{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T08:23:47Z","timestamp":1760171027672,"version":"3.40.3"},"publisher-location":"Cham","reference-count":24,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319561530"},{"type":"electronic","value":"9783319561547"}],"license":[{"start":{"date-parts":[[2017,1,1]],"date-time":"2017-01-01T00:00:00Z","timestamp":1483228800000},"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":[[2017]]},"DOI":"10.1007\/978-3-319-56154-7_42","type":"book-chapter","created":{"date-parts":[[2017,3,31]],"date-time":"2017-03-31T16:21:08Z","timestamp":1490977268000},"page":"469-479","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Towards a Universal Genomic Positioning System: Phylogenetics and Species IDentification"],"prefix":"10.1007","author":[{"given":"Max H.","family":"Garzon","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sambriddhi","family":"Mainali","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,4,1]]},"reference":[{"key":"42_CR1","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.1126\/science.7973651","volume":"266","author":"L Adleman","year":"1994","unstructured":"Adleman, L.: Molecular computation of solutions of combinatorial problems. Science 266, 1021\u20131024 (1994)","journal-title":"Science"},{"issue":"3","key":"42_CR2","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1023\/B:NACO.0000006772.32105.46","volume":"2","author":"H Bi","year":"2003","unstructured":"Bi, H., Chen, J., Deaton, R., Garzon, M., Rubin, H., Wood, D.H.: A PCR protocol for in Vitro selection of non-crosshybridizing oligonucleotides. J. Nat. Comput. 2(3), 417\u2013426 (2003)","journal-title":"J. Nat. Comput."},{"key":"42_CR3","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1007\/11925903_26","volume-title":"DNA Computing","author":"KC Bobba","year":"2006","unstructured":"Bobba, K.C., Neel, A.J., Phan, V., Garzon, M.H.: \u201cReasoning\u201d and \u201cTalking\u201d DNA: can DNA understand English? In: Mao, C., Yokomori, T. (eds.) DNA 2006. LNCS, vol. 4287, pp. 337\u2013349. Springer, Heidelberg (2006). doi:10.1007\/11925903_26"},{"issue":"13","key":"42_CR4","first-page":"381","volume":"17","author":"J Chen","year":"2016","unstructured":"Chen, J., Chen, S., Deng, L.-Y., Bowman, D., Shiau, J.-J., Wong, T.-Y., Madahian, B., Henry, L.: Phylogenetic tree construction using Trinucleotide Usage Profile (TUP). BMC 17(13), 381 (2016)","journal-title":"BMC"},{"key":"42_CR5","unstructured":"Deaton, J., Chen, J., Garzon, M., Wood, D.H.: Test Tube Selection of Large Independent Sets of DNA Oligonucleotides R, pp. 152\u2013166. World Publishing Co. Singapore (Volume dedicated to Ned Seeman on occasion of his 60th birthday)"},{"key":"42_CR6","unstructured":"Garzon, M.H., Mainali, S.: Towards reliable microarray analysis and design. In: The 9th International Conference on Bioinformatics and Computational Biology (2017)"},{"key":"42_CR7","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1007\/s11047-010-9232-y","volume":"10","author":"MH Garzon","year":"2011","unstructured":"Garzon, M.H., Wong, T.-Y., Garzon, M.H., Wong, T.Y.: DNA chips for species identification and biological phylogenies. Nat. Comput. 10, 375\u2013389 (2011)","journal-title":"Nat. Comput."},{"key":"42_CR8","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1007\/978-3-642-32208-2_6","volume-title":"DNA Computing and Molecular Programming","author":"MH Garzon","year":"2012","unstructured":"Garzon, M.H., Bobba, K.C.: A geometric approach to Gibbs energy landscapes and optimal DNA codeword design. In: Stefanovic, D., Turberfield, A. (eds.) DNA 2012. LNCS, vol. 7433, pp. 73\u201385. Springer, Heidelberg (2012). doi:10.1007\/978-3-642-32208-2_6"},{"key":"42_CR9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.4018\/jnmc.2009010101","volume":"1","author":"MH Garzon","year":"2009","unstructured":"Garzon, M.H., Phan, V., Neel, A.: Optimal codes for computing and self-assembly. Int. J. Nanotechnol. Mol. Comput. 1, 1\u201317 (2009)","journal-title":"Int. J. Nanotechnol. Mol. Comput."},{"key":"42_CR10","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-540-77962-9","volume-title":"DNA Computing","year":"2008","unstructured":"Garzon, M.H., Yan, H. (eds.): DNA 2007. LNCS, vol. 4848. Springer, Heidelberg (2008). doi:10.1007\/978-3-540-77962-9"},{"key":"42_CR11","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1007\/11925903_11","volume-title":"DNA Computing","author":"MH Garzon","year":"2006","unstructured":"Garzon, M.H., Phan, V., Roy, S., Neel, A.J.: In search of optimal codes for DNA computing. In: Mao, C., Yokomori, T. (eds.) DNA 2006. LNCS, vol. 4287, pp. 143\u2013156. Springer, Heidelberg (2006). doi:10.1007\/11925903_11"},{"key":"42_CR12","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1007\/11753681_7","volume-title":"DNA Computing","author":"MH Garzon","year":"2006","unstructured":"Garzon, M.H., Phan, V., Bobba, K.C., Kontham, R.: Sensitivity and capacity of microarray encodings. In: Carbone, A., Pierce, N.A. (eds.) DNA 2005. LNCS, vol. 3892, pp. 81\u201395. Springer, Heidelberg (2006). doi:10.1007\/11753681_7"},{"issue":"4","key":"42_CR13","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1007\/s11047-004-2642-y","volume":"3","author":"MH Garzon","year":"2004","unstructured":"Garzon, M.H., Blain, D., Neel, A.J.: Virtual test tubes for biomolecular computing. J. Nat. Comput. 3(4), 461\u2013477 (2004)","journal-title":"J. Nat. Comput."},{"key":"42_CR14","unstructured":"Hennig, W.: Grundz\u00fcge einer Theorie der Phylogenetischen Systematik (1950). English revision, Phylogenetic Systematics. (tr. D. Davis and R. Zangerl), Univ. of Illinois Press, Urbana 1966, reprinted 1979"},{"key":"42_CR15","series-title":"SCI","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1007\/978-3-540-78291-9_8","volume-title":"New Developments in Formal Languages and Applications","author":"AJ Neel","year":"2008","unstructured":"Neel, A.J., Garzon, M.H.: DNA-based memories: a survey. In: Bel-Enguix, G., Jim\u00e9nez-L\u00f3pez, M.D., Mart\u00edn-Vide, C. (eds.) New Developments in Formal Languages and Applications. SCI, vol. 113, pp. 259\u2013275. Springer, Heidelberg (2008)"},{"key":"42_CR16","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1007\/3-540-48017-X_22","volume-title":"DNA Computing","author":"H Reif","year":"2002","unstructured":"Reif,H., LaBean, T.H., Pirrung, M., Rana, V.S., Guo, B., Kingsford, C., Wickham, G.S.: Experimental construction of very large scale DNA databases with associative search capability. In: Jonoska, N., Seeman, N.C. (eds.) DNA 2001. LNCS, vol. 2340, pp. 231\u2013247. Springer, Heidelberg (2002). doi:10.1007\/3-540-48017-X_22"},{"key":"42_CR17","volume-title":"Microarray Analysis","author":"M Schena","year":"2003","unstructured":"Schena, M.: Microarray Analysis. Wiley, Hoboken (2003)"},{"key":"42_CR18","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1038\/nature01406","volume":"421","author":"N Seeman","year":"2003","unstructured":"Seeman, N.: DNA in a material world. Nature 421, 427\u2013431 (2003)","journal-title":"Nature"},{"key":"42_CR19","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511615535","volume-title":"Microarray Bioinformatics","author":"D Stekel","year":"2003","unstructured":"Stekel, D.: Microarray Bioinformatics. Cambridge University Press, Cambridge (2003)"},{"issue":"2","key":"42_CR20","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1111\/j.1574-6968.2000.tb09095.x","volume":"186","author":"JN Volff","year":"2000","unstructured":"Volff, J.N., Altenbuchner, J.: A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution. FEMS Microbiol. Lett. 186(2), 143\u2013150 (2000)","journal-title":"FEMS Microbiol. Lett."},{"issue":"35","key":"42_CR21","doi-asserted-by":"publisher","first-page":"15431","DOI":"10.1073\/pnas.1001454107","volume":"107","author":"JM Huget","year":"2010","unstructured":"Huget, J.M., Bizarro, C.V., Forns, N., Smith, S.B., Bustamante, C.A., Ritort, F.: Single-molecule derivation of salt-dependent base-pair free energies in DNA. PNAS 107(35), 15431\u201315436 (2010)","journal-title":"PNAS"},{"key":"42_CR22","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1038\/28998","volume":"394","author":"E Winfree","year":"1998","unstructured":"Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.C.: Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539\u2013544 (1998)","journal-title":"Nature"},{"key":"42_CR23","doi-asserted-by":"publisher","first-page":"5088","DOI":"10.1073\/pnas.74.11.5088","volume":"74","author":"C Woese","year":"1977","unstructured":"Woese, C., Fox, G.: Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. U.S.A. 74, 5088\u20135090 (1977)","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"42_CR24","unstructured":"http:\/\/en.wikipedia.org\/wiki\/Phylogenetics (2008). Accessed Feb 2017"}],"container-title":["Lecture Notes in Computer Science","Bioinformatics and Biomedical Engineering"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-56154-7_42","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,12]],"date-time":"2024-03-12T12:26:55Z","timestamp":1710246415000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-319-56154-7_42"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017]]},"ISBN":["9783319561530","9783319561547"],"references-count":24,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-56154-7_42","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2017]]},"assertion":[{"value":"1 April 2017","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"IWBBIO","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Bioinformatics and Biomedical Engineering","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Granada","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Spain","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2017","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"26 April 2017","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"28 April 2017","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"5","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"iwbbio2017","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"http:\/\/iwbbio.ugr.es\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}