Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data

Potential Mechanism of Action of meso-Dihydroguaiaretic Acid on Mycobacterium tuberculosis H37Rv

(2014) Aldo Clemente-Soto et al.   MOLECULES

Selection of human tissue-specific elementary flux modes using gene expression data

(2013) Alberto Rezola et al.   BIOINFORMATICS

A network-based approach for predicting key enzymes explaining metabolite abundance alterations in a disease phenotype

(2013) Jon Pey et al.   BMC Systems Biology

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

(2013) Ruchir A. Khandelwal et al.   PLoS One

Availability of public goods shapes the evolution of competing metabolic strategies

(2013) H. Bachmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Computational systems biology and in silico modeling of the human microbiome

(2012) E. Borenstein   BRIEFINGS IN BIOINFORMATICS

Towards metagenome-scale models for industrial applications—the case of Lactic Acid Bacteria

(2012) Filipe Branco dos Santos et al.   CURRENT OPINION IN BIOTECHNOLOGY

Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation

(2012) María-Eugenia Guazzaroni et al.   ISME Journal

Sizing up metatranscriptomics

(2012) Mary Ann Moran et al.   ISME Journal

Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli

(2012) L. Arike et al.   Journal of Proteomics

Expanding the chemical palate of cells by combining systems biology and metabolic engineering

(2012) Kathleen A. Curran et al.   METABOLIC ENGINEERING

Mathematical optimization applications in metabolic networks

(2012) Ali R. Zomorrodi et al.   METABOLIC ENGINEERING

In-silico-driven metabolic engineering of Pseudomonas putida for enhanced production of poly-hydroxyalkanoates

(2012) Ignacio Poblete-Castro et al.   METABOLIC ENGINEERING

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

(2012) Rasmus Agren et al.   PLoS Computational Biology

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

(2012) Ali R. Zomorrodi et al.   PLoS Computational Biology

Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks

(2012) Ana Rita Brochado et al.   PLoS Computational Biology

MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks

(2012) Edward Vitkin et al.   GENOME BIOLOGY

Bacteria-mediated PAH degradation in soil and sediment

(2011) Xiao-Ying Lu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Using the reconstructed genome-scale human metabolic network to study physiology and pathology

(2011) A. Bordbar et al.   JOURNAL OF INTERNAL MEDICINE

Pathway engineering via quorum sensing and sRNA riboregulators—Interconnected networks and controllers

(2011) Karen K. Carter et al.   METABOLIC ENGINEERING

Parts plus pipes: Synthetic biology approaches to metabolic engineering

(2011) Patrick M. Boyle et al.   METABOLIC ENGINEERING

iPath2.0: interactive pathway explorer

(2011) Takuji Yamada et al.   NUCLEIC ACIDS RESEARCH

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

(2011) S. Greenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gut microbiome-host interactions in health and disease

(2011) James M Kinross et al.   Genome Medicine

Systems approaches to microbial communities and their functioning

(2010) Wilfred FM Röling et al.   CURRENT OPINION IN BIOTECHNOLOGY

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism

(2010) Livnat Jerby et al.   Molecular Systems Biology

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

Metabolic systems biology

(2009) Bernhard Palsson   FEBS LETTERS

Geomicrobiology: Low life

(2009) Amanda Leigh Mascarelli   NATURE

anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data

(2008) Nicola Zamboni et al.   BMC BIOINFORMATICS

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

(2008) Juan Nogales et al.   BMC Systems Biology

Recent trends in industrial microbiology

(2008) Ana Beloqui et al.   CURRENT OPINION IN MICROBIOLOGY

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

iPath: interactive exploration of biochemical pathways and networks

(2008) Ivica Letunic et al.   TRENDS IN BIOCHEMICAL SCIENCES

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology