BioMed

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 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

Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm - It has been suggested that the mammalian genome is composed mainly of long compositionally homogeneous domains.

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

GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base - Summary: Rapid expansion of available data about G Protein Coupled Receptor (GPCR) dimers/oligomers over the past few years requires an effective system to organize this information electronically.

Integrative platform to translate gene sets to networks - Summary: We have implemented a computational platform (Moksiskaan) that integrates pathway, protein–protein interaction, genome and literature mining data to result in comprehensive networks for a list of genes or proteins.

ABC-SysBio--approximate Bayesian computation in Python with GPU support - Motivation: The growing field of systems biology has driven demand for flexible tools to model and simulate biological systems.