R. Aebersold and M. Mann, Mass spectrometry-based proteomics, Nature, vol.1, issue.6928, pp.198-207, 2003.
DOI : 10.1016/S0960-9822(01)00632-7

H. A. Almohamad and S. O. Duffuaa, A linear programming approach for the weighted graph matching problem, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.15, issue.5, pp.522-525, 1993.
DOI : 10.1109/34.211474

S. Bandyopadhyay, R. Sharan, and T. Ideker, Systematic identification of functional orthologs based on protein network comparison, Genome Research, vol.16, issue.3
DOI : 10.1101/gr.4526006

J. Berg and M. Lässig, Cross-species analysis of biological networks by Bayesian alignment, Proc. Natl. Acad. Sci. USA, pp.10967-10972, 2006.
DOI : 10.1073/pnas.0602294103

K. Brein, M. Remm, and E. Sonnhammer, Inparanoid: a comprehensive database of eukaryothic orthologs, Nucleic acids research, vol.33, 2005.

T. Caelli and S. Kosinov, An eigenspace projection clustering method for inexact graph matching, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.26, issue.4, pp.515-519, 2004.
DOI : 10.1109/TPAMI.2004.1265866

D. Conte, P. Foggia, C. Sansone, and M. Vento, THIRTY YEARS OF GRAPH MATCHING IN PATTERN RECOGNITION, International Journal of Pattern Recognition and Artificial Intelligence, vol.18, issue.03, pp.265-298, 2004.
DOI : 10.1142/S0218001404003228

URL : https://hal.archives-ouvertes.fr/hal-01408706

R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, 1998.
DOI : 10.1017/CBO9780511790492

S. Fields and O. Song, A novel genetic system to detect protein???protein interactions, Nature, vol.340, issue.6230, pp.245-246, 1989.
DOI : 10.1038/340245a0

J. Flannick, A. Novak, B. S. Srinivasan, H. H. Mcadams, and S. Batzoglou, Graemlin: General and robust alignment of multiple large interaction networks, Genome Research, vol.16, issue.9, pp.1169-1181, 2006.
DOI : 10.1101/gr.5235706

S. Gold and A. Rangarajan, A graduated assignment algorithm for graph matching, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.18, issue.4, pp.377-388, 1996.
DOI : 10.1109/34.491619

B. P. Kelley, R. Sharan, R. M. Karp, T. Sittler, D. E. Root et al., Conserved pathways within bacteria and yeast as revealed by global protein network alignment, Proc. Natl. Acad. Sci. USA, pp.10011394-11399, 2003.
DOI : 10.1073/pnas.1534710100

B. P. Kelley, B. Yuan, F. Lewitter, R. Sharan, B. R. Stockwell et al., PathBLAST: a tool for alignment of protein interaction networks, Nucleic Acids Research, vol.32, issue.Web Server, pp.83-88, 2004.
DOI : 10.1093/nar/gkh411

M. Koyutürk, Y. Kim, U. Topkara, S. Subramaniam, W. Szpankowski et al., Pairwise Alignment of Protein Interaction Networks, Journal of Computational Biology, vol.13, issue.2, pp.182-199, 2006.
DOI : 10.1089/cmb.2006.13.182

H. W. Kuhn, The Hungarian method for the assignment problem, Naval Research Logistics Quarterly, vol.3, issue.1-2, pp.83-97, 1955.
DOI : 10.1002/nav.3800020109

M. Remm, C. E. Storm, and E. L. Sonnhammer, Automatic clustering of orthologs and in-paralogs from pairwise species comparisons, Journal of Molecular Biology, vol.314, issue.5, pp.1041-1052, 2001.
DOI : 10.1006/jmbi.2000.5197

R. Sharan, S. Suthram, R. M. Kelley, T. Kuhn, S. Mccuine et al., Conserved patterns of protein interaction in multiple species, Proc. Natl. Acad. Sci. USA, pp.1974-1979, 2005.
DOI : 10.1073/pnas.0409522102

R. Singh, J. Xu, and B. Berger, Global alignment of multiple protein interaction networks with application to functional orthology detection, Proc. Natl. Acad. Sci. USA, pp.12763-12768, 2008.
DOI : 10.1073/pnas.0806627105

K. Sjölander, Phylogenomic inference of protein molecular function: advances and challenges, Bioinformatics, vol.20, issue.2, pp.170-179, 2004.
DOI : 10.1093/bioinformatics/bth021

S. Suthram, T. Sittler, and T. Ideker, The Plasmodium protein network diverges from those of other eukaryotes, Nature, vol.32, issue.7064, pp.108-112, 2005.
DOI : 10.1038/nature04135

S. Umeyama, An eigendecomposition approach to weighted graph matching problems, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.10, issue.5, pp.695-703, 1988.
DOI : 10.1109/34.6778

A. Viterbi, Error bounds for convolutional codes and an asymptotically optimum decoding algorithm, IEEE Transactions on Information Theory, vol.13, issue.2, pp.260-269, 1973.
DOI : 10.1109/TIT.1967.1054010

N. Yosef, R. Sharan, and W. S. Noble, Improved network-based identification of protein orthologs, Bioinformatics, vol.24, issue.16, pp.200-206, 2008.
DOI : 10.1093/bioinformatics/btn277

M. Zaslavskiy, F. Bach, and J. P. Vert, GRAPHM: Graph matching package, 2008.

M. Zaslavskiy, F. Bach, and J. P. Vert, A Path Following Algorithm for Graph Matching, Image and Signal Processing Proceedings of the 3rd International Conference, pp.329-337, 2008.
DOI : 10.1007/978-3-540-69905-7_38

URL : https://hal.archives-ouvertes.fr/hal-00433567

M. Zaslavskiy, F. Bach, and J. Vert, A Path Following Algorithm for the Graph Matching Problem, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.31, issue.12, 2008.
DOI : 10.1109/TPAMI.2008.245

URL : https://hal.archives-ouvertes.fr/hal-00433567