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.

GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base

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

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

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.