{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T06:42:24Z","timestamp":1768286544475,"version":"3.49.0"},"reference-count":37,"publisher":"Springer Science and Business Media LLC","issue":"S3","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/1752-0509-9-s3-s3","type":"journal-article","created":{"date-parts":[[2015,6,18]],"date-time":"2015-06-18T10:06:47Z","timestamp":1434622007000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["The hierarchical organization of natural protein interaction networks confers self-organization properties on pseudocells"],"prefix":"10.1186","volume":"9","author":[{"given":"Eugenia","family":"Galeota","sequence":"first","affiliation":[]},{"given":"Caius","family":"Gravila","sequence":"additional","affiliation":[]},{"given":"Filippo","family":"Castiglione","sequence":"additional","affiliation":[]},{"given":"Massimo","family":"Bernaschi","sequence":"additional","affiliation":[]},{"given":"Gianni","family":"Cesareni","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2015,6,1]]},"reference":[{"issue":"21","key":"1465_CR1","doi-asserted-by":"publisher","first-page":"E58","DOI":"10.1371\/journal.pbio.0000058","volume":"1","author":"RC Hardison","year":"2003","unstructured":"Hardison RC: Comparative Genomics. PLoS Biol. 2003, 1 (21): E58-","journal-title":"PLoS Biol"},{"issue":"7118","key":"1465_CR2","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1038\/nature05295","volume":"444","author":"LA Pennacchio","year":"2006","unstructured":"Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, et al: In vivo enhancer analysis of human conserved non-coding sequences. Nature. 2006, 444 (7118): 499-502. 10.1038\/nature05295.","journal-title":"Nature"},{"issue":"2","key":"1465_CR3","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1038\/35052548","volume":"2","author":"LA Pennacchio","year":"2001","unstructured":"Pennacchio LA, Rubin EM: Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet. 2001, 2 (2): 100-109. 10.1038\/35052548.","journal-title":"Nat Rev Genet"},{"issue":"5","key":"1465_CR4","doi-asserted-by":"publisher","first-page":"749","DOI":"10.1101\/gr.45502","volume":"12","author":"B G\u00f6ttgens","year":"2002","unstructured":"G\u00f6ttgens B, Barton LM, Chapman MA, Sinclair AM, Knudsen B, Grafham D, et al: Transcriptional regulation of the stem cell leukemia gene (SCL)--comparative analysis of five vertebrate SCL loci. Genome Res. 2002, 12 (5): 749-759. 10.1101\/gr.45502.","journal-title":"Genome Res"},{"issue":"7084","key":"1465_CR5","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1038\/nature04532","volume":"440","author":"A-C Gavin","year":"2006","unstructured":"Gavin A-C, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, et al: Proteome survey reveals modularity of the yeast cell machinery. Nature. 2006, 440 (7084): 631-636. 10.1038\/nature04532.","journal-title":"Nature"},{"issue":"7062","key":"1465_CR6","doi-asserted-by":"publisher","first-page":"1173","DOI":"10.1038\/nature04209","volume":"437","author":"JF Rual","year":"2005","unstructured":"Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, et al: Towards a proteome-scale map of the human protein-protein interaction network. Nature. 2005, 437 (7062): 1173-1178. 10.1038\/nature04209.","journal-title":"Nature"},{"issue":"7084","key":"1465_CR7","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1038\/nature04670","volume":"440","author":"NJ Krogan","year":"2006","unstructured":"Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, et al: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006, 440 (7084): 637-643. 10.1038\/nature04670.","journal-title":"Nature"},{"issue":"10","key":"1465_CR8","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1016\/j.tibtech.2007.08.002","volume":"25","author":"L Kiemer","year":"2007","unstructured":"Kiemer L, Cesareni G: Comparative interactomics: comparing apples and pears?. Trends Biotechnol. 2007, 25 (10): 448-454. 10.1016\/j.tibtech.2007.08.002.","journal-title":"Trends Biotechnol"},{"issue":"Pt 21","key":"1465_CR9","doi-asserted-by":"publisher","first-page":"4947","DOI":"10.1242\/jcs.02714","volume":"118","author":"R Albert","year":"2005","unstructured":"Albert R: Scale-free networks in cell biology. J Cell Sci. 2005, 118 (Pt 21): 4947-4957.","journal-title":"J Cell Sci"},{"issue":"5439","key":"1465_CR10","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1126\/science.286.5439.509","volume":"286","author":"AL Barabasi","year":"1999","unstructured":"Barabasi AL, Albert R: Emergence of scaling in random networks. Science. 1999, 286 (5439): 509-512. 10.1126\/science.286.5439.509.","journal-title":"Science"},{"issue":"2","key":"1465_CR11","doi-asserted-by":"publisher","first-page":"026112","DOI":"10.1103\/PhysRevE.67.026112","volume":"67","author":"E Ravasz","year":"2003","unstructured":"Ravasz E, Barab\u00e1si AL: Hierarchical organization in complex networks. Phys Rev E. 2003, 67 (2): 026112-","journal-title":"Phys Rev E"},{"issue":"Suppl 1","key":"1465_CR12","doi-asserted-by":"publisher","first-page":"S4","DOI":"10.1186\/1471-2105-8-S1-S4","volume":"8","author":"M Bernaschi","year":"2007","unstructured":"Bernaschi M, Castiglione F, Ferranti A, Gavrila C, Tinti M, Cesareni G: ProtNet: a tool for stochastic simulations of protein interaction networks dynamics. BMC Bioinformatics. 2007, 8 (Suppl 1): S4-10.1186\/1471-2105-8-S1-S4.","journal-title":"BMC Bioinformatics"},{"issue":"10","key":"1465_CR13","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1016\/S0968-0004(01)01938-7","volume":"26","author":"RJ Ellis","year":"2001","unstructured":"Ellis RJ: Macromolecular crowding: obvious but underappreciated. Trends Biochem Sci. 2001, 26 (10): 597-604. 10.1016\/S0968-0004(01)01938-7.","journal-title":"Trends Biochem Sci"},{"issue":"8","key":"1465_CR14","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1038\/nmeth.2561","volume":"10","author":"A Calderone","year":"2013","unstructured":"Calderone A, Castagnoli L, Cesareni G: mentha: a resource for browsing integrated protein-interaction networks. Nat Methods. 2013, 10 (8): 690-691. 10.1038\/nmeth.2561.","journal-title":"Nat Methods"},{"issue":"4","key":"1465_CR15","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1038\/nmeth.1931","volume":"9","author":"S Orchard","year":"2012","unstructured":"Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, et al: Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods. 2012, 9 (4): 345-350. 10.1038\/nmeth.1931.","journal-title":"Nat Methods"},{"issue":"Database issue","key":"1465_CR16","doi-asserted-by":"publisher","first-page":"D857","DOI":"10.1093\/nar\/gkr930","volume":"40","author":"L Licata","year":"2012","unstructured":"Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, Galeota E, et al: MINT, the molecular interaction database: 2012 update. Nucleic Acids Res. 2012, 40 (Database issue): D857-D861.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"1465_CR17","doi-asserted-by":"publisher","first-page":"D841","DOI":"10.1093\/nar\/gkr1088","volume":"40","author":"S Kerrien","year":"2012","unstructured":"Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, et al: The IntAct molecular interaction database in 2012. Nucleic Acids Res. 2012, 40 (Database issue): D841-D846.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"1465_CR18","doi-asserted-by":"publisher","first-page":"D449","DOI":"10.1093\/nar\/gkh086","volume":"32","author":"L Salwinski","year":"2004","unstructured":"Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2004, 32 (Database issue): D449-D451.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"1465_CR19","doi-asserted-by":"publisher","first-page":"D816","DOI":"10.1093\/nar\/gks1158","volume":"41","author":"A Chatr-Aryamontri","year":"2013","unstructured":"Chatr-Aryamontri A, Breitkreutz BJ, Heinicke S, Boucher L, Winter A, Stark C, et al: The BioGRID interaction database: 2013 update. Nucleic Acids Res. 2013, 41 (Database issue): D816-D823.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"1465_CR20","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1093\/bioinformatics\/btp025","volume":"25","author":"E Chautard","year":"2009","unstructured":"Chautard E, Ballut L, Thierry-Mieg N, Ricard-Blum S: MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. Bioinforma Oxf Engl. 2009, 25 (5): 690-691. 10.1093\/bioinformatics\/btp025.","journal-title":"Bioinforma Oxf Engl"},{"issue":"6","key":"1465_CR21","doi-asserted-by":"publisher","first-page":"932","DOI":"10.1002\/pmic.200600448","volume":"7","author":"L Kiemer","year":"2007","unstructured":"Kiemer L, Costa S, Ueffing M, Cesareni G: WI-PHI: a weighted yeast interactome enriched for direct physical interactions. Proteomics. 2007, 7 (6): 932-943. 10.1002\/pmic.200600448.","journal-title":"Proteomics"},{"key":"1465_CR22","first-page":"17","volume-title":"Publ Math Inst Hung Acad Sci","author":"P Erd\u00f6s","year":"1960","unstructured":"Erd\u00f6s P, R\u00e9nyi A: On the Evolution of Random Graphs. Publ Math Inst Hung Acad Sci. 1960, 17-61."},{"issue":"23-24","key":"1465_CR23","doi-asserted-by":"publisher","first-page":"4577","DOI":"10.1016\/j.physa.2011.06.052","volume":"390","author":"LS Heath","year":"2011","unstructured":"Heath LS, Parikh N: Generating random graphs with tunable clustering coefficients. Physica A: Statistical Mechanics and its Applications. 2011, 390 (23-24): 4577-4587. 10.1016\/j.physa.2011.06.052.","journal-title":"Physica A: Statistical Mechanics and its Applications"},{"issue":"2\/3","key":"1465_CR24","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1002\/rsa.3240060204","volume":"6","author":"M Molloy","year":"1995","unstructured":"Molloy M, Reed B: A critical point for random graphs with a given degree sequence. Random Struct Algorithms. 1995, 6 (2\/3): 161-180.","journal-title":"Random Struct Algorithms"},{"key":"1465_CR25","first-page":"10","volume-title":"IEEE","author":"W Guo","year":"2009","unstructured":"Guo W, Kraines SB: A Random Network Generator with Finely Tunable Clustering Coefficient for Small-World Social Networks. IEEE. 2009, 10-17."},{"issue":"17","key":"1465_CR26","doi-asserted-by":"publisher","first-page":"7640","DOI":"10.1073\/pnas.0912983107","volume":"107","author":"G Palla","year":"2010","unstructured":"Palla G, Lovasz L, Vicsek T: Multifractal network generator. Proc Natl Acad Sci. 2010, 107 (17): 7640-7645. 10.1073\/pnas.0912983107.","journal-title":"Proc Natl Acad Sci"},{"key":"1465_CR27","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1007\/s11590-011-0319-x","volume":"5","author":"CE Gounaris","year":"2011","unstructured":"Gounaris CE, Rajendran K, Kevrekidis IG, Floudas CA: Generation of networks with prescribed degree-dependent clustering. Optim Lett. 2011, 5: 435-451. 10.1007\/s11590-011-0319-x.","journal-title":"Optim Lett"},{"key":"1465_CR28","volume-title":"Phys Rev E","author":"E Volz","year":"2004","unstructured":"Volz E: Random networks with tunable degree distribution and clustering. Phys Rev E. 2004, 70:"},{"key":"1465_CR29","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4419-8819-5","volume-title":"Weighted Network Analysis Applications in Genomics and Systems Biology","author":"S Horvath","year":"2011","unstructured":"Horvath S: Weighted Network Analysis Applications in Genomics and Systems Biology. 2011, New York: Springer"},{"issue":"6684","key":"1465_CR30","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1038\/30918","volume":"393","author":"DJ Watts","year":"1998","unstructured":"Watts DJ, Strogatz SH: Collective dynamics of \"small-world\" networks. Nature. 1998, 393 (6684): 440-442. 10.1038\/30918.","journal-title":"Nature"},{"issue":"Suppl 1","key":"1465_CR31","doi-asserted-by":"publisher","first-page":"2566","DOI":"10.1073\/pnas.012582999","volume":"99","author":"MEJ Newman","year":"2002","unstructured":"Newman MEJ, Watts DJ, Strogatz SH: Random graph models of social networks. Proc Natl Acad Sci USA. 2002, 99 (Suppl 1): 2566-2572.","journal-title":"Proc Natl Acad Sci USA"},{"key":"1465_CR32","doi-asserted-by":"publisher","first-page":"265","DOI":"10.7155\/jgaa.00108","volume":"9","author":"T Schank","year":"2005","unstructured":"Schank T, Wagner D: Approximating Clustering Coefficient and Transitivity. J Graph Algorithms Appl. 2005, 9: 265-275. 10.7155\/jgaa.00108.","journal-title":"J Graph Algorithms Appl"},{"issue":"11","key":"1465_CR33","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13 (11): 2498-2504. 10.1101\/gr.1239303.","journal-title":"Genome Res"},{"issue":"2","key":"1465_CR34","doi-asserted-by":"publisher","first-page":"282","DOI":"10.1093\/bioinformatics\/btm554","volume":"24","author":"Y Assenov","year":"2008","unstructured":"Assenov Y, Ram\u00edrez F, Schelhorn SE, Lengauer T, Albrecht M: Computing topological parameters of biological networks. Bioinforma Oxf Engl. 2008, 24 (2): 282-284. 10.1093\/bioinformatics\/btm554.","journal-title":"Bioinforma Oxf Engl"},{"issue":"23","key":"1465_CR35","doi-asserted-by":"publisher","first-page":"8577","DOI":"10.1073\/pnas.0601602103","volume":"103","author":"MEJ Newman","year":"2006","unstructured":"Newman MEJ: Modularity and community structure in networks. Proc Natl Acad Sci USA. 2006, 103 (23): 8577-8582. 10.1073\/pnas.0601602103.","journal-title":"Proc Natl Acad Sci USA"},{"key":"1465_CR36","first-page":"1","volume-title":"Sitges Proc Complex Netw","author":"A Barab\u00e1si","year":"2003","unstructured":"Barab\u00e1si A, Dezso Z, Ravasz E, Oltvai Z: Scale-free and hierarchical structures in complex networks. Sitges Proc Complex Netw. 2003, Springer-Verlag, 1-16."},{"key":"1465_CR37","volume-title":"A Spatial Approach to Network Generation for Three Properties: Degree Distribution, Clustering Coefficient and Degree Assortativity","author":"Rob Badham","year":"2010","unstructured":"Badham Rob: A Spatial Approach to Network Generation for Three Properties: Degree Distribution, Clustering Coefficient and Degree Assortativity. 2010, 13 (1):"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-9-S3-S3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T19:41:54Z","timestamp":1630611714000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-9-S3-S3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,6,1]]},"references-count":37,"journal-issue":{"issue":"S3","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["1465"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-9-s3-s3","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,6,1]]},"assertion":[{"value":"1 June 2015","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S3"}}