Published in BMC Syst Biol on April 30, 2009
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Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc Natl Acad Sci U S A (2003) 3.15
Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem (2007) 3.03
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The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nat Biotechnol (2011) 2.87
Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst Biol (2009) 2.80
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Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis. Proc Natl Acad Sci U S A (2012) 1.75
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In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun (2012) 1.58
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The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. Biophys J (2004) 1.55
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst Biol (2011) 1.50
Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput Biol (2006) 1.48
Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol Syst Biol (2012) 1.41
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. BMC Syst Biol (2011) 1.37
Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nat Biotechnol (2013) 1.36
The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools. Biophys J (2003) 1.33
Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PLoS One (2012) 1.29
Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk. J Theor Biol (2004) 1.27
Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices. J Theor Biol (2003) 1.26
An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228. J Bacteriol (2011) 1.24
Network-based analysis of metabolic regulation in the human red blood cell. J Theor Biol (2003) 1.23
Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. PLoS Comput Biol (2006) 1.21
Optoinjection for efficient targeted delivery of a broad range of compounds and macromolecules into diverse cell types. J Biomed Opt (2006) 1.17
Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophys J (2003) 1.17
A road map for the development of community systems (CoSy) biology. Nat Rev Microbiol (2012) 1.16
Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content. J Bacteriol (2009) 1.14
Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology? Biotechnol Bioeng (2003) 1.14
Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J Bacteriol (2003) 1.13
PCR-based tandem epitope tagging system for Escherichia coli genome engineering. Biotechniques (2006) 1.12
Description and analysis of metabolic connectivity and dynamics in the human red blood cell. Biophys J (2002) 1.12
Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. Science (2013) 1.11
Proteomic analysis of Chinese hamster ovary cells. J Proteome Res (2012) 1.11
In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium. OMICS (2004) 1.10
Development of network-based pathway definitions: the need to analyze real metabolic networks. Trends Biotechnol (2003) 1.07
iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. BMC Syst Biol (2011) 1.05
A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution. Environ Microbiol (2011) 1.05
Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach. Prog Drug Res (2007) 1.04
Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. Mol Biosyst (2013) 1.02
Ion mobility-derived collision cross section as an additional measure for lipid fingerprinting and identification. Anal Chem (2014) 1.02
Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome. Mol Genet Metab (2007) 1.01
Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices. Biochemistry (2007) 1.01
Ion mobility derived collision cross sections to support metabolomics applications. Anal Chem (2014) 1.00
Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition. BMC Bioinformatics (2006) 0.92
Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features. BMC Genomics (2012) 0.92
The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models. BMC Syst Biol (2013) 0.92
Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction. PLoS One (2012) 0.92
Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution. Appl Microbiol Biotechnol (2012) 0.92
Three factors underlying incorrect in silico predictions of essential metabolic genes. BMC Syst Biol (2008) 0.91
Building the power house: recent advances in mitochondrial studies through proteomics and systems biology. Am J Physiol Cell Physiol (2006) 0.91
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. BMC Syst Biol (2014) 0.91
Genome-scale network analysis of imprinted human metabolic genes. Epigenetics (2009) 0.90
Microbial regulatory and metabolic networks. Curr Opin Biotechnol (2007) 0.88
Technologies and approaches to elucidate and model the virulence program of salmonella. Front Microbiol (2011) 0.88
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. BMC Syst Biol (2011) 0.86
Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst Biol (2013) 0.86
Multidimensional analytical approach based on UHPLC-UV-ion mobility-MS for the screening of natural pigments. Anal Chem (2015) 0.85
A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent. Biotechnol Bioeng (2013) 0.83
Multispecific drug transporter Slc22a8 (Oat3) regulates multiple metabolic and signaling pathways. Drug Metab Dispos (2013) 0.83
Characterization and efficacy of PKH26 as a probe to study the replication history of the human hematopoietic KG1a progenitor cell line. In Vitro Cell Dev Biol Anim (2002) 0.82
Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli. Biotechnol Lett (2003) 0.81
Isotopomer analysis of myocardial substrate metabolism: a systems biology approach. Biotechnol Bioeng (2006) 0.80
Capsule deletion via a λ-Red knockout system perturbs biofilm formation and fimbriae expression in Klebsiella pneumoniae MGH 78578. BMC Res Notes (2014) 0.80
Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant. FEMS Microbiol Lett (2013) 0.79
Metabolomic analysis of platelets during storage: a comparison between apheresis- and buffy coat-derived platelet concentrates. Transfusion (2014) 0.79
Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks. Nat Commun (2013) 0.79
In silico analysis of SNPs and other high-throughput data. Methods Mol Biol (2007) 0.78
Comprehensive metabolomic study of platelets reveals the expression of discrete metabolic phenotypes during storage. Transfusion (2014) 0.78
H. influenzae Consortium: integrative study of H. influenzae-human interactions. OMICS (2002) 0.78
Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling. Curr Top Microbiol Immunol (2013) 0.76
Microbiology. Topping off a multiscale balancing act. Science (2010) 0.75
Sensitive and accurate identification of protein-DNA binding events in ChIP-chip assays using higher order derivative analysis. Nucleic Acids Res (2010) 0.75