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).

• Benchmarking component choices for unpaired single cell RNA and epigenomic integration.

  PMID 41987329 · PMC13192178 · Genome biology · 2026 · 7 claims · 8 setups

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  Gene activity scores (GAS) show limited correlation with actual gene expression but effectively preserve cellular neighborhood structure and support clustering.

  e18 pbmc brain kidney scrna-seq share-seq gas

• ProtoCloud: A prototypical self-explaining model for single-cell analysis.

  PMID 41997134 · PMC13261663 · Cell genomics · 2026 · 8 claims · 8 setups

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  ProtoCloud matches or outperforms existing annotation methods across 11 large-scale datasets, particularly for rare cell types

  diverse pbmc10k pbmc30k tsca scrna-seq latent gene

• Identification of cycling regulatory T cell precursors as conductors of immune escape during breast carcinoma progression.

  PMID 41997138 · PMC13213619 · Cancer cell · 2026 · 8 claims · 8 setups

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  A novel proliferative Treg precursor state, cycling Treg (cycTreg: FOXP3^int, MKI67^hi, IKZF2/4^int-hi), is absent in normal breast, low in DCIS, and strongly expanded in IBC

  normal mammary dcis tumor-draining scrna-seq spatial multiplex

• Molecular signatures of cell diversity modulated by long noncoding RNAs in the human fetal spinal cord.

  PMID 42006319 · PMC13090696 · iScience · 2026 · 8 claims · 7 setups

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  Three neural stem cell (NSC) lineages (NSC1, NSC2, NSCs) were annotated in the human fetal spinal cord

  fetal nsc2 scrna-seq scstereo velocity

• Spatiotemporal Transcriptomics Characterizes Immune Microenvironment During Mouse Liver Aging.

  PMID 42010880 · PMC13096584 · Aging cell · 2026 · 8 claims · 8 setups

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  T cells are the immune cell population with the most pronounced transcriptomic alterations during liver aging

  liver nash cirrhotic hcc scrna-seq snrna-seq stereo-seq

• The landscape of responses to neoadjuvant immunotherapy in resectable Kirsten rat sarcoma viral oncogene homolog-mutant lung adenocarcinoma: Clinical heterogeneity and correlative immunologic analysis.

  PMID 42011021 · PMC13096693 · Clinical and translational medicine · 2026 · 6 claims · 8 setups

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  KRAS-mutant LUAD patients show significantly poorer pathological response and inferior long-term survival after neoadjuvant immunotherapy compared to KRAS-wildtype patients

  resected resectable epithelial cd4t_treg_tnfrsf4 scrna-seq retrospective cnv

• scSurvival: Single-Cell Survival Analysis of Clinical Cancer Cohort Data at Cellular Resolution.

  PMID 42013315 · PMC13133615 · Cancer discovery · 2026 · 8 claims · 7 setups

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  scSurvival, an attention-based multiple-instance Cox regression framework, models each tumor sample as an ensemble of cells to predict survival outcomes at both patient and single-cell levels

  simulated melanoma liver higher scrna-seq differential

• High-quality acinar cell isolation enables single-cell analysis of healthy and injured pancreas.

  PMID 42013858 · PMC13198085 · Cell reports methods · 2026 · 8 claims · 7 setups

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  The DCTC protocol isolates up to 90% acinar cells from healthy wild-type pancreatic tissue without cell fixation or dead-cell removal kits

  healthy pancreas epithelial kpc scrna-seq pseudobulk velocity

• SPP1(+) macrophage-driven interactions shape the tumor microenvironment in lymph node metastatic acral melanoma.

  PMID 42020397 · PMC13230793 · Cell death & disease · 2026 · 8 claims · 8 setups

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  LN+ acral melanoma shows preferential SPP1+ signaling, including autocrine amplification within SPP1+ macrophages and paracrine interaction with S100A8+ melanoma cells via the SPP1-CD44 axis

  tumor microarray thp-1 a375 scrna-seq immunofluorescence western

• Single-cell analysis highlights the role of CD4(+) IFN-I-related T cells in Behcet's uveitis during Interferonα-2a therapy.

  PMID 42021381 · PMC13238117 · Biology direct · 2026 · 6 claims · 8 setups

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  CD4+ IFN-I-related T cells are significantly decreased in active BD patients and restored after IFNα-2a therapy

  pbmcs sorted skin scrna-seq scrna-seq bulk cell-cell

• Single cell profiling reveals malignant states and immune landscapes in PCNSL and systemic DLBCL.

  PMID 42023148 · PMC13097095 · iScience · 2026 · 8 claims · 8 setups

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  PCNSL and sDLBCL contain five distinct malignant B-cell subtypes (B0-B4) with discrete differentiation trajectories

  pcnsl malignant bulk sdlbcl scrna-seq infercnv cytotrace2

• Development of a pediatric immune cell atlas and characterization of CD4+ T cells in food allergy.

  PMID 42025535 · PMC13105851 · Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology · 2026 · 8 claims · 8 setups

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  A pediatric single-cell PBMC reference atlas was developed from 57 healthy children across 8 public scRNA-seq studies.

  pbmcs cd3+ cd4+ memory scrna-seq pseudobulk bulk

• A spatially coordinated keratinocyte-fibroblast circuit recruits MMP9(+) myeloid cells to drive type I interferon-driven inflammation in photosensitive autoimmunity.

  PMID 42032302 · PMC13226071 · Nature immunology · 2026 · 8 claims · 8 setups

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  MMP9+CD14+ myeloid cells are critical mediators of photosensitivity, expanding in lesional skin, producing IFNβ, and colocalizing with cytotoxic CD4+ T cells at the dermal-epidermal junction

  skin blister punch donor scrna-seq 250-plex seqfish

• Single-cell profiling reveals distinct populations of tumor-associated macrophages and metastatic tumor cells in breast cancer brain metastasis.

  PMID 42034645 · PMC13247122 · Cell death & disease · 2026 · 8 claims · 8 setups

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  Single-cell profiling of BCBM identifies 12 tumor-associated macrophage (TAM) subtypes and 5 metastatic tumor cell (MTC) subtypes with distinct transcriptional profiles

  brain breast scrna-seq tams scrna-seq bulk copy

• Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

  PMID 42043480 · PMC13115984 · Cancer medicine · 2026 · 8 claims · 8 setups

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  EGFRI eligibility (defined by left-sidedness, RAS/BRAF wild-type, MSS) stratifies cancer cell transcriptomic characteristics more strongly than sidedness alone.

  crc epcam+ aggregated cancer scrna-seq copy pseudobulk

• CaHoT-GRN: context-aware high-order topology learning for robust single-cell gene regulatory network inference.

  PMID 42059479 · PMC13130071 · Briefings in bioinformatics · 2026 · 7 claims · 5 setups

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  CaHoT-GRN integrates pretrained biological language model embeddings (DNABERT for DNA, ESM for protein) with scRNA-seq expression data to improve GRN inference

  embryonic gene dataset-specific same scrna-seq-based sequence protein-protein

• A Cross-Species Single-Cell Atlas Reveals Conserved Regulatory Networks and Candidate Hearing Loss Genes in the Cochlea.

  PMID 42074555 · PMC13115875 · Genes · 2026 · 8 claims · 8 setups

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  A cross-species single-cell/single-nucleus RNA-seq atlas of human fetal and mouse postnatal cochlea identifies 19 conserved major cell types

  cochlea fetal top scrna-seq snrna-seq cell-cell

• Tumor reactivity assessment using clonal expression reveals tumor reactive CD8(+) T cell heterogeneity across solid tumors.

  PMID 42079667 · PMC13128579 · Frontiers in immunology · 2026 · 8 claims · 5 setups

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  TRACE, a clonotype-level CD8+ TRT classifier trained on an aggregated multi-study dataset, achieves robust holdout performance (mean MCC 0.84, F1 0.85)

  cd8+ expanded aggregated combined scrna-seq co-culture gene

• Divergent macrophage-regulated T cell states determine response to Bacillus Calmette-Guérin vaccine in high-risk bladder cancer.

  PMID 42081487 · PMC13262731 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  BCG responders show an increase in Th17-like Th1 CD4+ T cells with greater proinflammatory cytokine expression

  bladder pbmcs cd4+ separate scrna-seq trajectory flow

• TDAGENE: Inference of Gene Regulatory Network Based on Topological Data Analysis and Graph Attention Network for Single-Cell RNA Sequencing Data.

  PMID 42093817 · PMC13139726 · Computational and structural biotechnology journal · 2026 · 7 claims · 5 setups

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  TDAGENE combines TDA features with a multilayer GAT via gate-controlled fusion to improve GRN inference accuracy

  scrna-seq gene string chip-seq grn persistent prior