Designing Biological Circuits: From Principles to Applications

Discovering adaptation-capable biological network structures using control-theoretic approaches

(2022) Priyan Bhattacharya et al.   PLoS Computational Biology

Perfect adaptation in biology

(2021) Mustafa H. Khammash   Cell Systems

Design and Evaluation of Synthetic RNA-Based Incoherent Feed-Forward Loop Circuits

(2021) Seongho Hong et al.   Biomolecules

RBS and Promoter Strengths Determine the Cell-Growth-Dependent Protein Mass Fractions and Their Optimal Synthesis Rates

(2021) Fernando N. Santos-Navarro et al.   ACS Synthetic Biology

TopoFilter: a MATLAB package for mechanistic model identification in systems biology

(2020) Mikołaj Rybiński et al.   BMC BIOINFORMATICS

Tunable genetic devices through simultaneous control of transcription and translation

(2020) Vittorio Bartoli et al.   Nature Communications

Mechanistic Modeling of Biochemical Systems without A Priori Parameter Values Using the Design Space Toolbox v.3.0

(2020) Miguel Á. Valderrama-Gómez et al.   iScience

Distilling Robust Design Principles of Biocircuits Using Mixed Integer Dynamic Optimization

(2019) Irene Otero-Muras et al.   Processes

The effect of integral control in oscillatory and chaotic reaction kinetic networks

(2019) Kristian Thorsen et al.   PHYSICA D-NONLINEAR PHENOMENA

Adapting machine-learning algorithms to design gene circuits

(2019) Tom W. Hiscock   BMC BIOINFORMATICS

A universal biomolecular integral feedback controller for robust perfect adaptation

(2019) Stephanie K. Aoki et al.   NATURE

Building a global alliance of biofoundries

(2019) Nathan Hillson et al.   Nature Communications

A Model for the Spatiotemporal Design of Gene Regulatory Circuits

(2019) Ruud Stoof et al.   ACS Synthetic Biology

Design and Analysis of a Proportional-Integral-Derivative Controller with Biological Molecules

(2019) Michael Chevalier et al.   Cell Systems

Design, Fabrication, and Device Chemistry of a 3-Input-3-Output Synthetic Genetic Combinatorial Logic Circuit with a 3-Input AND Gate in a Single Bacterial Cell

(2019) Deepro Bonnerjee et al.   BIOCONJUGATE CHEMISTRY

Control Theory for Synthetic Biology: Recent Advances in System Characterization, Control Design, and Controller Implementation for Synthetic Biology

(2018) Victoria Hsiao et al.   IEEE CONTROL SYSTEMS MAGAZINE

Phenotype-centric modeling for elucidation of biological design principles

(2018) Miguel A. Valderrama-Gómez et al.   JOURNAL OF THEORETICAL BIOLOGY

The topological requirements for robust perfect adaptation in networks of any size

(2018) Robyn P. Araujo et al.   Nature Communications

Robustness of Clocks to Input Noise

(2018) Michele Monti et al.   PHYSICAL REVIEW LETTERS

Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells

(2017) Benjamin H Weinberg et al.   NATURE BIOTECHNOLOGY

Balancing a genetic toggle switch by real-time feedback control and periodic forcing

(2017) Jean-Baptiste Lugagne et al.   Nature Communications

Insulated transcriptional elements enable precise design of genetic circuits

(2017) Yeqing Zong et al.   Nature Communications

Engineered Control of Genetic Variability Reveals Interplay among Quorum Sensing, Feedback Regulation, and Biochemical Noise

(2017) Yadira Boada et al.   ACS Synthetic Biology

Adaptation with transcriptional regulation

(2017) Wenjia Shi et al.   Scientific Reports

Multi-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: an adaptive network case

(2016) Yadira Boada et al.   BMC Systems Biology

Synthetic biology routes to bio-artificial intelligence

(2016) Darren N. Nesbeth et al.   Essays in Biochemistry

Control theory meets synthetic biology

(2016) Domitilla Del Vecchio et al.   Journal of the Royal Society Interface

Genetic circuit design automation

(2016) A. A. K. Nielsen et al.   SCIENCE

Mechanistic links between cellular trade-offs, gene expression, and growth

(2015) Andrea Y. Weiße et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthesizing genetic sequential logic circuit with clock pulse generator

(2014) Chia-Hua Chuang et al.   BMC Systems Biology

The Energy Costs of Insulators in Biochemical Networks

(2013) John P. Barton et al.   BIOPHYSICAL JOURNAL

Time-scale separation - Michaelis and Menten's old idea, still bearing fruit

(2013) Jeremy Gunawardena   FEBS Journal

Contextualizing context for synthetic biology - identifying causes of failure of synthetic biological systems

(2012) Stefano Cardinale et al.   Biotechnology Journal

Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathways

(2011) Rui Alves et al.   Biotechnology & Genetic Engineering Reviews

Timing molecular motion and production with a synthetic transcriptional clock

(2011) E. Franco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’

(2010) Alvin Tamsir et al.   NATURE

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Defining Network Topologies that Can Achieve Biochemical Adaptation

(2009) Wenzhe Ma et al.   CELL

A Synthetic Genetic Edge Detection Program

(2009) Jeffrey J. Tabor et al.   CELL

OptCircuit: an optimization based method for computational design of genetic circuits

(2008) Madhukar S Dasika et al.   BMC Systems Biology

A fast, robust and tunable synthetic gene oscillator

(2008) Jesse Stricker et al.   NATURE