V. Acuna, Telling stories: enumerating maximal directed acyclic graphs with a constrained set of sources and targets, Theor. Comput. Sci, vol.457, pp.1-9, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00764025

A. V. Antonov, Ticl -a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics, FEBS J, vol.276, pp.2084-2094, 2009.

T. Blum and O. Kohlbacher, Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks, J. Comput. Biol, vol.15, pp.565-576, 2008.

M. Borassi, Telling stories fast: via linear-time delay pitch enumeration, 12th International Symposium, SEA 2013, 2013.

R. Caspi, The metacyc database of metabolic pathways and enzymes and the biocyc collection of pathway/genome databases, Nucleic Acids Res, vol.38, pp.473-479, 2010.

L. Cottret, Metexplore: a web server to link metabolomic experiments and genome-scale metabolic networks, Nucleic Acids Res, vol.38, pp.132-137, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00690651

D. Croes, Inferring meaningful pathways in weighted metabolic networks, J. Mol. Biol, vol.356, pp.222-236, 2006.
URL : https://hal.archives-ouvertes.fr/hal-01624320

M. T. Dittrich, Identifying functional modules in protein-protein interaction networks: an integrated exact approach, Bioinformatics, vol.24, pp.223-231, 2008.

M. Fauchon, Sulfur sparing in the yeast proteome in response to sulfur demand, Mol. Cell, vol.9, pp.713-723, 2002.

K. Faust, Pathway discovery in metabolic networks by subgraph extraction, Bioinformatics, vol.26, pp.1211-1218, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01624293

M. D. Groppa, Benavides. Nitric oxide, polyamines and cd-induced phytotoxicity in wheat roots, Phytochemistry, vol.69, pp.2609-2615, 2008.

P. Khatri, Ten years of pathway analysis: current approaches and outstanding challenges, PLoS Comput. Biol, vol.8, p.1002375, 2012.

V. Lacroix, An introduction to metabolic networks and their structural analysis, IEEE/ACM Trans. Comput. Biol. Bioinform, vol.5, pp.594-617, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00355497

A. Lafaye, Combined proteome and metabolite-profiling analyses reveal surprising insights into yeast sulfur metabolism, J. Biol. Chem, vol.280, pp.24723-24730, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00021888

D. P. Leader, Barrett. Pathos: a web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry, Rapid Commun. Mass Spectrom, vol.25, pp.3422-3426, 2011.

Z. Li, A new pathway for vacuolar cadmium sequestration in Saccharomyces cerevisiae: Ycf1-catalyzed transport of glutathionato cadmium, Proc. Natl Acad. Sci. USA, vol.94, pp.42-47, 1997.

G. Madalinski, Direct introduction of biological samples into a ltqorbitrap hybrid mass spectrometer as a tool for fast metabolome analysis, Anal. Chem, vol.80, pp.3291-3303, 2008.

S. Schuster, Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering, Trends Biotechnol, vol.17, pp.53-60, 1999.

S. Schuster and C. Hilgetag, On elementary flux modes in biochemical reaction systems at steady state, J. Biol. Syst, vol.2, pp.165-182, 1994.

B. Schwikowski and E. Speckenmeyer, On enumerating all minimal solutions of feedback problems, Discrete Appl. Math, vol.117, pp.253-265, 2002.

M. S. Scott, Identifying regulatory subnetworks for a set of genes, Mol. Cell. Proteomics, vol.4, pp.683-692, 2005.

A. Sekowska, Extracting biological information from DNA arrays: an unexpected link between arginine and methionine metabolism in bacillus subtilis, Genome Biol, vol.2, 2001.
URL : https://hal.archives-ouvertes.fr/hal-01219561

P. Shannon, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res, vol.13, pp.2498-2504, 2003.

A. Subramanian, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc. Natl Acad. Sci. USA, vol.102, pp.15545-15550, 2005.

L. W. Sumner, Proposed minimum reporting standards for chemical analysis, Metabolomics, vol.3, pp.211-221, 2007.

I. Thiele and B. O. Palsson, A protocol for generating a high-quality genomescale metabolic reconstruction, Nat. Protoc, vol.5, pp.93-121, 2010.

D. Thomas, Reverse methionine biosynthesis from s-adenosylmethionine in eukaryotic cells, J. Biol. Chem, vol.275, pp.40718-40724, 2000.

D. Thomas and Y. Surdin-kerjan, Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol, Mol. Biol. Rev, vol.61, pp.503-532, 1997.

J. Van-helden, Bioinformatics and Genome Analysis, Graph-Based Analysis of Metabolic Networks, vol.38, pp.245-274, 2002.

J. Xia, Metaboanalyst 2.0-a comprehensive server for metabolomic data analysis, Nucleic Acids Res, vol.40, pp.127-133, 2012.