{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T01:52:50Z","timestamp":1775872370858,"version":"3.50.1"},"publisher-location":"Cham","reference-count":35,"publisher":"Springer International Publishing","isbn-type":[{"value":"9783319947754","type":"print"},{"value":"9783319947761","type":"electronic"}],"license":[{"start":{"date-parts":[[2018,1,1]],"date-time":"2018-01-01T00:00:00Z","timestamp":1514764800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018]]},"DOI":"10.1007\/978-3-319-94776-1_34","type":"book-chapter","created":{"date-parts":[[2018,6,29]],"date-time":"2018-06-29T01:48:06Z","timestamp":1530236886000},"page":"403-415","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Partial Homology Relations - Satisfiability in Terms of Di-Cographs"],"prefix":"10.1007","author":[{"given":"Nikolai","family":"N\u00f8jgaard","sequence":"first","affiliation":[]},{"given":"Nadia","family":"El-Mabrouk","sequence":"additional","affiliation":[]},{"given":"Daniel","family":"Merkle","sequence":"additional","affiliation":[]},{"given":"Nicolas","family":"Wieseke","sequence":"additional","affiliation":[]},{"given":"Marc","family":"Hellmuth","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2018,6,29]]},"reference":[{"key":"34_CR1","unstructured":"https:\/\/arxiv.org\/abs\/1711.00504v3"},{"key":"34_CR2","doi-asserted-by":"publisher","first-page":"e1000262","DOI":"10.1371\/journal.pcbi.1000262","volume":"5","author":"AM Altenhoff","year":"2009","unstructured":"Altenhoff, A.M., Dessimoz, C.: Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput. Biol. 5, e1000262 (2009)","journal-title":"PLoS Comput. Biol."},{"issue":"1","key":"34_CR3","doi-asserted-by":"publisher","first-page":"e53786","DOI":"10.1371\/journal.pone.0053786","volume":"8","author":"AM Altenhoff","year":"2013","unstructured":"Altenhoff, A.M., Gil, M., Gonnet, G.H., Dessimoz, C.: Inferring hierarchical orthologous groups from orthologous gene pairs. PLoS ONE 8(1), e53786 (2013)","journal-title":"PLoS ONE"},{"issue":"D1","key":"34_CR4","doi-asserted-by":"publisher","first-page":"D240","DOI":"10.1093\/nar\/gku1158","volume":"43","author":"AM Altenhoff","year":"2015","unstructured":"Altenhoff, A.M., \u0160kunca, N., Glover, N., Train, C.M., Sueki, A., Pili\u017eota, I., Gori, K., Tomiczek, B., M\u00fcller, S., Redestig, H., Gonnet, G.H., Dessimoz, C.: The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Res. 43(D1), D240\u2013D249 (2015)","journal-title":"Nucleic Acids Res."},{"key":"34_CR5","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1006\/aima.1998.1743","volume":"138","author":"S B\u00f6cker","year":"1998","unstructured":"B\u00f6cker, S., Dress, A.W.M.: Recovering symbolically dated, rooted trees from symbolic ultrametrics. Adv. Math. 138, 105\u2013125 (1998)","journal-title":"Adv. Math."},{"key":"34_CR6","doi-asserted-by":"publisher","DOI":"10.1137\/1.9780898719796","volume-title":"Graph Classes: A Survey","author":"A Brandst\u00e4dt","year":"1999","unstructured":"Brandst\u00e4dt, A., Le, V.B., Spinrad, J.P.: Graph Classes: A Survey. Society for Industrial and Applied Mathematics, Philadelphia (1999)"},{"issue":"S1","key":"34_CR7","doi-asserted-by":"publisher","first-page":"D363","DOI":"10.1093\/nar\/gkj123","volume":"34","author":"F Chen","year":"2006","unstructured":"Chen, F., Mackey, A.J., Stoeckert, C.J., Roos, D.S.: OrthoMCL-db: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res. 34(S1), D363\u2013D368 (2006)","journal-title":"Nucleic Acids Res."},{"key":"34_CR8","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1016\/0166-218X(81)90013-5","volume":"3","author":"DG Corneil","year":"1981","unstructured":"Corneil, D.G., Lerchs, H., Steward Burlingham, L.: Complement reducible graphs. Discret. Appl. Math. 3, 163\u2013174 (1981)","journal-title":"Discret. Appl. Math."},{"key":"34_CR9","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1137\/0214065","volume":"14","author":"DG Corneil","year":"1985","unstructured":"Corneil, D.G., Perl, Y., Stewart, L.K.: A linear recognition algorithm for cographs. SIAM J. Comput. 14, 926\u2013934 (1985)","journal-title":"SIAM J. Comput."},{"key":"34_CR10","doi-asserted-by":"publisher","first-page":"1722","DOI":"10.1016\/j.dam.2006.03.005","volume":"154","author":"C Crespelle","year":"2006","unstructured":"Crespelle, C., Paul, C.: Fully dynamic recognition algorithm and certificate for directed cographs. Discret. Appl. Math. 154, 1722\u20131741 (2006)","journal-title":"Discret. Appl. Math."},{"key":"34_CR11","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1007\/978-3-540-78839-3_27","volume-title":"Research in Computational Molecular Biology","author":"C Dessimoz","year":"2008","unstructured":"Dessimoz, C., Margadant, D., Gonnet, G.H.: DLIGHT \u2013 lateral gene transfer detection using pairwise evolutionary distances in a statistical framework. In: Vingron, M., Wong, L. (eds.) RECOMB 2008. LNCS, vol. 4955, pp. 315\u2013330. Springer, Heidelberg (2008). https:\/\/doi.org\/10.1007\/978-3-540-78839-3_27"},{"key":"34_CR12","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1007\/978-3-319-43681-4_10","volume-title":"Algorithms in Bioinformatics","author":"R Dondi","year":"2016","unstructured":"Dondi, R., El-Mabrouk, N., Lafond, M.: Correction of weighted orthology and paralogy relations - complexity and algorithmic results. In: Frith, M., Storm Pedersen, C.N. (eds.) WABI 2016. LNCS, vol. 9838, pp. 121\u2013136. Springer, Cham (2016). https:\/\/doi.org\/10.1007\/978-3-319-43681-4_10"},{"key":"34_CR13","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1016\/0304-3975(94)00272-X","volume":"154","author":"J Engelfriet","year":"1996","unstructured":"Engelfriet, J., Harju, T., Proskurowski, A., Rozenberg, G.: Characterization and complexity of uniformly nonprimitive labeled 2-structures. Theor. Comp. Sci. 154, 247\u2013282 (1996)","journal-title":"Theor. Comp. Sci."},{"key":"34_CR14","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1016\/S0168-9525(00)02005-9","volume":"16","author":"WM Fitch","year":"2000","unstructured":"Fitch, W.M.: Homology: a personal view on some of the problems. Trends Genet. 16, 227\u2013231 (2000)","journal-title":"Trends Genet."},{"issue":"23","key":"34_CR15","doi-asserted-by":"publisher","first-page":"2763","DOI":"10.1016\/j.disc.2013.08.017","volume":"313","author":"Y Gao","year":"2013","unstructured":"Gao, Y., Hare, D.R., Nastos, J.: The cluster deletion problem for cographs. Discret. Math. 313(23), 2763\u20132771 (2013)","journal-title":"Discret. Math."},{"issue":"1","key":"34_CR16","doi-asserted-by":"publisher","first-page":"35","DOI":"10.19139\/soic.v5i1.260","volume":"5","author":"F Gurski","year":"2017","unstructured":"Gurski, F.: Dynamic programming algorithms on directed cographs. Stat. Optim. Inf. Comput. 5(1), 35\u201344 (2017)","journal-title":"Stat. Optim. Inf. Comput."},{"issue":"4","key":"34_CR17","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1093\/sysbio\/syq026","volume":"59","author":"K Hartmann","year":"2010","unstructured":"Hartmann, K., Wong, D., Stadler, T.: Sampling trees from evolutionary models. Syst. Biol. 59(4), 465\u2013476 (2010)","journal-title":"Syst. Biol."},{"issue":"1\u20132","key":"34_CR18","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1007\/s00285-012-0525-x","volume":"66","author":"M Hellmuth","year":"2013","unstructured":"Hellmuth, M., Hernandez-Rosales, M., Huber, K.T., Moulton, V., Stadler, P.F., Wieseke, N.: Orthology relations, symbolic ultrametrics, and cographs. J. Math. Biol. 66(1\u20132), 399\u2013420 (2013)","journal-title":"J. Math. Biol."},{"issue":"1","key":"34_CR19","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1007\/s00285-016-1084-3","volume":"75","author":"M Hellmuth","year":"2017","unstructured":"Hellmuth, M., Stadler, P.F., Wieseke, N.: The mathematics of xenology: Di-cographs, symbolic ultrametrics, 2-structures and tree- representable systems of binary relations. J. Math. Biol. 75(1), 199\u2013237 (2017)","journal-title":"J. Math. Biol."},{"key":"34_CR20","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1007\/978-3-319-41324-2_21","volume-title":"Evolutionary Biology","author":"M Hellmuth","year":"2016","unstructured":"Hellmuth, M., Wieseke, N.: From sequence data including orthologs, paralogs, and xenologs to gene and species trees. In: Pontarotti, P. (ed.) Evolutionary Biology, pp. 373\u2013392. Springer, Cham (2016). https:\/\/doi.org\/10.1007\/978-3-319-41324-2_21"},{"key":"34_CR21","doi-asserted-by":"crossref","unstructured":"Hellmuth, M., Wieseke, N.: On tree representations of relations and graphs: symbolic ultrametrics and cograph edge decompositions. J. Comb. Optim. 1\u201326 (2017)","DOI":"10.1007\/s10878-017-0111-7"},{"issue":"7","key":"34_CR22","doi-asserted-by":"publisher","first-page":"2058","DOI":"10.1073\/pnas.1412770112","volume":"112","author":"M Hellmuth","year":"2015","unstructured":"Hellmuth, M., Wieseke, N., Lechner, M., Lenhof, H.P., Middendorf, M., Stadler, P.F.: Phylogenomics with paralogs. Proc. Natl. Acad. Sci. 112(7), 2058\u20132063 (2015)","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"1","key":"34_CR23","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13015-016-0067-7","volume":"11","author":"M Lafond","year":"2016","unstructured":"Lafond, M., Dondi, R., El-Mabrouk, N.: The link between orthology relations and gene trees: a correction perspective. Algorithms Mol. Biol. 11(1), 1 (2016)","journal-title":"Algorithms Mol. Biol."},{"issue":"6","key":"34_CR24","doi-asserted-by":"publisher","first-page":"S12","DOI":"10.1186\/1471-2164-15-S6-S12","volume":"15","author":"M Lafond","year":"2014","unstructured":"Lafond, M., El-Mabrouk, N.: Orthology and paralogy constraints: satisfiability and consistency. BMC Genomics 15(6), S12 (2014)","journal-title":"BMC Genomics"},{"key":"34_CR25","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1007\/978-3-662-48221-6_5","volume-title":"Algorithms in Bioinformatics","author":"M Lafond","year":"2015","unstructured":"Lafond, M., El-Mabrouk, N.: Orthology relation and gene tree correction: complexity results. In: Pop, M., Touzet, H. (eds.) WABI 2015. LNCS, vol. 9289, pp. 66\u201379. Springer, Heidelberg (2015). https:\/\/doi.org\/10.1007\/978-3-662-48221-6_5"},{"issue":"3","key":"34_CR26","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1093\/genetics\/131.3.753","volume":"131","author":"JG Lawrence","year":"1992","unstructured":"Lawrence, J.G., Hartl, D.L.: Inference of horizontal genetic transfer from molecular data: an approach using the bootstrap. Genetics 131(3), 753\u2013760 (1992)","journal-title":"Genetics"},{"key":"34_CR27","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1186\/1471-2105-12-124","volume":"12","author":"M Lechner","year":"2011","unstructured":"Lechner, M., Findei\u00df, S., Steiner, L., Marz, M., Stadler, P.F., Prohaska, S.J.: Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinform. 12, 124 (2011)","journal-title":"BMC Bioinform."},{"issue":"8","key":"34_CR28","doi-asserted-by":"publisher","first-page":"e105015","DOI":"10.1371\/journal.pone.0105015","volume":"9","author":"M Lechner","year":"2014","unstructured":"Lechner, M., Hernandez-Rosales, M., Doerr, D., Wiesecke, N., Thevenin, A., Stoye, J., Hartmann, R.K., Prohaska, S.J., Stadler, P.F.: Orthology detection combining clustering and synteny for very large datasets. PLoS ONE 9(8), e105015 (2014)","journal-title":"PLoS ONE"},{"key":"34_CR29","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1016\/j.tcs.2011.11.040","volume":"461","author":"Y Liu","year":"2012","unstructured":"Liu, Y., Wang, J., Guo, J., Chen, J.: Complexity and parameterized algorithms for cograph editing. Theor. Comput. Sci. 461, 45\u201354 (2012)","journal-title":"Theor. Comput. Sci."},{"issue":"2","key":"34_CR30","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1016\/j.dam.2004.02.017","volume":"145","author":"RM McConnell","year":"2005","unstructured":"McConnell, R.M., De Montgolfier, F.: Linear-time modular decomposition of directed graphs. Discret. Appl. Math. 145(2), 198\u2013209 (2005)","journal-title":"Discret. Appl. Math."},{"issue":"suppl 1","key":"34_CR31","doi-asserted-by":"publisher","first-page":"D196","DOI":"10.1093\/nar\/gkp931","volume":"38","author":"G \u00d6stlund","year":"2010","unstructured":"\u00d6stlund, G., Schmitt, T., Forslund, K., K\u00f6stler, T., Messina, D.N., Roopra, S., Frings, O., Sonnhammer, E.L.: InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res. 38(suppl 1), D196\u2013D203 (2010)","journal-title":"Nucleic Acids Res."},{"issue":"5","key":"34_CR32","doi-asserted-by":"publisher","first-page":"e1004095","DOI":"10.1371\/journal.pcbi.1004095","volume":"11","author":"M Ravenhall","year":"2015","unstructured":"Ravenhall, M., \u0160kunca, N., Lassalle, F., Dessimoz, C.: Inferring horizontal gene transfer. PLoS Comput. Biol. 11(5), e1004095 (2015)","journal-title":"PLoS Comput. Biol."},{"issue":"12","key":"34_CR33","doi-asserted-by":"publisher","first-page":"1569","DOI":"10.1093\/bioinformatics\/btq228","volume":"26","author":"J Sukumaran","year":"2010","unstructured":"Sukumaran, J., Holder, M.T.: Dendropy: a python library for phylogenetic computing. Bioinformatics 26(12), 1569\u20131571 (2010)","journal-title":"Bioinformatics"},{"issue":"1","key":"34_CR34","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1093\/nar\/28.1.33","volume":"28","author":"RL Tatusov","year":"2000","unstructured":"Tatusov, R.L., Galperin, M.Y., Natale, D.A., Koonin, E.V.: The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28(1), 33\u201336 (2000)","journal-title":"Nucleic Acids Res."},{"issue":"10","key":"34_CR35","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1002\/bies.201100062","volume":"33","author":"K Trachana","year":"2011","unstructured":"Trachana, K., Larsson, T.A., Powell, S., Chen, W.H., Doerks, T., Muller, J., Bork, P.: Orthology prediction methods: a quality assessment using curated protein families. BioEssays 33(10), 769\u2013780 (2011)","journal-title":"BioEssays"}],"container-title":["Lecture Notes in Computer Science","Computing and Combinatorics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-94776-1_34","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,13]],"date-time":"2024-03-13T16:35:47Z","timestamp":1710347747000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-319-94776-1_34"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018]]},"ISBN":["9783319947754","9783319947761"],"references-count":35,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-94776-1_34","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018]]},"assertion":[{"value":"29 June 2018","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"COCOON","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Computing and Combinatorics Conference","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Qing Dao","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"China","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2018","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2 July 2018","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"4 July 2018","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"24","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"cocoon2018","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"http:\/\/cocoon2018.sdu.edu.cn\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}