Published in PLoS One on January 30, 2013
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Continuous-time Markov chain-based flux analysis in metabolism. J Comput Biol (2014) 0.75
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
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol (2003) 10.46
Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol (2005) 9.94
Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol (2004) 9.61
Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature (2004) 7.18
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng (2003) 6.81
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc (2007) 6.24
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res (2004) 6.21
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol (2008) 5.26
Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol (2003) 4.01
Energy balance for analysis of complex metabolic networks. Biophys J (2002) 3.46
Thermodynamics-based metabolic flux analysis. Biophys J (2006) 3.35
Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem (2007) 3.03
Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J (2008) 2.89
Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. J Bacteriol (2005) 2.82
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol (2006) 2.80
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Genome-scale thermodynamic analysis of Escherichia coli metabolism. Biophys J (2005) 2.70
Thermodynamic constraints for biochemical networks. J Theor Biol (2004) 2.19
Exploring the diversity of complex metabolic networks. Bioinformatics (2004) 1.93
Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry. Metab Eng (2005) 1.41
Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens. PLoS Comput Biol (2008) 1.30
Is there biological research beyond Systems Biology? A comparative analysis of terms. Mol Syst Biol (2005) 0.81
Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis. Biotechnol Bioeng (2012) 0.78
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol (2007) 6.21
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res (2007) 3.69
Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proc Natl Acad Sci U S A (2014) 2.42
Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature. Bioinformatics (2008) 1.58
The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal Genet Biol (2008) 1.56
Non-sterilized fermentative production of polymer-grade L-lactic acid by a newly isolated thermophilic strain Bacillus sp. 2-6. PLoS One (2009) 1.46
Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses. Biosystems (2005) 1.44
Bcl-2 enhances the formation of newborn striatal long-projection neurons in adult rat brain after a transient ischemic stroke. Neurosci Bull (2012) 1.42
Safety and immunogenicity of adenovirus-vectored near-consensus HIV type 1 clade B gag vaccines in healthy adults. AIDS Res Hum Retroviruses (2009) 1.36
Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales. Virus Res (2004) 1.26
Comparative cell-mediated immunogenicity of DNA/DNA, DNA/adenovirus type 5 (Ad5), or Ad5/Ad5 HIV-1 clade B gag vaccine prime-boost regimens. J Infect Dis (2010) 1.26
A double-blind, placebo-controlled study of the safety and immunogenicity of live, oral type 4 and type 7 adenovirus vaccines in adults. Vaccine (2008) 1.22
Novel (2R,3R)-2,3-butanediol dehydrogenase from potential industrial strain Paenibacillus polymyxa ATCC 12321. Appl Environ Microbiol (2011) 1.21
The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens. Biosystems (2004) 1.19
Biodiversity and evolution of primary carbon metabolism in Aspergillus nidulans and other Aspergillus spp. Fungal Genet Biol (2009) 1.18
Single-crystalline and monodisperse LaF3 triangular nanoplates from a single-source precursor. J Am Chem Soc (2005) 1.18
Safety and immunogenicity of the Merck adenovirus serotype 5 (MRKAd5) and MRKAd6 human immunodeficiency virus type 1 trigene vaccines alone and in combination in healthy adults. Clin Vaccine Immunol (2009) 1.13
Robust method for infrared small-target detection based on Boolean map visual theory. Appl Opt (2014) 1.13
MicroRNA genes derived from repetitive elements and expanded by segmental duplication events in mammalian genomes. PLoS One (2011) 1.10
The intra- and extracellular proteome of Aspergillus niger growing on defined medium with xylose or maltose as carbon substrate. Microb Cell Fact (2010) 1.10
TN curve: a novel 3D graphical representation of DNA sequence based on trinucleotides and its applications. J Theor Biol (2009) 1.08
Meta-analysis of several gene lists for distinct types of cancer: a simple way to reveal common prognostic markers. BMC Bioinformatics (2007) 1.04
Changes of brain morphometry in first-episode, drug-naïve, non-late-life adult patients with major depression: an optimized voxel-based morphometry study. Biol Psychiatry (2010) 1.03
Efficient and robust method for comparing the immunogenicity of candidate vaccines in randomized clinical trials. Vaccine (2008) 1.03
Copper catalyzing growth of single-walled carbon nanotubes on substrates. Nano Lett (2006) 1.02
Receiver-operating characteristic analyses of body mass index, waist circumference and waist-to-hip ratio for obesity: Screening in young adults in central south of China. Clin Nutr (2006) 1.02
Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid feature. Proteins (2011) 1.01
Genome sequence of the thermophilic strain Bacillus coagulans 2-6, an efficient producer of high-optical-purity L-lactic acid. J Bacteriol (2011) 1.00
Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey. BMC Genomics (2009) 1.00
Comparison of T cell immune responses induced by vectored HIV vaccines in non-human primates and humans. Vaccine (2010) 0.99
Origin and evolution of a placental-specific microRNA family in the human genome. BMC Evol Biol (2010) 0.99
A modified technology could significantly improve the visualization rate of the internal mammary sentinel lymph nodes in breast cancer patients. Breast Cancer Res Treat (2012) 0.98
Combined use of proteomic analysis and enzyme activity assays for metabolic pathway analysis of glycerol fermentation by Klebsiella pneumoniae. Biotechnol Bioeng (2003) 0.97
Cardioprotective effect of salvianolic acid B against arsenic trioxide-induced injury in cardiac H9c2 cells via the PI3K/Akt signal pathway. Toxicol Lett (2012) 0.94
Proteomic analysis of circulating monocytes in Chinese premenopausal females with extremely discordant bone mineral density. Proteomics (2008) 0.94
Coevolutionary analysis enabled rational deregulation of allosteric enzyme inhibition in Corynebacterium glutamicum for lysine production. Appl Environ Microbiol (2011) 0.94
Oxidative stress suppression by luteolin-induced heme oxygenase-1 expression. Toxicol Appl Pharmacol (2012) 0.93
RFRCDB-siRNA: improved design of siRNAs by random forest regression model coupled with database searching. Comput Methods Programs Biomed (2007) 0.93
Association mapping of starch physicochemical properties with starch biosynthesizing genes in waxy rice (Oryza sativa L.). J Agric Food Chem (2013) 0.93
Safety and Immunogenicity of the MRKAd5 gag HIV Type 1 Vaccine in a Worldwide Phase 1 Study of Healthy Adults. AIDS Res Hum Retroviruses (2010) 0.93
Metabolic modelling of syntrophic-like growth of a 1,3-propanediol producer, Clostridium butyricum, and a methanogenic archeon, Methanosarcina mazei, under anaerobic conditions. Bioprocess Biosyst Eng (2009) 0.93
Functional characterization of the gene PA2384 in large-scale gene regulation in response to iron starvation in Pseudomonas aeruginosa. J Biotechnol (2007) 0.92
A genome-wide study of two-component signal transduction systems in eight newly sequenced mutans streptococci strains. BMC Genomics (2012) 0.92
Phylogeography of Quercus variabilis based on chloroplast DNA sequence in East Asia: multiple glacial refugia and Mainland-migrated island populations. PLoS One (2012) 0.92
Biofuel production by in vitro synthetic enzymatic pathway biotransformation. Curr Opin Biotechnol (2010) 0.91
Integrating molecular dynamics and co-evolutionary analysis for reliable target prediction and deregulation of the allosteric inhibition of aspartokinase for amino acid production. J Biotechnol (2011) 0.91
A novel feature-based method for whole genome phylogenetic analysis without alignment: application to HEV genotyping and subtyping. Biochem Biophys Res Commun (2008) 0.90
Folding type specific secondary structure propensities of synonymous codons. IEEE Trans Nanobioscience (2003) 0.90
Synonymous codon usage in environmental chlamydia UWE25 reflects an evolutional divergence from pathogenic chlamydiae. Gene (2005) 0.90
Leukemia inhibitory factor is dysregulated in the endometrium and uterine flushing fluid of patients with adenomyosis during implantation window. Fertil Steril (2009) 0.89
An integrative method for identifying the over-annotated protein-coding genes in microbial genomes. DNA Res (2011) 0.88
[Neuron apoptosis induced by 3,4-methylenedioxy methamphetamine and expression of apoptosis-related factors in rat brain]. Sichuan Da Xue Xue Bao Yi Xue Ban (2009) 0.88
Exploring the allosteric mechanism of dihydrodipicolinate synthase by reverse engineering of the allosteric inhibitor binding sites and its application for lysine production. Appl Microbiol Biotechnol (2012) 0.87
Cleavage of Ni-(mu(2)-S)-Ni bridges in dinuclear nickel(II) dithiolate pincer complexes and related reactions. Inorg Chem (2009) 0.87
Sequence-based prediction of DNA-binding residues in proteins with conservation and correlation information. IEEE/ACM Trans Comput Biol Bioinform (2013) 0.87
STK31 maintains the undifferentiated state of colon cancer cells. Carcinogenesis (2012) 0.86
A novel method for quantitatively predicting non-covalent interactions from protein and nucleic acid sequence. J Mol Graph Model (2011) 0.86
Evolutionary origins of lymphocytes: ensembles of T cell and B cell transcriptional regulators in a cartilaginous fish. J Immunol (2004) 0.86
Inverse rectification in donor-acceptor molecular heterojunctions. ACS Nano (2011) 0.86
Absolute quantification of plasmid DNA by real-time PCR with genomic DNA as external standard and its application to a biodistribution study of an HIV DNA vaccine. Anal Sci (2009) 0.86
Identifying rare variants with optimal depth of coverage and cost-effective overlapping pool sequencing. Genet Epidemiol (2013) 0.85
Proteomic characterization of transient expression and secretion of a stress-related metalloprotease in high cell density culture of Bacillus megaterium. J Biotechnol (2006) 0.85
Design, characterization, and in vitro cellular inhibition and uptake of optimized genistein-loaded NLC for the prevention of posterior capsular opacification using response surface methodology. Int J Pharm (2013) 0.85
Diabetes synergistically exacerbates poststroke dementia and tau abnormality in brain. Neurochem Int (2010) 0.84
Lysimachia clethroides Duby extract attenuates inflammatory response in Raw 264.7 macrophages stimulated with lipopolysaccharide and in acute lung injury mouse model. J Ethnopharmacol (2013) 0.84
Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia. BMC Bioinformatics (2009) 0.84
Comparative study of one-step nucleic acid amplification assay, frozen section, and touch imprint cytology for intraoperative assessment of breast sentinel lymph node in Chinese patients. Cancer Sci (2012) 0.84
Study and reengineering of the binding sites and allosteric regulation of biosynthetic threonine deaminase by isoleucine and valine in Escherichia coli. Appl Microbiol Biotechnol (2012) 0.83
Association and linkage analysis of COL1A1 and AHSG gene polymorphisms with femoral neck bone geometric parameters in both Caucasian and Chinese nuclear families. Acta Pharmacol Sin (2007) 0.83
Cluster analysis of the codon use frequency of MHC genes from different species. Biosystems (2002) 0.83
Identification of common microRNA-mRNA regulatory biomodules in human epithelial cancers. Chin Sci Bull (2010) 0.83
Ursolic acid attenuates lipopolysaccharide-induced cognitive deficits in mouse brain through suppressing p38/NF-κB mediated inflammatory pathways. Neurobiol Learn Mem (2011) 0.83
IGFs mediate the action of LH on oocyte maturation in zebrafish. Mol Endocrinol (2015) 0.82
Global analysis of in vivo EGR1-binding sites in erythroleukemia cell using chromatin immunoprecipitation and massively parallel sequencing. Electrophoresis (2010) 0.82
Stress-induced anhedonia correlates with lower hippocampal serotonin transporter protein expression. Brain Res (2013) 0.82
Risk factors for sentinel lymph node metastasis and validation study of the MSKCC nomogram in breast cancer patients. Jpn J Clin Oncol (2012) 0.82
Engineering of recombinant Escherichia coli cells co-expressing poly-γ-glutamic acid (γ-PGA) synthetase and glutamate racemase for differential yielding of γ-PGA. Microb Biotechnol (2013) 0.82
An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks. Integr Biol (Camb) (2011) 0.82
Exercise promotes axon regeneration of newborn striatonigral and corticonigral projection neurons in rats after ischemic stroke. PLoS One (2013) 0.82
Comments on 'Sample size for equivalence trials: a case study from a vaccine lot consistency trial' by J. Ganju, A. Izu and A. Anemona. Stat Med (2012) 0.82
The (CA)n polymorphism of the TNFR2 gene is associated with peak bone density in Chinese nuclear families. J Hum Genet (2005) 0.82
Expression of integrin β3 and osteopontin in the eutopic endometrium of adenomyosis during the implantation window. Eur J Obstet Gynecol Reprod Biol (2013) 0.81
Protein identification from two-dimensional gel electrophoresis analysis of Klebsiella pneumoniae by combined use of mass spectrometry data and raw genome sequences. Proteome Sci (2003) 0.81
The mechanism of substrate inhibition in human indoleamine 2,3-dioxygenase. J Am Chem Soc (2012) 0.81
RF-DYMHC: detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features. Nucleic Acids Res (2007) 0.81
Decorating tetrathiafulvalene (TTF) with fluorinated phenyls through sulfur bridges: facile synthesis, properties, and aggregation through fluorine interactions. Chemistry (2014) 0.81
Characteristics of nucleosome core DNA and their applications in predicting nucleosome positions. Biophys J (2008) 0.81
Phenolic acids, anthocyanins, and antioxidant capacity in rice (Oryza sativa L.) grains at four stages of development after flowering. Food Chem (2013) 0.81
Diabetes-induced central neuritic dystrophy and cognitive deficits are associated with the formation of oligomeric reticulon-3 via oxidative stress. J Biol Chem (2013) 0.81
Support vector machine for classification of meiotic recombination hotspots and coldspots in Saccharomyces cerevisiae based on codon composition. BMC Bioinformatics (2006) 0.81
The contributions of lean tissue mass and fat mass to bone geometric adaptation at the femoral neck in Chinese overweight adults. Ann Hum Biol (2007) 0.81
Secular changes on the distribution of body mass index among Chinese children and adolescents, 1985-2010. Biomed Environ Sci (2013) 0.81
The patterns of histone modifications in the vicinity of transcription factor binding sites in human lymphoblastoid cell lines. PLoS One (2013) 0.80
Analysis of nucleosome positioning determined by DNA helix curvature in the human genome. BMC Genomics (2011) 0.80
A novel fluorescent assay for edaravone with aqueous functional CdSe quantum dots. Spectrochim Acta A Mol Biomol Spectrosc (2009) 0.80
Spatial resolution of a type II heterojunction in a single bipolar molecule. Nano Lett (2009) 0.80
Discovery and investigation of a new, second triose phosphate isomerase in Klebsiella pneumoniae. J Biotechnol (2006) 0.80
Reannotation of protein-coding genes based on an improved graphical representation of DNA sequence. J Comput Chem (2010) 0.80