Cell-free systems offer a promising approach to engineer biology since their open nature
allows for well-controlled and characterized reaction conditions. In this review, we discuss …

Living organisms are differentiated by their genetic material-millions to billions of DNA bases
encoding thousands of genes. These genes are translated into a vast array of proteins …

The considerable difficulty encountered in reproducing the results of published dynamical
models limits validation, exploration and reuse of this increasingly large biomedical …

We present a full-stack modeling, analysis, and parameter identification pipeline to guide the
modeling and design of biological systems starting from specifications to circuit …

Abstract Model reduction methods usually focus on the error performance analysis;
however, in presence of uncertainties, it is important to analyze the robustness properties of …

Forward engineering synthetic circuits are at the core of synthetic biology. Automated
solutions will be required to facilitate circuit design and implementation. Circuit design is …

We introduce a MATLAB-based simulation toolbox, called txtlsim, for an Escherichia coli-
based Transcription–Translation (TX–TL) system. This toolbox accounts for several cell-free …

Designing synthetic microbial consortia is an emerging area in synthetic biology and a major
goal is to realize stable and robust coexistence of multiple species. Cooperation and …

Targeted transcriptional repression with catalytically inactive Cas9 (CRISPRi) can be used
to build gene regulatory nets similar in principle to those made with traditional transcription …

We derive phenomenological models of gene expression from a mechanistic description of
chemical reactions using an automated model reduction method. Using this method, we get …