The precise nature of information flow through a biological network, which is governed by factors such as response sensitivities and noise propagation, greatly affects the operation of biological systems. Quantitative analysis of these properties is often difficult in naturally occurring systems but can be greatly facilitated by studying simple synthetic… (More)
Additional References: 1. Lecture slides by Ravi Tiruvury 2.
This paper analyzes how the delay and repression strength of negative feedback in single-gene and multigene transcriptional networks influences intrinsic noise propagation and oscillatory behavior. We simulate a variety of transcriptional networks using a stochastic model and report two main findings. First, intrinsic noise is not attenuated by the addition… (More)
In this paper, we review an emerging engineering discipline to program cell behaviors by embedding synthetic gene networks that perform computation, communications, and signal processing. To accomplish this goal, we begin with a genetic component library and a biocircuit design methodology for assembling these components into compound circuits. The main… (More)
Artificial genetic circuits are becoming important tools for controlling cellular behavior and studying molecular biosystems. To genetically optimize the properties of complex circuits in a practically feasible fashion, it is necessary to identify the best genes and/or their regulatory components as mutation targets to avoid the mutation experiments being… (More)
Quorum sensing (QS) enables bacterial multicellularity and selective advantage for communicating populations. While genetic "switching" phenomena are a common feature, their mechanistic underpinnings have remained elusive. The interplay between circuit components and their regulation are intertwined and embedded. Observable phenotypes are complex and… (More)
Writing secure code requires a programmer to think both as a defender and an attacker. One can draw a parallel between this model of thinking and techniques used in test-driven development, where students learn by thinking about how to effectively test their code and anticipate possible bugs. In this study, we analyzed the quality of both attack and defense… (More)
The flow of information through a biological network can greatly influence the operation and behavior of the system. Quantitative analysis of these properties is often difficult in naturally occurring systems, but can be greatly facilitated by studying simple synthetic networks. Here we present synthetic transcriptional cascades of various length and study… (More)