Measuring retroactivity from noise in gene regulatory networks.

[1]  D. Gillespie Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[2]  James W. Nilsson,et al.  Electric Circuits , 1983 .

[3]  Stephen Wolfram,et al.  Mathematica: a system for doing mathematics by computer (2nd ed.) , 1991 .

[4]  P. Bouloc,et al.  Degradation of carboxy-terminal-tagged cytoplasmic proteins by the Escherichia coli protease HflB (FtsH). , 1998, Genes & development.

[5]  A. Arkin,et al.  Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. , 1998, Genetics.

[6]  M. Elowitz,et al.  A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[7]  W. Hillen,et al.  Tet repressor induction without Mg2+. , 2000, Biochemistry.

[8]  T. Kepler,et al.  Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. , 2001, Biophysical journal.

[9]  C. Rao,et al.  Control, exploitation and tolerance of intracellular noise , 2002, Nature.

[10]  Ertugrul M. Ozbudak,et al.  Regulation of noise in the expression of a single gene , 2002, Nature Genetics.

[11]  P. Swain,et al.  Stochastic Gene Expression in a Single Cell , 2002, Science.

[12]  Hiroaki Kitano,et al.  Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. , 2003, Omics : a journal of integrative biology.

[13]  M. L. Simpson,et al.  Frequency domain analysis of noise in autoregulated gene circuits , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[14]  C. Rao,et al.  Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm , 2003 .

[15]  U. Alon,et al.  Detailed map of a cis-regulatory input function , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[16]  M. L. Simpson,et al.  Frequency domain chemical Langevin analysis of stochasticity in gene transcriptional regulation. , 2004, Journal of theoretical biology.

[17]  J. Raser,et al.  Control of Stochasticity in Eukaryotic Gene Expression , 2004, Science.

[18]  D. Endy Foundations for engineering biology , 2005, Nature.

[19]  P. Swain,et al.  Gene Regulation at the Single-Cell Level , 2005, Science.

[20]  M. Elowitz,et al.  Reconstruction of genetic circuits , 2005, Nature.

[21]  T. Elston,et al.  Stochasticity in gene expression: from theories to phenotypes , 2005, Nature Reviews Genetics.

[22]  Herbert M. Sauro,et al.  SBW - A Modular Framework for Systems Biology , 2006, Proceedings of the 2006 Winter Simulation Conference.

[23]  M. L. Simpson,et al.  Gene network shaping of inherent noise spectra , 2006, Nature.

[24]  Christopher A. Voigt,et al.  Genetic parts to program bacteria. , 2006, Current opinion in biotechnology.

[25]  J. Elf,et al.  Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell , 2007, Science.

[26]  Eduardo Sontag,et al.  Modular cell biology: retroactivity and insulation , 2008, Molecular systems biology.

[27]  M. Berger,et al.  The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters , 2008, Molecular microbiology.

[28]  J. Keasling Synthetic biology for synthetic chemistry. , 2008, ACS chemical biology.

[29]  Julien F. Ollivier,et al.  Colored extrinsic fluctuations and stochastic gene expression , 2008, Molecular systems biology.

[30]  M. Elowitz,et al.  Regulatory activity revealed by dynamic correlations in gene expression noise , 2008, Nature Genetics.

[31]  M. L. Simpson,et al.  Transient-mediated fate determination in a transcriptional circuit of HIV , 2007, Nature Genetics.

[32]  D. Endy,et al.  Refinement and standardization of synthetic biological parts and devices , 2008, Nature Biotechnology.

[33]  Deepak Chandran,et al.  TinkerCell: modular CAD tool for synthetic biology , 2009, Journal of biological engineering.

[34]  Nicolas E. Buchler,et al.  Protein sequestration generates a flexible ultrasensitive response in a genetic network , 2009, Molecular systems biology.

[35]  Domitilla Del Vecchio,et al.  On the compromise between retroactivity attenuation and noise amplification in gene regulatory networks , 2009, Proceedings of the 48h IEEE Conference on Decision and Control (CDC) held jointly with 2009 28th Chinese Control Conference.

[36]  Brian Munsky,et al.  Listening to the noise: random fluctuations reveal gene network parameters , 2009, Molecular systems biology.

[37]  Priscilla E. M. Purnick,et al.  The second wave of synthetic biology: from modules to systems , 2009, Nature Reviews Molecular Cell Biology.

[38]  Daniel C. Ducat,et al.  Insulation of a synthetic hydrogen metabolism circuit in bacteria , 2010, Journal of biological engineering.