Published in Metab Eng on July 01, 2005
Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol Syst Biol (2006) 3.04
Systematic assignment of thermodynamic constraints in metabolic network models. BMC Bioinformatics (2006) 2.26
Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev (2008) 1.97
Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks. BMC Syst Biol (2007) 1.71
Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli. Biophys Chem (2009) 1.64
Large-scale identification of genetic design strategies using local search. Mol Syst Biol (2009) 1.31
Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production. BMC Syst Biol (2010) 1.27
Thermodynamically feasible kinetic models of reaction networks. Biophys J (2007) 1.25
Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints. Biophys J (2006) 1.24
An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models. Nat Commun (2014) 1.13
A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks. PLoS Comput Biol (2012) 1.02
Exhaustive identification of steady state cycles in large stoichiometric networks. BMC Syst Biol (2008) 0.96
Prediction of metabolic fluxes by incorporating genomic context and flux-converging pattern analyses. Proc Natl Acad Sci U S A (2010) 0.94
Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models. Biophys J (2013) 0.85
Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks. Biophys J (2010) 0.84
Construction and analysis of the model of energy metabolism in E. coli. PLoS One (2013) 0.81
Predicting internal cell fluxes at sub-optimal growth. BMC Syst Biol (2015) 0.79
Reply to "Do genome-scale models need exact solvers or clearer standards?". Mol Syst Biol (2015) 0.76
The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization. PLoS Comput Biol (2016) 0.75
Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet (2010) 10.97
Macrophages regulate the angiogenic switch in a mouse model of breast cancer. Cancer Res (2006) 6.52
Energy balance for analysis of complex metabolic networks. Biophys J (2002) 3.46
DUX4, a candidate gene of facioscapulohumeral muscular dystrophy, encodes a transcriptional activator of PITX1. Proc Natl Acad Sci U S A (2007) 3.32
Molecular evidence for hierarchical transcriptional lineage priming in fetal and adult stem cells and multipotent progenitors. Immunity (2007) 3.26
Computer modeling of mitochondrial tricarboxylic acid cycle, oxidative phosphorylation, metabolite transport, and electrophysiology. J Biol Chem (2007) 2.61
A global evaluation of metabolic theory as an explanation for terrestrial species richness gradients. Ecology (2007) 2.29
Thermodynamic constraints for biochemical networks. J Theor Biol (2004) 2.19
Extreme pathways and Kirchhoff's second law. Biophys J (2002) 1.95
Acquired TNFRSF14 mutations in follicular lymphoma are associated with worse prognosis. Cancer Res (2010) 1.79
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data. BMC Bioinformatics (2007) 1.75
Stoichiometric network theory for nonequilibrium biochemical systems. Eur J Biochem (2003) 1.74
Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium. Biophys Chem (2004) 1.63
Kit regulates maintenance of quiescent hematopoietic stem cells. J Immunol (2008) 1.60
Phosphate metabolite concentrations and ATP hydrolysis potential in normal and ischaemic hearts. J Physiol (2008) 1.58
Relationship between thermodynamic driving force and one-way fluxes in reversible processes. PLoS One (2007) 1.58
Chromatin looping and the probability of transcription. Trends Genet (2006) 1.53
Minimum Information About a Simulation Experiment (MIASE). PLoS Comput Biol (2011) 1.48
Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism. Am J Physiol Endocrinol Metab (2004) 1.46
Multiple ion binding equilibria, reaction kinetics, and thermodynamics in dynamic models of biochemical pathways. Methods Enzymol (2009) 1.41
Cytokines regulate postnatal hematopoietic stem cell expansion: opposing roles of thrombopoietin and LNK. Genes Dev (2006) 1.40
Prognostic impact of inappropriate defibrillator shocks in a population cohort. Heart (2013) 1.38
Oxygen-sensitive {delta}-opioid receptor-regulated survival and death signals: novel insights into neuronal preconditioning and protection. J Biol Chem (2005) 1.26
Experimentally observed phenomena on cardiac energetics in heart failure emerge from simulations of cardiac metabolism. Proc Natl Acad Sci U S A (2009) 1.25
Oxidative ATP synthesis in skeletal muscle is controlled by substrate feedback. Am J Physiol Cell Physiol (2006) 1.25
Stochastic dynamics and non-equilibrium thermodynamics of a bistable chemical system: the Schlögl model revisited. J R Soc Interface (2008) 1.24
Analysis of cardiac mitochondrial Na+-Ca2+ exchanger kinetics with a biophysical model of mitochondrial Ca2+ handling suggests a 3:1 stoichiometry. J Physiol (2008) 1.22
ARC (apoptosis repressor with caspase recruitment domain) is a novel marker of human colon cancer. Cell Cycle (2008) 1.21
Population-based analysis of methadone distribution and metabolism using an age-dependent physiologically based pharmacokinetic model. J Pharmacokinet Pharmacodyn (2006) 1.20
Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm. J Comput Chem (2003) 1.20
Physical origins of entropy production, free energy dissipation, and their mathematical representations. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 1.19
Readmission rates of patients discharged against medical advice: a matched cohort study. PLoS One (2011) 1.19
The role of exotic species in homogenizing the North American flora. Ecol Lett (2006) 1.18
Computational biology of cardiac myocytes: proposed standards for the physiome. J Exp Biol (2007) 1.16
Identifying physiological origins of baroreflex dysfunction in salt-sensitive hypertension in the Dahl SS rat. Physiol Genomics (2010) 1.15
ErbB3-dependent motility and intravasation in breast cancer metastasis. Cancer Res (2006) 1.15
Phenotype reversion in fetal human liver epithelial cells identifies the role of an intermediate meso-endodermal stage before hepatic maturation. J Cell Sci (2008) 1.12
Generating rate equations for complex enzyme systems by a computer-assisted systematic method. BMC Bioinformatics (2009) 1.12
Computational modeling of physiological systems. Physiol Genomics (2005) 1.10
IL-7 mediates Ebf-1-dependent lineage restriction in early lymphoid progenitors. Blood (2011) 1.10
Regional differences in rates of plant speciation and molecular evolution: a comparison between eastern Asia and eastern North America. Evolution (2004) 1.09
Detailed kinetics and regulation of mammalian NAD-linked isocitrate dehydrogenase. Biochim Biophys Acta (2008) 1.07
A comparison of MS/MS-based, stable-isotope-labeled, quantitation performance on ESI-quadrupole TOF and MALDI-TOF/TOF mass spectrometers. Proteomics (2009) 1.07
Health disparities between island and mainland Puerto Ricans. Rev Panam Salud Publica (2006) 1.07
Differential tissue and subcellular expressionof ERM proteins in normal and malignant tissues: cytoplasmic ezrin expression has prognostic signficance for head and neck squamous cell carcinoma. Head Neck (2006) 1.05
Comparison of buffer and red blood cell perfusion of guinea pig heart oxygenation. Am J Physiol Heart Circ Physiol (2003) 1.05
Identification of tyrosine kinase, HCK, and tumor suppressor, BIN1, as potential mediators of AHI-1 oncogene in primary and transformed CTCL cells. Blood (2009) 1.04
Rapid hypoxia preconditioning protects cortical neurons from glutamate toxicity through delta-opioid receptor. Stroke (2006) 1.04
A biophysically based mathematical model for the kinetics of mitochondrial calcium uniporter. Biophys J (2009) 1.03
Use of Affymetrix mapping arrays in the diagnosis of gene copy number variation. Curr Protoc Hum Genet (2008) 1.03
In vitro and in vivo activity of R547: a potent and selective cyclin-dependent kinase inhibitor currently in phase I clinical trials. Mol Cancer Ther (2006) 1.02
A database of thermodynamic properties of the reactions of glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway. Database (Oxford) (2011) 1.01
A selective phosphatase of regenerating liver phosphatase inhibitor suppresses tumor cell anchorage-independent growth by a novel mechanism involving p130Cas cleavage. Cancer Res (2008) 1.01
Stochastic bistability and bifurcation in a mesoscopic signaling system with autocatalytic kinase. Biophys J (2010) 1.00
A quasistationary analysis of a stochastic chemical reaction: Keizer's paradox. Bull Math Biol (2007) 0.99
Grand canonical Markov model: a stochastic theory for open nonequilibrium biochemical networks. J Chem Phys (2006) 0.98
Kinetics and regulation of mammalian NADH-ubiquinone oxidoreductase (Complex I). Biophys J (2010) 0.97
Thermodynamic limit of a nonequilibrium steady state: Maxwell-type construction for a bistable biochemical system. Phys Rev Lett (2009) 0.96
Theoretical models for coronary vascular biomechanics: progress & challenges. Prog Biophys Mol Biol (2010) 0.96
Powering a burnt bridges Brownian ratchet: a model for an extracellular motor driven by proteolysis of collagen. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.96
The risks of post-operative complications following pre-operative infliximab therapy for Crohn's disease in patients undergoing abdominal surgery: a systematic review and meta-analysis. J Crohns Colitis (2013) 0.95
Kinetic timing: a novel mechanism that improves the accuracy of GTPase timers in endosome fusion and other biological processes. Traffic (2002) 0.95
Spatial heterogeneity in skeletal muscle microvascular blood flow distribution is increased in the metabolic syndrome. Am J Physiol Regul Integr Comp Physiol (2011) 0.95
Thermodynamically based profiling of drug metabolism and drug-drug metabolic interactions: a case study of acetaminophen and ethanol toxic interaction. Biophys Chem (2005) 0.95
A biophysically based mathematical model for the kinetics of mitochondrial Na+-Ca2+ antiporter. Biophys J (2010) 0.94
Detection of pathogenic copy number variants in children with idiopathic intellectual disability using 500 K SNP array genomic hybridization. BMC Genomics (2009) 0.94
Differentiation of dermal multipotent cells into odontogenic lineage induced by embryonic and neonatal tooth germ cell-conditioned medium. Stem Cells Dev (2010) 0.93
Bridging the genotype-phenotype gap: what does it take? J Physiol (2013) 0.93
Sensitivity and specificity amplification in signal transduction. Cell Biochem Biophys (2003) 0.92
Synchronized dynamics and non-equilibrium steady states in a stochastic yeast cell-cycle network. Math Biosci (2007) 0.91
Assessment of the proliferative status of epithelial cell types in the endometrium of young and menopausal transition women. Hum Reprod (2007) 0.90
Mitochondrial free [Ca2+] increases during ATP/ADP antiport and ADP phosphorylation: exploration of mechanisms. Biophys J (2010) 0.89
Nonequilibrium steady state of a nanometric biochemical system: determining the thermodynamic driving force from single enzyme turnover time traces. Nano Lett (2005) 0.89
NASA-approved rotary bioreactor enhances proliferation and osteogenesis of human periodontal ligament stem cells. Stem Cells Dev (2009) 0.89
The role of theoretical modeling in microcirculation research. Microcirculation (2008) 0.89
Characterization of Mg2+ inhibition of mitochondrial Ca2+ uptake by a mechanistic model of mitochondrial Ca2+ uniporter. Biophys J (2011) 0.89
Comparison of genome-wide array genomic hybridization platforms for the detection of copy number variants in idiopathic mental retardation. BMC Med Genomics (2011) 0.88
Stimulatory effects of calcium on respiration and NAD(P)H synthesis in intact rat heart mitochondria utilizing physiological substrates cannot explain respiratory control in vivo. J Biol Chem (2011) 0.88
Single-cell analysis of early B-lymphocyte development suggests independent regulation of lineage specification and commitment in vivo. Proc Natl Acad Sci U S A (2012) 0.88
Metabolic dynamics in skeletal muscle during acute reduction in blood flow and oxygen supply to mitochondria: in-silico studies using a multi-scale, top-down integrated model. PLoS One (2008) 0.88
Expression of integrin α2 receptor in human cord blood CD34+CD38-CD90+ stem cells engrafting long-term in NOD/SCID-IL2Rγ(c) null mice. Stem Cells (2013) 0.87
The effects of reversibility and noise on stochastic phosphorylation cycles and cascades. Biophys J (2008) 0.87
Delayed onset of positive feedback activation of Rab5 by Rabex-5 and Rabaptin-5 in endocytosis. PLoS One (2010) 0.87
Modeling to link regional myocardial work, metabolism and blood flows. Ann Biomed Eng (2012) 0.87
GABA and glycine are protective to mature but toxic to immature rat cortical neurons under hypoxia. Eur J Neurosci (2005) 0.87
Myocardial oxygenation and adenosine release in isolated guinea pig hearts during changes in contractility. Am J Physiol Heart Circ Physiol (2004) 0.87
Roles of the creatine kinase system and myoglobin in maintaining energetic state in the working heart. BMC Syst Biol (2009) 0.86
Down-regulation of delta-opioid receptors in Na+/H+ exchanger 1 null mutant mouse brain with epilepsy. Neurosci Res (2005) 0.86
Characterization of membrane potential dependency of mitochondrial Ca2+ uptake by an improved biophysical model of mitochondrial Ca2+ uniporter. PLoS One (2010) 0.86
Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences. Proc Natl Acad Sci U S A (2006) 0.85
Early B-cell factor 1 regulates the expansion of B-cell progenitors in a dose-dependent manner. J Biol Chem (2013) 0.85
Analysis of the kinetics and bistability of ubiquinol:cytochrome c oxidoreductase. Biophys J (2013) 0.85
Kinetic analysis and design of experiments to identify the catalytic mechanism of the monocarboxylate transporter isoforms 4 and 1. Biophys J (2011) 0.84
Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks. Biophys J (2010) 0.84
Computational analyses of intravascular tracer washout reveal altered capillary-level flow distributions in obese Zucker rats. J Physiol (2011) 0.84
A stochastic model of DNA fragments rejoining. PLoS One (2012) 0.83
Interleukin-7-induced Stat-5 acts in synergy with Flt-3 signaling to stimulate expansion of hematopoietic progenitor cells. J Biol Chem (2010) 0.83
Open-system thermodynamic analysis of DNA polymerase fidelity. Phys Biol (2009) 0.83
Lipopolysaccharide-induced fever depends on prostaglandin E2 production specifically in brain endothelial cells. Endocrinology (2012) 0.83
A perturbation analysis of rate theory of self-regulating genes and signaling networks. J Chem Phys (2011) 0.82