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

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