Burden-driven feedback control of gene expression

Genetic circuit characterization and debugging using RNA‐seq

(2017) Thomas E Gorochowski et al.   Molecular Systems Biology

Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit

(2017) Apoorv Gupta et al.   NATURE BIOTECHNOLOGY

Resource Competition Shapes the Response of Genetic Circuits

(2017) Yili Qian et al.   ACS Synthetic Biology

Overloaded and stressed: whole-cell considerations for bacterial synthetic biology

(2016) Olivier Borkowski et al.   CURRENT OPINION IN MICROBIOLOGY

Evaluation of TagSeq, a reliable low-cost alternative for RNAseq

(2016) Brian K. Lohman et al.   Molecular Ecology Resources

Using promoter libraries to reduce metabolic burden due to plasmid-encoded proteins in recombinant Escherichia coli

(2016) Martina Pasini et al.   New Biotechnology

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

(2016) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Genetic circuit design automation

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

DNAplotlib: Programmable Visualization of Genetic Designs and Associated Data

(2016) Bryan S. Der et al.   ACS Synthetic Biology

A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes

(2016) Thomas E. Gorochowski et al.   ACS Synthetic Biology

A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation

(2016) Iman Farasat et al.   PLoS Computational Biology

Isocost Lines Describe the Cellular Economy of Genetic Circuits

(2015) Andras Gyorgy et al.   BIOPHYSICAL JOURNAL

Quantifying cellular capacity identifies gene expression designs with reduced burden

(2015) Francesca Ceroni et al.   NATURE METHODS

Ribosome profiling reveals the what, when, where and how of protein synthesis

(2015) Gloria A. Brar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation

(2015) John R. Houser et al.   PLoS Computational Biology

Heat-Shock Response Transcriptional Program Enables High-Yield and High-Quality Recombinant Protein Production in Escherichia coli

(2014) Xin Zhang et al.   ACS Chemical Biology

A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase

(2014) T. H. Segall-Shapiro et al.   Molecular Systems Biology

Tunable protein degradation in bacteria

(2014) D Ewen Cameron et al.   NATURE BIOTECHNOLOGY

Evolutionary meandering of intermolecular interactions along the drift barrier

(2014) Michael Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

R2oDNA Designer: Computational Design of Biologically Neutral Synthetic DNA Sequences

(2014) Arturo Casini et al.   ACS Synthetic Biology

Visualization of Evolutionary Stability Dynamics and Competitive Fitness of Escherichia coli Engineered with Randomized Multigene Circuits

(2013) Sean C. Sleight et al.   ACS Synthetic Biology

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

(2012) Stefano Cardinale et al.   Biotechnology Journal

Genetic Circuit Performance under Conditions Relevant for Industrial Bioreactors

(2012) Felix Moser et al.   ACS Synthetic Biology

A synthetic biology approach to self-regulatory recombinant protein production in Escherichia coli

(2012) Martin Dragosits et al.   Journal of Biological Engineering

Empirical model and in vivo characterization of the bacterial response to synthetic gene expression show that ribosome allocation limits growth rate

(2011) Javier Carrera et al.   Biotechnology Journal

Transposase mediated construction of RNA-seq libraries

(2011) J. Gertz et al.   GENOME RESEARCH

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Cost of Unneeded Proteins in E. coli Is Reduced after Several Generations in Exponential Growth

(2010) Irit Shachrai et al.   MOLECULAR CELL

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics

(2010) Shaomei He et al.   NATURE METHODS

Emergent bistability by a growth-modulating positive feedback circuit

(2009) Cheemeng Tan et al.   Nature Chemical Biology

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS