Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design

MEMOTE for standardized genome-scale metabolic model testing

(2020) Christian Lieven et al.   NATURE BIOTECHNOLOGY

Endogenous carbohydrate esterases of Clostridium thermocellum are identified and disrupted for enhanced isobutyl acetate production from cellulose

(2020) Hyeongmin Seo et al.   BIOTECHNOLOGY AND BIOENGINEERING

Harnessing natural modularity of metabolism with goal attainment optimization to design a modular chassis cell for production of diverse chemicals

(2020) Sergio Garcia et al.   ACS Synthetic Biology

Modular design: Implementing proven engineering principles in biotechnology

(2019) Sergio Garcia et al.   BIOTECHNOLOGY ADVANCES

Comparison of Multi-Objective Evolutionary Algorithms to Solve the Modular Cell Design Problem for Novel Biocatalysis

(2019) Sergio Garcia et al.   Processes

Microbial biosynthesis of lactate esters

(2019) Jong-Won Lee et al.   Biotechnology for Biofuels

Thermodynamic analysis of the pathway for ethanol production from cellobiose in Clostridium thermocellum

(2019) Satyakam Dash et al.   METABOLIC ENGINEERING

Single mutation at a highly conserved region of chloramphenicol acetyltransferase enables isobutyl acetate production directly from cellulose by Clostridium thermocellum at elevated temperatures

(2019) Hyeongmin Seo et al.   Biotechnology for Biofuels

A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

(2019) Hongzhong Lu et al.   Nature Communications

Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints

(2018) Siu H J Chan et al.   BIOINFORMATICS

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

MinGenome: An In Silico Top-Down Approach for the Synthesis of Minimized Genomes

(2018) Lin Wang et al.   ACS Synthetic Biology

Multiobjective Strain Design: A Framework for Modular Cell Engineering

(2018) Sergio Garcia et al.   METABOLIC ENGINEERING

Engineering electron metabolism to increase ethanol production in Clostridium thermocellum

(2017) Jonathan Lo et al.   METABOLIC ENGINEERING

Glycolysis without pyruvate kinase in Clostridium thermocellum

(2017) Daniel G. Olson et al.   METABOLIC ENGINEERING

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

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

(2016) R. Adam Thompson et al.   Biotechnology for Biofuels

Simultaneous achievement of high ethanol yield and titer in Clostridium thermocellum

(2016) Liang Tian et al.   Biotechnology for Biofuels

Multi-omic data integration enables discovery of hidden biological regularities

(2016) Ali Ebrahim et al.   Nature Communications

Rescuing Those Left Behind: Recovering and Characterizing Underdigested Membrane and Hydrophobic Proteins To Enhance Proteome Measurement Depth

(2015) Richard J. Giannone et al.   ANALYTICAL CHEMISTRY

Alcohol Selectivity in a Synthetic Thermophilicn-Butanol Pathway Is Driven by Biocatalytic and Thermostability Characteristics of Constituent Enzymes

(2015) Andrew J. Loder et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Elimination of hydrogenase active site assembly blocks H2 production and increases ethanol yield in Clostridium thermocellum

(2015) Ranjita Biswas et al.   Biotechnology for Biofuels

Computational methods in metabolic engineering for strain design

(2015) Matthew R Long et al.   CURRENT OPINION IN BIOTECHNOLOGY

Advances in de novo strain design using integrated systems and synthetic biology tools

(2015) Chiam Yu Ng et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

A Quantitative System-Scale Characterization of the Metabolism of Clostridium acetobutylicum

(2015) Minyeong Yoo et al.   mBio

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

(2014) Satyakam Dash et al.   Biotechnology for Biofuels

The exometabolome of Clostridium thermocellum reveals overflow metabolism at high cellulose loading

(2014) Evert K Holwerda et al.   Biotechnology for Biofuels

Life on the edge: functional genomic response of Ignicoccus hospitalis to the presence of Nanoarchaeum equitans

(2014) Richard J Giannone et al.   ISME Journal

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

(2014) Daniel Machado et al.   PLoS Computational Biology

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

Constraint-based genome-scale metabolic modeling of Clostridium acetobutylicum behavior in an immobilized column

(2013) Janne Wallenius et al.   BIORESOURCE TECHNOLOGY

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii

(2013) Harish Nagarajan et al.   Microbial Cell Factories

Elucidating and reprogramming Escherichia coli metabolisms for obligate anaerobic n-butanol and isobutanol production

(2012) Cong T. Trinh   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

DanteR: an extensible R-based tool for quantitative analysis of -omics data

(2012) Tom Taverner et al.   BIOINFORMATICS

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

Redirecting carbon flux through exogenous pyruvate kinase to achieve high ethanol yields in Clostridium thermocellum

(2012) Yu Deng et al.   METABOLIC ENGINEERING

High Ethanol Titers from Cellulose by Using Metabolically Engineered Thermophilic, Anaerobic Microbes

(2011) D. Aaron Argyros et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

(2011) Jan Schellenberger et al.   BIOPHYSICAL JOURNAL

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

(2011) Caroline B Milne et al.   BMC Systems Biology

Recent progress in consolidated bioprocessing

(2011) Daniel G Olson et al.   CURRENT OPINION IN BIOTECHNOLOGY

Civil conflicts are associated with the global climate

(2011) Solomon M. Hsiang et al.   NATURE

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

Systems metabolic engineering: Genome-scale models and beyond

(2010) John Blazeck et al.   Biotechnology Journal

Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing

(2010) Fahimeh Salimi et al.   Biotechnology Journal

Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production

(2010) Seth B Roberts et al.   BMC Systems Biology

The surprising diversity of clostridial hydrogenases: a comparative genomic perspective

(2010) M. Calusinska et al.   MICROBIOLOGY-SGM

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes

(2010) Sergio Bordel et al.   PLoS Computational Biology

IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering

(2009) Ze-Qiang Ma et al.   JOURNAL OF PROTEOME RESEARCH

Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism

(2008) Cong T. Trinh et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Genome-scale model forClostridium acetobutylicum: Part I. Metabolic network resolution and analysis

(2008) Ryan S. Senger et al.   BIOTECHNOLOGY AND BIOENGINEERING

When will fossil fuel reserves be diminished?

(2008) Shahriar Shafiee et al.   ENERGY POLICY

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY