Modes and cuts in metabolic networks: Complexity and algorithms, Biosystems, issue.1, pp.9551-60, 2009. ,
Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets, Theoretical Computer Science, issue.0, pp.4571-4580, 2012. ,
Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks, Bioinformatics, vol.28, issue.19, 2012. ,
DOI : 10.1093/bioinformatics/bts423
TICL - a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics, FEBS Journal, vol.19, issue.7, pp.2762084-2094, 2009. ,
DOI : 10.1111/j.1742-4658.2009.06943.x
The metabolic world of Escherichia coli is not small, Proceedings of the National Academy of Sciences, vol.101, issue.6, pp.1543-1547, 2004. ,
DOI : 10.1073/pnas.0306458101
Complexity and Approximation: Combinatorial Optimization Problems and Their Approximability Properties, 1999. ,
DOI : 10.1007/978-3-642-58412-1
Directed Hypergraphs: Problems, Algorithmic Results, and a Novel Decremental Approach, Theoretical Computer Science, pp.312-328, 2001. ,
DOI : 10.1007/3-540-45446-2_20
Digraphs: Theory, Algorithms and Applications, 2010. ,
DOI : 10.1007/978-1-84800-998-1
Superessential reactions in metabolic networks, Proceedings of the National Academy of Sciences, 2012. ,
DOI : 10.1073/pnas.1113065109
Graphs and Hypergraphs. North-Holland Mathematical Library, 1976. ,
Steiner tree problems in the analysis of biological networks, 2005. ,
Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks, Journal of Computational Biology, vol.15, issue.6, pp.565-576, 2008. ,
DOI : 10.1089/cmb.2008.0044
Graph theory with applications, 1976. ,
DOI : 10.1007/978-1-349-03521-2
Large-scale reconstruction and phylogenetic analysis of metabolic environments, Proceedings of the National Academy of Sciences, vol.105, issue.38, pp.10514482-14487, 2008. ,
DOI : 10.1073/pnas.0806162105
Insect Symbiosis, 2008. ,
DOI : 10.1201/9780203009918
Ab initio reconstruction of metabolic pathways, ECCB, pp.26-34, 2003. ,
DOI : 10.1093/bioinformatics/btg1055
Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii, BMC Systems Biology, vol.3, issue.1, p.4, 2009. ,
DOI : 10.1016/0165-022X(81)90067-1
Systemic analysis of the symbiotic function of Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum, Comptes Rendus Biologies, vol.332, issue.11, pp.3321034-1049, 2009. ,
DOI : 10.1016/j.crvi.2009.09.007
URL : https://hal.archives-ouvertes.fr/hal-00539412
Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms, BMC Systems Biology, vol.6, issue.1, p.10, 2012. ,
DOI : 10.1016/j.cor.2003.11.014
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases, Nucleic Acids Research, vol.38, issue.Database, pp.473-479, 2010. ,
DOI : 10.1093/nar/gkp875
Chemical Organizations in the Central Sugar Metabolism of Escherichia coli, Mathematical Modeling of Biological Systems, Volume I, Modeling and Simulation in Science, Engineering and Technology, pp.105-119, 2007. ,
DOI : 10.1007/978-0-8176-4558-8_10
Computing chemical organizations in biological networks, Bioinformatics, vol.24, issue.14, pp.241611-1618, 2008. ,
DOI : 10.1093/bioinformatics/btn228
Enigmatic Microorganisms and Life in Extreme Environments , volume 1 of Cellular Origin and Life in Extreme Habitats, chapter Intracellular symbiotic bacteria within insects, pp.651-660, 1999. ,
The Universal Protein Resource (UniProt) 2009, Nucleic Acids Research, vol.37, issue.Database, pp.169-174, 2009. ,
DOI : 10.1093/nar/gkn664
Introduction To Algorithms, 2001. ,
Enumerating Precursor Sets of Target Metabolites in a Metabolic Network, WABI'2008, pp.233-244, 2008. ,
DOI : 10.1007/978-3-540-87361-7_20
URL : https://hal.archives-ouvertes.fr/hal-00428200
Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri, with Their Insect Host, Homalodisca coagulata, PLoS Computational Biology, vol.106, issue.9, p.1000904, 2010. ,
DOI : 10.1371/journal.pcbi.1000904.s030
URL : https://hal.archives-ouvertes.fr/hal-00690650
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks, Nucleic Acids Research, vol.38, issue.Web Server, pp.132-137, 2010. ,
DOI : 10.1093/nar/gkq312
URL : https://hal.archives-ouvertes.fr/hal-00690651
Inferring Meaningful Pathways in Weighted Metabolic Networks, Journal of Molecular Biology, vol.356, issue.1, pp.222-236, 2006. ,
DOI : 10.1016/j.jmb.2005.09.079
Java How to Program, 2007. ,
Identifying functional modules in protein-protein interaction networks: an integrated exact approach, Bioinformatics, vol.24, issue.13, pp.24-223, 2008. ,
DOI : 10.1093/bioinformatics/btn161
Chemical Organisation Theory, Bulletin of Mathematical Biology, vol.96, issue.25, pp.1199-1231, 2007. ,
DOI : 10.1007/s11538-006-9130-8
Relevant subgraph extraction from random walks in a graph, Research Report RR, vol.380167, pp.2006-2013, 2006. ,
Computational aspects of monotone dualization: A brief survey, Discrete Applied Mathematics, vol.156, issue.11, pp.2035-2049, 2008. ,
DOI : 10.1016/j.dam.2007.04.017
Approximating Minimum Feedback Sets and Multicuts in Directed Graphs, Algorithmica, vol.20, issue.2, pp.151-174, 1998. ,
DOI : 10.1007/PL00009191
Sulfur Sparing in the Yeast Proteome in Response to Sulfur Demand, Molecular Cell, vol.9, issue.4, pp.713-723, 2002. ,
DOI : 10.1016/S1097-2765(02)00500-2
Pathway discovery in metabolic networks by subgraph extraction, Bioinformatics, vol.26, issue.9, pp.1211-1218, 2010. ,
DOI : 10.1093/bioinformatics/btq105
The biomass objective function, Current Opinion in Microbiology, vol.13, issue.3, pp.344-349, 2010. ,
DOI : 10.1016/j.mib.2010.03.003
Reconstruction of biochemical networks in microorganisms, Nature Reviews Microbiology, vol.104, issue.2, pp.129-143, 2009. ,
DOI : 10.1038/nrmicro1949
In silico design and adaptive evolution of escherichia coli for production of lactic acid, Biotechnology and Bioengineering, issue.5, pp.91643-648, 2005. ,
The Arrival of the fittest: towards a theory of biological organization, Bull. Math. Biol, vol.56, pp.1-64, 1994. ,
Structural analyses of a hypothetical minimal metabolism, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.299, issue.5609, pp.3621751-1762, 1486. ,
DOI : 10.1126/science.299.5609.1006
Modular decomposition of protein-protein interaction networks, Genome Biology, vol.5, issue.8, p.57, 2004. ,
DOI : 10.1186/gb-2004-5-8-r57
Computers and Intractability; A Guide to the Theory of NP-Completeness, 1990. ,
Detection of stoichiometric inconsistencies in biomolecular models, Bioinformatics, vol.24, issue.19, pp.242245-2251, 2008. ,
DOI : 10.1093/bioinformatics/btn425
On generating the irredundant conjunctive and disjunctive normal forms of monotone Boolean functions, Discrete Applied Mathematics, vol.96, issue.97, pp.96-97363, 1999. ,
DOI : 10.1016/S0166-218X(99)00099-2
An environmental perspective on metabolism, Journal of Theoretical Biology, vol.252, issue.3, pp.530-537, 2008. ,
DOI : 10.1016/j.jtbi.2007.10.036
URL : https://hal.archives-ouvertes.fr/hal-00428159
Expanding Metabolic Networks: Scopes of Compounds, Robustness, and Evolution, Journal of Molecular Evolution, vol.268, issue.4, pp.498-512, 2005. ,
DOI : 10.1007/s00239-005-0027-1
Subnetwork hierarchies of biochemical pathways, Bioinformatics, vol.19, issue.4, pp.532-538, 2003. ,
DOI : 10.1093/bioinformatics/btg033
Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project, Systems Biology, vol.1, issue.1, pp.41-53, 2004. ,
DOI : 10.1049/sb:20045008
The Unified Software Development Process, 2012. ,
On generating all maximal independent sets, Information Processing Letters, vol.27, issue.3, pp.119-123, 1988. ,
DOI : 10.1016/0020-0190(88)90065-8
Predicting Gene Essentiality Using Genome-Scale in Silico Models, Microbial Gene Essentiality: Protocols and Bioinformatics, pp.433-457, 2008. ,
DOI : 10.1007/978-1-59745-321-9_30
Analyzing Molecular Reaction Networks: From Pathways to Chemical Organizations, Molecular Biotechnology, vol.34, issue.2, pp.117-123, 2006. ,
DOI : 10.1385/MB:34:2:117
Using chemical organization theory for model checking, Bioinformatics, vol.25, issue.15, pp.251915-1922, 2009. ,
DOI : 10.1093/bioinformatics/btp332
KEGG for linking genomes to life and the environment, Nucleic Acids Research, vol.36, issue.Database, pp.480-484, 2008. ,
DOI : 10.1093/nar/gkm882
Reducibility among combinatorial problems, Complexity of Computer Computations, pp.85-103, 1972. ,
DOI : 10.1007/978-3-540-68279-0_8
Advances in flux balance analysis, Current Opinion in Biotechnology, vol.14, issue.5, pp.491-496, 2003. ,
DOI : 10.1016/j.copbio.2003.08.001
Hypergraphs and Cellular Networks, PLoS Computational Biology, vol.9, issue.5, p.1000385, 2009. ,
DOI : 10.1371/journal.pcbi.1000385.g002
URL : http://doi.org/10.1371/journal.pcbi.1000385
Exploration of the core metabolism of symbiotic bacteria, BMC Genomics, vol.13, issue.1, p.438, 2012. ,
DOI : 10.1146/annurev.genet.41.110306.130119
URL : https://hal.archives-ouvertes.fr/hal-00784396
Structural and dynamical analysis of biological networks, Briefings in Functional Genomics, vol.11, issue.6, 2012. ,
DOI : 10.1093/bfgp/els030
URL : https://hal.archives-ouvertes.fr/hal-00737455
Centrality analysis methods for biological networks and their application to gene regulatory networks, Gene Regulation and Systems Biology, vol.2, pp.193-201, 2008. ,
An Introduction to Metabolic Networks and Their Structural Analysis, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.5, issue.4, pp.594-617, 2008. ,
DOI : 10.1109/TCBB.2008.79
URL : https://hal.archives-ouvertes.fr/hal-00355497
A new constraint-based description of the steady-state flux cone of metabolic networks, Discrete Applied Mathematics, vol.157, issue.10, pp.2257-2266, 2009. ,
DOI : 10.1016/j.dam.2008.06.039
Pathos: A web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry, Rapid Communications in Mass Spectrometry, vol.37, issue.22, pp.253422-3426, 2011. ,
DOI : 10.1002/rcm.5245
A new pathway for vacuolar cadmium sequestration in Saccharomyces cerevisiae: YCF1-catalyzed transport of bis(glutathionato)cadmium, Proceedings of the National Academy of Sciences, vol.94, issue.1, 1997. ,
DOI : 10.1073/pnas.94.1.42
Direct Introduction of Biological Samples into a LTQ-Orbitrap Hybrid Mass Spectrometer as a Tool for Fast Metabolome Analysis, Analytical Chemistry, vol.80, issue.9, pp.3291-3303, 2008. ,
DOI : 10.1021/ac7024915
Flux coupling analysis of metabolic networks is sensitive to missing reactions, Biosystems, vol.103, issue.1, pp.57-66, 2011. ,
DOI : 10.1016/j.biosystems.2010.09.011
Graph theory and networks in Biology, IET Systems Biology, vol.1, issue.2, pp.89-119, 2007. ,
DOI : 10.1049/iet-syb:20060038
Parallel genomic evolution and metabolic interdependence in an ancient symbiosis, Proceedings of the National Academy of Sciences, vol.104, issue.49, pp.19392-19397, 2007. ,
DOI : 10.1073/pnas.0708855104
Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms, Algorithms in Bioinformatics Lecture Notes in Computer Science, vol.6293, pp.226-237, 2010. ,
DOI : 10.1007/978-3-642-15294-8_19
URL : https://hal.archives-ouvertes.fr/hal-00751339
Finding the K shortest hyperpaths, Computers & Operations Research, vol.32, issue.6, pp.1477-1497, 2005. ,
DOI : 10.1016/j.cor.2003.11.014
Systematizing the generation of missing metabolic knowledge, Biotechnology and Bioengineering, vol.98, issue.14, pp.403-412, 2010. ,
DOI : 10.1002/bit.22844
Comparison of network-based pathway analysis methods, Trends in Biotechnology, vol.22, issue.8, pp.22400-405, 2004. ,
DOI : 10.1016/j.tibtech.2004.06.010
Using graph theory to analyze biological networks, BioData Mining, vol.19, issue.4, p.10, 2011. ,
DOI : 10.1186/1756-0381-4-10
OptStrain: A computational framework for redesign of microbial production systems, Genome Research, vol.14, issue.11, pp.2367-2376, 2004. ,
DOI : 10.1101/gr.2872004
Modular decomposition of metabolic systems via null-space analysis, Journal of Theoretical Biology, vol.249, issue.4, pp.691-705, 2007. ,
DOI : 10.1016/j.jtbi.2007.08.005
Genome-scale microbial in silico models: the constraints-based approach, Trends in Biotechnology, vol.21, issue.4, pp.162-169, 2003. ,
DOI : 10.1016/S0167-7799(03)00030-1
A sub-constant error-probability low-degree test, and a subconstant error-probability pcp characterization of np, Proceedings of the twenty-ninth annual ACM symposium on Theory of computing, STOC '97, pp.475-484, 1997. ,
Towards multidimensional genome annotation, Nature Reviews Genetics, vol.420, issue.2, pp.130-141, 2006. ,
DOI : 10.1038/nrg1769
NUTRIENT-RELATED ANALYSIS OF PATHWAY/GENOME DATABASES, Biocomputing 2001, pp.471-482, 2001. ,
DOI : 10.1142/9789814447362_0046
Optimization based automated curation of metabolic reconstructions, BMC Bioinformatics, vol.8, issue.1, p.212, 2007. ,
DOI : 10.1186/1471-2105-8-212
Optimization based automated curation of metabolic reconstructions, BMC Bioinformatics, vol.8, issue.1, p.212, 2007. ,
DOI : 10.1186/1471-2105-8-212
BRENDA, the enzyme information system in 2011, Nucleic Acids Research, vol.39, issue.Database, pp.670-676, 2011. ,
DOI : 10.1093/nar/gkq1089
Theory for the Systemic Definition of Metabolic Pathways and their use in Interpreting Metabolic Function from a Pathway-Oriented Perspective, Journal of Theoretical Biology, vol.203, issue.3, pp.229-248, 2000. ,
DOI : 10.1006/jtbi.2000.1073
Enumeration: algorithms and complexity, 2009. ,
Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering, Trends in Biotechnology, vol.17, issue.2, pp.53-60, 1999. ,
DOI : 10.1016/S0167-7799(98)01290-6
ON ELEMENTARY FLUX MODES IN BIOCHEMICAL REACTION SYSTEMS AT STEADY STATE, Journal of Biological Systems, vol.02, issue.02, pp.165-182, 1994. ,
DOI : 10.1142/S0218339094000131
On enumerating all minimal solutions of feedback problems, Discrete Applied Mathematics, vol.117, issue.1-3, pp.253-265, 2002. ,
DOI : 10.1016/S0166-218X(00)00339-5
Identifying Regulatory Subnetworks for a Set of Genes, Molecular & Cellular Proteomics, vol.4, issue.5, pp.683-692, 2005. ,
DOI : 10.1074/mcp.M400110-MCP200
Packing directed circuits fractionally, Combinatorica, vol.2, issue.2, pp.281-288, 1995. ,
DOI : 10.1007/BF01200760
Mathematical models in microbial systems biology, Current Opinion in Microbiology, vol.7, issue.5, pp.513-518, 2004. ,
DOI : 10.1016/j.mib.2004.08.004
Genome-scale gene/reaction essentiality and synthetic lethality analysis, Molecular Systems Biology, vol.177, 2009. ,
DOI : 10.1038/msb4100034
URL : http://doi.org/10.1038/msb.2009.56
An approximate solution for the steiner problem in graphs, Math Japan, vol.24, pp.573-577, 1980. ,
A protocol for generating a high-quality genome-scale metabolic reconstruction, Nature Protocols, vol.161, issue.1, pp.93-121, 2010. ,
DOI : 10.1186/1752-0509-3-37
Functional stoichiometric analysis of metabolic networks, Bioinformatics, vol.21, issue.22, pp.4176-4180, 2005. ,
DOI : 10.1093/bioinformatics/bti674
MaGe: a microbial genome annotation system supported by synteny results, Nucleic Acids Research, vol.34, issue.1, pp.53-65, 2006. ,
DOI : 10.1093/nar/gkj406
Graph-Based Analysis of Metabolic Networks, Ernst Schering Res Found Workshop, vol.38, pp.245-74, 2002. ,
DOI : 10.1007/978-3-662-04747-7_12
Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use, Bio/Technology, vol.43, issue.10, pp.994-998, 1994. ,
DOI : 10.1006/jtbi.1993.1203
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type escherichia coli w3110, Applied and Environmental Microbiology, issue.10, pp.603724-3731, 1994. ,
A new computational method to split large biochemical networks into coherent subnets, BMC Systems Biology, vol.5, issue.1, p.25, 2011. ,
DOI : 10.1186/1752-0509-5-25
Modular decomposition of metabolic reaction networks based on flux analysis and pathway projection, Bioinformatics, vol.23, issue.18, pp.232433-2440, 2007. ,
DOI : 10.1093/bioinformatics/btm374