Transcription factors (TFs) are key regulators of intrinsic cellular processes, such as
differentiation and development, and of the cellular response to external perturbation …

Proteomics is the large scale study of protein structure and function from biological systems
through protein identification and quantification.“Shotgun proteomics” or “bottom-up …

Motivation There is a need for easily accessible implementations that measure the strength
of both linear and non-linear relationships between metabolites in biological systems as an …

Gene co-expression analysis is a data analysis technique that helps identify groups of
genes with similar expression patterns across several different conditions. By means of …

Among the many approaches to build predictive models for bioprocesses, hybrid models
have gained increased attention due to their ability to combine data driven approaches with …

Gene co-expression networks can be constructed in multiple different ways, both in the use
of different measures of co-expression, and in the thresholds applied to the calculated co …

Motivation Identifying pathological metabolic changes in complex disease such as Dementia
with Lewy Bodies (DLB) requires a deep understanding of functional modifications in the …

Deep anaesthetisation is an important surgical and explorative tool in the study of
consciousness. Much work has been done to connect the deeply anaesthetised condition …

Even within well-studied organisms, many genes lack useful functional annotations. One
way to generate such functional information is to infer biological relationships between …

Nitrogen uptake in legumes is facilitated by bacteria such as Rhizobium leguminosarum. For
this bacterium, gene expression data are available, but functional gene annotation is less …