Functional synthetic biology

I Aldulijan, J Beal, S Billerbeck, J Bouffard… - Synthetic …, 2023 - academic.oup.com
Synthetic biologists have made great progress over the past decade in developing methods
for modular assembly of genetic sequences and in engineering biological systems with a …

Customizable gene sensing and response without altering endogenous coding sequences

F Caliendo, E Vitu, J Wang, SH Kuo, H Sandt… - Nature Chemical …, 2024 - nature.com
Synthetic biology aims to modify cellular behaviors by implementing genetic circuits that
respond to changes in cell state. Integrating genetic biosensors into endogenous gene …

Building the plant SynBio toolbox through combinatorial analysis of DNA regulatory elements

AC Pfotenhauer, A Occhialini, MA Nguyen… - ACS synthetic …, 2022 - ACS Publications
While the installation of complex genetic circuits in microorganisms is relatively routine, the
synthetic biology toolbox is severely limited in plants. Of particular concern is the absence of …

Synthetic gene circuits for cell state detection and protein tuning in human pluripotent stem cells

L Prochazka, YS Michaels, C Lau… - Molecular Systems …, 2022 - embopress.org
During development, cell state transitions are coordinated through changes in the identity of
molecular regulators in a cell type‐and dose‐specific manner. The ability to rationally …

Meeting measurement precision requirements for effective engineering of genetic regulatory networks

J Beal, B Teague, JT Sexton, S Castillo-Hair… - ACS synthetic …, 2022 - ACS Publications
Reliable, predictable engineering of cellular behavior is one of the key goals of synthetic
biology. As the field matures, biological engineers will become increasingly reliant on …

[HTML][HTML] Elucidating tumor-stromal metabolic crosstalk in colorectal cancer through integration of constraint-based models and LC-MS metabolomics

J Wang, A Delfarah, PE Gelbach, E Fong, P Macklin… - Metabolic …, 2022 - Elsevier
Colorectal cancer (CRC) is a major cause of morbidity and mortality in the United States.
Tumor-stromal metabolic crosstalk in the tumor microenvironment promotes CRC …

Quantitative characterization of recombinase-based digitizer circuits enables predictable amplification of biological signals

KA Kiwimagi, JH Letendre, BH Weinberg… - Communications …, 2021 - nature.com
Many synthetic gene circuits are restricted to single-use applications or require iterative
refinement for incorporation into complex systems. One example is the recombinase-based …

How retroactivity affects the behavior of incoherent feedforward loops

J Wang, C Belta, SA Isaacson - Iscience, 2020 - cell.com
An incoherent feedforward loop (IFFL) is a network motif known for its ability to accelerate
responses and generate pulses. It remains an open question to understand the behavior of …

DOSE-L1000: unveiling the intricate landscape of compound-induced transcriptional changes

J Wang, S Novick - Bioinformatics, 2023 - academic.oup.com
Abstract Motivation The LINCS L1000 project has collected gene expression profiles for
thousands of compounds across a wide array of concentrations, cell lines, and time points …

Inteins in the loop: a framework for engineering advanced biomolecular controllers for robust perfect adaptation

S Anastassov, M Filo, CH Chang, M Khammash - biorxiv, 2022 - biorxiv.org
Homeostasis is one of the cornerstones of life shaped by billions of years of evolution. A
notion that is similar to homeostasis, but yet more stringent, is Robust Perfect Adaptation …