Daphne van Ginneken, Valentijn Tromp, Lucas Stalder, Tudor-Stefan Cotet, Sophie Bakker, Anamay Samant, Sai T Reddy, Alexander Yermanos
{"title":"用AntibodyForests描述抗体库之间和内部的进化。","authors":"Daphne van Ginneken, Valentijn Tromp, Lucas Stalder, Tudor-Stefan Cotet, Sophie Bakker, Anamay Samant, Sai T Reddy, Alexander Yermanos","doi":"10.1093/bioinformatics/btaf560","DOIUrl":null,"url":null,"abstract":"<p><strong>Motivation: </strong>The rapid advancements in immune repertoire sequencing, powered by single-cell technologies and artificial intelligence, have created unprecedented opportunities to study B cell evolution at a novel scale and resolution. However, fully leveraging these data requires specialized software capable of performing inter- and intra-repertoire analyses to unravel the complex dynamics of B cell repertoire evolution during immune responses.</p><p><strong>Results: </strong>Here, we present AntibodyForests, software to infer B cell lineages, quantify inter- and intra-antibody repertoire evolution, and analyze somatic hypermutation using protein language models and protein structure.</p><p><strong>Availability: </strong>This R package is available on CRAN and Github at https://github.com/alexyermanos/AntibodyForests, a vignette is available at https://cran.case.edu/web/packages/AntibodyForests/vignettes/AntibodyForests_vignette.html.</p><p><strong>Supplementary information: </strong>Supplementary data are available at Bioinformatics online.</p>","PeriodicalId":93899,"journal":{"name":"Bioinformatics (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":5.4000,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Delineating inter- and intra-antibody repertoire evolution with AntibodyForests.\",\"authors\":\"Daphne van Ginneken, Valentijn Tromp, Lucas Stalder, Tudor-Stefan Cotet, Sophie Bakker, Anamay Samant, Sai T Reddy, Alexander Yermanos\",\"doi\":\"10.1093/bioinformatics/btaf560\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Motivation: </strong>The rapid advancements in immune repertoire sequencing, powered by single-cell technologies and artificial intelligence, have created unprecedented opportunities to study B cell evolution at a novel scale and resolution. However, fully leveraging these data requires specialized software capable of performing inter- and intra-repertoire analyses to unravel the complex dynamics of B cell repertoire evolution during immune responses.</p><p><strong>Results: </strong>Here, we present AntibodyForests, software to infer B cell lineages, quantify inter- and intra-antibody repertoire evolution, and analyze somatic hypermutation using protein language models and protein structure.</p><p><strong>Availability: </strong>This R package is available on CRAN and Github at https://github.com/alexyermanos/AntibodyForests, a vignette is available at https://cran.case.edu/web/packages/AntibodyForests/vignettes/AntibodyForests_vignette.html.</p><p><strong>Supplementary information: </strong>Supplementary data are available at Bioinformatics online.</p>\",\"PeriodicalId\":93899,\"journal\":{\"name\":\"Bioinformatics (Oxford, England)\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":5.4000,\"publicationDate\":\"2025-10-09\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Bioinformatics (Oxford, England)\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1093/bioinformatics/btaf560\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics (Oxford, England)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/bioinformatics/btaf560","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Delineating inter- and intra-antibody repertoire evolution with AntibodyForests.
Motivation: The rapid advancements in immune repertoire sequencing, powered by single-cell technologies and artificial intelligence, have created unprecedented opportunities to study B cell evolution at a novel scale and resolution. However, fully leveraging these data requires specialized software capable of performing inter- and intra-repertoire analyses to unravel the complex dynamics of B cell repertoire evolution during immune responses.
Results: Here, we present AntibodyForests, software to infer B cell lineages, quantify inter- and intra-antibody repertoire evolution, and analyze somatic hypermutation using protein language models and protein structure.
Availability: This R package is available on CRAN and Github at https://github.com/alexyermanos/AntibodyForests, a vignette is available at https://cran.case.edu/web/packages/AntibodyForests/vignettes/AntibodyForests_vignette.html.
Supplementary information: Supplementary data are available at Bioinformatics online.
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
