Can sugars be produced from fatty acids? A test case for pathway analysis tools.

Hypergraphs and cellular networks. PLoS Comput Biol (2009) 1.58

Path finding methods accounting for stoichiometry in metabolic networks. Genome Biol (2011) 0.96

Inferring branching pathways in genome-scale metabolic networks. BMC Syst Biol (2009) 0.93

Host-pathogen interactions between the human innate immune system and Candida albicans-understanding and modeling defense and evasion strategies. Front Microbiol (2015) 0.89

Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli. BMC Syst Biol (2012) 0.79

In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'. Bioinformatics (2009) 0.76

Projection to latent pathways (PLP): a constrained projection to latent variables (PLS) method for elementary flux modes discrimination. BMC Syst Biol (2011) 0.76

Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways. BMC Syst Biol (2013) 0.76

Metabolic network structure determines key aspects of functionality and regulation. Nature (2002) 6.64

Comparison of network-based pathway analysis methods. Trends Biotechnol (2004) 2.78

Metabolic pathways in the post-genome era. Trends Biochem Sci (2003) 2.57

Comparison of various approaches to calculating the optimal hematocrit in vertebrates. J Appl Physiol (1985) (2012) 2.15

Metatool 5.0: fast and flexible elementary modes analysis. Bioinformatics (2006) 2.12

A genome-scale metabolic model of Arabidopsis and some of its properties. Plant Physiol (2009) 1.95

Is maximization of molar yield in metabolic networks favoured by evolution? J Theor Biol (2007) 1.88

Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria. Biotechnol Bioeng (2002) 1.74

Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinformatics (2009) 1.54

Can sugars be produced from fatty acids? A test case for pathway analysis tools. Bioinformatics (2009) 1.53

Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. Mol Syst Biol (2011) 1.45

Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns. Genome Res (2009) 1.36

Game-theoretical approaches to studying the evolution of biochemical systems. Trends Biochem Sci (2005) 1.36

Integrated network reconstruction, visualization and analysis using YANAsquare. BMC Bioinformatics (2007) 1.32

YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC Bioinformatics (2005) 1.24

Role of sirtuins in lifespan regulation is linked to methylation of nicotinamide. Nat Chem Biol (2013) 1.23

In silico evidence for gluconeogenesis from fatty acids in humans. PLoS Comput Biol (2011) 1.18

A genome-scale metabolic model accurately predicts fluxes in central carbon metabolism under stress conditions. Plant Physiol (2010) 1.17

Structural robustness of metabolic networks with respect to multiple knockouts. J Theor Biol (2007) 1.11

The predictive start of hunting archer fish: a flexible and precise motor pattern performed with the kinematics of an escape C-start. J Exp Biol (2007) 1.11

Predicting three-dimensional target motion: how archer fish determine where to catch their dislodged prey. J Exp Biol (2002) 1.08

Topological analysis of metabolic networks based on Petri net theory. In Silico Biol (2003) 1.08

Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks. Curr Opin Biotechnol (2010) 1.04

Modeling and performance analysis of SAW reader systems for delay-line sensors. IEEE Trans Ultrason Ferroelectr Freq Control (2009) 1.04

Detection of stoichiometric inconsistencies in biomolecular models. Bioinformatics (2008) 1.03

Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis. BMC Syst Biol (2010) 1.02

Responses to light intensity in a genome-scale model of rice metabolism. Plant Physiol (2013) 1.02

Modelling the optimal timing in metabolic pathway activation-use of Pontryagin's Maximum Principle and role of the Golden section. Biosystems (2010) 1.00

A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions. Plant J (2013) 1.00

Computing chemical organizations in biological networks. Bioinformatics (2008) 0.99

Agent-based modeling approach of immune defense against spores of opportunistic human pathogenic fungi. Front Microbiol (2012) 0.99

Fruit-catching fish tune their fast starts to compensate for drift. Curr Biol (2008) 0.97

TassDB: a database of alternative tandem splice sites. Nucleic Acids Res (2006) 0.97

Less is more: selective advantages can explain the prevalent loss of biosynthetic genes in bacteria. Evolution (2014) 0.96

Small circuits for large tasks: high-speed decision-making in archerfish. Science (2008) 0.96

Elementary modes analysis of photosynthate metabolism in the chloroplast stroma. Eur J Biochem (2003) 0.95

Modular decomposition of metabolic systems via null-space analysis. J Theor Biol (2007) 0.93

TassDB2 - A comprehensive database of subtle alternative splicing events. BMC Bioinformatics (2010) 0.93

Can single knockouts accurately single out gene functions? BMC Syst Biol (2008) 0.93

Evolutionary game theory: cells as players. Mol Biosyst (2014) 0.93

Regulation of glycolytic flux in ischemic preconditioning. A study employing metabolic control analysis. J Biol Chem (2002) 0.92

Inhibition of alanine aminotransferase in silico and in vivo promotes mitochondrial metabolism to impair malignant growth. J Biol Chem (2011) 0.91

Metabolic costs of amino acid and protein production in Escherichia coli. Biotechnol J (2013) 0.91

A method for classifying metabolites in topological pathway analyses based on minimization of pathway number. Biosystems (2003) 0.91

Photonic crystal light collectors in fish retina improve vision in turbid water. Science (2012) 0.89

Selective regulation of cellular processes via protein cascades acting as band-pass filters for time-limited oscillations. FEBS Lett (2005) 0.89

Fungal alternative splicing is associated with multicellular complexity and virulence: a genome-wide multi-species study. DNA Res (2013) 0.89

More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coli. BMC Syst Biol (2011) 0.88

Quantitative model of cell cycle arrest and cellular senescence in primary human fibroblasts. PLoS One (2012) 0.88

Comparative analysis of sequence features involved in the recognition of tandem splice sites. BMC Genomics (2008) 0.88

Hunting archer fish match their take-off speed to distance from the future point of catch. J Exp Biol (2006) 0.88

Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism. Gene (2007) 0.86

Highly potent 5-aminotetrahydropyrazolopyridines: enantioselective dopamine D3 receptor binding, functional selectivity, and analysis of receptor-ligand interactions. J Med Chem (2011) 0.86

An example of the prisoner's dilemma in biochemistry. Naturwissenschaften (2003) 0.86

Dynamic optimization identifies optimal programmes for pathway regulation in prokaryotes. Nat Commun (2013) 0.86

NAD(+) biosynthesis and salvage--a phylogenetic perspective. FEBS J (2012) 0.86

Selection of human tissue-specific elementary flux modes using gene expression data. Bioinformatics (2013) 0.85

Biotechnological potential of respiring Zymomonas mobilis: a stoichiometric analysis of its central metabolism. J Biotechnol (2013) 0.85

Alternative splicing of mutually exclusive exons--a review. Biosystems (2013) 0.85

Detecting and investigating substrate cycles in a genome-scale human metabolic network. FEBS J (2012) 0.84

Modeling the seasonal adaptation of circadian clocks by changes in the network structure of the suprachiasmatic nucleus. PLoS Comput Biol (2012) 0.84

Pathway analysis of NAD+ metabolism. Biochem J (2011) 0.84

Combining metabolic pathway analysis with Evolutionary Game Theory: explaining the occurrence of low-yield pathways by an analytic optimization approach. Biosystems (2011) 0.83

Model of tryptophan metabolism, readily scalable using tissue-specific gene expression data. J Biol Chem (2013) 0.83

A minimal model for decoding of time-limited Ca2+ oscillations. Biophys Chem (2005) 0.82

Continuous model for the rock-scissors-paper game between bacteriocin producing bacteria. J Math Biol (2007) 0.82

Effect of substrate competition in kinetic models of metabolic networks. FEBS Lett (2013) 0.81

A theory of optimal differential gene expression. Biosystems (2004) 0.81

Visual search in hunting archerfish shares all hallmarks of human performance. J Exp Biol (2013) 0.81

Topological analysis of metabolic networks based on petri net theory. Stud Health Technol Inform (2011) 0.80

Commemorating the 1913 Michaelis-Menten paper Die Kinetik der Invertinwirkung: three perspectives. FEBS J (2013) 0.80

Kinetic modelling of the Zymomonas mobilis Entner-Doudoroff pathway: insights into control and functionality. Microbiology (2013) 0.80

Correlation between sequence, structure and function for trisporoid processing proteins in the model zygomycete Mucor mucedo. J Theor Biol (2012) 0.80

Modeling signal transduction in enzyme cascades with the concept of elementary flux modes. J Comput Biol (2009) 0.80

Under what conditions signal transduction pathways are highly flexible in response to external forcing? A case study on calcium oscillations. J Theor Biol (2003) 0.79

Dynamic simulation of pollutant effects on the threonine pathway in Escherichia coli. C R Biol (2003) 0.79

Theoretical model of the interactions between Ca2+, calmodulin and myosin light chain kinase. FEBS Lett (2005) 0.79

Theoretical study of lipid biosynthesis in wild-type Escherichia coli and in a protoplast-type L-form using elementary flux mode analysis. FEBS J (2010) 0.79

Evolutionary game theory: molecules as players. Mol Biosyst (2014) 0.79

Myocardial energy metabolism in ischemic preconditioning and cardioplegia: a metabolic control analysis. Mol Cell Biochem (2005) 0.79

Predicting novel pathways in genome-scale metabolic networks. Biochem Soc Trans (2010) 0.78

Detecting structural invariants in biological reaction networks. Methods Mol Biol (2012) 0.78

Metabolic control analysis of anaerobic glycolysis in human hibernating myocardium replaces traditional concepts of flux control. FEBS Lett (2002) 0.78

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a Petri net approach. In Silico Biol (2010) 0.78

Dim light vision--morphological and functional adaptations of the eye of the mormyrid fish, Gnathonemus petersii. J Physiol Paris (2008) 0.78

Biochemical frequency control by synchronisation of coupled repressilators: an in silico study of modules for circadian clock systems. Comput Intell Neurosci (2011) 0.78

A parallel algorithm to compute chemical organizations in biological networks. Bioinformatics (2010) 0.78

Protein phosphorylation can regulate metabolite concentrations rather than control flux: the example of glycogen synthase. Proc Natl Acad Sci U S A (2004) 0.78

Combinatorics of aliphatic amino acids. Naturwissenschaften (2010) 0.77