Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies

Engineering metabolism through dynamic control

(2015) Naveen Venayak et al.   CURRENT OPINION IN BIOTECHNOLOGY

Diversity in (p)ppGpp metabolism and effectors

(2015) Kuanqing Liu et al.   CURRENT OPINION IN MICROBIOLOGY

How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization

(2015) Evert Bosdriesz et al.   FEBS Journal

Many Means to a Common End: the Intricacies of (p)ppGpp Metabolism and Its Control of Bacterial Homeostasis

(2015) Anthony O. Gaca et al.   JOURNAL OF BACTERIOLOGY

Dynamic optimization of metabolic networks coupled with gene expression

(2015) Steffen Waldherr et al.   JOURNAL OF THEORETICAL BIOLOGY

A synthetic growth switch based on controlled expression of RNA polymerase

(2015) J. Izard et al.   Molecular Systems Biology

Recent functional insights into the role of (p)ppGpp in bacterial physiology

(2015) Vasili Hauryliuk et al.   NATURE REVIEWS MICROBIOLOGY

Microfluidics: reframing biological enquiry

(2015) Todd A. Duncombe 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

Understanding carbon catabolite repression in Escherichia coli using quantitative models

(2015) A. Kremling et al.   TRENDS IN MICROBIOLOGY

The unexhausted potential of E. coli

(2015) Zachary D Blount   eLife

Molecular physiology of the dynamic regulation of carbon catabolite repression in Escherichia coli

(2014) O. Borirak et al.   MICROBIOLOGY-SGM

Emergence of robust growth laws from optimal regulation of ribosome synthesis

(2014) M. Scott et al.   Molecular Systems Biology

Coordination of microbial metabolism

(2014) Victor Chubukov et al.   NATURE REVIEWS MICROBIOLOGY

Improving fatty acids production by engineering dynamic pathway regulation and metabolic control

(2014) P. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial growth laws reflect the evolutionary importance of energy efficiency

(2014) Arijit Maitra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Not Just a Theory—The Utility of Mathematical Models in Evolutionary Biology

(2014) Maria R. Servedio et al.   PLOS BIOLOGY

Promoter activity dynamics in the lag phase of Escherichia coli

(2013) Daniel Madar et al.   BMC Systems Biology

Engineering dynamic pathway regulation using stress-response promoters

(2013) Robert H Dahl et al.   NATURE BIOTECHNOLOGY

Optimal control of gene expression for fast proteome adaptation to environmental change

(2013) M. Y. Pavlov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular crowding limits translation and cell growth

(2013) S. Klumpp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Medium-dependent control of the bacterial growth rate

(2012) Måns Ehrenberg et al.   BIOCHIMIE

Optimality in the Development of Intestinal Crypts

(2012) Shalev Itzkovitz et al.   CELL

Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells

(2012) Somenath Bakshi et al.   MOLECULAR MICROBIOLOGY

ppGpp: magic beyond RNA polymerase

(2012) Zachary D. Dalebroux et al.   NATURE REVIEWS MICROBIOLOGY

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Multidimensional Optimality of Microbial Metabolism

(2012) R. Schuetz et al.   SCIENCE

Tradeoffs and Optimality in the Evolution of Gene Regulation

(2011) Frank J. Poelwijk et al.   CELL

Bacterial growth laws and their applications

(2011) Matthew Scott et al.   CURRENT OPINION IN BIOTECHNOLOGY

Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy

(2011) Jonathan W Young et al.   Nature Protocols

Single-molecule investigations of the stringent response machinery in living bacterial cells

(2011) B. P. English et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modelling the optimal timing in metabolic pathway activation—Use of Pontryagin's Maximum Principle and role of the Golden section

(2010) Martin Bartl et al.   BIOSYSTEMS

Resource allocation problem in a two-sector economic model of special form

(2010) Yu. N. Kiselev et al.   DIFFERENTIAL EQUATIONS

ppGpp is the major source of growth rate control in E. coli

(2010) Katarzyna Potrykus et al.   ENVIRONMENTAL MICROBIOLOGY

Survival of Escherichia coli in the environment: fundamental and public health aspects

(2010) Jan Dirk van Elsas et al.   ISME Journal

The trade-off between rate and yield in the design of microbial metabolism

(2010) S. A. FRANK   JOURNAL OF EVOLUTIONARY BIOLOGY

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Sequential Activation of Metabolic Pathways: a Dynamic Optimization Approach

(2009) Diego A. Oyarzún et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology

(p)ppGpp: Still Magical?

(2008) Katarzyna Potrykus et al.   Annual Review of Microbiology

The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli

(2008) Matthew F. Traxler et al.   MOLECULAR MICROBIOLOGY

Carbon catabolite repression in bacteria: many ways to make the most out of nutrients

(2008) Boris Görke et al.   NATURE REVIEWS MICROBIOLOGY

Is maximization of molar yield in metabolic networks favoured by evolution?

(2007) Stefan Schuster et al.   JOURNAL OF THEORETICAL BIOLOGY