Published in PLoS One on December 05, 2013
Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets. PLoS Comput Biol (2016) 1.43
A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database. BMC Syst Biol (2014) 0.99
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One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A (2000) 96.90
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Programming cells by multiplex genome engineering and accelerated evolution. Nature (2009) 6.64
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Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol (2006) 2.93
Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics (2007) 2.74
GrowMatch: an automated method for reconciling in silico/in vivo growth predictions. PLoS Comput Biol (2009) 2.41
Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides. Nat Biotechnol (2010) 2.38
E. coli genome manipulation by P1 transduction. Curr Protoc Mol Biol (2007) 2.25
Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol Syst Biol (2009) 2.11
Systematizing the generation of missing metabolic knowledge. Biotechnol Bioeng (2010) 1.85
Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets. J Bacteriol (2009) 1.51
Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery. Mol Syst Biol (2011) 1.50
Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation. PLoS Comput Biol (2010) 1.48
Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PLoS Genet (2011) 1.33
A universal TagModule collection for parallel genetic analysis of microorganisms. Nucleic Acids Res (2010) 1.11
Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks. Metab Eng (2009) 1.07
An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models. PLoS Comput Biol (2010) 1.05
Structure of the enzyme-acyl carrier protein (ACP) substrate gatekeeper complex required for biotin synthesis. Proc Natl Acad Sci U S A (2012) 1.03
MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks. Genome Biol (2012) 0.97
Computational tools for metabolic engineering. Metab Eng (2012) 0.94
YjjG, a dUMP phosphatase, is critical for thymine utilization by Escherichia coli K-12. J Bacteriol (2006) 0.89
A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm. PLoS One (2012) 0.85
FOCAL: an experimental design tool for systematizing metabolic discoveries and model development. Genome Biol (2012) 0.82
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol (2007) 11.03
Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol (2004) 9.61
Integrating high-throughput and computational data elucidates bacterial networks. Nature (2004) 7.72
Mast cells are essential intermediaries in regulatory T-cell tolerance. Nature (2006) 5.49
Towards environmental systems biology of Shewanella. Nat Rev Microbiol (2008) 4.37
Severe human lower respiratory tract illness caused by respiratory syncytial virus and influenza virus is characterized by the absence of pulmonary cytotoxic lymphocyte responses. J Infect Dis (2007) 3.62
Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. Trends Biochem Sci (2004) 3.31
Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol (2006) 2.93
Rapid antigen testing compares favorably with transcription-mediated amplification assay for the detection of Trichomonas vaginalis in young women. Clin Infect Dis (2007) 2.85
Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis. Proc Natl Acad Sci U S A (2010) 1.82
The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states. Proc Natl Acad Sci U S A (2005) 1.63
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst Biol (2011) 1.50
Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation. PLoS Comput Biol (2010) 1.48
OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. BMC Syst Biol (2010) 1.47
MEDI-563, a humanized anti-IL-5 receptor alpha mAb with enhanced antibody-dependent cell-mediated cytotoxicity function. J Allergy Clin Immunol (2010) 1.41
The evolution of metabolic networks of E. coli. BMC Syst Biol (2011) 1.32
Respiratory syncytial virus and influenza virus infections: observations from tissues of fatal infant cases. Pediatr Infect Dis J (2008) 1.31
Network-based analysis of metabolic regulation in the human red blood cell. J Theor Biol (2003) 1.23
Mycoplasma genitalium detected by transcription-mediated amplification is associated with Chlamydia trachomatis in adolescent women. Sex Transm Dis (2008) 1.17
Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophys J (2003) 1.17
Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli. PLoS Comput Biol (2007) 1.12
Isolation and characterization of monoclonal antibodies which neutralize human metapneumovirus in vitro and in vivo. J Virol (2006) 1.09
Safety and immunogenicity of a recombinant parvovirus B19 vaccine formulated with MF59C.1. J Infect Dis (2003) 1.05
An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models. PLoS Comput Biol (2010) 1.05
Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142. PLoS Comput Biol (2012) 1.05
Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling. BMC Syst Biol (2012) 1.02
Complex physiology and compound stress responses during fermentation of alkali-pretreated corn stover hydrolysate by an Escherichia coli ethanologen. Appl Environ Microbiol (2012) 1.00
Atlantoaxial rotary subluxation after minor trauma. Pediatr Emerg Care (2008) 0.99
Large-scale bi-level strain design approaches and mixed-integer programming solution techniques. PLoS One (2011) 0.99
Pyruvate and lactate metabolism by Shewanella oneidensis MR-1 under fermentation, oxygen limitation, and fumarate respiration conditions. Appl Environ Microbiol (2011) 0.98
Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli. Metab Eng (2010) 0.98
RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations. Genome Biol (2012) 0.97
iRsp1095: a genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network. BMC Syst Biol (2011) 0.95
Identification of functional differences in metabolic networks using comparative genomics and constraint-based models. PLoS One (2012) 0.94
Computational evaluation of Synechococcus sp. PCC 7002 metabolism for chemical production. Biotechnol J (2013) 0.90
Improving notification of sexually transmitted infections: a quality improvement project and planned experiment. Pediatrics (2012) 0.89
Randomized trial of Nordic walking in patients with moderate to severe heart failure. Can J Cardiol (2013) 0.85
Software platforms to facilitate reconstructing genome-scale metabolic networks. Environ Microbiol (2013) 0.85
Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models. Biophys J (2013) 0.85
Intrapersonal, social and physical environmental determinants of moderate-to-vigorous physical activity in working-age women: a systematic review protocol. Syst Rev (2014) 0.84
Inferring ancient metabolism using ancestral core metabolic models of enterobacteria. BMC Syst Biol (2013) 0.83
Individual, social and physical environmental correlates of sedentary behaviours in adults: a systematic review protocol. Syst Rev (2014) 0.83
Cytosolic, autocrine alpha-1 proteinase inhibitor (A1PI) inhibits caspase-1 and blocks IL-1β dependent cytokine release in monocytes. PLoS One (2012) 0.83
Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models. BMC Bioinformatics (2013) 0.82
Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering. Biotechnol J (2013) 0.82
FOCAL: an experimental design tool for systematizing metabolic discoveries and model development. Genome Biol (2012) 0.82
Point-of-care testing improves accuracy of STI care in an emergency department. Sex Transm Infect (2013) 0.81
Epitope mapping by random peptide phage display reveals essential residues for vaccinia extracellular enveloped virion spread. Virol J (2012) 0.81
Computational approaches in metabolic engineering. J Biomed Biotechnol (2011) 0.80
Effect of high dietary restraint on energy availability and menstrual status. Med Sci Sports Exerc (2013) 0.76
Mucosal antibody responses are directed by viral burden in children with acute influenza infection. Influenza Other Respir Viruses (2012) 0.75
Electronic cigarettes. CMAJ (2013) 0.75
Correction: Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. PLoS Genet (2016) 0.75
Improving flux predictions by integrating data from multiple strains. Bioinformatics (2017) 0.75
Do Adolescents With Higher Knowledge of HIV Have Lower Sexual Risk Behaviors? Pediatr Emerg Care (2016) 0.75