Published in FEBS Lett on April 24, 2010
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Elucidating the interactions between the human gut microbiota and its host through metabolic modeling. Front Genet (2014) 0.88
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. BMC Syst Biol (2014) 0.87
A constraint-based model of Scheffersomyces stipitis for improved ethanol production. Biotechnol Biofuels (2012) 0.86
Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production. J Ind Microbiol Biotechnol (2013) 0.82
Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27. Microb Cell Fact (2014) 0.79
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Reconstruction and analysis of the genome-scale metabolic model of schizochytrium limacinum SR21 for docosahexaenoic acid production. BMC Genomics (2015) 0.76
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Reconstruction of a Genome-scale Metabolic Network of Komagataeibacter nataicola RZS01 for Cellulose Production. Sci Rep (2017) 0.75
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Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res (2003) 7.22
Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol (2007) 6.21
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A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol (2008) 4.55
Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci U S A (2005) 4.40
A community-driven global reconstruction of human metabolism. Nat Biotechnol (2013) 3.89
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
Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat Commun (2012) 2.84
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Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. Gut (2011) 2.67
DTP vaccination and child survival in observational studies with incomplete vaccination data. Trop Med Int Health (2007) 2.64
Global metabolite analysis of yeast: evaluation of sample preparation methods. Yeast (2005) 2.64
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics (2013) 2.53
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res (2012) 2.53
Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae. Genome Biol (2006) 2.43
Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. OMICS (2003) 2.31
Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics (2005) 2.31
Mass spectrometry in metabolome analysis. Mass Spectrom Rev (2005) 2.14
Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol (2005) 2.14
Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries. Cell Mol Life Sci (2012) 2.06
Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods. Nucleic Acids Res (2013) 2.05
Does vitamin A supplementation interact with routine vaccinations? An analysis of the Ghana Vitamin A Supplementation Trial. Am J Clin Nutr (2009) 2.04
Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Res (2011) 2.03
Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res (2005) 2.03
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. BMC Syst Biol (2008) 2.02
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput Biol (2013) 2.00
In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metab Eng (2005) 1.96
Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT. PLoS Comput Biol (2012) 1.94
Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci U S A (2009) 1.79
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. BMC Syst Biol (2008) 1.73
Assessing the human gut microbiota in metabolic diseases. Diabetes (2013) 1.64
De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology. Microb Cell Fact (2012) 1.62
OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst Biol (2010) 1.61
Integration of metabolome data with metabolic networks reveals reporter reactions. Mol Syst Biol (2006) 1.60
Integration of gene expression data into genome-scale metabolic models. Metab Eng (2004) 1.59
The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal Genet Biol (2008) 1.56
A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proc Natl Acad Sci U S A (2008) 1.56
BioMet Toolbox: genome-wide analysis of metabolism. Nucleic Acids Res (2010) 1.55
Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metab Eng (2009) 1.55
Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes. PLoS Comput Biol (2010) 1.52
Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol Syst Biol (2008) 1.47
High-throughput metabolic state analysis: the missing link in integrated functional genomics of yeasts. Biochem J (2005) 1.47
Use of genome-scale microbial models for metabolic engineering. Curr Opin Biotechnol (2004) 1.45
Increased female-male mortality ratio associated with inactivated polio and diphtheria-tetanus-pertussis vaccines: Observations from vaccination trials in Guinea-Bissau. Pediatr Infect Dis J (2007) 1.44
TBscore: Signs and symptoms from tuberculosis patients in a low-resource setting have predictive value and may be used to assess clinical course. Scand J Infect Dis (2008) 1.44
The metabolic response of heterotrophic Arabidopsis cells to oxidative stress. Plant Physiol (2006) 1.43
Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae. Yeast (2010) 1.41
Microbial translocation correlates with the severity of both HIV-1 and HIV-2 infections. J Infect Dis (2010) 1.40
Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression saccharomyces cerevisiae strains: the comparison of two quantitative methods. J Proteome Res (2008) 1.39
Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae. Fungal Genet Biol (2009) 1.35
Simultaneous analysis of amino and nonamino organic acids as methyl chloroformate derivatives using gas chromatography-mass spectrometry. Anal Biochem (2003) 1.33
Testing the hypothesis that diphtheria-tetanus-pertussis vaccine has negative non-specific and sex-differential effects on child survival in high-mortality countries. BMJ Open (2012) 1.33
Systems biology of antibiotic production by microorganisms. Nat Prod Rep (2007) 1.27
A closer look at bacteroides: phylogenetic relationship and genomic implications of a life in the human gut. Microb Ecol (2011) 1.27
Establishing a platform cell factory through engineering of yeast acetyl-CoA metabolism. Metab Eng (2012) 1.27
Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling. Mol Syst Biol (2014) 1.26
Integration of clinical data with a genome-scale metabolic model of the human adipocyte. Mol Syst Biol (2013) 1.26
Production of plant sesquiterpenes in Saccharomyces cerevisiae: effect of ERG9 repression on sesquiterpene biosynthesis. Biotechnol Bioeng (2008) 1.26
Versatile enzyme expression and characterization system for Aspergillus nidulans, with the Penicillium brevicompactum polyketide synthase gene from the mycophenolic acid gene cluster as a test case. Appl Environ Microbiol (2011) 1.25
Sex differential effects of routine immunizations and childhood survival in rural Malawi. Pediatr Infect Dis J (2006) 1.25
From genomes to in silico cells via metabolic networks. Curr Opin Biotechnol (2005) 1.24
A systems biology approach to study glucose repression in the yeast Saccharomyces cerevisiae. Biotechnol Bioeng (2007) 1.23
EasyClone: method for iterative chromosomal integration of multiple genes in Saccharomyces cerevisiae. FEMS Yeast Res (2013) 1.22
In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network. Biotechnol Bioeng (2009) 1.22
Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J (2010) 1.21
Fifteen years of large scale metabolic modeling of yeast: developments and impacts. Biotechnol Adv (2011) 1.20
Analysis of Aspergillus nidulans metabolism at the genome-scale. BMC Genomics (2008) 1.20
Prospects of yeast systems biology for human health: integrating lipid, protein and energy metabolism. FEMS Yeast Res (2010) 1.20
Correlation between the presence of neutralizing antibodies against porcine circovirus 2 (PCV2) and protection against replication of the virus and development of PCV2-associated disease. BMC Vet Res (2006) 1.20
Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinformatics (2008) 1.20
Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design. BMC Genomics (2008) 1.19
Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans. Genome Biol (2006) 1.19
Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains. Nat Commun (2010) 1.18
Characterization of chromosomal integration sites for heterologous gene expression in Saccharomyces cerevisiae. Yeast (2009) 1.18
Molecular basis for mycophenolic acid biosynthesis in Penicillium brevicompactum. Appl Environ Microbiol (2011) 1.17
Genome-scale modeling of human metabolism - a systems biology approach. Biotechnol J (2013) 1.16
Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. BMC Syst Biol (2012) 1.16
Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae. BMC Genomics (2008) 1.15
Genome-wide transcriptional response of a Saccharomyces cerevisiae strain with an altered redox metabolism. Biotechnol Bioeng (2004) 1.15
Identification of in vivo enzyme activities in the cometabolism of glucose and acetate by Saccharomyces cerevisiae by using 13C-labeled substrates. Eukaryot Cell (2003) 1.15
A functional genomics approach using metabolomics and in silico pathway analysis. Biotechnol Bioeng (2002) 1.14
Understanding the interactions between bacteria in the human gut through metabolic modeling. Sci Rep (2013) 1.14
Opportunities for yeast metabolic engineering: Lessons from synthetic biology. Biotechnol J (2011) 1.14
Improvement of galactose uptake in Saccharomyces cerevisiae through overexpression of phosphoglucomutase: example of transcript analysis as a tool in inverse metabolic engineering. Appl Environ Microbiol (2005) 1.14
Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation. Appl Environ Microbiol (2006) 1.13
Microbial isoprenoid production: an example of green chemistry through metabolic engineering. Adv Biochem Eng Biotechnol (2005) 1.13
Metabolic engineering of recombinant protein secretion by Saccharomyces cerevisiae. FEMS Yeast Res (2012) 1.12
Metabolic engineering of ammonium assimilation in xylose-fermenting Saccharomyces cerevisiae improves ethanol production. Appl Environ Microbiol (2003) 1.12
Antibiotic overproduction in Streptomyces coelicolor A3 2 mediated by phosphofructokinase deletion. J Biol Chem (2008) 1.12
Functional expression and characterization of five wax ester synthases in Saccharomyces cerevisiae and their utility for biodiesel production. Biotechnol Biofuels (2012) 1.12
Metabolic engineering of beta-lactam production. Metab Eng (2003) 1.11