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The manner in which microorganisms utilize their metabolic processes can be predicted using constraint-based analysis of genome-scale metabolic networks. Herein, we present the constraint-based reconstruction and analysis toolbox, a software package running in the Matlab environment, which allows for quantitative prediction of cellular behavior using a(More)
Metabolism is a vital cellular process, and its malfunction is a major contributor to human disease. Metabolic networks are complex and highly interconnected, and thus systems-level computational approaches are required to elucidate and understand metabolic genotype-phenotype relationships. We have manually reconstructed the global human metabolic network(More)
Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling. Compared with its predecessors, the(More)
Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same(More)
Metabolomics has emerged as a powerful tool in the quantitative identification of physiological and disease-induced biological states. Extracellular metabolome or metabolic profiling data, in particular, can provide an insightful view of intracellular physiological states in a noninvasive manner. We used an updated genome-scale metabolic network model of(More)
The recent sequencing and annotation of the human genome enables a new era in biomedicine that will be based on an interdisciplinary, systemic approach to the elucidation and treatment of human disease. Reconstruction of genome-scale metabolic networks is an important part of this approach since networks represent the integration of diverse biological data(More)
Metabolic reconstructions (MRs) are common denominators in systems biology and represent biochemical, genetic, and genomic (BiGG) knowledge-bases for target organisms by capturing currently available information in a consistent, structured manner. Salmonella enterica subspecies I serovar Typhimurium is a human pathogen, causes various diseases and its(More)
Macrophages are central players in immune response, manifesting divergent phenotypes to control inflammation and innate immunity through release of cytokines and other signaling factors. Recently, the focus on metabolism has been reemphasized as critical signaling and regulatory pathways of human pathophysiology, ranging from cancer to aging, often converge(More)
The intricate nature of human physiology renders its study a difficult undertaking, and a systems biology approach is necessary to understand the complex interactions involved. Network reconstruction is a key step in systems biology and represents a common denominator because all systems biology research on a target organism relies on such a representation.(More)
The main kidney transporter of many commonly prescribed drugs (e.g. penicillins, diuretics, antivirals, methotrexate, and non-steroidal anti-inflammatory drugs) is organic anion transporter-1 (OAT1), originally identified as NKT (Lopez-Nieto, C. E., You, G., Bush, K. T., Barros, E. J., Beier, D. R., and Nigam, S. K. (1997) J. Biol. Chem. 272, 6471-6478).(More)