Thrombotic disorders, such as myocardial infarction, ischemic stroke, peripheral arterial disease, deep venous thrombosis, pulmonary embolism, or other embolic diseases that are responsible for worldwide mortality and morbidity, are manifestations of the formed thrombi by blood clots during a pathologic blood coagulation process. Once thrombi are formed, the only way to resolve the blood clot i...

Coevolution analyses identify residues that co-vary with each other during evolution, revealing sequence relationships unobservable from traditional multiple sequence alignments. Here we describe a coevolutionary analysis of phosphomannomutase/phosphoglucomutase (PMM/PGM), a widespread and diverse enzyme family involved in carbohydrate biosynthesis. Mutual information and graph theory were util...

Understanding the architecture of physiological functions from annotated genome sequences is a major task for postgenomic biology. From the annotated genome sequence of the microbe Escherichia coli, we propose a general quantitative definition of enzyme importance in a metabolic network. Using a graph analysis of its metabolism, we relate the extent of the topological damage generated in the me...

Motivation: Development of mathematical models that adequately describe moleculargenetic mechanisms is one of the main tasks in modern bioinformatics. Not only should a model be sensitive to the particulars of enzyme reactions underlying cell life activity, but also to regulation exerted on enzyme activity by metabolites and specialized cell proteins. Results: The gene network for branched-chai...

Determining the entire complement of enzymes and their enzymatic functions is a fundamental step for reconstructing the metabolic network of cells. High quality enzyme annotation helps in enhancing metabolic networks reconstructed from the genome, especially by reducing gaps and increasing the enzyme coverage. Currently, structure-based and network-based approaches can only cover a limited numb...