Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome
Published 2016 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome
Authors
Keywords
<em class=EmphasisTypeItalic >Clostridium thermocellum</em>, Genome-scale model, Consolidated bioprocessing, Biofuels, Bioenergetics, Elementary mode analysis, Flux balance analysis, Rational strain design, Minimal cut sets
Journal
Biotechnology for Biofuels
Volume 9, Issue 1, Pages -
Publisher
Springer Nature
Online
2016-09-06
DOI
10.1186/s13068-016-0607-x
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Reassessment of the Transhydrogenase/Malate Shunt Pathway in Clostridium thermocellum ATCC 27405 through Kinetic Characterization of Malic Enzyme and Malate Dehydrogenase
- (2015) M. Taillefer et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- FluxModeCalculator: an efficient tool for large-scale flux mode computation: Table 1.
- (2015) Jan Bert van Klinken et al. BIOINFORMATICS
- Clostridium thermocellum DSM 1313 transcriptional responses to redox perturbation
- (2015) Kyle Sander et al. Biotechnology for Biofuels
- Elimination of hydrogenase active site assembly blocks H2 production and increases ethanol yield in Clostridium thermocellum
- (2015) Ranjita Biswas et al. Biotechnology for Biofuels
- Elimination of formate production in Clostridium thermocellum
- (2015) Thomas Rydzak et al. JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
- Genome-scale modeling for metabolic engineering
- (2015) Evangelos Simeonidis et al. JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
- Rational design of efficient modular cells
- (2015) Cong T. Trinh et al. METABOLIC ENGINEERING
- Elucidating central metabolic redox obstacles hindering ethanol production in Clostridium thermocellum
- (2015) R. Adam Thompson et al. METABOLIC ENGINEERING
- Elimination of metabolic pathways to all traditional fermentation products increases ethanol yields in Clostridium thermocellum
- (2015) Beth Papanek et al. METABOLIC ENGINEERING
- Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum
- (2015) Paul P. Lin et al. METABOLIC ENGINEERING
- HMMER web server: 2015 update
- (2015) Robert D. Finn et al. NUCLEIC ACIDS RESEARCH
- Insights into electron flux through manipulation of fermentation conditions and assessment of protein expression profiles in Clostridium thermocellum
- (2014) Thomas Rydzak et al. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
- Role of transcription and enzyme activities in redistribution of carbon and electron flux in response to N2 and H2 sparging of open-batch cultures of Clostridium thermocellum ATCC 27405
- (2014) Carlo R. Carere et al. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
- Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition
- (2014) Kristopher A. Hunt et al. BIOINFORMATICS
- The exometabolome of Clostridium thermocellum reveals overflow metabolism at high cellulose loading
- (2014) Evert K Holwerda et al. Biotechnology for Biofuels
- Increase in Ethanol Yield via Elimination of Lactate Production in an Ethanol-Tolerant Mutant of Clostridium thermocellum
- (2014) Ranjita Biswas et al. PLoS One
- optGpSampler: An Improved Tool for Uniformly Sampling the Solution-Space of Genome-Scale Metabolic Networks
- (2014) Wout Megchelenbrink et al. PLoS One
- Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds
- (2014) Henrik Marcus Geertz-Hansen et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks
- (2014) Axel von Kamp et al. PLoS Computational Biology
- A review of genome-scale metabolic flux modeling of anaerobiosis in biotechnology
- (2014) Ryan S Senger et al. Current Opinion in Chemical Engineering
- The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications
- (2014) Hannah Akinosho et al. Frontiers in Chemistry
- Atypical Glycolysis in Clostridium thermocellum
- (2013) Jilai Zhou et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks
- (2013) M. Ganter et al. BIOINFORMATICS
- Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass
- (2013) Charlotte M Wilson et al. Biotechnology for Biofuels
- Characterization of Clostridium thermocellum strains with disrupted fermentation end-product pathways
- (2013) Douwe van der Veen et al. JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
- The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum
- (2013) Rasmus Agren et al. PLoS Computational Biology
- Nitrogen and sulfur requirements for Clostridium thermocellum and Caldicellulosiruptor bescii on cellulosic substrates in minimal nutrient media
- (2012) Donna M. Kridelbaugh et al. BIORESOURCE TECHNOLOGY
- Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression
- (2012) Thomas Rydzak et al. BMC MICROBIOLOGY
- Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico
- (2012) Michael J McAnulty et al. BMC Systems Biology
- Reconciliation of metabolites and biochemical reactions for metabolic networks
- (2012) T. Bernard et al. BRIEFINGS IN BIOINFORMATICS
- A defined growth medium with very low background carbon for culturing Clostridium thermocellum
- (2012) Evert K. Holwerda et al. JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
- Redirecting carbon flux through exogenous pyruvate kinase to achieve high ethanol yields in Clostridium thermocellum
- (2012) Yu Deng et al. METABOLIC ENGINEERING
- End-product induced metabolic shifts in Clostridium thermocellum ATCC 27405
- (2011) Thomas Rydzak et al. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
- Transcriptomic analysis of Clostridium thermocellum ATCC 27405 cellulose fermentation
- (2011) Babu Raman et al. BMC MICROBIOLOGY
- Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052
- (2011) Caroline B Milne et al. BMC Systems Biology
- Complete Genome Sequence of the Cellulolytic Thermophile Clostridium thermocellum DSM1313
- (2011) L. Feinberg et al. JOURNAL OF BACTERIOLOGY
- Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
- (2011) Jan Schellenberger et al. Nature Protocols
- The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
- (2011) R. Caspi et al. NUCLEIC ACIDS RESEARCH
- TSdb: A database of transporter substrates linking metabolic pathways and transporter systems on a genome scale via their shared substrates
- (2011) Min Zhao et al. Science China-Life Sciences
- Global Gene Expression Patterns inClostridium thermocellumas Determined by Microarray Analysis of Chemostat Cultures on Cellulose or Cellobiose
- (2010) Allison Riederer et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Development of pyrF-Based Genetic System for Targeted Gene Deletion in Clostridium thermocellum and Creation of a pta Mutant
- (2010) S. A. Tripathi et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing
- (2010) Fahimeh Salimi et al. Biotechnology Journal
- Genome-scale metabolic model integrated with RNAseq data to identify metabolic states ofClostridium thermocellum
- (2010) Christopher M. Gowen et al. Biotechnology Journal
- Economic impact of total solids loading on enzymatic hydrolysis of dilute acid pretreated corn stover
- (2010) David Humbird et al. BIOTECHNOLOGY PROGRESS
- Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production
- (2010) Seth B Roberts et al. BMC Systems Biology
- Computing complex metabolic intervention strategies using constrained minimal cut sets
- (2010) Oliver Hädicke et al. METABOLIC ENGINEERING
- A protocol for generating a high-quality genome-scale metabolic reconstruction
- (2010) Ines Thiele et al. Nature Protocols
- BRENDA, the enzyme information system in 2011
- (2010) M. Scheer et al. NUCLEIC ACIDS RESEARCH
- A new bioinformatics analysis tools framework at EMBL-EBI
- (2010) M. Goujon et al. NUCLEIC ACIDS RESEARCH
- Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes
- (2010) Sergio Bordel et al. PLoS Computational Biology
- Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network
- (2009) Bevan Chung et al. BMC Systems Biology
- Growth phase-dependant enzyme profile of pyruvate catabolism and end-product formation in Clostridium thermocellum ATCC 27405
- (2009) Thomas Rydzak et al. JOURNAL OF BIOTECHNOLOGY
- Biosolutions to the energy problem
- (2009) Arnold L. Demain JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
- Impact of Pretreated Switchgrass and Biomass Carbohydrates on Clostridium thermocellum ATCC 27405 Cellulosome Composition: A Quantitative Proteomic Analysis
- (2009) Babu Raman et al. PLoS One
- Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses
- (2008) C. T. Trinh et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Cellodextrin and Laminaribiose ABC Transporters in Clostridium thermocellum
- (2008) Y. Nataf et al. JOURNAL OF BACTERIOLOGY
- Use of Randomized Sampling for Analysis of Metabolic Networks
- (2008) Jan Schellenberger et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
- (2008) Adam M Feist et al. NATURE BIOTECHNOLOGY
- How biotech can transform biofuels
- (2008) Lee R Lynd et al. NATURE BIOTECHNOLOGY
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started