance, integrated software for single-cell allele-specific expression data.

  PMID 41851619 · PMC13169709 · BMC bioinformatics · 2026 · 8 claims · 6 setups

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  DAESC+ is a dual-module, end-to-end software package (DAESC-P for preprocessing, DAESC-GPU for differential analysis) for single-cell ASE data

  onek1k endoderm simulated single-cell differential runtime

• Metabolic Adaptation of CD8⁺ T Cells Limits the Efficacy of Fatty Acid Oxidation Inhibition in Type 1 Diabetes.

  PMID 41800251 · PMC12965062 · International journal of biological sciences · 2026 · 8 claims · 8 setups

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  TMZ enhances mitochondrial membrane potential and suppresses fatty acid oxidation (FAO) in human T cells

  peripheral endoc-βh5 nod pancreatic mitochondrial extracellular glucose-stimulated

• Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

  PMID 41865369 · PMC13207208 · Cell reports · 2026 · 8 claims · 6 setups

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  Memory CD4+ T cells show enhanced chromatin accessibility proximal to rapid-recall genes compared to naive cells

  blood-derived computational pseudobulk cd4+ single-nuclei maxatac grn

• Telomerase-Associated Genes as Prognostic Markers in High-Grade Serous Ovarian Cancer.

  PMID 42050900 · PMC13137916 · Medical science monitor : international medical journal of experimental and clinical research · 2026 · 8 claims · 8 setups

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  TAGs are linked to HGSOC progression and yield a candidate prognostic model

  hgsoc tcga-ov scrna-seq-derived single-cell bulk cellchat

• 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

• MECP2 mutations rewire human ESC fate and bias cortical lineage commitment.

  PMID 42030940 · PMC13163216 · Stem cell reports · 2026 · 8 claims · 8 setups

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  MECP2 mutations induce an early naïve-like transcriptional drift in human ESCs, marked by upregulation of ZFP42/REX1 and other naïve-enriched markers

  isogenic undifferentiated 3-month bulk bulk single-cell single-nucleus

• Single-cell and spatial profiling highlights TB-induced myofibroblasts as drivers of lung pathology.

  PMID 41489684 · PMC12767585 · The Journal of experimental medicine · 2026 · 8 claims · 8 setups

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  MMP1+CXCL5+ fibroblasts and SPP1+ macrophages are linked to TB disease and TB lung granuloma and reveal targetable cellular cross talk underlying TB immunopathology

  lung ffpe lymph nonhuman scrna-seq spatial bulk

• Single-cell mitophagy signature-based artificial intelligence model enhances prediction of prognosis and immunotherapy response in non-small-cell lung cancer.

  PMID 41851738 · PMC13112628 · Respiratory research · 2026 · 8 claims · 8 setups

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  A six-gene MRG panel (FOS, CANX, EIF4G1, CALCOCO2, HSP90AB1, PRKAR1A) was selected via LASSO regression as prognostic markers in NSCLC.

  nsclc tcga external immunotherapy single-cell bulk transcriptomic

• Translation factor eIF4G2 directs CD8(+) T cell lineage commitment by selectively enabling the IL-7 receptor response.

  PMID 41940334 · PMC13049607 · iScience · 2026 · 8 claims · 8 setups

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  eIF4G2 expression is markedly upregulated in DP thymocytes relative to DN thymocytes

  thymocytes peripheral eif4g2 cd4+cd8lo single-cell western flow

• PD-1 blockade potentiates neoadjuvant chemotherapy in NSCLC via increasing CD127(+) and KLRG1(+) CD8 T cells.

  PMID 37231145 · PMC10213055 · NPJ precision oncology · 2023 · 8 claims · 5 setups

  Has reproduction · 40

  NAPC produces higher major pathological response (MPR) and pathological complete response (pCR) rates and longer DFS/OS than NAC alone

  cd45+ ffpe scrna-seq cd8+ single-cell multiplex gene

• An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.

  PMID 36548438 · PMC9822106 · PLoS computational biology · 2022 · 8 claims · 6 setups

  Has reproduction · 67

  An individualized Bayesian causal discovery framework can learn tumor-specific intercellular communication networks (ICNs) by combining single-cell gene expression module (GEM) discovery, bulk tumor deconvolution, and individualized causal network learning.

  hnscc cd45+ cd8+ tcga single-cell bulk pseudo-time

• 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 multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

  PMID 41528844 · PMC12971065 · Cell reports · 2026 · 8 claims · 8 setups

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  Generated a single-cell gene expression and chromatin accessibility (multiome) atlas of human RPE and choroid from control and AMD eyes

  rpe-choroid rpe arpe-19 scatac-seq joint h3k27ac activity-by-contact

• Single-Cell RNA-Seq Profiling of Transposable Element Expression in Human Peripheral Blood Cells During Viral Infections.

  PMID 41683713 · PMC12898442 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

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  TE expression is significantly higher in PBMCs from viral infection cohorts (and recovered individuals) compared to healthy controls

  pbmcs pbmc cd8+ single-cell cell-type expression

• Peripheral Immune and Metabolic Dysregulation in Migraine, Ménière's Disease, and Vestibular Migraine: A Single-Cell Atlas Study.

  PMID 41953397 · PMC13054517 · Human mutation · 2026 · 8 claims · 8 setups

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  T cell abundance is significantly increased in MI compared to HC, while monocyte abundance is reduced, identifying T cells as a key pathogenic cell type

  pbmcs pbmc-derived degs pbmc single-cell differential kegg

• Single-cell spatial analysis stratifies lung adenocarcinoma with rare actionable mutations and reveals immune-modulatory cellular crosstalk.

  PMID 42013848 · PMC13198233 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  Consensus meta-program (MP) expression patterns stratify LUAD patients with rare and reference oncogenic mutations into ICI-MP-H and ICI-MP-L subgroups reflecting differential predicted ICI benefit

  luad matched tcga epithelial single-cell multiplex bulk

• Integrating single-cell and bulk transcriptomes to reveal prognostic and immunological features of ecDNA-related genes in osteosarcoma.

  PMID 42047819 · PMC13125642 · Cancer immunology, immunotherapy : CII · 2026 · 7 claims · 8 setups

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  A novel ecDNA-related Gene Prognostic Score Model (EGPSM) was constructed using an integrated framework of 101 machine learning algorithm combinations and validated in training, testing, and external cohorts.

  osteosarcoma treatment-naive bulk 143b bulk single-cell cibersort

• Airway injury induces alveolar epithelial responses mediated by macrophages.

  PMID 41579370 · PMC13090803 · Cell reports · 2026 · 8 claims · 8 setups

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  Club cell injury (naphthalene) induces transient proliferation of distal AT2 progenitor cells

  lung bronchoalveolar club alveolar-enriched single-cell immunofluorescence flow