Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca

Optimal selection of 2D reversed-phase–reversed-phase HPLC separation techniques in bottom-up proteomics

(2012) Peter McQueen et al.   Expert Review of Proteomics

Analysis of omics data with genome-scale models of metabolism

(2012) Daniel R. Hyduke et al.   Molecular BioSystems

Update on activities at the Universal Protein Resource (UniProt) in 2013

(2012)   NUCLEIC ACIDS RESEARCH

In silico method for modelling metabolism and gene product expression at genome scale

(2012) Joshua A. Lerman et al.   Nature Communications

Exploration and Mining of the Bacterial Terpenome

(2011) David E. Cane et al.   ACCOUNTS OF CHEMICAL RESEARCH

rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks

(2011) S. G. Thorleifsson et al.   BIOINFORMATICS

MBRole: enrichment analysis of metabolomic data

(2011) M. Chagoyen et al.   BIOINFORMATICS

Siderophore production by actinomycetes isolates from two soil sites in Western Australia

(2011) Joanna Lee et al.   BIOMETALS

Terpenoids are Widespread in Actinomycetes: A Correlation of Secondary Metabolism and Genome Data

(2011) Christian A. Citron et al.   CHEMBIOCHEM

Metabolic engineering of Thermobifida fusca for direct aerobic bioconversion of untreated lignocellulosic biomass to 1-propanol

(2011) Yu Deng et al.   METABOLIC ENGINEERING

EMILiO: A fast algorithm for genome-scale strain design

(2011) Laurence Yang et al.   METABOLIC ENGINEERING

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Reveromycin A biosynthesis uses RevG and RevJ for stereospecific spiroacetal formation

(2011) Shunji Takahashi et al.   Nature Chemical Biology

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Biotechnological doxorubicin production: pathway and regulation engineering of strains for enhanced production

(2010) Narayan Prasad Niraula et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Genome-scale metabolic model integrated with RNAseq data to identify metabolic states ofClostridium thermocellum

(2010) Christopher M. Gowen et al.   Biotechnology Journal

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

A Genome-Scale Metabolic Model of Cryptosporidium hominis

(2010) Niti Vanee et al.   CHEMISTRY & BIODIVERSITY

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Sridhar Ranganathan et al.   PLoS Computational Biology

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

(2009) Caroline Colijn et al.   PLoS Computational Biology

Practical Implementation of 2D HPLC Scheme with Accurate Peptide Retention Prediction in Both Dimensions for High-Throughput Bottom-Up Proteomics

(2008) Ravi C. Dwivedi et al.   ANALYTICAL CHEMISTRY

Third Generation Biofuels via Direct Cellulose Fermentation

(2008) Carlo Carere et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY