Recent advances in reconstruction and applications of genome-scale metabolic models
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August 2012 |
Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
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September 2010 |
In Vitro Binding of the Pleiotropic Transcriptional Regulatory Protein, FruR, to the fru, pps, ace, pts and icd Operons of Escherichia coli and Salmonella typhimurium
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November 1993 |
Metabolic ensemble modeling for strain engineers
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October 2011 |
Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology
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December 2009 |
A Whole-Cell Computational Model Predicts Phenotype from Genotype
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July 2012 |
Extensive In Vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses
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November 2010 |
MediaDB: A Database of Microbial Growth Conditions in Defined Media
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August 2014 |
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach
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June 2010 |
Constraint-based models predict metabolic and associated cellular functions
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January 2014 |
A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell
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December 2007 |
BioMog: A Computational Framework for the De Novo Generation or Modification of Essential Biomass Components
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December 2013 |
Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models
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October 2014 |
‘Unknown’ proteins and ‘orphan’ enzymes: the missing half of the engineering parts list – and how to find it
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December 2009 |
Shared control of gene expression in bacteria by transcription factors and global physiology of the cell
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January 2013 |
OptStrain: A computational framework for redesign of microbial production systems
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November 2004 |
Understanding Metabolic Regulation and Its Influence on Cell Physiology
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February 2013 |
Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction
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January 2013 |
Shrinking the Metabolic Solution Space Using Experimental Datasets
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August 2012 |
Coordination of microbial metabolism
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March 2014 |
Bacterial regulatory networks are extremely flexible in evolution
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July 2006 |
Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection
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January 2014 |
Evolutionary Dynamics of Prokaryotic Transcriptional Regulatory Networks
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April 2006 |
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
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December 2009 |
Ensemble Modeling of Metabolic Networks
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December 2008 |
In silico method for modelling metabolism and gene product expression at genome scale
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January 2012 |
A methodology for the structural and functional analysis of signaling and regulatory networks
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February 2006 |
Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk
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March 2004 |
AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation
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January 2013 |
A system‐level model for the microbial regulatory genome
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July 2014 |
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
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July 2008 |
Acetylation of Metabolic Enzymes Coordinates Carbon Source Utilization and Metabolic Flux
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February 2010 |
Structural kinetic modeling of metabolic networks
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July 2006 |
In vitro Phosphorylation of Key Metabolic Enzymes from <i>Bacillus subtilis:</i> PrkC Phosphorylates Enzymes from Different Branches of Basic Metabolism
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January 2010 |
Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use
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October 1994 |
Analysis of optimality in natural and perturbed metabolic networks
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November 2002 |
A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information
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January 2007 |
Modeling formalisms in Systems Biology
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January 2011 |
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
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September 2010 |
The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum
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March 2013 |
Indirect and suboptimal control of gene expression is widespread in bacteria
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January 2013 |
The MiST2 database: a comprehensive genomics resource on microbial signal transduction
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November 2009 |
A genome‐scale computational study of the interplay between transcriptional regulation and metabolism
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January 2007 |
E-CELL: software environment for whole-cell simulation
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January 1999 |
Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles
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January 2007 |
The Phosphoproteome of the Minimal Bacterium Mycoplasma pneumoniae : ANALYSIS OF THE COMPLETE KNOWN SER/THR KINOME SUGGESTS THE EXISTENCE OF NOVEL KINASES
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January 2010 |
Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation
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April 2007 |
Regulation and control of metabolic fluxes in microbes
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August 2011 |
Control of Proteobacterial Central Carbon Metabolism by the HexR Transcriptional Regulator: A CASE STUDY IN
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August 2011 |
Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization
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March 2009 |
Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: Identifying ChIP-quality p300 monoclonal antibodies
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June 2014 |
Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks
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December 2013 |
The allosteric regulation of pyruvate kinase by fructose-1,6-bisphosphate
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February 1998 |
Integrative Features of the Yeast Phosphoproteome and Protein–Protein Interaction Map
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January 2011 |
The challenges of in silico biology
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November 2000 |
Wisdom of crowds for robust gene network inference
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July 2012 |
Nucleotide sequence of the argR gene of Escherichia coli K-12 and isolation of its product, the arginine repressor.
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October 1987 |
Phenotypic Landscape of a Bacterial Cell
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January 2011 |
OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains
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January 2010 |
Constraints-based models: Regulation of Gene Expression Reduces the Steady-state Solution Space
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April 2003 |
Applications of genome‐scale metabolic reconstructions
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January 2009 |
Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models
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February 2011 |
Revealing strengths and weaknesses of methods for gene network inference
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March 2010 |
Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data
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June 2007 |
Advantages and limitations of current network inference methods
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August 2010 |
The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli
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June 1995 |
Genome-Scale In Silico Models of E. coli Have Multiple Equivalent Phenotypic States: Assessment of Correlated Reaction Subsets That Comprise Network States
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September 2004 |
Dialogue on Reverse-Engineering Assessment and Methods: The DREAM of High-Throughput Pathway Inference
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October 2007 |
High-throughput generation, optimization and analysis of genome-scale metabolic models
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August 2010 |
Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism
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April 2014 |
A Global Metabolite Profiling Approach to Identify Protein−Metabolite Interactions
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October 2008 |
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
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October 2003 |
Phenotype MicroArrays for High-Throughput Phenotypic Testing and Assay of Gene Function
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July 2001 |
Towards genome-scale signalling-network reconstructions
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February 2010 |
Regulatory on/off minimization of metabolic flux changes after genetic perturbations
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May 2005 |
A protocol for generating a high-quality genome-scale metabolic reconstruction
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January 2010 |
Integrating high-throughput and computational data elucidates bacterial networks
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May 2004 |
An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models
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October 2010 |
Identification of lysine succinylation as a new post-translational modification
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December 2010 |
Kinetic Modeling of Metabolic Networks
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January 2012 |
An integrative, multi‐scale, genome‐wide model reveals the phenotypic landscape of E scherichia coli
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July 2014 |
Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli
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May 2005 |
Carbon catabolite repression in bacteria: many ways to make the most out of nutrients
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August 2008 |
Global insights into energetic and metabolic networks in Rhodobacter sphaeroides
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January 2013 |
Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms
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September 2009 |
Regulators of oxidative stress response genes in Escherichia coli and their functional conservation in bacteria
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September 2012 |
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
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November 2010 |
The control of pyruvate kinase of Escherichia coli. Binding of substrate and allosteric effectors to the enzyme activated by fructose 1,6-bisphosphate
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January 1976 |
Oxidative stress responses in Escherichia coli and Salmonella typhimurium.
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January 1991 |
The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks
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January 2011 |
Crotonylation of key metabolic enzymes regulates carbon catabolite repression in Streptomyces roseosporus
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April 2020 |
Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection
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January 2014 |
The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks
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June 2011 |
Acetylation of Metabolic Enzymes Coordinates Carbon Source Utilization and Metabolic Flux
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January 2010 |
Revealing strengths and weaknesses of methods for gene network inference
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January 2010 |
Accomplishments in Genome-Scale In Silico Modeling for Industrial and Medical Biotechnology
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January 2009 |
Structural Kinetic Modeling of Metabolic Networks
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January 2006 |
Whole-cell simulation: a grand challenge of the 21st century
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June 2001 |
Computational methods for biomolecular docking
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June 1996 |
Systems biology from micro-organisms to human metabolic diseases: the role of detailed kinetic models
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September 2010 |
Genome Scanning for Conditionally Essential Genes in Salmonella enterica Serotype Typhimurium
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February 2012 |
CceR and AkgR Regulate Central Carbon and Energy Metabolism in Alphaproteobacteria
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February 2015 |
Oxidative stress responses in Escherichia coli and Salmonella typhimurium
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December 1991 |