Morten Muhlig Nielsen

circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA

This paper identifies circHIPK3 as a competing endogenous RNA that sequesters IGF2BP2 to regulate target mRNAs, including STAT3, and shows its correlation with bladder cancer survival.

miRNA activity inferred from single cell mRNA expression

The paper estimates miRNA activity from single-cell RNA sequencing data by analyzing motif enrichment, validated on bulk and single-cell datasets.

Transcriptome-wide profiles of circular RNA and RNA binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

The paper identifies circRNA-RBP interactions in cancer, showing their role in circRNA biogenesis and cancer gene expression, with implications for bladder cancer prognosis.

Unique genomic features and deeply-conserved functions of long non-coding RNAs in the Cancer LncRNA Census (CLC)

The paper introduces the Cancer LncRNA Census (CLC), a curated resource of lncRNAs with causative roles in cancer, and shows their genomic and evolutionary features.

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

Integrative pathway enrichment analysis of multivariate omics data

ActivePathways integrates multivariate omics data to identify enriched pathways, revealing cancer driver genes and prognostic pathways in breast cancer.

Regmex, Motif analysis in ranked lists of sequences

Regmex identifies overrepresented motifs in ranked sequence lists using regular expressions and Markov models, with options for enrichment evaluation.

A Site Specific Model And Analysis Of The Neutral Somatic Mutation Rate In Whole-Genome Cancer Data

The paper develops a site-specific model to predict mutation rates in cancer genomes, showing it outperforms regional models by incorporating local genomic variables.

Passenger mutations in 2500 cancer genomes: Overall molecular functional impact and consequences

The paper analyzes 2500 cancer genomes to assess the molecular functional impact of mutations, finding that some putative passenger variants may influence gene activity and contribute to cancer phenotypes.

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

The paper identifies and characterizes coding and non-coding driver mutations across 2,500 cancer genomes, revealing new candidates and questioning previous findings.