Boolean network models are one of the simplest models to study complex dynamic behavior
in biological systems. They can be applied to unravel the mechanisms regulating the …

Cellular decision making is the process whereby cells assume different, functionally
important and heritable fates without an associated genetic or environmental difference …

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 …

Transcription regulation networks control the expression of genes. The transcription
networks of well-studied microorganisms appear to be made up of a small set of recurring …

Mass cytometry facilitates high-dimensional, quantitative analysis of the effects of bioactive
molecules on human samples at single-cell resolution, but instruments process only one …

Many signaling systems show adaptation—the ability to reset themselves after responding to
a stimulus. We computationally searched all possible three-node enzyme network …

This paper advances a psychophysiological systems view of pain in which physical injury, or
wounding, generates a complex stress response that extends beyond the nervous system …

MicroRNAs (miRNAs) are regulatory molecules that participate in diverse biological
processes in animals and plants. While thousands of mammalian genes are potentially …

Background The production of peroxide and superoxide is an inevitable consequence of
aerobic metabolism, and while these particular'reactive oxygen species'(ROSs) can exhibit a …

In this essay I will sketch some ideas for how to think about models in biology. I will begin by
trying to dispel the myth that quantitative modeling is somehow foreign to biology. I will then …