H. Yu, P. Braun, M. Yildirim, I. Lemmens, K. Venkatesan et al., High-Quality Binary Protein Interaction Map of the Yeast Interactome Network, Science, vol.3, issue.4, pp.104-114, 2008.
DOI : 10.1371/journal.pcbi.0030059

T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori et al., A comprehensive two-hybrid analysis to explore the yeast protein interactome, Proceedings of the National Academy of Sciences, vol.18, issue.12, pp.4569-74, 2001.
DOI : 10.1038/82360

N. Krogan, G. Cagney, H. Yu, G. Zhong, X. Guo et al., Global landscape of protein complexes in the yeast Saccharomyces cerevisiae, JF. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae, pp.637-680, 2006.
DOI : 10.1016/0092-8674(85)90117-5

A. Gavin, P. Aloy, P. Grandi, R. Krause, M. Boesche et al., Proteome survey reveals modularity of the yeast cell machinery, Nature, vol.134, issue.7084, pp.631-637, 2006.
DOI : 10.1534/genetics.104.040063

D. Las, R. Fontanillo, and C. , Protein-protein interactions essentials: key concepts to building and analyzing interactome networks, PLoS Comput Biol, vol.6, p.1000807, 2010.

H. Heide and I. Wittig, Methods to analyse composition and dynamics of macromolecular complexes, Biochemical Society Transactions, vol.681, issue.5, pp.1235-1276, 2013.
DOI : 10.1007/978-1-60761-913-0_2

V. Mering, C. Krause, R. Snel, B. Cornell, M. Oliver et al., Comparative assessment of large-scale data sets of protein???protein interactions, Nature, vol.417, pp.399-403, 2002.
DOI : 10.1038/nature750

J. Gillis, S. Ballouz, and P. Pavlidis, Bias tradeoffs in the creation and analysis of protein???protein interaction networks, Journal of Proteomics, vol.100, pp.44-54, 2014.
DOI : 10.1016/j.jprot.2014.01.020

J. Chang, Y. Zhou, M. Qamar, L. Chen, and Y. Ding, Prediction of Protein???Protein Interactions by Evidence Combining Methods, International Journal of Molecular Sciences, vol.350, issue.11
DOI : 10.1038/nature11503

D. Merico, D. Gfeller, and G. Bader, How to visually interpret biological data using networks, Nature Biotechnology, vol.9, issue.10, pp.921-925, 2009.
DOI : 10.1126/science.1087447

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4154490

G. Agapito, P. Guzzi, and M. Cannataro, Visualization of protein interaction networks: problems and solutions, BMC Bioinformatics, vol.14, issue.Suppl 1, p.1, 2013.
DOI : 10.1093/bioinformatics/bti551

D. Szklarczyk, A. Franceschini, S. Wyder, K. Forslund, D. Heller et al., STRING v10: protein-protein interaction networks, integrated over the tree of life, Nucleic Acids Research, vol.43, issue.D1, pp.447-52, 2015.
DOI : 10.1093/nar/gku1003

K. Mitra, A. Carvunis, S. Ramesh, and T. Ideker, Integrative approaches for finding modular structure in biological networks, Nature Reviews Genetics, vol.333, issue.10, pp.719-751, 2013.
DOI : 10.1186/1471-2105-11-95

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3940161

M. Mete, F. Tang, X. Xu, and N. Yuruk, A structural approach for finding functional modules from large biological networks, BMC Bioinformatics, vol.9, issue.Suppl 9, p.19, 2008.
DOI : 10.1186/1471-2105-9-S9-S19

URL : http://doi.org/10.1186/1471-2105-9-s9-s19

S. Srihari, C. Yong, A. Patil, and L. Wong, Methods for protein complex prediction and their contributions towards understanding the organisation, function and dynamics of complexes, FEBS Letters, vol.24, issue.19PartA, 2015.
DOI : 10.1093/bioinformatics/btm630

S. Srihari and H. Leong, Temporal dynamics of protein complexes in PPI networks: a case study using yeast cell cycle dynamics, BMC Bioinformatics, vol.13, p.16, 2012.

S. Brohée and J. Van-helden, Evaluation of clustering algorithms for protein-protein interaction networks, BMC Bioinformatics, vol.7, issue.1, pp.488-507, 2006.
DOI : 10.1186/1471-2105-7-488

X. Li, M. Wu, C. Kwoh, and S. Ng, Computational approaches for detecting protein complexes from protein interaction networks: a survey, BMC Genomics, vol.11, issue.Suppl 1, p.3, 2010.
DOI : 10.1186/1471-2164-11-S1-S3

URL : http://doi.org/10.1186/1471-2164-11-s1-s3

J. Wang, M. Li, Y. Deng, and Y. Pan, Recent advances in clustering methods for protein interaction networks, BMC Genomics, vol.11, issue.Suppl 3, p.10, 2010.
DOI : 10.1186/1471-2164-11-S3-S10

C. Yong, G. Liu, H. Chua, and L. Wong, Supervised maximum-likelihood weighting of composite protein networks for complex prediction, BMC Systems Biology, vol.6, issue.Suppl 2, p.13, 2012.
DOI : 10.1101/gr.1239303

H. Ahmed, D. Battacharyya, and J. Kalita, Core and peripheral connectivity based cluster analysis over PPI network, Computational Biology and Chemistry, vol.59, 2015.
DOI : 10.1016/j.compbiolchem.2015.08.008

S. Glatt, J. Létoquart, C. Faux, N. Taylor, B. Séraphin et al., The Elongator subcomplex Elp456 is a hexameric RecA-like ATPase, Nature Structural & Molecular Biology, vol.13, issue.3, pp.314-334, 2012.
DOI : 10.1038/13732

S. Glatt and C. Müller, Structural insights into Elongator function, Current Opinion in Structural Biology, vol.23, issue.2, pp.235-277, 2013.
DOI : 10.1016/j.sbi.2013.02.009

Z. Lin, W. Zhao, W. Diao, X. Xie, Z. Wang et al., Crystal Structure of Elongator Subcomplex Elp4???6, Journal of Biological Chemistry, vol.10, issue.25, pp.21501-21509, 2012.
DOI : 10.1073/pnas.181342398

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3375571

L. Larivière, C. Plaschka, M. Seizl, L. Wenzeck, F. Kurth et al., Structure of the Mediator head module, Nature, vol.5, issue.7429, pp.448-51, 2012.
DOI : 10.1002/0471250953.bi0506s15

Y. Takagi, G. Calero, H. Komori, J. Brown, A. Ehrensberger et al., Head Module Control of Mediator Interactions, Molecular Cell, vol.23, issue.3, pp.355-64, 2006.
DOI : 10.1016/j.molcel.2006.06.007

URL : http://doi.org/10.1016/j.molcel.2006.06.007

T. Imasaki, G. Calero, G. Cai, K. Tsai, K. Yamada et al., Architecture of the Mediator head module, Nature, vol.16, issue.7355, pp.240-243, 2011.
DOI : 10.1038/nsmb.1532

C. Lange and C. Hunte, Crystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c, Proceedings of the National Academy of Sciences, vol.355, issue.6359, pp.2800-2805, 2002.
DOI : 10.1038/355472a0

P. Smith, J. Fox, and D. Winge, Biogenesis of the cytochrome bc1 complex and role of assembly factors, Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol.1817, issue.2, pp.872-82, 2012.
DOI : 10.1016/j.bbabio.2011.11.009

V. Zara, L. Conte, and B. Trumpower, Biogenesis of the yeast cytochrome bc1 complex, Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol.1793, issue.1, pp.89-96, 2009.
DOI : 10.1016/j.bbamcr.2008.04.011

A. Conte, B. Papa, A. Ferramosca, and V. Zara, The dimerization of the yeast cytochrome bc1 complex is an early event and is independent of Rip1, Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol.1853, issue.5, pp.987-95, 2015.
DOI : 10.1016/j.bbamcr.2015.02.006

S. Kerrien, Y. Alam-faruque, B. Aranda, I. Bancarz, A. Bridge et al., IntAct--open source resource for molecular interaction data, Nucleic Acids Research, vol.35, issue.Database, pp.561-566, 2007.
DOI : 10.1093/nar/gkl958

URL : http://doi.org/10.1093/nar/gkl958

J. Villaveces, R. Jiménez, P. Porras, N. Del-toro, M. Duesbury et al., Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study, Database, vol.2015, issue.0, pp.1-12, 2015.
DOI : 10.1093/database/bau131

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316181

G. Bader and C. Hogue, An automated method for finding molecular complexes in large protein interaction networks, BMC Bioinformatics, vol.4, issue.2, 2003.

T. Nepusz, H. Yu, and A. Paccanaro, Detecting overlapping protein complexes in protein-protein interaction networks, Nature Methods, vol.57, issue.5, pp.471-473, 2012.
DOI : 10.1093/bioinformatics/btn376

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3543700

P. Gambette and A. Guénoche, Bootstrap clustering for graph partitioning, RAIRO - Operations Research, vol.45, issue.4, pp.339-52, 2011.
DOI : 10.1051/ro/2012001

URL : https://hal.archives-ouvertes.fr/hal-00676989

Q. Zhang, D. Petrey, L. Deng, L. Qiang, Y. Shi et al., Structure-based prediction of protein???protein interactions on a genome-wide scale, Nature, vol.374, issue.7421, pp.556-60, 2012.
DOI : 10.1186/1471-2105-6-247

Q. Zhang, D. Petrey, J. Garzón, L. Deng, and B. Honig, PrePPI: a structure-informed database of protein-protein interactions, Nucleic Acids Research, vol.41, issue.D1, pp.828-861, 2013.
DOI : 10.1093/nar/gks1231

C. Plaschka, L. Larivière, L. Wenzeck, M. Seizl, M. Hemann et al., Architecture of the RNA polymerase II???Mediator core initiation complex, Nature, vol.38, issue.7539, pp.376-80, 2015.
DOI : 10.1093/nar/gkq029

A. Belle, A. Tanay, L. Bitincka, R. Shamir, O. Shea et al., Quantification of protein half-lives in the budding yeast proteome, Proceedings of the National Academy of Sciences, vol.3, issue.11, pp.13004-13013, 2006.
DOI : 10.1074/mcp.M400099-MCP200

M. Wang, M. Weiss, M. Simonovic, G. Haertinger, S. Schrimpf et al., PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life, Molecular & Cellular Proteomics, vol.6, issue.8, pp.492-500, 2012.
DOI : 10.1126/science.1158441

N. Zaki and A. Mora, A comparative analysis of computational approaches and algorithms for protein subcomplex identification, Scientific Reports, vol.37, issue.1, p.4262, 2014.
DOI : 10.1093/nar/gkn1005

B. Chen, W. Fan, J. Liu, and F. Wu, Identifying protein complexes and functional modules--from static PPI networks to dynamic PPI networks, Briefings in Bioinformatics, vol.15, issue.2, pp.177-94, 2014.
DOI : 10.1093/bib/bbt039

X. Shen, L. Yi, X. Jiang, Y. Zhao, X. Hu et al., Neighbor affinity based algorithm for discovering temporal protein complex from dynamic PPI network, Methods, vol.110, issue.16, pp.1046-202330174, 2016.
DOI : 10.1016/j.ymeth.2016.06.010

S. Razick, G. Magklaras, and I. Donaldson, iRefIndex: A consolidated protein interaction database with provenance, BMC Bioinformatics, vol.9, issue.1, p.405, 2008.
DOI : 10.1186/1471-2105-9-405

URL : http://doi.org/10.1186/1471-2105-9-405

C. Stark, B. Breitkreutz, T. Reguly, L. Boucher, A. Breitkreutz et al., BioGRID: a general repository for interaction datasets, Nucleic Acids Research, vol.34, issue.90001, pp.535-539, 2006.
DOI : 10.1093/nar/gkj109

URL : http://doi.org/10.1093/nar/gkj109

A. Guénoche and H. Garretta, Representation and evaluation of partitions In classification, clustering, and data analysis, part of the series studies in classification, data analysis, and knowledge organization, pp.131-139, 2002.

M. Longtine, A. Mckenzie, D. Demarini, N. Shah, A. Wach et al., Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae, Yeast, vol.10, pp.953-61, 1998.

C. Lemaire and G. Dujardin, Preparation of Respiratory Chain Complexes from Saccharomyces cerevisiae Wild-Type and Mutant Mitochondria, Methods Mol Biol, vol.432, pp.65-81, 2008.
DOI : 10.1007/978-1-59745-028-7_5

C. Hunte, J. Koepke, C. Lange, T. Rossmanith, and H. Michel, Structure at 2.3 ?? resolution of the cytochrome bc1 complex from the yeast Saccharomyces cerevisiae co-crystallized with an antibody Fv fragment, Structure, vol.8, issue.6, pp.669-84, 2000.
DOI : 10.1016/S0969-2126(00)00152-0

C. Nouet, G. Truan, L. Mathieu, and G. Dujardin, Functional Analysis of Yeast bcs1 Mutants Highlights the Role of Bcs1p-Specific Amino Acids in the AAA Domain, Journal of Molecular Biology, vol.388, issue.2, pp.252-61, 2009.
DOI : 10.1016/j.jmb.2009.03.018