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).

• Comprehensive analysis of m(6)A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing.

  PMID 38510975 · PMC10950754 · Computational and structural biotechnology journal · 2024 · 8 claims · 6 setups

  Has reproduction

  m6A site number and m6A levels are significantly lower in post-treatment complete remission (CR) bone marrow than in pre-treatment AML bone marrow

  paired hl-60 gene aml nanopore functional kaplan-meier

• Single-cell analysis highlights the significance of malignant cell IFN/MHC-II for immunotherapy response in head and neck squamous cell carcinoma.

  PMID 41923630 · PMC13130666 · Cell reports. Medicine · 2026 · 8 claims · 4 setups

  Full-text index only

  A malignant cell subset expressing IFN-response and MHC-II genes (IFN/MHC-II) increases in proportion after pembrolizumab treatment and is associated with response

  hnscc ffpe syngeneic independent single-cell multiplexed tumor

• Neoadjuvant sintilimab plus chemotherapy in EGFR-mutant NSCLC: Phase 2 trial interim results (NEOTIDE/CTONG2104).

  PMID 38897205 · PMC11293361 · Cell reports. Medicine · 2024 · 8 claims · 8 setups

  Has reproduction · 72

  Neoadjuvant sintilimab plus carboplatin/nab-paclitaxel is clinically feasible and tolerable in resectable EGFR-mutant NSCLC, with all 18 patients completing treatment and undergoing radical surgery.

  pre resected tumor serial whole-exome bulk single-cell

• PD-1 blockade plus tyrosine kinase inhibitor remodels the tumor microenvironment in advanced renal cell carcinoma.

  PMID 41916996 · PMC13199584 · Nature communications · 2026 · 8 claims · 8 setups

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  Non-responders to TKI±ICI therapy show increased neutrophil infiltration and enrichment of SAA+ tumor cells after treatment.

  arcc pre post-treatment tumor single-cell multiplex ligand-receptor

• GRIP-Lung: Generative Model of Response to Drug-Induced Perturbation in Lung Cancer.

  PMID 41977443 · PMC13072768 · International journal of molecular sciences · 2026 · 8 claims · 7 setups

  Full-text index only

  GRIP-Lung, a GAN framework embedding cell-line identity and drug conditions, predicts drug-induced gene expression profiles in lung cancer cell lines

  lung nsclc a549 nci-60 bulk five-fold differential

• Comprehensive Transcriptome Analysis Reveals Genome-Wide Changes Associated with Endoplasmic Reticulum (ER) Stress in Potato (Solanum tuberosum L.).

  PMID 36430273 · PMC9696714 · International journal of molecular sciences · 2022 · 8 claims · 3 setups

  Has reproduction · 62

  TM treatment of potato leaves produces widespread, time-dependent differential gene expression associated with ER stress and the UPR

  potato rna-seq gene alternative

• Enabling Single-Cell Drug Response Annotations from Bulk RNA-Seq Using SCAD.

  PMID 36762572 · PMC10104628 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023 · 7 claims · 7 setups

  Has reproduction · 81

  SCAD, a transfer learning framework integrating adversarial discriminative domain adaptation (ADDA), can infer single-cell drug sensitivities by transferring knowledge from bulk RNA-seq pharmacogenomic data (GDSC) to scRNA-seq target domains

  pan-cancer pc9 451lu a375 bulk scrna-seq computational

• DAGFormer: A graph-based domain adaptation approach for single-cell cancer drug response prediction.

  PMID 41417875 · PMC12795466 · PLoS computational biology · 2025 · 7 claims · 5 setups

  Has reproduction

  DAGFormer constructs cellular neighbor graphs using diverse topological strategies to represent intercellular interactions for drug response prediction

  pan-cancer jhu006 scc47 pc9 bulk scrna-seq

• Sequential transcriptional waves and NF-κB-driven chromatin remodeling direct drug-induced dedifferentiation in cancer.

  PMID 41986344 · PMC13083995 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  BRAFi (vemurafenib) treatment drives BRAF-mutant melanoma cells through a reversible dedifferentiation transition from a melanocytic state through a neural crest-like state to a drug-tolerant mesenchymal state

  m397 patient-derived longitudinal time-series atac-seq chip-seq

• A longitudinal, multi-omic atlas reveals the emergence of a spatially organized immunosuppressive ecosystem in resistant melanoma.

  PMID 41916292 · PMC13130630 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  Resistant tumors undergo convergent evolution toward a shared, spatially organized immunosuppressive ecosystem despite genetic heterogeneity.

  longitudinal rois tumor exome rna-seq nanostring

• Reinvigorating COTL1(high) NK cells via GITR signalling overcomes immune checkpoint blockade resistance in tsMHC-I-impaired tumours.

  PMID 41912896 · PMC13179135 · Nature cell biology · 2026 · 8 claims · 8 setups

  Full-text index only

  A COTL1-high NK cell subset mediates immune checkpoint blockade responsiveness in tsMHC-I impaired tumours

  hcc sorted orthotopic multiplex bulk 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

  Full-text index only

  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