{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T07:46:20Z","timestamp":1777621580432,"version":"3.51.4"},"reference-count":30,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2015,3,27]],"date-time":"2015-03-27T00:00:00Z","timestamp":1427414400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004079","type":"journal-article","created":{"date-parts":[[2015,3,28]],"date-time":"2015-03-28T22:34:46Z","timestamp":1427582086000},"page":"e1004079","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":9,"title":["3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics"],"prefix":"10.1371","volume":"11","author":[{"given":"Deborah A","family":"Weighill","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel A","family":"Jacobson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2015,3,27]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nrg1272","article-title":"Network biology: understanding the cell\u2019s functional organization","volume":"5","author":"AL Barabasi","year":"2004","journal-title":"Nature Reviews Genetics"},{"key":"ref2","first-page":"1601","article-title":"Learning with hypergraphs: Clustering, classification, and embedding","author":"D Zhou","year":"2006","journal-title":"Advances in neural information processing systems"},{"key":"ref3","first-page":"61","article-title":"Hypergraph partitioning and clustering","author":"DA Papa","year":"2007","journal-title":"Approximation algorithms and metaheuristics"},{"key":"ref4","unstructured":"Karypis G, Kumar V (1998). hmetis\u2014hypergraph and circuit partitioning. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/glaros.dtc.umn.edu\/gkhome\/metis\/hmetis\/overview\" xlink:type=\"simple\">http:\/\/glaros.dtc.umn.edu\/gkhome\/metis\/hmetis\/overview<\/ext-link>. Accessed November 16, 2014."},{"key":"ref5","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1098\/rsbl.2006.0553","article-title":"A multiple-site similarity measure","volume":"3","author":"OH Diserud","year":"2007","journal-title":"Biology letters"},{"key":"ref6","doi-asserted-by":"crossref","unstructured":"Santini G, SoldanoH, PothierJ(2010) Use of ternary similarities in graph based clustering for protein structural family classification. In: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology. ACM, pp. 457\u2013459.","DOI":"10.1145\/1854776.1854856"},{"key":"ref7","doi-asserted-by":"crossref","unstructured":"Zhang L, Gao Y, Hong C, Feng Y, Zhu J, et al. (2013) Feature correlation hypergraph: Exploiting high-order potentials for multimodal recognition. IEEE Transactions on Cybernetics.","DOI":"10.1109\/TCYB.2013.2285219"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1831","DOI":"10.1093\/bioinformatics\/btp269","article-title":"Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison","volume":"25","author":"A Mithani","year":"2009","journal-title":"Bioinformatics"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"984","DOI":"10.1109\/TCBB.2013.115","article-title":"Decomposition of flux distributions into metabolic pathways","volume":"10","author":"O Seref","year":"2013","journal-title":"Computational Biology and Bioinformatics, IEEE\/ACM Transactions on"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1186\/1471-2164-7-100","article-title":"Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria","volume":"7","author":"Z Wang","year":"2006","journal-title":"BMC genomics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/1752-0509-7-47","article-title":"Constructing higher-order mirna-mrna interaction networks in prostate cancer via hypergraph-based learning","volume":"7","author":"SJ Kim","year":"2013","journal-title":"BMC systems biology"},{"key":"ref12","doi-asserted-by":"crossref","unstructured":"Kim SJ, Ha JW, Zhang BT (2014) Bayesian evolutionary hypergraph learning for predicting cancer clinical outcomes. Journal of biomedical informatics.","DOI":"10.1016\/j.jbi.2014.02.002"},{"key":"ref13","doi-asserted-by":"crossref","DOI":"10.1201\/9780203490204","article-title":"Handbook of graph theory","author":"JL Gross","year":"2003"},{"key":"ref14","first-page":"1","article-title":"A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons","volume":"5","author":"T S\u00f8rensen","year":"1948","journal-title":"Biol skr"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1007\/BF00344966","article-title":"Similarity indices, sample size and diversity","volume":"50","author":"H Wolda","year":"1981","journal-title":"Oecologia"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"325","DOI":"10.2307\/1942268","article-title":"An ordination of the upland forest communities of southern wisconsin","volume":"27","author":"JR Bray","year":"1957","journal-title":"Ecological monographs"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1093\/nar\/30.7.1575","article-title":"An efficient algorithm for large-scale detection of protein families","volume":"30","author":"A Enright","year":"2002","journal-title":"Nucleic acids research"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"39","DOI":"10.2307\/2342435","article-title":"The logic of inductive inference","author":"RA Fisher","year":"1935","journal-title":"Journal of the Royal Statistical Society"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"S Altschul","year":"1990","journal-title":"Journal of molecular biology"},{"key":"ref20","first-page":"W5","article-title":"Nucleic acids research","volume":"36","author":"M Johnson","year":"2008"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1128\/JB.01778-12","article-title":"Gene conservation among endospore-forming bacteria reveals additional sporulation genes in bacillus subtilis","volume":"195","author":"BA Traag","year":"2013","journal-title":"Journal of bacteriology"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1146\/annurev.genet.30.1.297","article-title":"Molecular genetics of sporulation in bacillus subtilis","volume":"30","author":"P Stragier","year":"1996","journal-title":"Annual review of genetics"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1093\/jb\/mvh151","article-title":"Characterization of a polysaccharide deacetylase gene homologue (pdab) on sporulation of bacillus subtilis","volume":"136","author":"T Fukushima","year":"2004","journal-title":"Journal of biochemistry"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"6007","DOI":"10.1128\/JB.184.21.6007-6015.2002","article-title":"A polysaccharide deacetylase gene (pdaa) is required for germination and for production of muramic \u03b4-lactam residues in the spore cortex of bacillus subtilis","volume":"184","author":"T Fukushima","year":"2002","journal-title":"Journal of bacteriology"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1038\/nrmicro1288","article-title":"A comparative genomic view of clostridial sporulation and physiology","volume":"3","author":"CJ Paredes","year":"2005","journal-title":"Nature Reviews Microbiology"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"2864","DOI":"10.1128\/JB.01581-08","article-title":"Whole-genome-based phylogeny and divergence of the genus brucella","volume":"191","author":"JT Foster","year":"2009","journal-title":"Journal of bacteriology"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"2178","DOI":"10.1101\/gr.1224503","article-title":"Orthomcl: identification of ortholog groups for eukaryotic genomes","volume":"13","author":"L Li","year":"2003","journal-title":"Genome research"},{"key":"ref28","unstructured":"van Dongen S (2000) Graph clustering by flow simulation. Ph.D. thesis, University of Utrecht."},{"key":"ref29","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"P Shannon","year":"2003","journal-title":"Genome research"},{"key":"ref30","first-page":"65","article-title":"A simple sequentially rejective multiple test procedure","author":"S Holm","year":"1979","journal-title":"Scandinavian journal of statistics"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004079","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,22]],"date-time":"2019-08-22T11:06:07Z","timestamp":1566471967000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004079"}},"subtitle":[],"editor":[{"given":"Christos A.","family":"Ouzounis","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2015,3,27]]},"references-count":30,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2015,3,27]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004079","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,3,27]]}}}