Towards computational prediction of microRNA function and activity

Towards computational prediction of microRNA function and activity - While it has been established that microRNAs (miRNAs) play key roles throughout development and are dysregulated in many human pathologies, the specific processes and pathways regulated by individual miRNAs are mostly unknown.

An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes

An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes - Motivation: Evolutionarily conserved non-coding genomic sequences represent a potentially rich source for the discovery of gene regulatory region such as transcriptional enhancers.

Genome-wide functional element detection using pairwise statistical alignment outperforms multi-genome footprinting techniques

Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques - Motivation: Comparative genomic sequence analysis is a powerful approach for identifying putative functional elements in silico.

Mining metabolic pathways through gene expression

Mining metabolic pathways through gene expression - Motivation: An observed metabolic response is the result of the coordinated activation and interaction between multiple genetic pathways.

Integration of pathway knowledge into a weighted recursive feature elimination approach for cancer patients risk stratification

Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients - Motivation: One of the main goals of high-throughput gene-expression studies in cancer research is to identify prognostic gene signatures, which have the potential t

A Poisson model for random multigraphs

A Poisson model for random multigraphs - Motivation: Biological networks are often modeled by random graphs. A better modeling vehicle is a multigraph where each pair of nodes is connected by a Poisson number of edges.

A Bayesian approach using covariance of SNP data to detect differences in linkage disequilibrium patterns between groups

A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals - Motivation: Quantifying differences in linkage disequilibrium (LD) between sub-groups can highlight genetic regions or sites under sele

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor - Summary: A tool to predict the effect that newly discovered genomic variants have on known transcripts is indispensible in prioritizing and categorizing such variants.

Over-optimism in bioinformatics: an illustration

Over-optimism in bioinformatics: an illustration - Motivation: In statistical bioinformatics research, different optimization mechanisms potentially lead to ‘over-optimism’ in published papers.