Cancer-related molecular mechanisms research

GDCRNATools provides an R/Bioconductor package for analyzing lncRNA, miRNA, and mRNA data from the GDC to study ceRNA regulatory networks in cancers.

The paper introduces ASSA, a computational pipeline that predicts RNA-RNA interactions by combining sequence alignment and thermodynamics, outperforming existing tools.

The paper identifies RNA sequences responsible for nuclear enrichment in lncRNAs using a modified MPRA approach and validates findings with smRNA-FISH.

The paper analyzes natural antisense transcripts (NATs) in breast cancer using RNA sequencing to identify their potential role in gene regulation and survival outcomes.

This study identifies that a significant portion of human lincRNAs may originate from pseudogenized protein-coding genes through comparative genomic analysis.

The paper translates ceRNA susceptibilities into correlation functions to estimate crosstalk strength and validates this approach using simulations and TCGA data.

lncRNA-screen is a pipeline for computationally screening lncRNAs in large genomics datasets, generating interactive reports for further experimental validation.

Evolinc identifies and characterizes sequence-conserved lincRNAs across species to prioritize candidates for functional analysis.

The paper clusters head and neck squamous cell carcinomas based on lncRNA expression and identifies molecular and clinical associations.

LncATLAS provides a database of lncRNA subcellular localization in human cells using RNA-seq data, offering tools to query and compare localization across cell types and organelles.

The paper identifies differences in chromatin environment, transcriptional regulation, and splicing between lincRNAs and mRNAs in human cell lines.