Published in BMC Bioinformatics on May 19, 2008
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol (2012) 3.56
Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev (2008) 1.97
Identifying essential genes in Escherichia coli from a metabolic optimization principle. Proc Natl Acad Sci U S A (2009) 1.02
A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks. PLoS Comput Biol (2012) 1.02
Dispensability of Escherichia coli's latent pathways. Proc Natl Acad Sci U S A (2011) 0.96
A novel methodology to estimate metabolic flux distributions in constraint-based models. Metabolites (2013) 0.88
Optimal fluxes, reaction replaceability, and response to enzymopathies in the human red blood cell. J Biomed Biotechnol (2010) 0.83
Uniform sampling of steady states in metabolic networks: heterogeneous scales and rounding. PLoS One (2015) 0.83
Energy metabolism and glutamate-glutamine cycle in the brain: a stoichiometric modeling perspective. BMC Syst Biol (2013) 0.80
Identifying all moiety conservation laws in genome-scale metabolic networks. PLoS One (2014) 0.78
Obstructions to Sampling Qualitative Properties. PLoS One (2015) 0.76
Quantitative constraint-based computational model of tumor-to-stroma coupling via lactate shuttle. Sci Rep (2015) 0.75
Estimating Metabolic Fluxes Using a Maximum Network Flexibility Paradigm. PLoS One (2015) 0.75
An analytic approximation of the feasible space of metabolic networks. Nat Commun (2017) 0.75
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35
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An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol (2003) 10.46
Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci U S A (2002) 8.41
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature (2002) 7.38
Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature (2004) 7.18
The small world of metabolism. Nat Biotechnol (2000) 6.35
Analytic and algorithmic solution of random satisfiability problems. Science (2002) 4.06
Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors. J Theor Biol (1993) 2.39
Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. J Biol Chem (2004) 2.26
Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space. J Theor Biol (2004) 2.24
Thermodynamic constraints for biochemical networks. J Theor Biol (2004) 2.19
Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. Biophys J (2004) 2.12
Coloring random graphs. Phys Rev Lett (2002) 1.57
Structural comparison of metabolic networks in selected single cell organisms. BMC Bioinformatics (2005) 1.49
Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints. Biophys J (2006) 1.24
Efficient supervised learning in networks with binary synapses. Proc Natl Acad Sci U S A (2007) 1.01
Correctness of belief propagation in Gaussian graphical models of arbitrary topology. Neural Comput (2001) 0.86
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
Protein 3D structure computed from evolutionary sequence variation. PLoS One (2011) 4.71
Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A (2011) 4.08
Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments. Proc Natl Acad Sci U S A (2013) 2.13
Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells. Genome Biol (2013) 1.22
Modelling Competing Endogenous RNA Networks. PLoS One (2013) 1.21
Predicting protein functions with message passing algorithms. Bioinformatics (2004) 1.13
Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem. J Comput Biol (2013) 1.10
Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach. BMC Bioinformatics (2010) 0.99
Threshold values, stability analysis, and high-q asymptotics for the coloring problem on random graphs. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.94
Zero-temperature properties of RNA secondary structures. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 0.91
Bridging the gaps in systems biology. Mol Genet Genomics (2014) 0.90
A stochastic local search algorithm for distance-based phylogeny reconstruction. Mol Biol Evol (2010) 0.85
Optimally designed quantum transport across disordered networks. Phys Rev Lett (2013) 0.84
Sharing information to reconstruct patient-specific pathways in heterogeneous diseases. Pac Symp Biocomput (2014) 0.79
Reaction networks as systems for resource allocation: a variational principle for their non-equilibrium steady states. PLoS One (2012) 0.78
Inter-individual variation in nucleotide excision repair pathway is modulated by non-synonymous polymorphisms in ERCC4 and MBD4 genes. Mutat Res (2013) 0.77
SLAMF1 regulation of chemotaxis and autophagy determines CLL patient response. J Clin Invest (2015) 0.77
Stochastic approximation to the T cell mediated specific response of the immune system. J Theor Biol (2011) 0.75
Inference algorithm for finite-dimensional spin glasses: belief propagation on the dual lattice. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.75
Efficiency scaling of non-coherent upconversion in a one-dimensional model system. J Chem Phys (2013) 0.75