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Constrained Allocation Flux Balance Analysis
Matteo Mori, Terence Hwa, Olivier C. Martin +2
New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement F…
Dissecting the Specificity of Protein-Protein Interaction in Bacterial Two-Component Signaling: Orphans and Crosstalks
Andrea Procaccini, Bryan Lunt, Hendrik Szurmant +2
Predictive understanding of the myriads of signal transduction pathways in a cell is an outstanding challenge of systems biology. Such pathways are primarily mediated by specific b…
Deterministic characterization of stochastic genetic circuits
Matthew Scott, Terence Hwa, Brian Ingalls
For cellular biochemical reaction systems where the numbers of molecules is small, significant noise is associated with chemical reaction events. This molecular noise can give rise…
Stochastic fluctuations in metabolic pathways
Erel Levine, Terence Hwa
Fluctuations in the abundance of molecules in the living cell may affect its growth and well being. For regulatory molecules (e.g., signaling proteins or transcription factors), fl…
Quantitative Characterization of Combinatorial Transcriptional Control of the Lactose Operon of E. coli
T. E. Kuhlman, Z. Zhang, M. H. Saier +1
It is the goal of systems biology to understand the behavior of the whole in terms of the knowledge of the parts. This is hard to achieve in many cases due to the difficulty of cha…
Designing sequential transcription logic: a simple genetic circuit for conditional memory
Georg Fritz, Nicolas E. Buchler, Terence Hwa +1
The ability to learn and respond to recurrent events depends on the capacity to remember transient biological signals received in the past. Moreover, it may be desirable to remembe…
Nonlinear Protein Degradation and the Function of Genetic Circuits
Nicolas E. Buchler, Ulrich Gerland, Terence Hwa
The functions of most genetic circuits require sufficient degrees of cooperativity in the circuit components. While mechanisms of cooperativity have been studied most extensively i…
Transcriptional Regulation by the Numbers 2: Applications
Lacramioara Bintu, Nicolas E. Buchler, Hernan G. Garcia +5
With the increasing amount of experimental data on gene expression and regulation, there is a growing need for quantitative models to describe the data and relate them to the diffe…
Transcriptional Regulation by the Numbers 1: Models
Lacramioara Bintu, Nicolas E. Buchler, Hernan G. Garcia +4
The study of gene regulation and expression is often discussed in quantitative terms. In particular, the expression of genes is regularly characterized with respect to how much, ho…