There has been a renewed interest for metabolism in the computational biology community,
leading to an avalanche of papers coming from methodological network analysis as well as …

We consider the problem of aligning two metabolic pathways. Unlike traditional approaches,
we do not restrict the alignment to one-to-one mappings between the molecules (nodes) of …

A critical challenge for environmental chemical risk assessment is the characterization and
reduction of uncertainties introduced when extrapolating inferences from one species to …

Background Wnt signal transduction pathway (Wnt STP) is a crucial intracellular pathway
mainly due to its participation in important biological processes, functions, and diseases, ie …

Motivation: Recent results related to horizontal gene transfer suggest that phylogenetic
reconstruction cannot be determined conclusively from sequence data, resulting in a shift …

The electrostatic potential of an enzyme is a key determinant of its substrate interactions and
catalytic turnover. Here we invoke comparative analysis of protein electrostatic potentials …

Background Pathways provide topical descriptions of cellular circuitry. Comparing
analogous pathways reveals intricate insights into individual functional differences among …

Using a metabolic pathway alignment method we developed, we studied highly conserved
reactions in different groups of organisms and found out that biological functions vital for …

Pathways show how different biochemical entities interact with one another to perform vital
functions for the survival of an organism. Comparative analysis of pathways is crucial in …

Background Given the increasing amount of biomedical resources that are being annotated
with concepts from more than one ontology and covering multiple domains of knowledge, it …