{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T16:23:36Z","timestamp":1722702216105},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2011,11,1]],"date-time":"2011-11-01T00:00:00Z","timestamp":1320105600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"DOI":"10.1186\/1471-2105-12-426","type":"journal-article","created":{"date-parts":[[2011,12,7]],"date-time":"2011-12-07T21:20:29Z","timestamp":1323292829000},"source":"Crossref","is-referenced-by-count":24,"title":["A Bayesian model for gene family evolution"],"prefix":"10.1186","volume":"12","author":[{"given":"Liang","family":"Liu","sequence":"first","affiliation":[]},{"given":"Lili","family":"Yu","sequence":"additional","affiliation":[]},{"given":"Venugopal","family":"Kalavacharla","sequence":"additional","affiliation":[]},{"given":"Zhanji","family":"Liu","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,11,1]]},"reference":[{"issue":"1","key":"4950_CR1","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1002\/bies.080085","volume":"31","author":"JP Demuth","year":"2009","unstructured":"Demuth JP, Hahn MW: The life and death of gene families. BioEssays: news and reviews in molecular, cellular and developmental biology 2009, 31(1):29\u201339. 10.1002\/bies.080085","journal-title":"BioEssays: news and reviews in molecular, cellular and developmental biology"},{"key":"4950_CR2","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1016\/S0378-1119(00)00428-5","volume":"259","author":"T Ohta","year":"2000","unstructured":"Ohta T: Evolution of gene families. Gene 2000, 259: 45\u201352. 10.1016\/S0378-1119(00)00428-5","journal-title":"Gene"},{"key":"4950_CR3","volume-title":"Evolution","author":"M Ridley","year":"2003","unstructured":"Ridley M: Evolution. Hoboken: Wiley-Blackwell; 2003."},{"key":"4950_CR4","doi-asserted-by":"crossref","DOI":"10.1142\/3049","volume-title":"Gene Families: Structure, Function, Genetics and Evolution","author":"RS Holmes","year":"1996","unstructured":"Holmes RS, Lim HA: Gene Families: Structure, Function, Genetics and Evolution. Singapore: World Scientific Publisher; 1996."},{"issue":"3","key":"4950_CR5","doi-asserted-by":"publisher","first-page":"1941","DOI":"10.1534\/genetics.107.080077","volume":"177","author":"MW Hahn","year":"2007","unstructured":"Hahn MW, Demuth JP, Han SG: Accelerated rate of gene gain and loss in primates. Genetics 2007, 177(3):1941\u20139. 10.1534\/genetics.107.080077","journal-title":"Genetics"},{"issue":"1","key":"4950_CR6","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1093\/genetics\/132.1.247","volume":"132","author":"CJ Basten","year":"1992","unstructured":"Basten CJ, Ohta T: Simulation study of a multigene family, with special reference to the evolution of compensatory advantageous mutations. Genetics 1992, 132(1):247\u201352.","journal-title":"Genetics"},{"key":"4950_CR7","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1186\/1471-2148-4-32","volume":"4","author":"GP Karev","year":"2004","unstructured":"Karev GP, Wolf YI, Berezovskaya FS, Koonin EV: Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models. BMC Evol Biol 2004, 4: 32. 10.1186\/1471-2148-4-32","journal-title":"BMC Evol Biol"},{"issue":"8","key":"4950_CR8","doi-asserted-by":"publisher","first-page":"1153","DOI":"10.1101\/gr.3567505","volume":"15","author":"MW Hahn","year":"2005","unstructured":"Hahn MW, De Bie T, Stajich JE, Nguyen C, Cristianini N: Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res 2005, 15(8):1153\u201360. 10.1101\/gr.3567505","journal-title":"Genome Res"},{"issue":"12","key":"4950_CR9","doi-asserted-by":"publisher","first-page":"2641","DOI":"10.1103\/PhysRevLett.85.2641","volume":"85","author":"I Yanai","year":"2000","unstructured":"Yanai I, Camacho CJ, DeLisi C: Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification. Phys Rev Lett 2000, 85(12):2641\u20134. 10.1103\/PhysRevLett.85.2641","journal-title":"Phys Rev Lett"},{"issue":"5494","key":"4950_CR10","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1126\/science.290.5494.1151","volume":"290","author":"M Lynch","year":"2000","unstructured":"Lynch M, Conery JS: The evolutionary fate and consequences of duplicate genes. Science 2000, 290(5494):1151\u20135. 10.1126\/science.290.5494.1151","journal-title":"Science"},{"issue":"3","key":"4950_CR11","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1093\/genetics\/91.3.591","volume":"91","author":"T Ohta","year":"1979","unstructured":"Ohta T: An Extension of a Model for the Evolution of Multigene Families by Unequal Crossing over. Genetics 1979, 91(3):591\u2013607.","journal-title":"Genetics"},{"issue":"Suppl 1","key":"4950_CR12","doi-asserted-by":"publisher","first-page":"i7","DOI":"10.1093\/bioinformatics\/btg1000","volume":"19","author":"L Arvestad","year":"2003","unstructured":"Arvestad L, Berglund AC, Lagergren J, Sennblad B: Bayesian gene\/species tree reconciliation and orthology analysis using MCMC. Bioinformatics 2003, 19(Suppl 1):i7\u201315. 10.1093\/bioinformatics\/btg1000","journal-title":"Bioinformatics"},{"key":"4950_CR13","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1146\/annurev.genet.39.073003.112240","volume":"39","author":"M Nei","year":"2005","unstructured":"Nei M, Rooney AP: Concerted and Birth-and-Death Evolution in Multigene Families. Ann Rev Genet 2005, 39: 121\u2013152. 10.1146\/annurev.genet.39.073003.112240","journal-title":"Ann Rev Genet"},{"issue":"1","key":"4950_CR14","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/genetics\/115.1.207","volume":"115","author":"T Ohta","year":"1987","unstructured":"Ohta T: Simulating evolution by gene duplication. Genetics 1987, 115(1):207\u201313.","journal-title":"Genetics"},{"issue":"7","key":"4950_CR15","doi-asserted-by":"publisher","first-page":"E207","DOI":"10.1371\/journal.pbio.0020207","volume":"2","author":"A Fortna","year":"2004","unstructured":"Fortna A, Kim Y, MacLaren E, Marshall K, Hahn G, Meltesen L, Brenton M, Hink R, Burgers S, Hernandez-Boussard T, Karimpour-Fard A, Glueck D, McGavran L, Berry R, Pollack J, Sikela JM: Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol 2004, 2(7):E207. 10.1371\/journal.pbio.0020207","journal-title":"PLoS Biol"},{"issue":"15","key":"4950_CR16","doi-asserted-by":"publisher","first-page":"1910","DOI":"10.1093\/bioinformatics\/btq315","volume":"26","author":"M Csuros","year":"2010","unstructured":"Csuros M: Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics 2010, 26(15):1910\u20132. 10.1093\/bioinformatics\/btq315","journal-title":"Bioinformatics"},{"issue":"9","key":"4950_CR17","doi-asserted-by":"publisher","first-page":"2087","DOI":"10.1093\/molbev\/msp123","volume":"26","author":"M Csuros","year":"2009","unstructured":"Csuros M, Miklos I: Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model. Molecular biology and evolution 2009, 26(9):2087\u201395. 10.1093\/molbev\/msp123","journal-title":"Molecular biology and evolution"},{"issue":"3","key":"4950_CR18","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1093\/molbev\/msp240","volume":"27","author":"O Cohen","year":"2010","unstructured":"Cohen O, Pupko T: Inference and characterization of horizontally transferred gene families using stochastic mapping. Molecular Biology and Evolution 2010, 27(3):703\u201313. 10.1093\/molbev\/msp240","journal-title":"Molecular Biology and Evolution"},{"key":"4950_CR19","volume-title":"An introduction to probability theory and its application","author":"W Feller","year":"1968","unstructured":"Feller W: An introduction to probability theory and its application. New York: John Wiley & Sons; 1968."},{"issue":"22","key":"4950_CR20","doi-asserted-by":"publisher","first-page":"2914","DOI":"10.1093\/bioinformatics\/btq549","volume":"26","author":"O Cohen","year":"2010","unstructured":"Cohen O, Ashkenazy H, Belinky F, Huchon D, Pupko T: GLOOME: gain loss mapping engine. Bioinformatics 2010, 26(22):2914\u20135. 10.1093\/bioinformatics\/btq549","journal-title":"Bioinformatics"},{"issue":"13","key":"4950_CR21","doi-asserted-by":"publisher","first-page":"i230","DOI":"10.1093\/bioinformatics\/btm165","volume":"23","author":"W Iwasaki","year":"2007","unstructured":"Iwasaki W, Takagi T: Reconstruction of highly heterogeneous gene-content evolution across the three domains of life. Bioinformatics 2007, 23(13):i230\u20139. 10.1093\/bioinformatics\/btm165","journal-title":"Bioinformatics"},{"issue":"5","key":"4950_CR22","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1093\/oxfordjournals.molbev.a025959","volume":"15","author":"MA Huynen","year":"1998","unstructured":"Huynen MA, van Nimwegen E: The frequency distribution of gene family sizes in complete genomes. Mol Biol Evol 1998, 15(5):583\u20139. 10.1093\/oxfordjournals.molbev.a025959","journal-title":"Mol Biol Evol"},{"issue":"11","key":"4950_CR23","doi-asserted-by":"publisher","first-page":"e197","DOI":"10.1371\/journal.pgen.0030197","volume":"3","author":"MW Hahn","year":"2007","unstructured":"Hahn MW, Han MV, Han SG: Gene family evolution across 12 Drosophila genomes. PLoS Genet 2007, 3(11):e197. 10.1371\/journal.pgen.0030197","journal-title":"PLoS Genet"},{"key":"4950_CR24","volume-title":"Graphical models","author":"SL Lauritzen","year":"2001","unstructured":"Lauritzen SL: Graphical models. Oxford, UK: Clarendon Press; 2001."},{"key":"4950_CR25","doi-asserted-by":"publisher","first-page":"e85","DOI":"10.1371\/journal.pone.0000085","volume":"1","author":"JP Demuth","year":"2006","unstructured":"Demuth JP, De Bie T, Stajich JE, Cristianini N, Hahn MW: The evolution of mammalian gene families. PLoS One 2006, 1: e85. 10.1371\/journal.pone.0000085","journal-title":"PLoS One"},{"issue":"9","key":"4950_CR26","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1093\/bioinformatics\/14.9.819","volume":"14","author":"RD Page","year":"1998","unstructured":"Page RD: GeneTree: comparing gene and species phylogenies using reconciled trees. Bioinformatics 1998, 14(9):819\u201320. 10.1093\/bioinformatics\/14.9.819","journal-title":"Bioinformatics"},{"issue":"7","key":"4950_CR27","doi-asserted-by":"publisher","first-page":"R141","DOI":"10.1186\/gb-2007-8-7-r141","volume":"8","author":"MW Hahn","year":"2007","unstructured":"Hahn MW: Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biol 2007, 8(7):R141. 10.1186\/gb-2007-8-7-r141","journal-title":"Genome Biol"},{"key":"4950_CR28","doi-asserted-by":"publisher","first-page":"1142","DOI":"10.1214\/aos\/1176325622","volume":"22","author":"X Meng","year":"1994","unstructured":"Meng X: Posterior predictive p-value. Ann Statist 1994, 22: 1142\u20131160. 10.1214\/aos\/1176325622","journal-title":"Ann Statist"},{"key":"4950_CR29","doi-asserted-by":"crossref","DOI":"10.1201\/9780429258480","volume-title":"Bayesian data analysis","author":"A Gelman","year":"2003","unstructured":"Gelman A, Carlin JB, Stern HS, Rubin DB: Bayesian data analysis. 2nd edition. New York: Chapman and Hall\/CRC; 2003.","edition":"2"},{"key":"4950_CR30","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1093\/biomet\/57.1.97","volume":"57","author":"WK Hastings","year":"1970","unstructured":"Hastings WK: Monte Carlo sampling methods using Markov chains and their applications. Biometrika 1970, 57: 97\u2013109. 10.1093\/biomet\/57.1.97","journal-title":"Biometrika"},{"key":"4950_CR31","doi-asserted-by":"publisher","first-page":"1087","DOI":"10.1063\/1.1699114","volume":"21","author":"N Metropolis","year":"1950","unstructured":"Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E: Equations of State Calculations by Fast Computing Machines. J Chem Phys 1950, 21: 1087\u20131092.","journal-title":"J Chem Phys"},{"key":"4950_CR32","volume-title":"Random and Restricted Walks: Theory and Applications","author":"MN Barber","year":"1970","unstructured":"Barber MN, Ninham BW: Random and Restricted Walks: Theory and Applications. New York: Gordon and Breach Publisher; 1970."},{"key":"4950_CR33","doi-asserted-by":"publisher","first-page":"883","DOI":"10.1080\/01621459.1996.10476956","volume":"91","author":"MK Cowles","year":"1996","unstructured":"Cowles MK, Carlin BP: Markov Chain Monte Carlo convergence diagnostics. JASA 1996, 91: 883\u2013904. 10.1080\/01621459.1996.10476956","journal-title":"JASA"},{"key":"4950_CR34","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1080\/01621459.1996.10476672","volume":"91","author":"VE Johnson","year":"1996","unstructured":"Johnson VE: Studying convergence of Markov Chain Monte Carlo algorithms using coupled sample paths. JASA 1996, 91: 154\u2013166. 10.1080\/01621459.1996.10476672","journal-title":"JASA"},{"key":"4950_CR35","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1007\/978-1-4612-6079-0_14","volume-title":"RA Fisher: An appreciation","author":"DL Wallace","year":"1980","unstructured":"Wallace DL: The Behrens-Fisher and Feiller-Creasy problems. In RA Fisher: An appreciation. Edited by: Fienberg SF, Hinkley DV. Springer: New York; 1980:119\u2013147."},{"issue":"1","key":"4950_CR36","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1093\/bib\/bbk006","volume":"7","author":"AS Novozhilov","year":"2006","unstructured":"Novozhilov AS, Karev GP, Koonin EV: Biological applications of the theory of birth-and-death processes. Briefings in bioinformatics 2006, 7(1):70\u201385. 10.1093\/bib\/bbk006","journal-title":"Briefings in bioinformatics"},{"key":"4950_CR37","doi-asserted-by":"publisher","DOI":"10.1002\/9780470316870","volume-title":"Bayesian Theory","author":"J Bernardo","year":"1994","unstructured":"Bernardo J, Smith AFM: Bayesian Theory. New York: John Wiley; 1994."},{"key":"4950_CR38","volume-title":"The Theory of Probability","author":"H Jeffreys","year":"1961","unstructured":"Jeffreys H: The Theory of Probability. UK: Oxford Publisher; 1961."},{"issue":"10","key":"4950_CR39","doi-asserted-by":"publisher","first-page":"1269","DOI":"10.1093\/bioinformatics\/btl097","volume":"22","author":"T De Bie","year":"2006","unstructured":"De Bie T, Cristianini N, Demuth JP, Hahn MW: CAFE: a computational tool for the study of gene family evolution. Bioinformatics 2006, 22(10):1269\u201371. 10.1093\/bioinformatics\/btl097","journal-title":"Bioinformatics"},{"issue":"1512","key":"4950_CR40","doi-asserted-by":"publisher","first-page":"3903","DOI":"10.1098\/rstb.2008.0177","volume":"363","author":"O Cohen","year":"2008","unstructured":"Cohen O, Rubinstein ND, Stern A, Gophna U, Pupko T: A likelihood framework to analyse phyletic patterns. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2008, 363(1512):3903\u201311. 10.1098\/rstb.2008.0177","journal-title":"Philosophical transactions of the Royal Society of London. Series B, Biological sciences"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-426.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-12-426\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-426.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,12,19]],"date-time":"2021-12-19T05:07:03Z","timestamp":1639890423000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-426"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,11,1]]},"references-count":40,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4950"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-426","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,11,1]]},"article-number":"426"}}