Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves

Cellular perception of growth rate and the mechanistic origin of bacterial growth law

(2022) Chenhao Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shaping bacterial gene expression by physiological and proteome allocation constraints

(2022) Matthew Scott et al.   NATURE REVIEWS MICROBIOLOGY

Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria

(2022) Rohan Balakrishnan et al.   SCIENCE

Macro-nutrients recovery from liquid waste as a sustainable resource for production of recovered mineral fertilizer: Uncovering alternative options to sustain global food security cost-effectively

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A unifying autocatalytic network-based framework for bacterial growth laws

(2021) Anjan Roy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robust surface-to-mass coupling and turgor-dependent cell width determine bacterial dry-mass density

(2021) Enno R. Oldewurtel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An analytical theory of balanced cellular growth

(2020) Hugo Dourado et al.   Nature Communications

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

(2020) Daan H. de Groot et al.   PLoS Computational Biology

A universal trade-off between growth and lag in fluctuating environments

(2020) Markus Basan et al.   NATURE

Proteome reallocation from amino acid biosynthesis to ribosomes enables yeast to grow faster in rich media

(2020) Johan Björkeroth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Growth strategy of microbes on mixed carbon sources

(2019) Xin Wang et al.   Nature Communications

Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase

(2019) Patricia Sanchez-Vazquez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli

(2019) Mattia Zampieri et al.   Nature Communications

Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health

(2019) Kaitlyn Oliphant et al.   Microbiome

Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics based on Acid Extraction

(2019) Joerg Doellinger et al.   MOLECULAR & CELLULAR PROTEOMICS

Regulation underlying hierarchical and simultaneous utilization of carbon substrates by flux sensors in Escherichia coli

(2019) Hiroyuki Okano et al.   Nature Microbiology

Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial

(2018) Christina Ludwig et al.   Molecular Systems Biology

A global resource allocation strategy governs growth transition kinetics of Escherichia coli

(2017) David W. Erickson et al.   NATURE

Quantifying the benefit of a proteome reserve in fluctuating environments

(2017) Matteo Mori et al.   Nature Communications

The E. coli molecular phenotype under different growth conditions

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The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

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Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth

(2016) Xiongfeng Dai et al.   Nature Microbiology

Review article: insights into colonic protein fermentation, its modulation and potential health implications

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Proteome reallocation in Escherichia coli with increasing specific growth rate

(2015) Karl Peebo et al.   Molecular BioSystems

Relation between chemotaxis and consumption of amino acids in bacteria

(2015) Yiling Yang et al.   MOLECULAR MICROBIOLOGY

Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria

(2015) S. Hui et al.   Molecular Systems Biology

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

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

(2015) Vasili Hauryliuk et al.   NATURE REVIEWS MICROBIOLOGY

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

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

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The metabolic potential of Escherichia coli BL21 in defined and rich medium

(2014) Zhaopeng Li et al.   Microbial Cell Factories

Emergence of robust growth laws from optimal regulation of ribosome synthesis

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

Visual account of protein investment in cellular functions

(2014) W. Liebermeister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chemodiversity of dissolved organic matter in lakes driven by climate and hydrology

(2014) Anne M. Kellerman et al.   Nature Communications

What is the total number of protein molecules per cell volume? A call to rethink some published values

(2013) Ron Milo   BIOESSAYS

Coordination of bacterial proteome with metabolism by cyclic AMP signalling

(2013) Conghui You et al.   NATURE

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

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

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Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA

(2011) J. J. Lemke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology

(p)ppGpp: Still Magical?

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