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).

• Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma.

  PMID 34654806 · PMC8519947 · Nature communications · 2021 · 6 claims · 8 setups

  Has reproduction · 100

  A pathway-based super signature from on-treatment samples (PASS-ON) predicts anti-PD1 response with high accuracy (validation AUC 0.85-0.89, combined AUC 0.88) and outperforms existing signatures across all four datasets.

  metastatic pathway bulk gene elastic-net

• Annotation-free prediction of immunotherapy response in melanoma using single-cell transcriptomic data.

  PMID 41758825 · PMC12948085 · PloS one · 2026 · 8 claims · 6 setups

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  AI-based predictive models built on unannotated scRNA-seq data (cell-by-gene expression matrices) can classify melanoma patients as ICI responders vs. non-responders

  cd45+ scrna-seq independent scrna-seq single-gene-level pathway-level

• Nuclear Myosin 1 links genomic architecture to adipose tissue remodeling, metabolic inflammation and obesity in mice.

  PMID 41748556 · PMC13004839 · Cell death & disease · 2026 · 8 claims · 8 setups

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  NM1 is required for metabolic homeostasis during adipocyte differentiation

  nm1 epididymal mefs het atac-seq bulk rna-seq

• PFOS and PFOA exposure induces liver injury and sex-dependent immune effects in C57BL/6 mice.

  PMID 41641100 · PMC12865548 · iScience · 2026 · 7 claims · 7 setups

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  PFOA and PFOS exposure induces hepatotoxicity, including hepatomegaly and elevated serum liver injury biomarkers (ALP, ALT), across sexes and durations

  plasma liver serum thymus lc-ms organ serum

• An AIB1 isoform rewires glucocorticoid receptor signaling to promote TNBC progression.

  PMID 41704785 · PMC12907120 · iScience · 2026 · 8 claims · 10 setups

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  GR antagonists (RU486, relacorilant) inhibit AIB1Δ4-driven invasion of DCIS cells in 3D invasion assays, zebrafish extravasation, and mouse xenograft models

  dcis kdrl nod e0771 sphere rt-qpcr shrna

• Pathway-specific canalization and plasticity of gene expression during C. elegans dauer development.

  PMID 41890963 · PMC13014971 · iScience · 2026 · 8 claims · 7 setups

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  Dauers induced by different environmental (starvation, pheromone, heat) or genetic (daf-2, daf-7, ilc-17.1, cep-1 OE) stimuli are transcriptionally distinct from each other and from continuously developing WT L2/L3 and adults

  elegans bulk principal likelihood

• CeLLTra: aligning cell names with gene expression via a pathway-informed transformer.

  PMID 41652996 · PMC12881829 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

  Full-text index only

  Grouping genes into pathway-defined gene sets as Transformer input tokens (instead of using individual genes or discretized bins) mitigates the long-sequence problem and improves representation learning of scRNA-Seq gene expression profiles.

  tabula tumor-infiltrating scrna-seq

• MicroRNA Enrichment and Docking-Based Evaluation of Ilomastat Targeting of MMP-2 in Esophageal Squamous Cell Carcinoma: Insights from a South African Cohort.

  PMID 42158110 · PMC13181172 · Computational and structural biotechnology journal · 2026 · 7 claims · 5 setups

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  The miR-29 family inhibits MMP-2 and represents a key regulatory axis in tumor invasion

  paired deg mmp-2 escc bulk pathway molecular

• WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization.

  PMID 25254103 · PMC4168754 · F1000Research · 2014 · 8 claims · 7 setups

  Has reproduction · 76

  The open-source WikiPathways app for Cytoscape imports biological pathways from WikiPathways for data visualization and network analysis.

  cardiac cytoscape rna-seq pathway network

• Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra.

  PMID 33779545 · PMC8049744 · eLife · 2021 · 8 claims · 5 setups

  Has reproduction · 100

  The initial transcriptional response to amputation is identical during head and foot regeneration at 3 hpa

  hydra atac-seq rna-seq chromvar

• STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.

  PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 8 claims · 6 setups

  Has reproduction · 66

  Low STAT3 expression in primary PCa is associated with increased OXPHOS and ribosomal biosynthesis at the transcriptomic level

  prostate bulk weighted reverse

• Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.

  PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 8 claims · 8 setups

  Has reproduction · 71

  AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)

  aml hovon cancer tcga bulk consensus machine

• Splice-switching of the oncogenic BCS1L isoform suppresses ovarian cancer progression by disrupting mitochondrial function.

  PMID 41771836 · PMC13039997 · Cell death & disease · 2026 · 7 claims · 8 setups

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  BCS1L is alternatively spliced into a full-length isoform (BCS1L-L) and an exon 2-skipped short isoform (BCS1L-S)

  tcga-ov ovarian clinical fte187 gsea single-cell qpcr

• Coding and non-coding roles of MOCCI (C15ORF48) coordinate to regulate host inflammation and immunity.

  PMID 33837217 · PMC8035321 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 68

  MOCCI (encoded by C15ORF48) is a mito-SEP upregulated during inflammation and infection that promotes host-protective resolution

  aortic failing colon hek293t ribo-seq wgcna-gsea gene

• Differential Gene Expression and Methylation Analysis of Melanoma in TCGA Database to Further Study the Expression Pattern of KYNU in Melanoma.

  PMID 35893303 · PMC9329910 · Journal of personalized medicine · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  Oncogenes MITF, KIT, CDH1, NRAS, AKT1, EGFR, TP53, and CDK4 are elevated while tumor suppressors PTEN, cAMP, and BCL2 are reduced in melanoma

  tcga-skcm melanoma-related intradermal keratinocytes rna-seq kegg copy

• Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

  PMID 41758938 · PMC12947870 · Science advances · 2026 · 8 claims · 8 setups

  Has reproduction · 84

  MYOD1 L122R-mutant SRMS tumors contain three coexisting, conserved cell states (progenitor, transition, differentiated) reflecting aberrant myogenic differentiation

  patient-derived tumor single paired single-nucleus infercnv aracne-ap

• Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.

  PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 6 setups

  Has reproduction · 67

  PSPred-ALE outperforms state-of-the-art SARS-CoV-2 phosphorylation site predictors (e.g. DeepIPs) and handcrafted feature-based methods in benchmarking comparisons

  a549 sequence same bulk pathway gene

• Research and experimental verification on the mechanisms of cellular senescence in triple-negative breast cancer.

  PMID 38435998 · PMC10909353 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 67

  TNBC can be classified into three molecular subtypes (clusters 1, 2, 3) based on cellular senescence-related pathway scores

  tnbc tcga tcga-tnbc mda-mb-468 scrna-seq ssgsea unsupervised

• Comparative Transcriptomic Profiling Identifies IL-1β as a Non-Canonical Driver of Human Dendritic Cell Maturation.

  PMID 41472934 · PMC12745711 · Iranian journal of biotechnology · 2026 · 8 claims · 7 setups

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  IL-1β can substitute for PAMPs in inducing DC maturation via a non-canonical pathway distinct from classical TLR-mediated activation

  monocyte-derived dendritic bulk principal pathway

• TEAD4 and RXRA Regulate the Function of Nucleus Pulposus Cells in Intervertebral Disc Degeneration Via the TNF-α/NF-κB Pathway: An Integrated Analysis of Single-Cell RNA-Seq, Bulk RNA-Seq, and In Vitro Validation.

  PMID 41511606 · PMC12995935 · Applied biochemistry and biotechnology · 2026 · 8 claims · 8 setups

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  TEAD4 and RXRA play critical roles in IDD progression, likely regulating NP cell behavior and ECM metabolism via the TNF-α/NF-κB pathway

  differential il-1β-induced scrna-seq bulk gsea