List of works - Frank J Bruggeman

A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803.

scientific article

A turbo engine with automatic transmission? How to marry chemicomotion to the subtleties and robustness of life

scientific article

Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength

scientific article published on 10 January 2019

AmtB-mediated NH3 transport in prokaryotes must be active and as a consequence regulation of transport by GlnK is mandatory to limit futile cycling of NH4(+)/NH3.

scientific article

Attractive models: how to make the silicon cell relevant and dynamic

scientific article published on January 2003

Basic concepts and principles of stoichiometric modeling of metabolic networks

scientific article

Binding proteins enhance specific uptake rate by increasing the substrate-transporter encounter rate

scientific article published on 24 April 2015

Biphasic Cell-Size and Growth-Rate Homeostasis by Single Bacillus subtilis Cells

scientific article published on 04 May 2020

Cancer: a Systems Biology disease

scientific article

Community flux balance analysis for microbial consortia at balanced growth

scientific article

Comparative systems biology: from bacteria to man ⬇️

scientific article published on September 1, 2010

Constraint-based stoichiometric modelling from single organisms to microbial communities.

scientific article published on November 2016

Control of MAPK signalling: from complexity to what really matters

Design principles of nuclear receptor signaling: how complex networking improves signal transduction.

scientific article

Design principles of nuclear receptor signalling: How complex networking improves signal transduction

article

ECA: control in ecosystems

scientific article published in January 2002

Ecological control analysis: being(s) in control of mass flux and metabolite concentrations in anaerobic degradation processes

scientific article published on February 2007

Effects of growth rate and promoter activity on single-cell protein expression

scientific article published on 24 July 2017

Effects of sequestration on signal transduction cascades

scientific article published in March 2006

Elementary Growth Modes provide a molecular description of cellular self-fabrication

scientific article published on 27 January 2020

Emergence of the silicon human and network targeting drugs

article

Evolutionary pressures on microbial metabolic strategies in the chemostat

scientific article

Exploration of the spontaneous fluctuating activity of single enzyme molecules

scientific article published on 12 July 2013

Fast flux module detection using matroid theory.

scientific article published on 7 January 2015

Fatal attraction in glycolysis: how Saccharomyces cerevisiae manages sudden transitions to high glucose.

scientific article published on 20 February 2014

From Silicon Cellsilicon cell to Silicon Humansilicon human

Gene network requirements for regulation of metabolic gene expression to a desired state

scientific article published on January 2013

Growth-rate and protein-synthesis dynamics of single Bacillus subtilis cells along their cell-cycle

article

How biochemical constraints of cellular growth shape evolutionary adaptations in metabolism.

scientific article

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

scientific article published on 26 March 2015

How molecular competition influences fluxes in gene expression networks

scientific article

Integrative biology of persister cell formation: molecular circuitry, phenotypic diversification and fitness effects

scientific article published in 2022

Inter-level relations in computer science, biology, and psychology

scholarly article by Fred Boogerd et al published December 2002 in Philosophical Psychology

Interplay between constraints, objectives, and optimality for genome-scale stoichiometric models

scientific article published on 7 April 2015

Introduction to systems biology

scientific article published on 01 January 2007

Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of Nongrowing Cells

scientific article published in Science

Maintaining maximal metabolic flux by gene expression control

article

Maximal growth rate requires minimal metabolic complexity

Metabolic control analysis to identify optimal drug targets

scientific article published on January 2007

Metabolic control analysis to identify optimal drug targets

article

Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield

scientific article published on 16 February 2018

Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield

Metabolic states with maximal specific rate carry flux through an elementary flux mode

scientific article published on 12 February 2014

Metabolism at evolutionary optimal States.

scientific article published on 02 June 2015

Model-based quantification of metabolic interactions from dynamic microbial-community data

scientific article

Modular interaction strengths in regulatory networks; an example

scientific article published in January 2002

Modular response analysis of cellular regulatory networks.

scientific article

Multi-tasking of biosynthetic and energetic functions of glycolysis explained by supply and demand logic

scientific article

Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism

scientific article published on 24 April 2015

Network-based selectivity of antiparasitic inhibitors

scientific article published on 01 January 2002

Noise management by molecular networks

scientific article

Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks

scientific article published on 15 August 2012

Optimality principles in the regulation of metabolic networks

scientific article published on 29 August 2012

Optimization of stress response through the nuclear receptor-mediated cortisol signalling network

scientific article

Population-level transcription cycles derive from stochastic timing of single-cell transcription

scientific article

Principles behind the multifarious control of signal transduction

scientific article published on 01 January 2005

Public goods and metabolic strategies

scientific article

Restriction point control of the mammalian cell cycle via the cyclin E/Cdk2:p27 complex

scientific article published on 10 December 2009

Searching for principles of microbial physiology

scientific article published on 21 September 2020

Selection for Cell Yield Does Not Reduce Overflow Metabolism in <i>Escherichia coli</i>

scientific article published in 2021

Silence on the relevant literature and errors in implementation

scientific article published in April 2015

Single yeast cells vary in transcription activity not in delay time after a metabolic shift

scientific article

Single-cell imaging of ERK and Akt activation dynamics and heterogeneity induced by G-protein-coupled receptors

scientific article published on 11 March 2022

Statistics and simulation of growth of single bacterial cells: illustrations with B. subtilis and E. coli

scientific article

StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes

scientific article

Systems biology and the reconstruction of the cell: from molecular components to integral function

scientific article published on January 2007

Systems biology from micro-organisms to human metabolic diseases: the role of detailed kinetic models.

scientific article published in October 2010

Systems biology towards life in silico: mathematics of the control of living cells.

scientific article published on 16 February 2008

Systems biology: the elements and principles of life

scientific article published on December 2009

Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure

scientific article published on 19 March 2015

Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments

scientific article

The Fundamental Equations of Change in Statistical Ensembles and Biological Populations

scientific article published on 10 December 2020

The common message of constraint-based optimization approaches: overflow metabolism is caused by two growth-limiting constraints

scientific article published on 22 November 2019

The multifarious short-term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replica

scientific article

The nature of systems biology

scientific article

The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

scientific article published on 11 March 2019

Towards building the silicon cell: a modular approach

scientific article published on 19 October 2005

Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model.

scientific article

Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico.

scientific article published on 7 December 2012

Understanding bistability in yeast glycolysis using general properties of metabolic pathways.

scientific article published on 21 June 2014

Understanding start-up problems in yeast glycolysis

scientific article published on 14 March 2018

Untangling the wires: a strategy to trace functional interactions in signaling and gene networks

scientific article

Vertical systems biology: from DNA to flux and back

scientific article published in January 2008

What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform

scientific article published on 8 December 2010

Whole-cell metabolic control analysis

scientific article published in December 2023

Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

scientific article published on 10 February 2022

List of works by Frank J Bruggeman

A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803.

A turbo engine with automatic transmission? How to marry chemicomotion to the subtleties and robustness of life

Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength

AmtB-mediated NH3 transport in prokaryotes must be active and as a consequence regulation of transport by GlnK is mandatory to limit futile cycling of NH4(+)/NH3.

Attractive models: how to make the silicon cell relevant and dynamic

Basic concepts and principles of stoichiometric modeling of metabolic networks

Binding proteins enhance specific uptake rate by increasing the substrate-transporter encounter rate

Biphasic Cell-Size and Growth-Rate Homeostasis by Single Bacillus subtilis Cells

Cancer: a Systems Biology disease

Community flux balance analysis for microbial consortia at balanced growth

Comparative systems biology: from bacteria to man ⬇️

Constraint-based stoichiometric modelling from single organisms to microbial communities.

Control of MAPK signalling: from complexity to what really matters

Design principles of nuclear receptor signaling: how complex networking improves signal transduction.

Design principles of nuclear receptor signalling: How complex networking improves signal transduction

ECA: control in ecosystems

Ecological control analysis: being(s) in control of mass flux and metabolite concentrations in anaerobic degradation processes

Effects of growth rate and promoter activity on single-cell protein expression

Effects of sequestration on signal transduction cascades

Elementary Growth Modes provide a molecular description of cellular self-fabrication

Emergence of the silicon human and network targeting drugs

Evolutionary pressures on microbial metabolic strategies in the chemostat

Exploration of the spontaneous fluctuating activity of single enzyme molecules

Fast flux module detection using matroid theory.

Fatal attraction in glycolysis: how Saccharomyces cerevisiae manages sudden transitions to high glucose.

From Silicon Cellsilicon cell to Silicon Humansilicon human

Gene network requirements for regulation of metabolic gene expression to a desired state

Growth-rate and protein-synthesis dynamics of single Bacillus subtilis cells along their cell-cycle

How biochemical constraints of cellular growth shape evolutionary adaptations in metabolism.

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

How molecular competition influences fluxes in gene expression networks

Integrative biology of persister cell formation: molecular circuitry, phenotypic diversification and fitness effects

Inter-level relations in computer science, biology, and psychology

Interplay between constraints, objectives, and optimality for genome-scale stoichiometric models

Introduction to systems biology

Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of Nongrowing Cells

Maintaining maximal metabolic flux by gene expression control

Maximal growth rate requires minimal metabolic complexity

Metabolic control analysis to identify optimal drug targets

Metabolic control analysis to identify optimal drug targets

Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield

Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield

Metabolic states with maximal specific rate carry flux through an elementary flux mode

Metabolism at evolutionary optimal States.

Model-based quantification of metabolic interactions from dynamic microbial-community data

Modular interaction strengths in regulatory networks; an example

Modular response analysis of cellular regulatory networks.

Multi-tasking of biosynthetic and energetic functions of glycolysis explained by supply and demand logic

Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism

Network-based selectivity of antiparasitic inhibitors

Noise management by molecular networks

Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks

Optimality principles in the regulation of metabolic networks

Optimization of stress response through the nuclear receptor-mediated cortisol signalling network

Population-level transcription cycles derive from stochastic timing of single-cell transcription

Principles behind the multifarious control of signal transduction

Public goods and metabolic strategies

Restriction point control of the mammalian cell cycle via the cyclin E/Cdk2:p27 complex

Searching for principles of microbial physiology

Selection for Cell Yield Does Not Reduce Overflow Metabolism in <i>Escherichia coli</i>

Silence on the relevant literature and errors in implementation

Single yeast cells vary in transcription activity not in delay time after a metabolic shift

Single-cell imaging of ERK and Akt activation dynamics and heterogeneity induced by G-protein-coupled receptors

Statistics and simulation of growth of single bacterial cells: illustrations with B. subtilis and E. coli

StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes

Systems biology and the reconstruction of the cell: from molecular components to integral function

Systems biology from micro-organisms to human metabolic diseases: the role of detailed kinetic models.

Systems biology towards life in silico: mathematics of the control of living cells.

Systems biology: the elements and principles of life

Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure

Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments

The Fundamental Equations of Change in Statistical Ensembles and Biological Populations

The common message of constraint-based optimization approaches: overflow metabolism is caused by two growth-limiting constraints

The multifarious short-term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replica

The nature of systems biology

The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

Towards building the silicon cell: a modular approach

Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model.

Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico.