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 lncRNA-mRNA competitive regulatory network in human islet tissue exosomes of a type 1 diabetes model reveals exosome miRNA markers.

  PMID 36440209 · PMC9682028 · Frontiers in endocrinology · 2022 · 7 claims · 7 setups

  Has reproduction · 50

  LncRNA-mRNA competitive regulatory network topology and function differ substantially between control and cytokine-treated (IL-1β+IFN-γ) islet exosomes

  pancreatic starbase islet mrnas bulk database-derived cerna

• 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

• Identification of a novel lncRNA prognostic signature and analysis of functional lncRNA AC115619.1 in hepatocellular carcinoma.

  PMID 37614318 · PMC10442647 · Frontiers in pharmacology · 2023 · 8 claims · 8 setups

  Has reproduction · 87

  A six-lncRNA prognostic signature (LINC02428, LINC02163, AC008549.1, AC115619.1, CASC9, LINC02362) predicts overall survival in HCC patients

  hcc tcga paired snu-449 lncrna sequencing univariate

• 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

  Full-text index only

  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

• Bioinformatic Analysis of Differentially Expressed Long Non-Coding RNAs in Skeletal Muscle Following Aerobic and Resistance Exercise.

  PMID 41595529 · PMC12840796 · Genes · 2026 · 8 claims · 3 setups

  Full-text index only

  Distinct lncRNA expression profiles exist in skeletal muscle between acute AE and RE, suggesting modality-specific lncRNA roles in exercise adaptation.

  skeletal aggregated bulk database

• A urine extracellular vesicle lncRNA classifier for high-grade prostate cancer and increased risk of progression: A multi-center study.

  PMID 37852185 · PMC10591064 · Cell reports. Medicine · 2023 · 8 claims · 8 setups

  Has reproduction · 65

  A 3-lncRNA urine extracellular vesicle classifier (Clnc: AC015987.1, CTD-2589M5.4, RP11-363E6.3) detects high-grade PCa with higher accuracy than PCA3, mpMRI, PCPT-RC 2.0, and ERSPC-RC

  urinary tcga paired urine sequencing lncrna qrt-pcr

• 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

• Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network.

  PMID 36855106 · PMC9976425 · BMC medical genomics · 2023 · 8 claims · 7 setups

  Has reproduction · 86

  RNA-seq of peripheral blood from 23 sepsis patients and 10 healthy controls identifies 1,044 DEmRNAs, 66 DEmiRNAs and 155 DElncRNAs.

  peripheral demrnas blood thp-1 rna-seq annotation wgcna

• Multiomic machine learning on lactylation for molecular typing and prognosis of lung adenocarcinoma.

  PMID 39856156 · PMC11760357 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 83

  Ten multiomics clustering algorithms identify two distinct lactylation cancer subtypes (CS1 and CS2) in LUAD

  tcga gse13213 gse31210 multiomics closest ssgsea

• Long non-coding RNA profiling of hypertrophic cardiomyopathy in mice.

  PMID 41942516 · PMC13230700 · Scientific data · 2026 · 6 claims · 8 setups

  Full-text index only

  This study presents a transcriptome-wide RNA-Seq dataset delineating differentially expressed lncRNAs in left ventricle of the TNNT2 ∆160 HCM mouse model (n=31 TG, n=33 nTG).

  left fastq rna-seq lncrna bulk fastqc read

• EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology.

  PMID 41805684 · PMC12975130 · eLife · 2026 · 8 claims · 8 setups

  Full-text index only

  EPB41L4A-AS1 acts in cis to enhance transcription of the proximal EPB41L4A gene

  mcf-7 epb41l4a-as1 rna-seq rt-qpcr single-molecule

• A cross-scale multimodal framework identifies clinically actionable immunotherapy biomarkers in melanoma through bulk to single-cell and spatial transcriptomics integration.

  PMID 41840725 · PMC13104449 · Human genomics · 2026 · 7 claims · 8 setups

  Full-text index only

  Multi-omics consensus clustering (MOVICS) identifies two distinct SKCM molecular subtypes, CS1 and CS2

  tcga-skcm meta-geo gtex melanoma multi-omics bulk transcriptome-wide

• BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization.

  PMID 41266599 · PMC12635123 · Communications biology · 2025 · 8 claims · 8 setups

  Has reproduction · 50

  BiRNA-BERT uses adaptive dual-tokenization that dynamically selects nucleotide-level (NUC) or byte-pair encoding (BPE) tokens based on input sequence length

  rfam plant lncrna-mirna sequences unsupervised mirna-lncrna length-binned

• 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

  Full-text index only

  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

• 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

  Full-text index only

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

  peripheral pancreatic predicted bulk weighted single-cell

• lncEvo: automated identification and conservation study of long noncoding RNAs.

  PMID 33563213 · PMC7871587 · BMC bioinformatics · 2021 · 8 claims · 5 setups

  Has reproduction · 61

  lncEvo is an integrated Nextflow/Docker pipeline combining transcriptome assembly, lncRNA identification, and cross-species conservation analysis into a single workflow.

  chimp assembled pairwise raw bulk lncrna comparative

• Systematic and computational identification of Androctonus crassicauda long non-coding RNAs.

  PMID 33633149 · PMC7907363 · Scientific reports · 2021 · 8 claims · 6 setups

  Has reproduction · 71

  13,401 lncRNAs were identified in the A. crassicauda transcriptome using the ECF pipeline

  crassicauda rna-seq coding sequence

• Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

  PMID 30010758 · PMC6065499 · GigaScience · 2018 · 8 claims · 6 setups

  Has reproduction · 91

  A draft genome (Ogye_1.1) was assembled using a hybrid de novo method combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X)

  yeonsan ogye_1.1 locus tissues whole-genome genome structural

• Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene.

  PMID 35447887 · PMC9027897 · Non-coding RNA · 2022 · 6 claims · 7 setups

  Has reproduction · 64

  A computational pipeline intersecting immune gene coordinates with Alu element coordinates can identify candidate Alu-lncRNAs

  peripheral genome blood bulk illumina ion

• annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.

  PMID 36472574 · PMC9724561 · GigaScience · 2022 · 7 claims · 8 setups

  Has reproduction · 78

  annotate_my_genomes is an easy-to-use genome-guided pipeline that uses hybrid (PacBio+Illumina) assembled transcripts to distinguish coding genes from long non-coding RNAs and reconcile them with prior annotations.

  chick real simulated pacbio illumina hybrid