Published in Metab Eng on March 01, 2005
Recent developments in parameter estimation and structure identification of biochemical and genomic systems. Math Biosci (2009) 2.58
An integrated network approach identifies the isobutanol response network of Escherichia coli. Mol Syst Biol (2009) 1.66
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Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source. Proc Natl Acad Sci U S A (2005) 1.54
Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli. Proc Natl Acad Sci U S A (2007) 1.49
Factor analysis for gene regulatory networks and transcription factor activity profiles. BMC Bioinformatics (2007) 1.44
Furfural inhibits growth by limiting sulfur assimilation in ethanologenic Escherichia coli strain LY180. Appl Environ Microbiol (2009) 1.35
Inferring yeast cell cycle regulators and interactions using transcription factor activities. BMC Genomics (2005) 1.26
Synthetic biology: tools to design, build, and optimize cellular processes. J Biomed Biotechnol (2010) 1.26
Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast. PLoS Comput Biol (2009) 1.08
A dynamic network of transcription in LPS-treated human subjects. BMC Syst Biol (2009) 1.07
Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities. BMC Bioinformatics (2011) 1.00
Bioinformatics analysis of the early inflammatory response in a rat thermal injury model. BMC Bioinformatics (2007) 0.96
Trimming of mammalian transcriptional networks using network component analysis. BMC Bioinformatics (2010) 0.90
An Overview of NCA-Based Algorithms for Transcriptional Regulatory Network Inference. Microarrays (Basel) (2015) 0.85
Transcription factor network reconstruction using the living cell array. J Theor Biol (2008) 0.83
Reconstructing repressor protein levels from expression of gene targets in Escherichia coli. Proc Natl Acad Sci U S A (2006) 0.82
Iterative sub-network component analysis enables reconstruction of large scale genetic networks. BMC Bioinformatics (2015) 0.81
Inferring a transcriptional regulatory network of the cytokinesis-related genes by network component analysis. BMC Syst Biol (2009) 0.81
Behavior training reverses asymmetry in hippocampal transcriptome of the cav3.2 knockout mice. PLoS One (2015) 0.80
An integrated machine learning approach for predicting DosR-regulated genes in Mycobacterium tuberculosis. BMC Syst Biol (2010) 0.79
Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic. Bioinformatics (2012) 0.79
Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli. BMC Bioinformatics (2009) 0.77
Regulatory component analysis: a semi-blind extraction approach to infer gene regulatory networks with imperfect biological knowledge. Signal Processing (2011) 0.77
Dynamics of regulatory networks in gastrin-treated adenocarcinoma cells. PLoS One (2014) 0.76
Accuracy and application of the motif expression decomposition method in dissecting transcriptional regulation. Nucleic Acids Res (2008) 0.76
Reconstruction of temporal activity of microRNAs from gene expression data in breast cancer cell line. BMC Genomics (2015) 0.76
Using temporal correlation in factor analysis for reconstructing transcription factor activities. EURASIP J Bioinform Syst Biol (2008) 0.76
Past Roadblocks and New Opportunities in Transcription Factor Network Mapping. Trends Genet (2016) 0.76
Topology of transcriptional regulatory networks: testing and improving. PLoS One (2012) 0.75
Dynamic regulatory network reconstruction for Alzheimer's disease based on matrix decomposition techniques. Comput Math Methods Med (2014) 0.75
An extended data mining method for identifying differentially expressed assay-specific signatures in functional genomic studies. BioData Min (2010) 0.75
Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature (2008) 6.68
Metabolite-enabled eradication of bacterial persisters by aminoglycosides. Nature (2011) 4.06
Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde. Nat Biotechnol (2009) 3.63
A synthetic gene-metabolic oscillator. Nature (2005) 3.26
Metabolic engineering of Escherichia coli for 1-butanol production. Metab Eng (2007) 3.17
Global expression profiling of acetate-grown Escherichia coli. J Biol Chem (2002) 2.61
Co-expression pattern from DNA microarray experiments as a tool for operon prediction. Nucleic Acids Res (2002) 2.50
Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli. Appl Environ Microbiol (2011) 2.19
Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis. Proc Natl Acad Sci U S A (2003) 2.03
Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes. Appl Microbiol Biotechnol (2009) 1.94
Conversion of proteins into biofuels by engineering nitrogen flux. Nat Biotechnol (2011) 1.91
Expanding metabolism for biosynthesis of nonnatural alcohols. Proc Natl Acad Sci U S A (2008) 1.86
Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Mol Syst Biol (2010) 1.75
Metabolic engineering for advanced biofuels production from Escherichia coli. Curr Opin Biotechnol (2008) 1.69
ATP drives direct photosynthetic production of 1-butanol in cyanobacteria. Proc Natl Acad Sci U S A (2012) 1.68
An integrated network approach identifies the isobutanol response network of Escherichia coli. Mol Syst Biol (2009) 1.66
Engineering Corynebacterium glutamicum for isobutanol production. Appl Microbiol Biotechnol (2010) 1.65
Metabolic control of persister formation in Escherichia coli. Mol Cell (2013) 1.62
Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide. Metab Eng (2011) 1.62
Resistance to diet-induced obesity in mice with synthetic glyoxylate shunt. Cell Metab (2009) 1.56
Single-gene disorders: what role could moonlighting enzymes play? Am J Hum Genet (2005) 1.52
Dormancy is not necessary or sufficient for bacterial persistence. Antimicrob Agents Chemother (2013) 1.51
Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli. Proc Natl Acad Sci U S A (2007) 1.49
Heterogeneous bacterial persisters and engineering approaches to eliminate them. Curr Opin Microbiol (2011) 1.47
Directed evolution of Methanococcus jannaschii citramalate synthase for biosynthesis of 1-propanol and 1-butanol by Escherichia coli. Appl Environ Microbiol (2008) 1.45
Ensemble modeling of metabolic networks. Biophys J (2008) 1.44
Integrated electromicrobial conversion of CO2 to higher alcohols. Science (2012) 1.42
Microbial production of advanced transportation fuels in non-natural hosts. Curr Opin Biotechnol (2009) 1.41
Design of artificial cell-cell communication using gene and metabolic networks. Proc Natl Acad Sci U S A (2004) 1.40
Nitric oxide is consumed, rather than conserved, by reaction with oxyhemoglobin under physiological conditions. Proc Natl Acad Sci U S A (2002) 1.30
Production of 2-methyl-1-butanol in engineered Escherichia coli. Appl Microbiol Biotechnol (2008) 1.29
A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis. J Biol Chem (2005) 1.26
Inferring yeast cell cycle regulators and interactions using transcription factor activities. BMC Genomics (2005) 1.26
Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature (2013) 1.24
Next generation biofuel engineering in prokaryotes. Curr Opin Chem Biol (2013) 1.23
Metabolic engineering of Clostridium cellulolyticum for production of isobutanol from cellulose. Appl Environ Microbiol (2011) 1.22
Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proc Natl Acad Sci U S A (2013) 1.21
High-flux isobutanol production using engineered Escherichia coli: a bioreactor study with in situ product removal. Appl Microbiol Biotechnol (2011) 1.21
Transcriptome network component analysis with limited microarray data. Bioinformatics (2006) 1.21
Engineering of an Escherichia coli strain for the production of 3-methyl-1-butanol. Appl Environ Microbiol (2008) 1.20
Zebrafish larvae exhibit rheotaxis and can escape a continuous suction source using their lateral line. PLoS One (2012) 1.20
Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J (2007) 1.18
Engineering metabolic systems for production of advanced fuels. J Ind Microbiol Biotechnol (2009) 1.17
Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations. Biotechnol Biofuels (2012) 1.16
Differential association of hemoglobin with proinflammatory high density lipoproteins in atherogenic/hyperlipidemic mice. A novel biomarker of atherosclerosis. J Biol Chem (2007) 1.16
Enantioselective synthesis of pure (R,R)-2,3-butanediol in Escherichia coli with stereospecific secondary alcohol dehydrogenases. Org Biomol Chem (2009) 1.14
Expanding metabolism for total biosynthesis of the nonnatural amino acid L-homoalanine. Proc Natl Acad Sci U S A (2010) 1.13
Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator. Mol Syst Biol (2007) 1.11
Genomic library screens for genes involved in n-butanol tolerance in Escherichia coli. PLoS One (2011) 1.10
Acetolactate synthase from Bacillus subtilis serves as a 2-ketoisovalerate decarboxylase for isobutanol biosynthesis in Escherichia coli. Appl Environ Microbiol (2009) 1.10
Improvement of isopropanol production by metabolically engineered Escherichia coli using gas stripping. J Biosci Bioeng (2010) 1.09
Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models. Biophys Chem (2007) 1.09
Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast. PLoS Comput Biol (2009) 1.08
3-Methyl-1-butanol production in Escherichia coli: random mutagenesis and two-phase fermentation. Appl Microbiol Biotechnol (2010) 1.08
Microbial synthesis of n-butanol, isobutanol, and other higher alcohols from diverse resources. Bioresour Technol (2012) 1.08
Nitric oxide reaction with red blood cells and hemoglobin under heterogeneous conditions. Proc Natl Acad Sci U S A (2002) 1.06
Erythrocyte nitric oxide transport reduced by a submembrane cytoskeletal barrier. Biochim Biophys Acta (2005) 1.04
Heat shock response of Archaeoglobus fulgidus. J Bacteriol (2005) 1.03
Rainbow trout consume less oxygen in turbulence: the energetics of swimming behaviors at different speeds. J Exp Biol (2011) 1.03
Glycerol kinase deficiency alters expression of genes involved in lipid metabolism, carbohydrate metabolism, and insulin signaling. Eur J Hum Genet (2007) 1.03
A selection platform for carbon chain elongation using the CoA-dependent pathway to produce linear higher alcohols. Metab Eng (2012) 1.01
Targeted disruption of glycerol kinase gene in mice: expression analysis in liver shows alterations in network partners related to glycerol kinase activity. Hum Mol Genet (2005) 1.01
Establishment of a method to rapidly assay bacterial persister metabolism. Antimicrob Agents Chemother (2013) 1.00
Engineering synthetic recursive pathways to generate non-natural small molecules. Nat Chem Biol (2012) 1.00
Engineering a synthetic pathway in cyanobacteria for isopropanol production directly from carbon dioxide and light. Metab Eng (2013) 0.99
Evolutionary engineering of Saccharomyces cerevisiae for enhanced tolerance to hydrolysates of lignocellulosic biomass. Biotechnol Bioeng (2013) 0.98
Rhodopseudomonas palustris CGA009 has two functional ppsR genes, each of which encodes a repressor of photosynthesis gene expression. Biochemistry (2006) 0.98
Extending carbon chain length of 1-butanol pathway for 1-hexanol synthesis from glucose by engineered Escherichia coli. J Am Chem Soc (2011) 0.96
Energy biotechnology. Curr Opin Biotechnol (2012) 0.96
A synthetic recursive "+1" pathway for carbon chain elongation. ACS Chem Biol (2012) 0.95
Analysis of nitric oxide consumption by erythrocytes in blood vessels using a distributed multicellular model. Ann Biomed Eng (2003) 0.95
A generalized framework for network component analysis. IEEE/ACM Trans Comput Biol Bioinform (2006) 0.94
Visualizing evolution in real time to determine the molecular mechanisms of n-butanol tolerance in Escherichia coli. Metab Eng (2012) 0.94
Global metabolic effects of glycerol kinase overexpression in rat hepatoma cells. Mol Genet Metab (2007) 0.94
Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites. Bioinformatics (2004) 0.93
An evolutionary strategy for isobutanol production strain development in Escherichia coli. Metab Eng (2011) 0.93
Isobutanol production as an alternative metabolic sink to rescue the growth deficiency of the glycogen mutant of Synechococcus elongatus PCC 7942. Photosynth Res (2014) 0.92
Biofuels: biomolecular engineering fundamentals and advances. Annu Rev Chem Biomol Eng (2010) 0.91
Engineering a cyanobacterium as the catalyst for the photosynthetic conversion of CO2 to 1,2-propanediol. Microb Cell Fact (2013) 0.91
Ensemble modeling for strain development of L-lysine-producing Escherichia coli. Metab Eng (2009) 0.91
A software package for cDNA microarray data normalization and assessing confidence intervals. OMICS (2003) 0.90
Trimming of mammalian transcriptional networks using network component analysis. BMC Bioinformatics (2010) 0.90
Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux. Metab Eng (2010) 0.90
Evolutionary dynamics of Candida albicans during in vitro evolution. Eukaryot Cell (2011) 0.90
Transcriptional analysis of Lactobacillus brevis to N-butanol and ferulic acid stress responses. PLoS One (2011) 0.89
Regulation of nitric oxide consumption by hypoxic red blood cells. Proc Natl Acad Sci U S A (2003) 0.89
Metabolic ensemble modeling for strain engineers. Biotechnol J (2011) 0.89
Determination of the Escherichia coli S-nitrosoglutathione response network using integrated biochemical and systems analysis. J Biol Chem (2007) 0.88
Heterogeneity and dynamics of lateral line afferent innervation during development in zebrafish (Danio rerio). J Comp Neurol (2012) 0.86
Synergy as design principle for metabolic engineering of 1-propanol production in Escherichia coli. Metab Eng (2013) 0.86
Transcriptomic and network component analysis of glycerol kinase in skeletal muscle using a mouse model of glycerol kinase deficiency. Mol Genet Metab (2009) 0.86
Stochastic modeling of the phase-variable pap operon regulation in uropathogenic Escherichia coli. Biotechnol Bioeng (2004) 0.85
A kinetic platform to determine the fate of nitric oxide in Escherichia coli. PLoS Comput Biol (2013) 0.85
An information theoretic exploratory method for learning patterns of conditional gene coexpression from microarray data. IEEE/ACM Trans Comput Biol Bioinform (2008) 0.85
Reconstruction of the archaeal isoprenoid ether lipid biosynthesis pathway in Escherichia coli through digeranylgeranylglyceryl phosphate. Metab Eng (2009) 0.85