{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T04:28:45Z","timestamp":1773289725377,"version":"3.50.1"},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Theory Biosci."],"published-print":{"date-parts":[[2009,8]]},"DOI":"10.1007\/s12064-009-0067-y","type":"journal-article","created":{"date-parts":[[2009,6,25]],"date-time":"2009-06-25T10:55:26Z","timestamp":1245927326000},"page":"165-170","source":"Crossref","is-referenced-by-count":19,"title":["Defining genes: a computational framework"],"prefix":"10.1007","volume":"128","author":[{"given":"Peter F.","family":"Stadler","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sonja J.","family":"Prohaska","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian V.","family":"Forst","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David C.","family":"Krakauer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,6,26]]},"reference":[{"key":"67_CR1","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/0304-3975(92)90185-I","volume":"96","author":"G Berry","year":"1992","unstructured":"Berry G, Boudol G (1992) The chemical abstract machine. Theor Comput Sci 96:217\u2013248","journal-title":"Theor Comput Sci"},{"key":"67_CR2","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1007\/s10539-007-9094-6","volume":"22","author":"I Brigandt","year":"2007","unstructured":"Brigandt I, Griffiths P (2007) The importance of homology for biology and philosophy. Biol Philos 22:633\u2013641","journal-title":"Biol Philos"},{"key":"67_CR3","doi-asserted-by":"crossref","first-page":"1960","DOI":"10.1111\/j.1742-4658.2008.06366.x","volume":"275","author":"E Dicou","year":"2008","unstructured":"Dicou E (2008) Biologically active, non membrane-anchored precursors: an overview. FEBS J 275:1960\u20131975","journal-title":"FEBS J"},{"key":"67_CR4","doi-asserted-by":"crossref","first-page":"1653","DOI":"10.1126\/science.1126316","volume":"312","author":"L Duret","year":"2006","unstructured":"Duret L, Chureau C, Samain S, Weissenbach J, Avner P (2006) The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science 312:1653\u20131655","journal-title":"Science"},{"key":"67_CR5","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1186\/1471-2105-7-67","volume":"7","author":"CV Forst","year":"2006","unstructured":"Forst CV, Flamm C, Hofacker IL, Stadler PF (2006) Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinf 7:67","journal-title":"BMC Bioinf"},{"key":"67_CR6","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1186\/1479-7364-2-4-266","volume":"2","author":"TS Furey","year":"2006","unstructured":"Furey TS (2006) Comparison of human (and other) genome browsers. Hum Genomics 2:266\u2013270","journal-title":"Hum Genomics"},{"key":"67_CR7","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1101\/gr.6339607","volume":"17","author":"MB Gerstein","year":"2007","unstructured":"Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M (2007) What is a gene, post-ENCODE? History and updated definition. Genome Res 17:669\u2013681","journal-title":"Genome Res"},{"key":"67_CR8","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1101\/gr.6525007","volume":"17","author":"TR Gingeras","year":"2007","unstructured":"Gingeras TR (2007) Origin of phenotypes: genes and transcripts. Genome Res 17:682\u2013690","journal-title":"Genome Res"},{"key":"67_CR9","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gkm952","volume":"36","author":"S Griffiths-Jones","year":"2008","unstructured":"Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154\u2013D158","journal-title":"Nucleic Acids Res"},{"key":"67_CR10","doi-asserted-by":"crossref","first-page":"D773","DOI":"10.1093\/nar\/gkm966","volume":"36","author":"D Karolchik","year":"2008","unstructured":"Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ (2008) The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res 36:D773\u2013D779","journal-title":"Nucleic Acids Res"},{"key":"67_CR11","doi-asserted-by":"crossref","first-page":"3036","DOI":"10.1093\/emboj\/20.12.3036","volume":"20","author":"MM Krem","year":"2001","unstructured":"Krem MM, Di Cera E (2001) Molecular markers of serine protease evolution. EMBO J 20:3036\u20133045","journal-title":"EMBO J"},{"key":"67_CR12","first-page":"777","volume":"40","author":"MD Laubichler","year":"2000","unstructured":"Laubichler MD (2000) Homology in development and the development of the homology concept. Int Comp Biol 40:777\u2013788","journal-title":"Int Comp Biol"},{"key":"67_CR13","unstructured":"Maggiora GM, Shanmugasundaram V (2004) Molecular similarity measures. In: Bajorath J (ed) Chemoinformatics: concepts, methods, and tools for drug discovery. Methods in molecular biology, vol 275. Springer, Heidelberg, pp 1\u201350"},{"key":"67_CR14","unstructured":"NC-ICBMB, Webb EC (ed) (1992) Enzyme Nomenclature 1992: Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. Academic Press, San Diego"},{"key":"67_CR15","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511790515","volume-title":"Systems biology","author":"BO Palsson","year":"2006","unstructured":"Palsson BO (2006) Systems biology. Cambridge University Press, Cambridge"},{"key":"67_CR16","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1038\/441398a","volume":"441","author":"H Pearson","year":"2006","unstructured":"Pearson H (2006) Genetics: what is a gene? Nature 441:398\u2013401","journal-title":"Nature"},{"key":"67_CR17","doi-asserted-by":"crossref","first-page":"1556","DOI":"10.1126\/science.316.5831.1556","volume":"316","author":"E Pennisi","year":"2007","unstructured":"Pennisi E (2007) DNA study forces rethink of what it means to be a gene. Science 316:1556\u20131557","journal-title":"Science"},{"key":"67_CR18","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1007\/s12064-008-0025-0","volume":"127","author":"SJ Prohaska","year":"2008","unstructured":"Prohaska SJ, Stadler PF (2008) Genes. Theor Biosci 127:215\u2013221","journal-title":"Theor Biosci"},{"key":"67_CR19","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1007\/s12064-007-0012-x","volume":"126","author":"K Scherrer","year":"2007","unstructured":"Scherrer K, Jost J (2007) The gene and the genon concept: a conceptual and information-theoretic analysis of genetic storage and expression in the light of modern molecular biology. Theor Biosci 126:65\u2013113","journal-title":"Theor Biosci"},{"key":"67_CR20","volume-title":"Models of computation and formal languages","author":"RG Taylor","year":"1998","unstructured":"Taylor RG (1998) Models of computation and formal languages. Oxford University Press, New York"},{"key":"67_CR21","doi-asserted-by":"crossref","first-page":"736","DOI":"10.2197\/ipsjdc.3.736","volume":"3","author":"Y Tohsato","year":"2007","unstructured":"Tohsato Y, Nishimura Y (2007) Metabolic pathway alignment based on similarity between chemical structures. IPSJ Digit Courier 3:736\u2013745","journal-title":"IPSJ Digit Courier"},{"key":"67_CR22","doi-asserted-by":"crossref","first-page":"1406","DOI":"10.1016\/j.phytochem.2006.05.033","volume":"67","author":"JD Walton","year":"2006","unstructured":"Walton JD (2006) HC-toxin. Phytochemistry 67:1406\u20131413","journal-title":"Phytochemistry"}],"container-title":["Theory in Biosciences"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s12064-009-0067-y.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,4,19]],"date-time":"2019-04-19T00:28:50Z","timestamp":1555633730000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s12064-009-0067-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,6,26]]},"references-count":22,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2009,8]]}},"alternative-id":["67"],"URL":"https:\/\/doi.org\/10.1007\/s12064-009-0067-y","relation":{},"ISSN":["1431-7613","1611-7530"],"issn-type":[{"value":"1431-7613","type":"print"},{"value":"1611-7530","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,6,26]]}}}