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).

• Cell type- and species-specific regulation of hepatic lncRNAs by TCDD-activated aryl hydrocarbon receptor.

  PMID 41136526 · PMC12552753 · Scientific reports · 2025 · 8 claims · 6 setups

  Has reproduction · 71

  AHR-mediated lncRNA dysregulation may be a contributing mechanism in TCDD-elicited progression of steatosis to steatohepatitis with fibrosis

  liver mm39 bulk single-nuclei ahr

• Integrated transcriptome and single-cell sequencing analysis identify blood-pancreas shared lncRNA biomarkers in new-onset T2DM.

  PMID 41915667 · PMC13037964 · PloS one · 2026 · 8 claims · 6 setups

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  1,709 lncRNAs are differentially expressed in peripheral blood of new-onset T2DM patients vs controls

  peripheral pancreatic predicted bulk weighted single-cell

• Distinct lncRNA transcriptional fingerprints characterize progressive stages of multiple myeloma.

  PMID 26895470 · PMC4924754 · Oncotarget · 2016 · 8 claims · 8 setups

  Has reproduction · 36

  160 lncRNAs are differentially expressed between normal plasma cells and MGUS, SMM, MM, or PCL patients, with 31 lncRNAs shared across at least three comparisons

  bone gene plasma normal microarray custom unsupervised

• Genome-wide reprogramming of sRNA and lncRNA in the epigenetic regulation following interspecific hybridization in the Brassica species.

  PMID 41668146 · PMC12892563 · Molecular horticulture · 2026 · 6 claims · 5 setups

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  Regulatory differences in sRNAs between the two F1 hybrids are mainly driven by maternal inheritance, with Hybrid-sh showing more maternal influence and Hybrid-yh showing transgressive regulation

  brassica s70 small strand-specific atac-seq

• A novel deep learning-driven framework for improving lncRNA comprehensive annotation with LncADeep 2.0.

  PMID 41923359 · PMC13090826 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  LncADeep 2.0 outperforms LncADeep and other existing tools for lncRNA identification on both GENCODE annotated transcripts and independent RNA-seq data

  lncrna hypertrophic gencode lncrna-protein-mirna mlp-based independent ablation

• FLYNC: a machine-learning-driven framework for discovering long noncoding RNAs in Drosophila melanogaster.

  PMID 41551930 · PMC12805895 · NAR genomics and bioinformatics · 2026 · 7 claims · 8 setups

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  FLYNC, an explainable boosting machine (EBM) model, accurately predicts the probability that a newly identified RNA transcript in D. melanogaster is a lncRNA

  melanogaster drosophila automated ebm hyperparameter

• Integrated spatial transcriptomics and pan-cancer XGBoost modeling uncover spatial drivers of immune exclusion and predict immunotherapy response.

  PMID 41925746 · PMC13046951 · Cancer immunology, immunotherapy : CII · 2026 · 8 claims · 8 setups

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  A three-step computational framework (ImmCeRNA) identified 6,070 immune-related ceRNA interactions across 27 cancer types by integrating expression correlation and experimental validation data.

  cancer pan-cancer single lung bulk database single-cell