{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,20]],"date-time":"2024-09-20T16:20:36Z","timestamp":1726849236437},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"S8","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,6]]},"DOI":"10.1186\/s12859-017-1659-z","type":"journal-article","created":{"date-parts":[[2017,6,7]],"date-time":"2017-06-07T09:40:17Z","timestamp":1496828417000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["ATria: a novel centrality algorithm applied to biological networks"],"prefix":"10.1186","volume":"18","author":[{"given":"Trevor","family":"Cickovski","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eli","family":"Peake","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vanessa","family":"Aguiar-Pulido","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giri","family":"Narasimhan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,6,7]]},"reference":[{"key":"1659_CR1","doi-asserted-by":"crossref","DOI":"10.1093\/acprof:oso\/9780199206650.001.0001","volume-title":"Networks: an introduction","author":"MEJ Newman","year":"2010","unstructured":"Newman MEJ. Networks: an introduction. Oxford: Oxford University Press; 2010."},{"issue":"14","key":"1659_CR2","doi-asserted-by":"crossref","first-page":"4935","DOI":"10.1073\/pnas.0502024102","volume":"102","author":"E Davidson","year":"2005","unstructured":"Davidson E, Levin M. Gene regulatory networks. Proc Natl Acad Sci U S A. 2005; 102(14):4935.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"12","key":"1659_CR3","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1038\/82360","volume":"18","author":"B Schwikowski","year":"2000","unstructured":"Schwikowski B, Uetz P, Fields S. A network of protein-protein interactions in yeast. Nat Biotech. 2000; 18(12):1257\u201361.","journal-title":"Nat Biotech"},{"issue":"6","key":"1659_CR4","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1038\/scientificamerican0612-36","volume":"306","author":"J Ackerman","year":"2012","unstructured":"Ackerman J. The ultimate social network. Sci Am. 2012; 306(6):36\u201343.","journal-title":"Sci Am"},{"issue":"40","key":"1659_CR5","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1098\/rsif.2009.0203","volume":"6","author":"S Atkinson","year":"2009","unstructured":"Atkinson S, Williams P. Quorum sensing and social networking in the microbial world. J R Soc Interface. 2009; 6(40):959\u201378.","journal-title":"J R Soc Interface"},{"issue":"11","key":"1659_CR6","doi-asserted-by":"crossref","first-page":"S6","DOI":"10.1186\/1471-2164-16-S11-S6","volume":"16","author":"M Fernandez","year":"2015","unstructured":"Fernandez M, Riveros JD, Campos M, Mathee K, Narasimhan G. Microbial \u201cSocial Networks\u201d. BMC Genomics. 2015; 16(11):S6. (Special Issue).","journal-title":"BMC Genomics"},{"issue":"4","key":"1659_CR7","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1111\/j.1365-2958.1993.tb01737.x","volume":"9","author":"BL Bassler","year":"1993","unstructured":"Bassler BL, Wright M, Showalter RE, Silverman MR. Intercellular signalling in Vibrio Harveyi: sequence and function of genes regulating expression of luminescence. Mol Microbiol. 1993; 9(4):773\u201386.","journal-title":"Mol Microbiol"},{"issue":"3","key":"1659_CR8","first-page":"1","volume":"26","author":"SCP Williams","year":"2013","unstructured":"Williams SCP. Microbial social networks. HHMI Bulletin. 2013; 26(3):1\u20136.","journal-title":"HHMI Bulletin"},{"issue":"2","key":"1659_CR9","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1111\/j.1574-6976.2012.00345.x","volume":"37","author":"CS Pereira","year":"2013","unstructured":"Pereira CS, Thompson JA, Xavier KB. Ai-2-mediated signalling in bacteria. FEMS Microbiol Rev. 2013; 37(2):156\u201381.","journal-title":"FEMS Microbiol Rev"},{"issue":"12","key":"1659_CR10","doi-asserted-by":"crossref","first-page":"1002340","DOI":"10.1371\/journal.pcbi.1002340","volume":"7","author":"PJ Kim","year":"2011","unstructured":"Kim PJ, Price ND. Genetic Co-Occurrence Network across Sequenced Microbes. PLoS Comput Biol. 2011; 7(12):1002340.","journal-title":"PLoS Comput Biol"},{"issue":"11","key":"1659_CR11","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1002\/spe.4380211102","volume":"21","author":"TMJ Fruchterman","year":"1991","unstructured":"Fruchterman TMJ, Reingold EM. Graph drawing by force-directed placement. Softw Pract Experience. 1991; 21(11):1129\u201364.","journal-title":"Softw Pract Experience"},{"issue":"11","key":"1659_CR12","doi-asserted-by":"crossref","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, Amin N, Schwikowski B, Ideker T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498\u2013504.","journal-title":"Genome Res"},{"key":"1659_CR13","first-page":"193","volume":"2","author":"D Koschutzki","year":"2008","unstructured":"Koschutzki D, Schreiber F. Centrality analysis methods for biological networks and their application to gene regulatory networks. Gene Regul Syst Bio. 2008; 2:193\u2013201.","journal-title":"Gene Regul Syst Bio"},{"key":"1659_CR14","first-page":"1","volume":"2013","author":"Q Wu","year":"2013","unstructured":"Wu Q, Qi X, Fuller E, Zhang CQ. Follow the leader: A centrality guided clustering and its application to social network analysis. Sci World J. 2013; 2013:1\u20139.","journal-title":"Sci World J"},{"key":"1659_CR15","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511761942","volume-title":"Networks, Crowds, and Markets: Reasoning About a Highly Connected World","author":"D Easley","year":"2010","unstructured":"Easley D, Kleinberg J. Networks, Crowds, and Markets: Reasoning About a Highly Connected World. Cambridge: Cambridge University Press; 2010."},{"key":"1659_CR16","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1086\/228631","volume":"92","author":"P Bonacich","year":"1987","unstructured":"Bonacich P. Power and centrality: A family of measures. Am J Sociol. 1987; 92:1170\u201382.","journal-title":"Am J Sociol"},{"key":"1659_CR17","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1080\/15427951.2013.865686","volume":"10","author":"P Boldi","year":"2014","unstructured":"Boldi P, Vigna S. Axioms for centrality. Internet Math. 2014; 10:222\u201362.","journal-title":"Internet Math"},{"issue":"18","key":"1659_CR18","doi-asserted-by":"crossref","first-page":"3825","DOI":"10.1016\/j.comnet.2012.10.007","volume":"56","author":"S Brin","year":"2012","unstructured":"Brin S, Page L. Reprint of: The anatomy of a large-scale hypertextual web search engine. Comput Netw. 2012; 56(18):3825\u201333.","journal-title":"Comput Netw"},{"key":"1659_CR19","volume-title":"Proceedings of the Second Annual Conference on Communication Networks and Services Research","author":"W Xing","year":"2004","unstructured":"Xing W, Ghorbani A. Weighted PageRank algorithm. In: Proceedings of the Second Annual Conference on Communication Networks and Services Research. Washington: IEEE: 2004. p. 305\u201314."},{"key":"1659_CR20","volume-title":"Proceedings SIAM Data Mining Conference (SDM2008)","author":"C de Kerchove","year":"2008","unstructured":"de Kerchove C, Van Dooren P. The PageTrust algorithm: How to rank web pages when negative links are allowed? In: Proceedings SIAM Data Mining Conference (SDM2008). Atlanta: SIAM: 2008. p. 346\u201352."},{"key":"1659_CR21","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/j.socnet.2014.03.005","volume":"38","author":"MG Everett","year":"2014","unstructured":"Everett MG, Borgatti SP. Networks containing negative ties. Soc Networks. 2014; 38:111\u201320.","journal-title":"Soc Networks"},{"key":"1659_CR22","volume-title":"International Conference on Computational Advances in Bio and Medical Sciences (short Abstract). ICCABS \u201915","author":"T Cickovski","year":"2015","unstructured":"Cickovski T, Peake E, Aguiar-Pulido V, Narasimhan G. ATria: A novel centrality algorithm applied to biological networks. In: International Conference on Computational Advances in Bio and Medical Sciences (short Abstract). ICCABS \u201915. Miami: IEEE: 2015. p. 1."},{"issue":"5439","key":"1659_CR23","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1126\/science.286.5439.509","volume":"286","author":"AL Barab\u00e1si","year":"1999","unstructured":"Barab\u00e1si AL, Albert R. Emergence of scaling in random networks. Science. 1999; 286(5439):509\u201312.","journal-title":"Science"},{"issue":"1","key":"1659_CR24","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1006\/jeth.1996.0108","volume":"71","author":"MO Jackson","year":"1996","unstructured":"Jackson MO, Wolinsky A. A strategic model of social and economic networks. J Econ Theory. 1996; 71(1):44\u201374.","journal-title":"J Econ Theory"},{"key":"1659_CR25","volume-title":"Introduction to Algorithms","author":"T Cormen","year":"2009","unstructured":"Cormen T, Leiserson C, Rivest R, Stein C. Introduction to Algorithms. Cambridge: MIT press; 2009."},{"issue":"21","key":"1659_CR26","doi-asserted-by":"crossref","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(21):4947\u201357.","journal-title":"J Cell Sci"},{"issue":"6684","key":"1659_CR27","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/30918","volume":"393","author":"DJ Watts","year":"1998","unstructured":"Watts DJ, Strogatz SH. Collective dynamics of\u2019small-world\u2019networks,. Nature. 1998; 393(6684):409\u201310.","journal-title":"Nature"},{"issue":"suppl 1","key":"1659_CR28","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1093\/nar\/gkq1234","volume":"39","author":"D Park","year":"2011","unstructured":"Park D, Singh R, Baym M, Liao CS, Berger B. Isobase: a database of functionally related proteins across PPI networks. Nucleic Acids Res. 2011; 39(suppl 1):295\u2013300.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"1659_CR29","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1016\/S0968-0004(98)01201-8","volume":"23","author":"SN Maity","year":"1998","unstructured":"Maity SN, de Crombrugghe B. Role of the ccaat-binding protein cbf\/nf-y in transcription. Trends Biochem Sci. 1998; 23(5):174\u20138.","journal-title":"Trends Biochem Sci"},{"key":"1659_CR30","doi-asserted-by":"crossref","first-page":"2140","DOI":"10.1093\/emboj\/20.9.2140","volume":"20","author":"A Reymond","year":"2001","unstructured":"Reymond A, Meroni G, Fantozzi A, Merla G, Cairo S, Luzi L, Riganelli D, Zanaria E, Messali S, Cainarca S, Guffanti A, Minucci S, Pelicci PG, Ballabio A. The tripartite motif family identifies cell compartments. EMBO J. 2001; 20:2140\u201351.","journal-title":"EMBO J"},{"issue":"D1","key":"1659_CR31","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1093\/nar\/gku989","volume":"43","author":"TU Consortium","year":"2015","unstructured":"Consortium TU. Uniprot: a hub for protein information. Nucleic Acids Res. 2015; 43(D1):204\u201312.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"1659_CR32","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1038\/nsmb.2771","volume":"21","author":"EJ Worden","year":"2014","unstructured":"Worden EJ, Padovani C, Martin A. Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation. Nat Struct Mol Biol. 2014; 21(3):220\u20137.","journal-title":"Nat Struct Mol Biol"},{"key":"1659_CR33","unstructured":"Ciechanover A, Hershko A, Rose I. For the Discovery of Ubiquitin-Mediated Protein Degradation. 2004. Available at \n                        http:\/\/www.nobelprize.org\/nobel_prizes\/chemistry\/laureates\/2004\/\n                        \n                    . Accessed 2015."},{"issue":"21","key":"1659_CR34","doi-asserted-by":"crossref","first-page":"2857","DOI":"10.1093\/bioinformatics\/btp517","volume":"25","author":"G Scardoni","year":"2009","unstructured":"Scardoni G, Petterlini M, Laudanna C. Analyzing biological network parameters with CentiScaPe. Bioinformatics. 2009; 25(21):2857\u20139.","journal-title":"Bioinformatics"},{"key":"1659_CR35","volume-title":"International Work Conference on Bioinformatics and Biomedical Engineering. IWBBIO \u201916","author":"T Cickovski","year":"2016","unstructured":"Cickovski T, Aguiar-Pulido V, Huang W, Mahmoud S, Narasimhan G. Lightweight microbiome analysis pipelines In: Guzman FO, I. R. Ruiz GSLP, editors. International Work Conference on Bioinformatics and Biomedical Engineering. IWBBIO \u201916. Granada: Springer: 2016. p. 225\u20137."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1659-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,7]],"date-time":"2017-06-07T12:29:40Z","timestamp":1496838580000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1659-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,6]]},"references-count":35,"journal-issue":{"issue":"S8","published-print":{"date-parts":[[2017,6]]}},"alternative-id":["1659"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1659-z","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,6]]},"article-number":"239"}}