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Trade-offs between the instantaneous growth rate and long-term fitness: Consequences for microbial physiology and predictive computational models

BioEssays, 2023-10, Vol.45 (10), p.e2300015-e2300015

2023

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

PLoS computational biology, 2018-02, Vol.14 (2), p.e1006010-e1006010

2018

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Transcription Stochasticity of Complex Gene Regulation Models

Biophysical journal, 2012-09, Vol.103 (6), p.1152-1161

2012

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

PLoS computational biology, 2019-03, Vol.15 (3), p.e1006858-e1006858

2019

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Community flux balance analysis for microbial consortia at balanced growth

PloS one, 2013-05, Vol.8 (5), p.e64567-e64567

2013

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

Science (American Association for the Advancement of Science), 2014-02, Vol.343 (6174), p.987-987

2014

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

PLoS computational biology, 2020-01, Vol.16 (1), p.e1007559-e1007559

2020

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

Nature communications, 2022-02, Vol.13 (1), p.801-801, Article 801

2022

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Contributions of Cell Growth and Biochemical Reactions to Nongenetic Variability of Cells

Biophysical journal, 2014-07, Vol.107 (2), p.301-313

2014

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

Journal of the Royal Society interface, 2017-07, Vol.14 (132), p.20170141

2017

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

PloS one, 2013-11, Vol.8 (11), p.e79345-e79345

2013

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Understanding and computational design of genetic circuits of metabolic networks

Essays in biochemistry, 2024-04, Vol.68 (1), p.41-51

2024

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The Fundamental Equations of Change in Statistical Ensembles and Biological Populations

Entropy (Basel, Switzerland), 2020-12, Vol.22 (12), p.1395

2020

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Elongation dynamics shape bursty transcription and translation

Proceedings of the National Academy of Sciences - PNAS, 2009-02, Vol.106 (8), p.2583-2588

2009

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

PloS one, 2017-03, Vol.12 (3), p.e0173183-e0173183

2017

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

Scientific reports, 2017-07, Vol.7 (1), p.6299-11, Article 6299

2017

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A yeast FRET biosensor enlightens cAMP signalling

Molecular biology of the cell, 2021-06, Vol.32 (13), p.mbcE20050319-1240

2021

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Maintaining maximal metabolic flux by gene expression control

PLoS computational biology, 2018-09, Vol.14 (9), p.e1006412-e1006412

2018

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

BioEssays, 2015-01, Vol.37 (1), p.34-45

2015

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Noise management by molecular networks

PLoS computational biology, 2009-09, Vol.5 (9), p.e1000506-e1000506

2009

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

Frontiers in microbiology, 2015-03, Vol.6, p.213-213

2015

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How molecular competition influences fluxes in gene expression networks

PloS one, 2011-12, Vol.6 (12), p.e28494-e28494

2011

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Searching for principles of microbial physiology

FEMS microbiology reviews, 2020-11, Vol.44 (6), p.821-844

2020

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Escherichia coli robustly expresses ATP synthase at growth rate‐maximizing concentrations

The FEBS journal, 2022-08, Vol.289 (16), p.4925-4934

2022

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

The FEBS journal, 2015-06, Vol.282 (12), p.2394-2407

2015

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Trade-offs between the instantaneous growth rate and long-term fitness: Consequences for microbial physiology and predictive computational models

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

Transcription Stochasticity of Complex Gene Regulation Models

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

Community flux balance analysis for microbial consortia at balanced growth

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

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

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

Contributions of Cell Growth and Biochemical Reactions to Nongenetic Variability of Cells

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

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

Understanding and computational design of genetic circuits of metabolic networks

The Fundamental Equations of Change in Statistical Ensembles and Biological Populations

Elongation dynamics shape bursty transcription and translation

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

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

A yeast FRET biosensor enlightens cAMP signalling

Maintaining maximal metabolic flux by gene expression control

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

Noise management by molecular networks

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

How molecular competition influences fluxes in gene expression networks

Searching for principles of microbial physiology

Escherichia coli robustly expresses ATP synthase at growth rate‐maximizing concentrations

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

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