相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Resource Reallocation in Bacteria by Reengineering the Gene Expression Machinery
Hidde de Jong et al.
TRENDS IN MICROBIOLOGY (2017)
Invariance of Initiation Mass and Predictability of Cell Size in Escherichia coli
Fangwei Si et al.
CURRENT BIOLOGY (2017)
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
Socorro Gama-Castro et al.
NUCLEIC ACIDS RESEARCH (2016)
Necessary and sufficient conditions for protocell growth
Erwan Bigan et al.
JOURNAL OF MATHEMATICAL BIOLOGY (2016)
Constraint-based stoichiometric modelling from single organisms to microbial communities
Willi Gottstein et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2016)
The post-transcriptional regulatory system CSR controls the balance of metabolic pools in upper glycolysis of Escherichia coli
Manon Morin et al.
MOLECULAR MICROBIOLOGY (2016)
Single-cell characterization of metabolic switching in the sugar phosphotransferase system of Escherichia coli
Sonja A. Westermayer et al.
MOLECULAR MICROBIOLOGY (2016)
Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies
Nils Giordano et al.
PLOS COMPUTATIONAL BIOLOGY (2016)
Constrained Allocation Flux Balance Analysis
Matteo Mori et al.
PLOS COMPUTATIONAL BIOLOGY (2016)
Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution
Jose Utrilla et al.
CELL SYSTEMS (2016)
Genomic analysis and D-xylose fermentation of three novel Spathaspora species: Spathaspora girioi sp nov., Spathaspora hagerdaliae f. a., sp nov and Spathaspora gorwiae f. a., sp nov.
Mariana R. Lopes et al.
FEMS YEAST RESEARCH (2016)
Cell-Size Control and Homeostasis in Bacteria
Sattar Taheri-Araghi et al.
CURRENT BIOLOGY (2015)
How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization
Evert Bosdriesz et al.
FEBS JOURNAL (2015)
Methods and advances in metabolic flux analysis: a mini-review
Maciek R. Antoniewicz
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY (2015)
Dynamic optimization of metabolic networks coupled with gene expression
Steffen Waldherr et al.
JOURNAL OF THEORETICAL BIOLOGY (2015)
A growth-rate composition formula for the growth of E. coli on co-utilized carbon substrates
Rutger Hermsen et al.
MOLECULAR SYSTEMS BIOLOGY (2015)
Inflating bacterial cells by increased protein synthesis
Markus Basan et al.
MOLECULAR SYSTEMS BIOLOGY (2015)
Real-time metabolome profiling of the metabolic switch between starvation and growth
Hannes Link et al.
NATURE METHODS (2015)
Mechanistic links between cellular trade-offs, gene expression, and growth
Andrea Y. Weisse et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Why Build Whole-Cell Models?
Javier Carrera et al.
TRENDS IN CELL BIOLOGY (2015)
Understanding carbon catabolite repression in Escherichia coli using quantitative models
A. Kremling et al.
TRENDS IN MICROBIOLOGY (2015)
From the selfish gene to selfish metabolism: Revisiting the central dogma
Victor de Lorenzo
BIOESSAYS (2014)
Division in Escherichia coli is triggered by a size-sensing rather than a timing mechanism
Lydia Robert et al.
BMC BIOLOGY (2014)
Models in biology: 'accurate descriptions of our pathetic thinking'
Jeremy Gunawardena
BMC BIOLOGY (2014)
Global dynamic optimization approach to predict activation in metabolic pathways
Gundian M. de Hijas-Liste et al.
BMC SYSTEMS BIOLOGY (2014)
A Constant Size Extension Drives Bacterial Cell Size Homeostasis
Manuel Campos et al.
CELL (2014)
Reverse engineering and identification in systems biology: strategies, perspectives and challenges
Alejandro F. Villaverde et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2014)
Bacterial sugar utilization gives rise to distinct single-cell behaviours
Taliman Afroz et al.
MOLECULAR MICROBIOLOGY (2014)
Phenotypic bistability in Escherichia coli's central carbon metabolism
Oliver Kotte et al.
MOLECULAR SYSTEMS BIOLOGY (2014)
Emergence of robust growth laws from optimal regulation of ribosome synthesis
Matthew Scott et al.
MOLECULAR SYSTEMS BIOLOGY (2014)
Stochasticity of metabolism and growth at the single-cell level
Daniel J. Kiviet et al.
NATURE (2014)
Constraint-based models predict metabolic and associated cellular functions
Aarash Bordbar et al.
NATURE REVIEWS GENETICS (2014)
Coordination of microbial metabolism
Victor Chubukov et al.
NATURE REVIEWS MICROBIOLOGY (2014)
optGpSampler: An Improved Tool for Uniformly Sampling the Solution-Space of Genome-Scale Metabolic Networks
Wout Megchelenbrink et al.
PLOS ONE (2014)
DRUM: A New Framework for Metabolic Modeling under Non-Balanced Growth. Application to the Carbon Metabolism of Unicellular Microalgae
Caroline Baroukh et al.
PLOS ONE (2014)
Concerted control of Escherichia coli cell division
Matteo Osella et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of Nongrowing Cells
Johan H. van Heerden et al.
SCIENCE (2014)
Medium-dependent control of the bacterial growth rate
Mans Ehrenberg et al.
BIOCHIMIE (2013)
Overview of the Oldest Existing Set of Substrate-optimized Anaerobic Processes: Digestive Tracts
Jean-Jacques Godon et al.
BIOENERGY RESEARCH (2013)
Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells
Yi Zhou et al.
BMC SYSTEMS BIOLOGY (2013)
On the identifiability of metabolic network models
Sara Berthoumieux et al.
JOURNAL OF MATHEMATICAL BIOLOGY (2013)
Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
Edward J. O'Brien et al.
MOLECULAR SYSTEMS BIOLOGY (2013)
Coordination of bacterial proteome with metabolism by cyclic AMP signalling
Conghui You et al.
NATURE (2013)
Changes in substrate availability in Escherichia coli lead to rapid metabolite, flux and growth rate responses
Hilal Taymaz-Nikerel et al.
METABOLIC ENGINEERING (2013)
Dynamic models of metabolism: Review of the cybernetic approach
Doraiswami Ramkrishna et al.
AICHE JOURNAL (2012)
A Whole-Cell Computational Model Predicts Phenotype from Genotype
Jonathan R. Karr et al.
CELL (2012)
Influence of peptide dipoles and hydrogen bonds on reactive cysteine pKa values in fission yeast DJ-1
Peter Madzelan et al.
FEBS JOURNAL (2012)
Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks
Steven M. Kelk et al.
SCIENTIFIC REPORTS (2012)
Bacterial growth rate reflects a bottleneck in resource allocation
A. Goelzer et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2011)
Bacterial growth laws and their applications
Matthew Scott et al.
CURRENT OPINION IN BIOTECHNOLOGY (2011)
Economics of membrane occupancy and respiro-fermentation
Kai Zhuang et al.
MOLECULAR SYSTEMS BIOLOGY (2011)
Condition-Dependent Cell Volume and Concentration of Escherichia coli to Facilitate Data Conversion for Systems Biology Modeling
Benjamin Volkmer et al.
PLOS ONE (2011)
Development of an artificial cell, from self-organization to computation and self-reproduction
Vincent Noireaux et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
The biomass objective function
Adam M. Feist et al.
CURRENT OPINION IN MICROBIOLOGY (2010)
Classic and contemporary approaches to modeling biochemical reactions
William W. Chen et al.
GENES & DEVELOPMENT (2010)
Mathematical modelling of carbohydrate degradation by human colonic microbiota
Rafael Munoz-Tamayo et al.
JOURNAL OF THEORETICAL BIOLOGY (2010)
What is flux balance analysis?
Jeffrey D. Orth et al.
NATURE BIOTECHNOLOGY (2010)
Interdependence of Cell Growth and Gene Expression: Origins and Consequences
Matthew Scott et al.
SCIENCE (2010)
The Carbon Assimilation Network in Escherichia coli Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes
Valentina Baldazzi et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm
Sean R. McGuffee et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions
Tobias Bollenbach et al.
CELL (2009)
Growth Rate-Dependent Global Effects on Gene Expression in Bacteria
Stefan Klumpp et al.
CELL (2009)
Systems biology: parameter estimation for biochemical models
Maksat Ashyraliyev et al.
FEBS JOURNAL (2009)
Coordination of gene expression with growth rate: A feedback or a feed-forward strategy?
Sagi Levy et al.
FEBS LETTERS (2009)
Shifts in growth strategies reflect tradeoffs in cellular economics
Douwe Molenaar et al.
MOLECULAR SYSTEMS BIOLOGY (2009)
Emergent bistability by a growth-modulating positive feedback circuit
Cheemeng Tan et al.
NATURE CHEMICAL BIOLOGY (2009)
Invariant Distribution of Promoter Activities in Escherichia coli
Alon Zaslaver et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
(p)ppGpp: Still Magical?
Katarzyna Potrykus et al.
ANNUAL REVIEW OF MICROBIOLOGY (2008)
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
Markus W. Covert et al.
BIOINFORMATICS (2008)
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation:: a scaffold to query lipid metabolism
Intawat Nookaew et al.
BMC SYSTEMS BIOLOGY (2008)
Is maximization of molar yield in metabolic networks favoured by evolution?
Stefan Schuster et al.
JOURNAL OF THEORETICAL BIOLOGY (2008)
Carbon catabolite repression in bacteria:: many ways to make the most out of nutrients
Boris Goerke et al.
NATURE REVIEWS MICROBIOLOGY (2008)
Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks
Neema Jamshidi et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity
Q. K. Beg et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
Robert Schuetz et al.
MOLECULAR SYSTEMS BIOLOGY (2007)
Bacterial gene regulation in diauxic and non-diauxic growth
Atul Narang et al.
JOURNAL OF THEORETICAL BIOLOGY (2007)
Whole-cell modeling framework in which biochemical dynamics impact aspects of cellular geometry
Ivan V. Surovstev et al.
JOURNAL OF THEORETICAL BIOLOGY (2007)
Stochastic simulation of chemical kinetics
Daniel T. Gillespie
ANNUAL REVIEW OF PHYSICAL CHEMISTRY (2007)
Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model
Bas Teusink et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2006)
A comprehensive library of fluorescent transcriptional reporters for Escherichia coli
Alon Zaslaver et al.
NATURE METHODS (2006)
Stochasticity in gene expression:: From theories to phenotypes
M Kærn et al.
NATURE REVIEWS GENETICS (2005)
Genome-scale models of microbial cells: Evaluating the consequences of constraints
ND Price et al.
NATURE REVIEWS MICROBIOLOGY (2004)
Uniform sampling of steady-state flux spaces: Means to design experiments and to interpret enzymopathies
ND Price et al.
BIOPHYSICAL JOURNAL (2004)
Dynamic metabolic modelling under the balanced growth condition
A Provost et al.
JOURNAL OF PROCESS CONTROL (2004)
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
RU Ibarra et al.
NATURE (2002)
Dynamic flux balance analysis of diauxic growth in Escherichia coli
R Mahadevan et al.
BIOPHYSICAL JOURNAL (2002)
Optimal allocation of building blocks between nutrient uptake systems in a microbe
HA van den Berg et al.
JOURNAL OF MATHEMATICAL BIOLOGY (2002)
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
JS Edwards et al.
NATURE BIOTECHNOLOGY (2001)
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
S Schuster et al.
NATURE BIOTECHNOLOGY (2000)
分享论文
