Metabolism is highly complex and involves thousands of different connected reactions; it is
therefore necessary to use mathematical models for holistic studies. The use of …

When faced with a shortage of oxygen, many bacterial species use nitrate to support
respiration via the process of denitrification. This takes place extensively in nitrogen-rich …

Praise for the first edition:… superb, beautifully written and organized work that takes an
engineering approach to systems biology. Alon provides nicely written appendices to …

Direct in vivo investigation of mammalian metabolism is complicated by the distinct
metabolic functions of different tissues. We present a computational method that successfully …

Many properties of complex networks cannot be understood from monitoring the
components—not even when comprehensively monitoring all protein or metabolite …

The advent of functional genomics has enabled the molecular biosciences to come a long
way towards characterizing the molecular constituents of life. Yet, the challenge for biology …

Maximization of growth rate is an important fitness strategy for bacteria. Bacteria can achieve
this by expressing proteins at optimal concentrations, such that resources are not wasted …

iMAT is an Integrative Metabolic Analysis Tool, enabling the integration of transcriptomic and
proteomic data with genome-scale metabolic network models to predict enzymes' metabolic …

Adaptation of cells to environmental changes requires dynamic interactions between
metabolic and regulatory networks, but studies typically address only one or a few layers of …

Motivation: The availability of modern sequencing techniques has led to a rapid increase in
the amount of reconstructed metabolic networks. Using these models as a platform for the …