4.7 Article

Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data

Brian J. Schmidt et al.

BIOINFORMATICS (2013)

Article Biotechnology & Applied Microbiology

The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum

Keerthi P. Venkataramanan et al.

BMC GENOMICS (2013)

Article Mathematical & Computational Biology

Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow

Thomas J. Mueller et al.

BMC SYSTEMS BIOLOGY (2013)

Article Biotechnology & Applied Microbiology

Engineering Clostridium acetobutylicum for alcohol production

Xiaohu Hou et al.

JOURNAL OF BIOTECHNOLOGY (2013)

Article Multidisciplinary Sciences

Model-based identification of drug targets that revert disrupted metabolism and its application to ageing

Keren Yizhak et al.

NATURE COMMUNICATIONS (2013)

Article Biotechnology & Applied Microbiology

New insights into the butyric acid metabolism of Clostridium acetobutylicum

Doerte Lehmann et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2012)

Article Biotechnology & Applied Microbiology

Disruption of the acetate kinase (ack) gene of Clostridium acetobutylicum results in delayed acetate production

Wouter Kuit et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2012)

Article Biochemical Research Methods

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

Akhil Kumar et al.

BMC BIOINFORMATICS (2012)

Article Mathematical & Computational Biology

Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico

Michael J. McAnulty et al.

BMC SYSTEMS BIOLOGY (2012)

Review Biochemical Research Methods

Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications

Bryan P. Tracy et al.

CURRENT OPINION IN BIOTECHNOLOGY (2012)

Article Biotechnology & Applied Microbiology

A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum - Cellular behavior in adaptation to n-butanol

Katrin M. Schwarz et al.

JOURNAL OF BIOTECHNOLOGY (2012)

Article Biotechnology & Applied Microbiology

Targeted mutagenesis of the Clostridium acetobutylicum acetone-butanol-ethanol fermentation pathway

Clare M. Cooksley et al.

METABOLIC ENGINEERING (2012)

Article Biotechnology & Applied Microbiology

Metabolome Remodeling during the Acidogenic-Solventogenic Transition in Clostridium acetobutylicum

Daniel Amador-Noguez et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)

Article Biophysics

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

Jan Schellenberger et al.

BIOPHYSICAL JOURNAL (2011)

Article Biotechnology & Applied Microbiology

Switching Clostridium acetobutylicum to an ethanol producer by disruption of the butyrate/butanol fermentative pathway

Doerte Lehmann et al.

METABOLIC ENGINEERING (2011)

Article Biotechnology & Applied Microbiology

High-throughput generation, optimization and analysis of genome-scale metabolic models

Christopher S. Henry et al.

NATURE BIOTECHNOLOGY (2010)

Article Biotechnology & Applied Microbiology

What is flux balance analysis?

Jeffrey D. Orth et al.

NATURE BIOTECHNOLOGY (2010)

Article Biochemical Research Methods

A protocol for generating a high-quality genome-scale metabolic reconstruction

Ines Thiele et al.

NATURE PROTOCOLS (2010)

Article Multidisciplinary Sciences

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis

Sriram Chandrasekaran et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemical Research Methods

An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models

Dipak Barua et al.

PLOS COMPUTATIONAL BIOLOGY (2010)

Article Biochemical Research Methods

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions

Sridhar Ranganathan et al.

PLOS COMPUTATIONAL BIOLOGY (2010)

Review Microbiology

Reconstruction of biochemical networks in microorganisms

Adam M. Feist et al.

NATURE REVIEWS MICROBIOLOGY (2009)

Article Biochemical Research Methods

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

Caroline Colijn et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Biotechnology & Applied Microbiology

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network

Joungmin Lee et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2008)

Article Biotechnology & Applied Microbiology

Genome-Scale Model for Clostridium acetobutylicum: Part I. Metabolic Network Resolution and Analysis

Ryan S. Senger et al.

BIOTECHNOLOGY AND BIOENGINEERING (2008)

Review Biochemical Research Methods

Engineering solventogenic clostridia

Eleftherios T. Papoutsakis

CURRENT OPINION IN BIOTECHNOLOGY (2008)

Article Biochemistry & Molecular Biology

Predicting synthetic rescues in metabolic networks

Adilson E. Motter et al.

MOLECULAR SYSTEMS BIOLOGY (2008)

Article Biotechnology & Applied Microbiology

The transcriptional program underlying the physiology of clostridial sporulation

Shawn W. Jones et al.

GENOME BIOLOGY (2008)

Article Biochemistry & Molecular Biology

A genome-scale computational study of the interplay between transcriptional regulation and metabolism

Tomer Shlomi et al.

MOLECULAR SYSTEMS BIOLOGY (2007)

Article Biochemistry & Molecular Biology

The TIGR plant transcript assemblies database

Kevin L. Childs et al.

NUCLEIC ACIDS RESEARCH (2007)

Review Genetics & Heredity

Towards multidimensional genome annotation

JL Reed et al.

NATURE REVIEWS GENETICS (2006)

Article Biochemistry & Molecular Biology

Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri

Adam M. Feist et al.

MOLECULAR SYSTEMS BIOLOGY (2006)

Article Microbiology

Modeling Lactococcus lactis using a genome-scale flux model -: art. no. 39

AP Oliveira et al.

BMC MICROBIOLOGY (2005)

Article Biotechnology & Applied Microbiology

Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli

H Alper et al.

METABOLIC ENGINEERING (2005)

Article Multidisciplinary Sciences

Global organization of metabolic fluxes in the bacterium Escherichia coli

E Almaas et al.

NATURE (2004)

Article Biochemistry & Molecular Biology

Flux coupling analysis of genome-scale metabolic network reconstructions

AP Burgard et al.

GENOME RESEARCH (2004)

Article Biotechnology & Applied Microbiology

Stoichiometric network constraints on xylose metabolism by recombinant Saccharomyces cerevisiae

YS Jin et al.

METABOLIC ENGINEERING (2004)

Article Biotechnology & Applied Microbiology

OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

AP Burgard et al.

BIOTECHNOLOGY AND BIOENGINEERING (2003)

Article Biochemistry & Molecular Biology

Transcriptional regulation in constraints-based metabolic models of Escherichia coli

MW Covert et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2002)

Article Biology

Regulation of gene expression in flux balance models of metabolism

MW Covert et al.

JOURNAL OF THEORETICAL BIOLOGY (2001)

Article Multidisciplinary Sciences

Significance analysis of microarrays applied to the ionizing radiation response

VG Tusher et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)