{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T07:33:02Z","timestamp":1791271982436,"version":"4.1.0"},"reference-count":43,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2011,2,10]],"date-time":"2011-02-10T00:00:00Z","timestamp":1297296000000},"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 Syst Biol"],"published-print":{"date-parts":[[2011,12]]},"DOI":"10.1186\/1752-0509-5-27","type":"journal-article","created":{"date-parts":[[2011,2,10]],"date-time":"2011-02-10T23:16:19Z","timestamp":1297379779000},"source":"Crossref","is-referenced-by-count":31,"title":["The whole-organism heavy chain B cell repertoire from Zebrafish self-organizes into distinct network features"],"prefix":"10.1186","volume":"5","author":[{"given":"Rotem","family":"Ben-Hamo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sol","family":"Efroni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2011,2,10]]},"reference":[{"key":"616_CR1","volume-title":"KUBY IMMUNOLOGY","author":"A Richard","year":"2000","unstructured":"Richard A, Goldsby TJK, Barbara A, Osborne : KUBY IMMUNOLOGY. W.H. Freeman & Company; 2000."},{"key":"616_CR2","volume-title":"Tending Adam's garden: evolving the cognitive immune self","author":"IR Cohen","year":"2000","unstructured":"Cohen IR: Tending Adam's garden: evolving the cognitive immune self. San Diego, CA: Academic Press; 2000."},{"key":"616_CR3","volume-title":"The immune System","author":"P Parham","year":"2009","unstructured":"Parham P: The immune System. New York, Garland Publishing Press; 2009."},{"issue":"3","key":"616_CR4","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1007\/s002510050357","volume":"47","author":"E Andersson","year":"1998","unstructured":"Andersson E, Matsunaga T: Evolutionary stability of the immunoglobulin heavy chain variable region gene families in teleost. Immunogenetics 1998,47(3):272-277. 10.1007\/s002510050357","journal-title":"Immunogenetics"},{"key":"616_CR5","first-page":"111","volume":"248","author":"JD Hansen","year":"2000","unstructured":"Hansen JD, McBlane JF: Recombination-activating genes, transposition, and the lymphoid-specific combinatorial immune system: a common evolutionary connection. Curr Top Microbiol Immunol 2000, 248: 111-135.","journal-title":"Curr Top Microbiol Immunol"},{"issue":"7","key":"616_CR6","doi-asserted-by":"publisher","first-page":"1793","DOI":"10.1016\/j.molimm.2006.07.295","volume":"44","author":"Z Li","year":"2007","unstructured":"Li Z, Chang Y: V(D)J recombination in zebrafish: Normal joining products with accumulation of unresolved coding ends and deleted signal ends. Mol Immunol 2007,44(7):1793-1802. 10.1016\/j.molimm.2006.07.295","journal-title":"Mol Immunol"},{"issue":"1","key":"616_CR7","doi-asserted-by":"publisher","first-page":"333","DOI":"10.4049\/jimmunol.177.1.333","volume":"177","author":"LA Clark","year":"2006","unstructured":"Clark LA, Ganesan S, Papp S, van Vlijmen HW: Trends in antibody sequence changes during the somatic hypermutation process. J Immunol 2006,177(1):333-340.","journal-title":"J Immunol"},{"issue":"1","key":"616_CR8","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1006\/jtbi.1993.1139","volume":"164","author":"TB Kepler","year":"1993","unstructured":"Kepler TB, Perelson AS: Somatic hypermutation in B cells: an optimal control treatment. J Theor Biol 1993,164(1):37-64. 10.1006\/jtbi.1993.1139","journal-title":"J Theor Biol"},{"issue":"12","key":"616_CR9","doi-asserted-by":"publisher","first-page":"4011","DOI":"10.1002\/(SICI)1521-4141(199912)29:12<4011::AID-IMMU4011>3.0.CO;2-W","volume":"29","author":"SJ Foster","year":"1999","unstructured":"Foster SJ, Dorner T, Lipsky PE: Somatic hypermutation of VkappaJkappa rearrangements: targeting of RGYW motifs on both DNA strands and preferential selection of mutated codons within RGYW motifs. Eur J Immunol 1999,29(12):4011-4021. 10.1002\/(SICI)1521-4141(199912)29:12<4011::AID-IMMU4011>3.0.CO;2-W","journal-title":"Eur J Immunol"},{"key":"616_CR10","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1111\/j.1600-065X.1988.tb00763.x","volume":"105","author":"C Berek","year":"1988","unstructured":"Berek C, Milstein C: The dynamic nature of the antibody repertoire. Immunol Rev 1988, 105: 5-26. 10.1111\/j.1600-065X.1988.tb00763.x","journal-title":"Immunol Rev"},{"issue":"9","key":"616_CR11","doi-asserted-by":"publisher","first-page":"4639","DOI":"10.4049\/jimmunol.171.9.4639","volume":"171","author":"SH Kleinstein","year":"2003","unstructured":"Kleinstein SH, Louzoun Y, Shlomchik MJ: Estimating hypermutation rates from clonal tree data. J Immunol 2003,171(9):4639-4649.","journal-title":"J Immunol"},{"issue":"3","key":"616_CR12","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1006\/smim.1996.0020","volume":"8","author":"CJ Jolly","year":"1996","unstructured":"Jolly CJ, Wagner SD, Rada C, Klix N, Milstein C, Neuberger MS: The targeting of somatic hypermutation. Semin Immunol 1996,8(3):159-168. 10.1006\/smim.1996.0020","journal-title":"Semin Immunol"},{"issue":"14","key":"616_CR13","doi-asserted-by":"publisher","first-page":"1469","DOI":"10.1016\/S1286-4579(02)00029-1","volume":"4","author":"JA Yoder","year":"2002","unstructured":"Yoder JA, Nielsen ME, Amemiya CT, Litman GW: Zebrafish as an immunological model system. Microbes Infect 2002,4(14):1469-1478. 10.1016\/S1286-4579(02)00029-1","journal-title":"Microbes Infect"},{"issue":"6","key":"616_CR14","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1007\/s002510050221","volume":"45","author":"CE Willett","year":"1997","unstructured":"Willett CE, Cherry JJ, Steiner LA: Characterization and expression of the recombination activating genes (rag1 and rag2) of zebrafish. Immunogenetics 1997,45(6):394-404. 10.1007\/s002510050221","journal-title":"Immunogenetics"},{"issue":"4","key":"616_CR15","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1016\/S1074-7613(04)00084-6","volume":"20","author":"NS Trede","year":"2004","unstructured":"Trede NS, Langenau DM, Traver D, Look AT, Zon LI: The use of zebrafish to understand immunity. Immunity 2004,20(4):367-379. 10.1016\/S1074-7613(04)00084-6","journal-title":"Immunity"},{"issue":"5928","key":"616_CR16","doi-asserted-by":"publisher","first-page":"807","DOI":"10.1126\/science.1170020","volume":"324","author":"JA Weinstein","year":"2009","unstructured":"Weinstein JA, Jiang N, White RA, Fisher DS, Quake SR: High-throughput sequencing of the zebrafish antibody repertoire. Science 2009,324(5928):807-810. 10.1126\/science.1170020","journal-title":"Science"},{"issue":"3","key":"616_CR17","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1038\/10343","volume":"22","author":"S Tavazoie","year":"1999","unstructured":"Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM: Systematic determination of genetic network architecture. Nat Genet 1999,22(3):281-285. 10.1038\/10343","journal-title":"Nat Genet"},{"issue":"6833","key":"616_CR18","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/35075138","volume":"411","author":"H Jeong","year":"2001","unstructured":"Jeong H, Mason SP, Barabasi AL, Oltvai ZN: Lethality and centrality in protein networks. Nature 2001,411(6833):41-42. 10.1038\/35075138","journal-title":"Nature"},{"issue":"5","key":"616_CR19","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1038\/nbt0503-490","volume":"21","author":"O Ozier","year":"2003","unstructured":"Ozier O, Amin N, Ideker T: Global architecture of genetic interactions on the protein network. Nat Biotechnol 2003,21(5):490-491. 10.1038\/nbt0503-490","journal-title":"Nat Biotechnol"},{"issue":"5939","key":"616_CR20","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1126\/science.1173299","volume":"325","author":"AL Barabasi","year":"2009","unstructured":"Barabasi AL: Scale-free networks: a decade and beyond. Science 2009,325(5939):412-413. 10.1126\/science.1173299","journal-title":"Science"},{"issue":"12","key":"616_CR21","doi-asserted-by":"publisher","first-page":"7821","DOI":"10.1073\/pnas.122653799","volume":"99","author":"M Girvan","year":"2002","unstructured":"Girvan M, Newman ME: Community structure in social and biological networks. Proc Natl Acad Sci USA 2002,99(12):7821-7826. 10.1073\/pnas.122653799","journal-title":"Proc Natl Acad Sci USA"},{"issue":"8","key":"616_CR22","doi-asserted-by":"publisher","first-page":"e1000140","DOI":"10.1371\/journal.pcbi.1000140","volume":"4","author":"E Zotenko","year":"2008","unstructured":"Zotenko E, Mestre J, O'Leary DP, Przytycka TM: Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput Biol 2008,4(8):e1000140. 10.1371\/journal.pcbi.1000140","journal-title":"PLoS Comput Biol"},{"issue":"6","key":"616_CR23","doi-asserted-by":"publisher","first-page":"826","DOI":"10.1371\/journal.pgen.0020088","volume":"2","author":"XL He","year":"2006","unstructured":"He XL, Zhang JZ: Why do hubs tend to be essential in protein networks? Plos Genetics 2006,2(6):826-834. 10.1371\/journal.pgen.0020088","journal-title":"Plos Genetics"},{"issue":"6833","key":"616_CR24","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/35075138","volume":"411","author":"H Jeong","year":"2001","unstructured":"Jeong H, Mason SP, Barabasi AL, Oltvai ZN: Lethality and centrality in protein networks. Nature 2001,411(6833):41-42. 10.1038\/35075138","journal-title":"Nature"},{"issue":"46","key":"616_CR25","doi-asserted-by":"publisher","first-page":"17916","DOI":"10.1073\/pnas.0705081104","volume":"104","author":"JY Park","year":"2007","unstructured":"Park JY, Barabasi AL: Distribution of node characteristics in complex networks. Proceedings of the National Academy of Sciences of the United States of America 2007,104(46):17916-17920. 10.1073\/pnas.0705081104","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"4","key":"616_CR26","doi-asserted-by":"publisher","first-page":"928","DOI":"10.1002\/pmic.200300636","volume":"4","author":"SH Yook","year":"2004","unstructured":"Yook SH, Oltvai ZN, Barabasi AL: Functional and topological characterization of protein interaction networks. Proteomics 2004,4(4):928-942. 10.1002\/pmic.200300636","journal-title":"Proteomics"},{"issue":"12","key":"616_CR27","doi-asserted-by":"publisher","first-page":"5405","DOI":"10.1073\/pnas.1001705107","volume":"107","author":"T Mora","year":"2010","unstructured":"Mora T, Walczak AM, Bialek W, Callan CG Jr: Maximum entropy models for antibody diversity. Proc Natl Acad Sci USA 2010,107(12):5405-5410. 10.1073\/pnas.1001705107","journal-title":"Proc Natl Acad Sci USA"},{"issue":"9","key":"616_CR28","doi-asserted-by":"publisher","first-page":"1467","DOI":"10.1084\/jem.20042483","volume":"201","author":"NY Zheng","year":"2005","unstructured":"Zheng NY, Wilson K, Jared M, Wilson PC: Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation. J Exp Med 2005,201(9):1467-1478. 10.1084\/jem.20042483","journal-title":"J Exp Med"},{"issue":"9","key":"616_CR29","doi-asserted-by":"publisher","first-page":"1193","DOI":"10.1084\/jem.20011858","volume":"195","author":"FN Papavasiliou","year":"2002","unstructured":"Papavasiliou FN, Schatz DG: The activation-induced deaminase functions in a postcleavage step of the somatic hypermutation process. J Exp Med 2002,195(9):1193-1198. 10.1084\/jem.20011858","journal-title":"J Exp Med"},{"issue":"26","key":"616_CR30","doi-asserted-by":"publisher","first-page":"18470","DOI":"10.1074\/jbc.274.26.18470","volume":"274","author":"M Muramatsu","year":"1999","unstructured":"Muramatsu M, Sankaranand VS, Anant S, Sugai M, Kinoshita K, Davidson NO, Honjo T: Specific expression of activation-induced cytidine deaminase (AID), a novel member of the RNA-editing deaminase family in germinal center B cells. J Biol Chem 1999,274(26):18470-18476. 10.1074\/jbc.274.26.18470","journal-title":"J Biol Chem"},{"key":"616_CR31","doi-asserted-by":"crossref","unstructured":"Tanaka A, Shen HM, Ratnam S, Kodgire P, Storb U: Attracting AID to targets of somatic hypermutation. J Exp Med 207(2):405-415. 10.1084\/jem.20090821","DOI":"10.1084\/jem.20090821"},{"issue":"43","key":"616_CR32","doi-asserted-by":"publisher","first-page":"15963","DOI":"10.1073\/pnas.0607581103","volume":"103","author":"U Hershberg","year":"2006","unstructured":"Hershberg U, Shlomchik MJ: Differences in potential for amino acid change after mutation reveals distinct strategies for kappa and lambda light-chain variation. Proc Natl Acad Sci USA 2006,103(43):15963-15968. 10.1073\/pnas.0607581103","journal-title":"Proc Natl Acad Sci USA"},{"issue":"9","key":"616_CR33","doi-asserted-by":"publisher","first-page":"1351","DOI":"10.1101\/gr.144700","volume":"10","author":"WB Barbazuk","year":"2000","unstructured":"Barbazuk WB, Korf I, Kadavi C, Heyen J, Tate S, Wun E, Bedell JA, McPherson JD, Johnson SL: The syntenic relationship of the zebrafish and human genomes. Genome Res 2000,10(9):1351-1358. 10.1101\/gr.144700","journal-title":"Genome Res"},{"issue":"12","key":"616_CR34","doi-asserted-by":"publisher","first-page":"1890","DOI":"10.1101\/gr.164800","volume":"10","author":"JH Postlethwait","year":"2000","unstructured":"Postlethwait JH, Woods IG, Ngo-Hazelett P, Yan YL, Kelly PD, Chu F, Huang H, Hill-Force A, Talbot WS: Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res 2000,10(12):1890-1902. 10.1101\/gr.164800","journal-title":"Genome Res"},{"issue":"9","key":"616_CR35","doi-asserted-by":"publisher","first-page":"6136","DOI":"10.1073\/pnas.072560099","volume":"99","author":"TX Liu","year":"2002","unstructured":"Liu TX, Zhou Y, Kanki JP, Deng M, Rhodes J, Yang HW, Sheng XM, Zon LI, Look AT: Evolutionary conservation of zebrafish linkage group 14 with frequently deleted regions of human chromosome 5 in myeloid malignancies. Proc Natl Acad Sci USA 2002,99(9):6136-6141. 10.1073\/pnas.072560099","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"616_CR36","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1007\/BF00188428","volume":"41","author":"E Andersson","year":"1995","unstructured":"Andersson E, Matsunaga T: Evolution of immunoglobulin heavy chain variable region genes: a VH family can last for 150-200 million years or longer. Immunogenetics 1995,41(1):18-28. 10.1007\/BF00188428","journal-title":"Immunogenetics"},{"issue":"5","key":"616_CR37","doi-asserted-by":"publisher","first-page":"1345","DOI":"10.1073\/pnas.57.5.1345","volume":"57","author":"EA Kabat","year":"1967","unstructured":"Kabat EA: The paucity of species-specific amino acid residues in the variable regions of human and mouse Bence-Jones proteins and its evolutionary and genetic implications. Proc Natl Acad Sci USA 1967,57(5):1345-1349. 10.1073\/pnas.57.5.1345","journal-title":"Proc Natl Acad Sci USA"},{"issue":"6","key":"616_CR38","doi-asserted-by":"publisher","first-page":"527","DOI":"10.1093\/intimm\/3.6.527","volume":"3","author":"E Andersson","year":"1991","unstructured":"Andersson E, Tormanen V, Matsunaga T: Evolution of a VH gene family in low vertebrates. Int Immunol 1991,3(6):527-533. 10.1093\/intimm\/3.6.527","journal-title":"Int Immunol"},{"issue":"20","key":"616_CR39","doi-asserted-by":"publisher","first-page":"9248","DOI":"10.1073\/pnas.91.20.9248","volume":"91","author":"JP Rast","year":"1994","unstructured":"Rast JP, Litman GW: T-cell receptor gene homologs are present in the most primitive jawed vertebrates. Proc Natl Acad Sci USA 1994,91(20):9248-9252. 10.1073\/pnas.91.20.9248","journal-title":"Proc Natl Acad Sci USA"},{"key":"616_CR40","doi-asserted-by":"crossref","unstructured":"Mora T, Walczak AM, Bialek W, Callan CG Jr: Maximum entropy models for antibody diversity. Proc Natl Acad Sci USA 107(12):5405-5410. 10.1073\/pnas.1001705107","DOI":"10.1073\/pnas.1001705107"},{"issue":"3","key":"616_CR41","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1038\/ni1166","volume":"6","author":"N Danilova","year":"2005","unstructured":"Danilova N, Bussmann J, Jekosch K, Steiner LA: The immunoglobulin heavy-chain locus in zebrafish: identification and expression of a previously unknown isotype, immunoglobulin Z. Nat Immunol 2005,6(3):295-302. 10.1038\/ni1166","journal-title":"Nat Immunol"},{"key":"616_CR42","doi-asserted-by":"crossref","unstructured":"McGinnis S, Madden TL: BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004, (32 Web Server):W20-25. 10.1093\/nar\/gkh435","DOI":"10.1093\/nar\/gkh435"},{"key":"616_CR43","first-page":"47","volume-title":"Connections","author":"VMA Batagelj","year":"1998","unstructured":"Batagelj VMA: Pajek: A program for large network analysis. Connections 1998, 47-57."}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-5-27.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1752-0509-5-27\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-5-27.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,6,8]],"date-time":"2019-06-08T13:54:12Z","timestamp":1560002052000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-5-27"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,2,10]]},"references-count":43,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["616"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-5-27","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,2,10]]},"article-number":"27"}}