{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,23]],"date-time":"2026-02-23T23:11:38Z","timestamp":1771888298466,"version":"3.50.1"},"reference-count":62,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2017,8,31]],"date-time":"2017-08-31T00:00:00Z","timestamp":1504137600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["31003A_143869, 31003A_170110"],"award-info":[{"award-number":["31003A_143869, 31003A_170110"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The evolution of antibody repertoires represents a hallmark feature of adaptive B-cell immunity. Recent advancements in high-throughput sequencing have dramatically increased the resolution to which we can measure the molecular diversity of antibody repertoires, thereby offering for the first time the possibility to capture the antigen-driven evolution of B cells. However, there does not exist a repertoire simulation framework yet that enables the comparison of commonly utilized phylogenetic methods with regard to their accuracy in inferring antibody evolution.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we developed AbSim, a time-resolved antibody repertoire simulation framework, which we exploited for testing the accuracy of methods for the phylogenetic reconstruction of B-cell lineages and antibody molecular evolution. AbSim enables the (i) simulation of intermediate stages of antibody sequence evolution and (ii) the modeling of immunologically relevant parameters such as duration of repertoire evolution, and the method and frequency of mutations. First, we validated that our repertoire simulation framework recreates replicates topological similarities observed in experimental sequencing data. Second, we leveraged Absim to show that current methods fail to a certain extent to predict the true phylogenetic tree correctly. Finally, we formulated simulation-validated guidelines for antibody evolution, which in the future will enable the development of accurate phylogenetic methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/cran.r-project.org\/web\/packages\/AbSim\/index.html<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx533","type":"journal-article","created":{"date-parts":[[2017,8,30]],"date-time":"2017-08-30T11:09:29Z","timestamp":1504091369000},"page":"3938-3946","source":"Crossref","is-referenced-by-count":55,"title":["Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim)"],"prefix":"10.1093","volume":"33","author":[{"given":"Alexander","family":"Yermanos","sequence":"first","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Z\u00fcrich, Basel, Switzerland"}]},{"given":"Victor","family":"Greiff","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Z\u00fcrich, Basel, Switzerland"}]},{"given":"Nike Julia","family":"Krautler","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, ETH Z\u00fcrich, Z\u00fcrich, Switzerland"}]},{"given":"Ulrike","family":"Menzel","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Z\u00fcrich, Basel, Switzerland"}]},{"given":"Andreas","family":"Dounas","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Applied Biosciences, ETH Z\u00fcrich, Z\u00fcrich, Switzerland"}]},{"given":"Enkelejda","family":"Miho","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Z\u00fcrich, Basel, Switzerland"}]},{"given":"Annette","family":"Oxenius","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, ETH Z\u00fcrich, Z\u00fcrich, Switzerland"}]},{"given":"Tanja","family":"Stadler","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Z\u00fcrich, Basel, Switzerland"}]},{"given":"Sai T","family":"Reddy","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Z\u00fcrich, Basel, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2017,8,31]]},"reference":[{"key":"2023020207510249600_btx533-B1","doi-asserted-by":"crossref","first-page":"63308","DOI":"10.1128\/JVI.02871-14","article-title":"High preexisting serological antibody levels correlate with diversification of the influenza vaccine response","volume":"89","author":"Andrews","year":"2015","journal-title":"J. Virol"},{"key":"2023020207510249600_btx533-B2","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.jim.2008.06.006","article-title":"IgTree\u00a9: Creating Immunoglobulin variable region gene lineage trees","volume":"338","author":"Barak","year":"2008","journal-title":"J. Immunol. Methods"},{"key":"2023020207510249600_btx533-B3","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1038\/nmeth.3364","article-title":"MiXCR: software for comprehensive adaptive immunity profiling","volume":"12","author":"Bolotin","year":"2015","journal-title":"Nat. Methods"},{"key":"2023020207510249600_btx533-B4","doi-asserted-by":"crossref","first-page":"e1003537.","DOI":"10.1371\/journal.pcbi.1003537","article-title":"BEAST 2: a software platform for Bayesian evolutionary analysis","volume":"10","author":"Bouckaert","year":"2014","journal-title":"PLoS Comput. Biol"},{"key":"2023020207510249600_btx533-B5","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"2023020207510249600_btx533-B6","doi-asserted-by":"crossref","first-page":"20140236.","DOI":"10.1098\/rstb.2014.0236","article-title":"The mouse antibody heavy chain repertoire is germline-focused and highly variable between inbred strains","volume":"370","author":"Collins","year":"2015","journal-title":"Philos. Trans. R. Soc. B"},{"key":"2023020207510249600_btx533-B7","doi-asserted-by":"crossref","first-page":"3566","DOI":"10.4049\/jimmunol.1502263","article-title":"A model of somatic hypermutation targeting in mice based on high-throughput Ig sequencing data","volume":"197","author":"Cui","year":"2016","journal-title":"J. Immunol"},{"key":"2023020207510249600_btx533-B8","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1093\/molbev\/msi103","article-title":"Bayesian coalescent inference of past population dynamics from molecular sequences","volume":"22","author":"Drummond","year":"2005","journal-title":"Mol. Biol. Evol"},{"key":"2023020207510249600_btx533-B9","doi-asserted-by":"crossref","first-page":"e88.","DOI":"10.1371\/journal.pbio.0040088","article-title":"Relaxed phylogenetics and dating with confidence","volume":"4","author":"Drummond","year":"2006","journal-title":"PLoS Biol"},{"key":"2023020207510249600_btx533-B10","doi-asserted-by":"crossref","first-page":"20140243.","DOI":"10.1098\/rstb.2014.0243","article-title":"Inferring processes underlying B-cell repertoire diversity","volume":"370","author":"Elhanati","year":"2015","journal-title":"Phil. Trans. R. Soc. B"},{"key":"2023020207510249600_btx533-B11","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.1038\/ni.3533","article-title":"Defining antigen-specific plasmablast and memory B cell subsets in human blood after viral infection or vaccination","volume":"17","author":"Ellebedy","year":"2016","journal-title":"Nat. Immunol"},{"key":"2023020207510249600_btx533-B12","doi-asserted-by":"crossref","first-page":"1377","DOI":"10.1084\/jem.172.5.1377","article-title":"Lack of N regions in fetal and neonatal mouse immunoglobulin V-D-J junctional sequences","volume":"172","author":"Feeney","year":"1990","journal-title":"J. Exp. Med"},{"key":"2023020207510249600_btx533-B13","doi-asserted-by":"crossref","first-page":"401.","DOI":"10.2307\/2412923","article-title":"Cases in which parsimony or compatibility methods will be positively misleading","volume":"27","author":"Felsenstein","year":"1978","journal-title":"Syst. Zool"},{"key":"2023020207510249600_btx533-B14","first-page":"164","article-title":"PHYLIP \u2013 Phylogeny Inference Package (Version 3.2)","volume":"5","author":"Felsenstein","year":"1989","journal-title":"Cladistics"},{"key":"2023020207510249600_btx533-B15","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1038\/nbt.2782","article-title":"The promise and challenge of high-throughput sequencing of the antibody repertoire","volume":"32","author":"Georgiou","year":"2014","journal-title":"Nat. Biotechnol"},{"key":"2023020207510249600_btx533-B16","doi-asserted-by":"crossref","first-page":"W435","DOI":"10.1093\/nar\/gkh412","article-title":"IMGT\/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis","volume":"32","author":"Giudicelli","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023020207510249600_btx533-B17","doi-asserted-by":"crossref","first-page":"20066","DOI":"10.1073\/pnas.1107498108","article-title":"Naive antibody gene-segment frequencies are heritable and unaltered by chronic lymphocyte ablation","volume":"108","author":"Glanville","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020207510249600_btx533-B18","doi-asserted-by":"crossref","first-page":"1604","DOI":"10.1182\/blood-2012-09-457283","article-title":"Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma","volume":"121","author":"Green","year":"2013","journal-title":"Blood"},{"key":"2023020207510249600_btx533-B19","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/s13073-015-0169-8","article-title":"A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status","volume":"7","author":"Greiff","year":"2015","journal-title":"Genome Med"},{"key":"2023020207510249600_btx533-B20","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1016\/j.it.2015.09.006","article-title":"Bioinformatic and statistical analysis of adaptive immune repertoires","volume":"36","author":"Greiff","year":"2015","journal-title":"Trends Immunol"},{"key":"2023020207510249600_btx533-B21","doi-asserted-by":"crossref","first-page":"40.","DOI":"10.1186\/s12865-014-0040-5","article-title":"Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice","volume":"15","author":"Greiff","year":"2014","journal-title":"BMC Immunol"},{"key":"2023020207510249600_btx533-B22","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1016\/j.celrep.2017.04.054","article-title":"Systems analysis reveals high genetic and antigen-driven predetermination of antibody repertoires throughout B-cell development","volume":"19","author":"Greiff","year":"2017","journal-title":"Cell Rep"},{"key":"2023020207510249600_btx533-B23","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1534\/genetics.116.196303","article-title":"A phylogenetic codon substitution model for antibody lineages","volume":"206","author":"Hoehn","year":"2017","journal-title":"Genetics"},{"key":"2023020207510249600_btx533-B24","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.chom.2014.05.013","article-title":"Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements","volume":"16","author":"Jackson","year":"2014","journal-title":"Cell Host Microbe"},{"key":"2023020207510249600_btx533-B25","volume-title":"Janeway\u2018s Immunobiology 8th Revised Edition","author":"Janeway","year":"2011"},{"key":"2023020207510249600_btx533-B26","doi-asserted-by":"crossref","first-page":"1458","DOI":"10.1126\/science.aad9195","article-title":"HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen","volume":"351","author":"Jardine","year":"2016","journal-title":"Science"},{"key":"2023020207510249600_btx533-B27","doi-asserted-by":"crossref","first-page":"4221","DOI":"10.4049\/jimmunol.176.7.4221","article-title":"Complete sequence assembly and characterization of the C57BL\/6 mouse Ig heavy chain V region","volume":"176","author":"Johnston","year":"2006","journal-title":"J. Immunol"},{"key":"2023020207510249600_btx533-B28","doi-asserted-by":"crossref","DOI":"10.1111\/1755-0998.12676","article-title":"treespace: Statistical exploration of landscapes of phylogenetic trees","author":"Jombart","year":"2017","journal-title":"Mol. Ecol. Resour"},{"key":"2023020207510249600_btx533-B29","doi-asserted-by":"crossref","first-page":"2735","DOI":"10.1093\/molbev\/msw124","article-title":"Mapping phylogenetic trees to reveal distinct patterns of evolution","volume":"33","author":"Kendall","year":"2016","journal-title":"Mol. Biol. Evol"},{"key":"2023020207510249600_btx533-B30","doi-asserted-by":"crossref","first-page":"e1501371","DOI":"10.1126\/sciadv.1501371","article-title":"Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting","volume":"2","author":"Khan","year":"2016","journal-title":"Sci. Adv"},{"key":"2023020207510249600_btx533-B31","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/S0022-1759(96)00208-6","article-title":"Reliable cloning of functional antibody variable domains from hybridomas and spleen cell repertoires employing a reengineered phage display system","volume":"201","author":"Krebber","year":"1997","journal-title":"J. Immunol. Methods"},{"key":"2023020207510249600_btx533-B32","doi-asserted-by":"crossref","DOI":"10.1038\/nature12053","article-title":"Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus","volume":"496","author":"Liao","year":"2013","journal-title":"Nature"},{"key":"2023020207510249600_btx533-B33","doi-asserted-by":"crossref","first-page":"111","DOI":"10.32614\/RJ-2014-011","article-title":"The stringdist package for approximate string matching","volume":"6","author":"Loo","year":"2014","journal-title":"R. J"},{"key":"2023020207510249600_btx533-B34","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1038\/40540","article-title":"Lifetime of plasma cells in the bone marrow","volume":"388","author":"Manz","year":"1997","journal-title":"Nature"},{"key":"2023020207510249600_btx533-B35","doi-asserted-by":"crossref","first-page":"3180","DOI":"10.1073\/pnas.81.10.3180","article-title":"Generation of antibody diversity in the immune response of BALB\/c mice to influenza virus hemagglutinin","volume":"81","author":"McKean","year":"1984","journal-title":"Proc. Natl. Acad. Sci, USA"},{"key":"2023020207510249600_btx533-B36","doi-asserted-by":"crossref","first-page":"e96727","DOI":"10.1371\/journal.pone.0096727","article-title":"Comprehensive evaluation and optimization of amplicon library preparation methods for high-throughput antibody sequencing","volume":"9","author":"Menzel","year":"2014","journal-title":"PLoS ONE"},{"key":"2023020207510249600_btx533-B37","first-page":"msu340","article-title":"Antibody-specific model of amino acid substitution for immunological inferences from alignments of antibody sequences","author":"Mirsky","year":"2014","journal-title":"Mol. Biol. Evol"},{"key":"2023020207510249600_btx533-B38","doi-asserted-by":"crossref","first-page":"5405","DOI":"10.1073\/pnas.1001705107","article-title":"Maximum entropy models for antibody diversity","volume":"107","author":"Mora","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020207510249600_btx533-B39","first-page":"96.","article-title":"Differences in the composition of the human antibody repertoire by B cell subsets in the blood","volume":"5","author":"Mroczek","year":"2014","journal-title":"B Cell Biol"},{"key":"2023020207510249600_btx533-B40","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1016\/S0092-8674(00)00078-7","article-title":"Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme","volume":"102","author":"Muramatsu","year":"2000","journal-title":"Cell"},{"key":"2023020207510249600_btx533-B41","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1038\/nri1896","article-title":"Targeting of somatic hypermutation","volume":"6","author":"Odegard","year":"2006","journal-title":"Nat. Rev. Immunol"},{"key":"2023020207510249600_btx533-B42","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1093\/bioinformatics\/btg412","article-title":"APE: Analyses of Phylogenetics and Evolution in R language","volume":"20","author":"Paradis","year":"2004","journal-title":"Bioinformatics"},{"key":"2023020207510249600_btx533-B43","doi-asserted-by":"crossref","first-page":"e1005086.","DOI":"10.1371\/journal.pcbi.1005086","article-title":"Likelihood-based inference of B cell clonal families","volume":"12","author":"Ralph","year":"2016","journal-title":"PLOS Comput. Biol"},{"key":"2023020207510249600_btx533-B44","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1111\/j.2041-210X.2011.00169.x","article-title":"phytools: an R package for phylogenetic comparative biology (and other things): phytools: R package","volume":"3","author":"Revell","year":"2012","journal-title":"Methods Ecol. Evol"},{"key":"2023020207510249600_btx533-B45","doi-asserted-by":"crossref","first-page":"976","DOI":"10.1111\/2041-210X.12233","article-title":"Rphylip: an R interface for PHYLIP","volume":"5","author":"Revell","year":"2014","journal-title":"Methods Ecol. Evol"},{"key":"2023020207510249600_btx533-B46","doi-asserted-by":"crossref","first-page":"2349","DOI":"10.1002\/eji.201343566","article-title":"Non-neutralizing antibodies protect from chronic LCMV infection independently of activating Fc\u03b3R or complement: Immunity to infection","volume":"43","author":"Richter","year":"2013","journal-title":"Eur. J. Immunol"},{"key":"2023020207510249600_btx533-B47","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/sj.icb.7100055","article-title":"Models for antigen receptor gene rearrangement: CDR3 length","volume":"85","author":"Saada","year":"2007","journal-title":"Immunol. Cell Biol"},{"key":"2023020207510249600_btx533-B48","doi-asserted-by":"crossref","first-page":"i53","DOI":"10.1093\/bioinformatics\/btv238","article-title":"IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis","volume":"31","author":"Safonova","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020207510249600_btx533-B49","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1093\/bioinformatics\/btq706","article-title":"phangorn: phylogenetic analysis in R","volume":"27","author":"Schliep","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020207510249600_btx533-B50","doi-asserted-by":"crossref","first-page":"2659","DOI":"10.1084\/jem.20091087","article-title":"Molecular footprints of a germinal center derivation of human IgM\u2009+\u2009(IgD+)CD27+ B cells and the dynamics of memory B cell generation","volume":"206","author":"Seifert","year":"2009","journal-title":"J Exp Med"},{"key":"2023020207510249600_btx533-B51","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega","volume":"7","author":"Sievers","year":"2014","journal-title":"Mol. Syst. Biol"},{"key":"2023020207510249600_btx533-B52","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020207510249600_btx533-B53","doi-asserted-by":"crossref","first-page":"248ra107","DOI":"10.1126\/scitranslmed.3008879","article-title":"B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes","volume":"6","author":"Stern","year":"2014","journal-title":"Sci. Transl. Med"},{"key":"2023020207510249600_btx533-B54","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1038\/ni.3175","article-title":"Diversity, cellular origin and autoreactivity of antibody-secreting cell population expansions in acute systemic lupus erythematosus","volume":"16","author":"Tipton","year":"2015","journal-title":"Nat. Immunol"},{"key":"2023020207510249600_btx533-B55","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/302575a0","article-title":"Somatic generation of antibody diversity","volume":"302","author":"Tonegawa","year":"1983","journal-title":"Nature"},{"key":"2023020207510249600_btx533-B56","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1073\/pnas.1415875112","article-title":"B-cell repertoire responses to varicella-zoster vaccination in human identical twins","volume":"112","author":"Wang","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020207510249600_btx533-B57","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1126\/science.1170020","article-title":"High-throughput sequencing of the zebrafish antibody repertoire","volume":"324","author":"Weinstein","year":"2009","journal-title":"Science"},{"key":"2023020207510249600_btx533-B58","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1016\/j.cell.2015.03.004","article-title":"Maturation and diversity of the VRC01-antibody lineage over 15\u2009years of chronic HIV-1 infection","volume":"161","author":"Wu","year":"2015","journal-title":"Cell"},{"key":"2023020207510249600_btx533-B59","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/S1074-7613(00)00006-6","article-title":"Diversity in the CDR3 region of VH is sufficient for most antibody specificities","volume":"13","author":"Xu","year":"2000","journal-title":"Immunity"},{"key":"2023020207510249600_btx533-B60","first-page":"358","article-title":"Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput Immunoglobulin sequencing data","volume":"4","author":"Yaari","year":"2013","journal-title":"Front. B Cell Biol"},{"key":"2023020207510249600_btx533-B61","doi-asserted-by":"crossref","first-page":"121.","DOI":"10.1186\/s13073-015-0243-2","article-title":"Practical guidelines for B-cell receptor repertoire sequencing analysis","volume":"7","author":"Yaari","year":"2015","journal-title":"Genome Med"},{"key":"2023020207510249600_btx533-B62","doi-asserted-by":"crossref","first-page":"6470","DOI":"10.1073\/pnas.1219320110","article-title":"Mining the antibodyome for HIV-1\u2013neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy\/light chains","volume":"110","author":"Zhu","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/24\/3938\/49042073\/bioinformatics_33_24_3938.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/24\/3938\/49042073\/bioinformatics_33_24_3938.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T07:54:27Z","timestamp":1675324467000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/24\/3938\/4100159"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,8,31]]},"references-count":62,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2017,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx533","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,12,15]]},"published":{"date-parts":[[2017,8,31]]}}}