Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator

Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes

(2021) Johannes Asplund-Samuelsson et al.   PLoS Computational Biology

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

(2020) Pierre Salvy et al.   Nature Communications

Pooled CRISPRi screening of the cyanobacterium Synechocystis sp PCC 6803 for enhanced industrial phenotypes

(2020) Lun Yao et al.   Nature Communications

Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle

(2020) Nico J. Claassens et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Underground isoleucine biosynthesis pathways in E. coli

(2020) Charles AR Cotton et al.   eLife

Perspectives for the biotechnological production of biofuels from CO2 and H2 using Ralstonia eutropha and other ‘Knallgas’ bacteria

(2019) Christopher Brigham   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Allosteric Feedback Inhibition Enables Robust Amino Acid Biosynthesis in E. coli by Enforcing Enzyme Overabundance

(2019) Timur Sander et al.   Cell Systems

Quantitative insights into the cyanobacterial cell economy

(2019) Tomáš Zavřel et al.   eLife

Automated generation of bacterial resource allocation models

(2019) Ana Bulović et al.   METABOLIC ENGINEERING

Temporal Dynamics of the Soil Metabolome and Microbiome During Simulated Anaerobic Soil Disinfestation

(2019) Shashika S. Hewavitharana et al.   Frontiers in Microbiology

Reserve Flux Capacity in the Pentose Phosphate Pathway Enables Escherichia coli 's Rapid Response to Oxidative Stress

(2018) Dimitris Christodoulou et al.   Cell Systems

Kinetic modeling of the Calvin cycle identifies flux control and stable metabolomes in Synechocystis carbon fixation

(2018) Markus Janasch et al.   JOURNAL OF EXPERIMENTAL BOTANY

Growth of Cyanobacteria Is Constrained by the Abundance of Light and Carbon Assimilation Proteins

(2018) Michael Jahn et al.   Cell Reports

CbbR and RegA regulate cbb operon transcription in Ralstonia eutropha H16

(2017) Steffen Gruber et al.   JOURNAL OF BIOTECHNOLOGY

Targeted Feature Detection for Data-Dependent Shotgun Proteomics

(2017) Hendrik Weisser et al.   JOURNAL OF PROTEOME RESEARCH

13C-assisted metabolic flux analysis to investigate heterotrophic and mixotrophic metabolism in Cupriavidus necator H16

(2017) Swathi Alagesan et al.   Metabolomics

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

(2017) Benjamín J Sánchez et al.   Molecular Systems Biology

Quantifying the benefit of a proteome reserve in fluctuating environments

(2017) Matteo Mori et al.   Nature Communications

Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity

(2017) Ed Reznik et al.   Cell Reports

Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points

(2017) Uri Barenholz et al.   eLife

Principles of cellular resource allocation revealed by condition-dependent proteome profiling

(2017) Eyal Metzl-Raz et al.   eLife

The formate bio-economy

(2016) Oren Yishai et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

(2016) Hannes L Röst et al.   NATURE METHODS

Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitrokcatmeasurements

(2016) Dan Davidi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization

(2016) Elad Noor et al.   PLoS Computational Biology

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

(2016) Edward J. O’Brien et al.   PLoS Computational Biology

Quantitative prediction of genome-wide resource allocation in bacteria

(2015) Anne Goelzer et al.   METABOLIC ENGINEERING

Proteome reallocation in Escherichia coli with increasing specific growth rate

(2015) Karl Peebo et al.   Molecular BioSystems

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

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

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

The essential gene set of a photosynthetic organism

(2015) Benjamin E. Rubin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons

(2015) Kelly M. Wetmore et al.   mBio

New Insight into the Role of the Calvin Cycle: Reutilization of CO2 Emitted through Sugar Degradation

(2015) Rie Shimizu et al.   Scientific Reports

Coping with Anoxia: A Comprehensive Proteomic and Transcriptomic Survey of Denitrification

(2014) Yvonne Kohlmann et al.   JOURNAL OF PROTEOME RESEARCH

Emergence of robust growth laws from optimal regulation of ribosome synthesis

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

Kinetic and stoichiometric characterization of organoautotrophic growth of R alstonia eutropha on formic acid in fed-batch and continuous cultures

(2014) Stephan Grunwald et al.   Microbial Biotechnology

Carbon dioxide fixation by Calvin-Cycle enzymes improves ethanol yield in yeast

(2013) Víctor Guadalupe-Medina et al.   Biotechnology for Biofuels

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Fast and Accurate Database Searches with MS-GF+Percolator

(2013) Viktor Granholm et al.   JOURNAL OF PROTEOME RESEARCH

Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production

(2011) Jong Park et al.   BMC Systems Biology

Identification of mutation points in Cupriavidus necator NCIMB 11599 and genetic reconstitution of glucose-utilization ability in wild strain H16 for polyhydroxyalkanoate production

(2011) Izumi Orita et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Analyses of Soluble and Membrane Proteomes ofRalstonia eutrophaH16 Reveal Major Changes in the Protein Complement in Adaptation to Lithoautotrophy

(2011) Yvonne Kohlmann et al.   JOURNAL OF PROTEOME RESEARCH

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology

A proteomic view of the facultatively chemolithoautotrophic lifestyle ofRalstonia eutrophaH16

(2009) Edward Schwartz et al.   PROTEOMICS

The Genome Organization of Ralstonia eutropha Strain H16 and Related Species of the Burkholderiaceae

(2008) Wolfgang Florian Fricke et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Genomic View of Energy Metabolism in Ralstonia eutropha H16

(2008) Rainer Cramm   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY