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VBASE2, an integrative V gene database

I. Retter
<span title="2004-12-17">2004</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
It acts as an interconnecting platform between several existing self-contained data systems: VBASE2 integrates genome sequence data and links to the V genes in the Ensembl Genome Browser.  ...  The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes.  ...  We thank Ian Tomlinson for allowing us to call our database 'VBASE2' and for his helpful discussion.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki088">doi:10.1093/nar/gki088</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15608286">pmid:15608286</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC540042/">pmcid:PMC540042</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dvkd6qy4wng2bguwzu4x6yhrty">fatcat:dvkd6qy4wng2bguwzu4x6yhrty</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20051025213928/http://nar.oxfordjournals.org:80/cgi/reprint/33/suppl_1/D671.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/72/60/7260d0967ca07097dbb5a0d5d6744f08c7aa0e73.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki088"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540042" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Immunoglobulin class switching appears to be regulated by B-cell antigen receptor-specific T-cell action

Hans Lange, Oliver Hecht, Michael Zemlin, Ahmad Trad, Radu I. Tanasa, Harry W. Schroeder, Hilmar Lemke
<span title="">2012</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/skuoqxf27fhphjuj4apy7wodla" style="color: black;">European Journal of Immunology</a> </i> &nbsp;
To test this view, we analyzed the variable gene repertoires of natural monoclonal antibodies to the hapten 2-phenyloxazolone (phOx) as well as those generated after phOx protein carrier-induced thymus-dependent  ...  VBASE2, an integrative V gene database. Nucleic Acids Res. 2005; 33:D671-D674.  ...  b Indicates the VH or VL gene family.In the integrative database VBASE2, the genes are classified: for class 1 genes there is genomic and rearranged evidence, for class 2 genes only genomic evidence  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/eji.201141857">doi:10.1002/eji.201141857</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22531925">pmid:22531925</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3688080/">pmcid:PMC3688080</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u2vcbfmhqzadzmapsxk4b4ayxu">fatcat:u2vcbfmhqzadzmapsxk4b4ayxu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200206145626/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3688080&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ac/b3/acb3e98cb59a412128aacf7d3e2087d5866fbcba.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/eji.201141857"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3688080" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Human/Murine Chimeric Fab Antibody Neutralizes Anthrax Lethal ToxinIn Vitro

Guipeng Ding, Ximin Chen, Jin Zhu, Nicholas S. Duesbery, Xunjia Cheng, Brian Cao
<span title="">2013</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cl6j3vzo2rcephhjrywq7cktkq" style="color: black;">Clinical and Developmental Immunology</a> </i> &nbsp;
The LF8-Fab expressed inEscherichia colicould specifically identify LF with an affinity of3.46×107 L/mol and could neutralize LeTx with an EC50of 85 μg/mL.  ...  This is an integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse, while all variable gene sequences are extracted from the EMBL-Bank [34] .  ...  The complementary determining region (CDR) and framework region (FR) of V H and V L were determined by VBASE2 database (Figure 2) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2013/475809">doi:10.1155/2013/475809</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23861692">pmid:23861692</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3687597/">pmcid:PMC3687597</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/enwlcfvh2jg2talqdcrnmqavhq">fatcat:enwlcfvh2jg2talqdcrnmqavhq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190227024716/http://pdfs.semanticscholar.org/75a3/1a5a13612b014943acb1f0f3dde565c4f6db.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/75/a3/75a31a5a13612b014943acb1f0f3dde565c4f6db.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2013/475809"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3687597" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Generation of "LYmph Node Derived Antibody Libraries" (LYNDAL) for selecting fully human antibody fragments with therapeutic potential

Philipp Diebolder, Armin Keller, Stephanie Haase, Anne Schlegelmilch, Jonathan D Kiefer, Tamana Karimi, Tobias Weber, Gerhard Moldenhauer, Roland Kehm, Anna M Eis-Hübinger, Dirk Jäger, Philippe A Federspil (+5 others)
<span title="2013-11-20">2013</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/34ng7d3sk5bmlcnpsyiueeatim" style="color: black;">mAbs</a> </i> &nbsp;
As the source for variable antibody genes, we cloned immunoglobulin G (IgG)-derived B cell repertoires from lymph nodes of 20 individuals undergoing surgery for head and neck cancer.  ...  Sequence analysis of unselected "LYmph Node Derived Antibody Libraries" (LYNDAL) revealed a naturally occurring distribution pattern of rearranged antibody sequences, representing all known variable gene  ...  gene family occurrences of sequenced LYNDAL clones were calculated and compared with the mean distribution of all functional V gene entries of human antibody databases VBASE, VBASE2, and IMGT-GENE. 65  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4161/mabs.27236">doi:10.4161/mabs.27236</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24256717">pmid:24256717</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3929437/">pmcid:PMC3929437</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4tjawk2xsjgmxcgl2paoq7cmna">fatcat:4tjawk2xsjgmxcgl2paoq7cmna</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3929437/PMC3929437-mabs.27236.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4a/17/4a17794fa919d411ae351c9d671d4d1a6d64cc99.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4161/mabs.27236"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929437" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

SAIVGeM: spreadsheet analysis of immunoglobulin VH gene mutations

Bradley T. Messmer
<span title="">2005</span> <i title="Future Science, LTD"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6t7cfvh76ranblnkx6doquvcyq" style="color: black;">BioTechniques</a> </i> &nbsp;
/V-QUEST, imgt.cines.fr/textes/vquest (11) ; VBASE2, www.dnaplot.de/ vbase2 (12) ], but there are currently no publicly available tools for the simultaneous analysis of many sequences.  ...  The sheet germline RGYW potential is a reference database that indicates, for each germline gene, which nucleotides reside in an RGYW motif on the template (+), nontemplate (-), or both strands (+/-).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2144/05393st03">doi:10.2144/05393st03</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16206907">pmid:16206907</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hxyn564zlvgvfbzels24xyjvvi">fatcat:hxyn564zlvgvfbzels24xyjvvi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809093257/http://www.biotechniques.com/multimedia/archive/00004/BTN_A_05393ST03_O_4703a.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f0/c1/f0c15290c74800477a5e6796947321ab34a99e82.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2144/05393st03"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data

Felix Breden, Eline T. Luning Prak, Bjoern Peters, Florian Rubelt, Chaim A. Schramm, Christian E. Busse, Jason A. Vander Heiden, Scott Christley, Syed Ahmad Chan Bukhari, Adrian Thorogood, Frederick A. Matsen IV, Yariv Wine (+11 others)
<span title="2017-11-01">2017</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t7exsmmojvgjnhq3pflf7pk6zq" style="color: black;">Frontiers in Immunology</a> </i> &nbsp;
The purpose of this perspective is to provide an overview of the AIRR Community's founding principles and present the progress that the AIRR Community has made in developing standards of practice and data  ...  VBASE2, an integrative V gene database. Nucleic Acids Res (2005) 33(Database issue):D671-4. doi:10.1093/ nar/gki088 https://www.b-t.cr. 2 https://www.b-t.cr/t/317. 3 https://www.b-t.cr/t/426.  ...  Immunoglobulin and T-cell receptor sequences have been studied for decades and several established databases exist including Kabat-Wu and Vbase2 (9, 10).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fimmu.2017.01418">doi:10.3389/fimmu.2017.01418</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29163494">pmid:29163494</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5671925/">pmcid:PMC5671925</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ifsiphj5uvbvfpe66r52uxkduu">fatcat:ifsiphj5uvbvfpe66r52uxkduu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190307135358/http://pdfs.semanticscholar.org/e119/009a47ba07584e17484157beb98d8b5b7cf1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e1/19/e119009a47ba07584e17484157beb98d8b5b7cf1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fimmu.2017.01418"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5671925" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Review on Computational Tools and Databases for the Development of Vaccines Against Infectious Diseases

Qazi Mohammad Sajid Jamal
<span title="">2019</span> <i title="Turk Immunoloji Dernegi"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4vikkcnwobaepet7qxny6mggni" style="color: black;">Turkish Journal of Immunology</a> </i> &nbsp;
Many databases and tools with huge molecular level information are freely available to utilize in the outgoing research work.  ...  Thus, the article provides information about online resources, database and tools which could be helpful in vaccine designing.  ...  Acknowledgement: Author is thankful to the all database curator for the maintenance and development of informative portal to the scientific community and students.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.25002/tji.2019.1182">doi:10.25002/tji.2019.1182</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cjo5wbc3rvcypot3byqzxkcpsi">fatcat:cjo5wbc3rvcypot3byqzxkcpsi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200928211433/http://turkishimmunology.org/pdf/7_3_137_148.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/60/70/607069068c14242d36fe9494316bbdf884caed15.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.25002/tji.2019.1182"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Clonal Progression during the T Cell-Dependent B Cell Antibody Response Depends on the Immunoglobulin DH Gene Segment Repertoire

Ahmad Trad, Radu Iulian Tanasa, Hans Lange, Michael Zemlin, Harry W. Schroeder, Hilmar Lemke
<span title="2014-08-11">2014</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t7exsmmojvgjnhq3pflf7pk6zq" style="color: black;">Frontiers in Immunology</a> </i> &nbsp;
Neither of the D-altered strains demonstrated the restriction in the V H /V L repertoire, the elimination of V H 1 family-encoded antibodies, the focusing of the distribution of CDR-H3 lengths, or the  ...  An increased prevalence of IgM-producing hybridomas from late primary, secondary, and tertiary memory responses suggested either impaired class switch recombination (CSR) or impaired clonal expansion of  ...  is designated V H 171/V κ 072 in the integrative database VBASE2.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fimmu.2014.00385">doi:10.3389/fimmu.2014.00385</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25157256">pmid:25157256</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4128299/">pmcid:PMC4128299</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qemd7qa3p5adpmnaki6jiiutj4">fatcat:qemd7qa3p5adpmnaki6jiiutj4</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC4128299/PMC4128299-fimmu.2014.00385.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/85/c2/85c233e2f57d04e2efaba39ffd23779c9ec5a24e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fimmu.2014.00385"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4128299" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles

Daniel Gadala-Maria, Gur Yaari, Mohamed Uduman, Steven H. Kleinstein
<span title="2015-02-09">2015</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
Current V(D)J assignment methods work by aligning sequences to a database of known germline V(D)J segment alleles.  ...  The integration of TIgGER into Rep-Seq processing pipelines will increase the accuracy of V segment assignments, thus improving B-cell repertoire analyses. next-generation sequencing | B-cell repertoire  ...  Some of these V alleles have been incorporated into the IMGT database or alternative databases of germline alleles [such as VBASE2 (22) or the UNSWIg human heavy chain repertoire (23) ].  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1417683112">doi:10.1073/pnas.1417683112</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25675496">pmid:25675496</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4345584/">pmcid:PMC4345584</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tmccevrq5rby7b6uxccysfx5iy">fatcat:tmccevrq5rby7b6uxccysfx5iy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180728160439/http://www.pnas.org/content/pnas/112/8/E862.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2e/7c/2e7c398c62eed7d7892a3512b196636c223c52ba.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1417683112"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4345584" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Development of human antibody fragments using antibody phage display for the detection and diagnosis of Venezuelan equine encephalitis virus (VEEV)

Martina Kirsch, Birgit Hülseweh, Christoph Nacke, Torsten Rülker, Thomas Schirrmann, Hans-Jürgen Marschall, Michael Hust, Stefan Dübel
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rxfgte5g2bcizdvltz5dfdp7zi" style="color: black;">BMC Biotechnology</a> </i> &nbsp;
The objective of this work was the generation of recombinant antibodies for the detection of VEEV after a potential bioterrorism assault or an natural outbreak of VEEV.  ...  Results: In this work, human anti-VEEV single chain Fragments variable (scFv) were isolated for the first time from a human naïve antibody gene library using optimized selection processes.  ...  We gratefully acknowledge the kind help of Svetlana Mollova, Ida Retter and Werner Müller for adapting VBASE2 to analysis of antibody V-gene sequences directly derived from antibody selection projects.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6750-8-66">doi:10.1186/1472-6750-8-66</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18764933">pmid:18764933</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2543005/">pmcid:PMC2543005</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fckywzeqfraifos6wcirnq64fy">fatcat:fckywzeqfraifos6wcirnq64fy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830032014/https://bmcbiotechnol.biomedcentral.com/track/pdf/10.1186/1472-6750-8-66?site=http://bmcbiotechnol.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/86/f2/86f2973cee9053541e5b4185335a3f8e375dedb1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6750-8-66"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2543005" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Camelid Ig V genes reveal significant human homology not seen in therapeutic target genes, providing for a powerful therapeutic antibody platform

Alex Klarenbeek, Khalil El Mazouari, Aline Desmyter, Christophe Blanchetot, Anna Hultberg, Natalie de Jonge, Rob C Roovers, Christian Cambillau, Sylvia Spinelli, Jurgen Del-Favero, Theo Verrips, Hans J de Haard (+1 others)
<span title="2015-05-27">2015</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/34ng7d3sk5bmlcnpsyiueeatim" style="color: black;">mAbs</a> </i> &nbsp;
We therefore leveraged the publicly available HTG and WGS databases of Lama pacos and Camelus ferus to retrieve the germline repertoire of V genes using human IGV genes as reference.  ...  Interestingly, this sequence homology seemed largely restricted to the Ig V genes and was far less apparent in other genes: 6 therapeutically relevant target genes differed significantly from their human  ...  Human germline V gene sequences are derived from the publicly available human reference genome (Build 37, hg 19), Vbase2 database (www.vbase2.org/vbdownload.php) and NCBI Igblast database (www.ncbi.nlm.nih.gov  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/19420862.2015.1046648">doi:10.1080/19420862.2015.1046648</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26018625">pmid:26018625</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4622956/">pmcid:PMC4622956</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vvuzlfrjajc5lfscmsd4yzgmaq">fatcat:vvuzlfrjajc5lfscmsd4yzgmaq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200505185334/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4622956&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6a/3b/6a3b890282b325537ea357c8b6e525412ff0c5e4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/19420862.2015.1046648"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> tandfonline.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4622956" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences

<span title="2020-03-01">2019</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
We found that only 73/183 (40%) V, D and J human genes were shared between the reference germline sets used by the tools. We found that the annotation results differed between tools.  ...  IgBLAST and MiXCR, in terms of reproducibility of annotation output, accuracy and speed using simulated and experimental high-throughput sequencing datasets.We analyzed changes in IMGT reference germline database  ...  Briefly, after HTS data are collected, the sequences are aligned to V, (D) and J genes from a reference germline database (e.g.GenBank, IMGT, VBASE2).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btz845">doi:10.1093/bioinformatics/btz845</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31873728">pmid:31873728</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7075533/">pmcid:PMC7075533</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/53kvuphbirdnjgfmet5xlam3ki">fatcat:53kvuphbirdnjgfmet5xlam3ki</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210715071704/https://www.duo.uio.no/bitstream/handle/10852/83279/Postnr+1812070_Smakaj_Greiff_Bioinformatics_btz845.pdf?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/af/81/af81bc03dc370ce0fd670a13e0fd6de678b0e13d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btz845"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7075533" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Novel Allele Detection Tool Benchmark and Application With Antibody Repertoire Sequencing Dataset

Xiujia Yang, Yan Zhu, Sen Chen, Huikun Zeng, Junjie Guan, Qilong Wang, Chunhong Lan, Deqiang Sun, Xueqing Yu, Zhenhai Zhang
<span title="2021-10-26">2021</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t7exsmmojvgjnhq3pflf7pk6zq" style="color: black;">Frontiers in Immunology</a> </i> &nbsp;
Here, we developed a tool to simulate repertoires by integrating the full spectrum features of an antibody repertoire such as germline gene usage, junctional modification, position-specific SHM and clonal  ...  Detailed knowledge of the diverse immunoglobulin germline genes is critical for the study of humoral immunity.  ...  GENE-DB, http://www.imgt.org/genedb/; IgPdb, https:// cgi.cse.unsw.edu.au/~ihmmune/IgPdb/information.php; VBASE2 (23) , http://www.vbase2.org/; Lym1K (24) , http://maths.nuigalway. ie/biocluster/database  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fimmu.2021.739179">doi:10.3389/fimmu.2021.739179</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34764956">pmid:34764956</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8576399/">pmcid:PMC8576399</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2eahjibowrf7bimxld7p7nfzce">fatcat:2eahjibowrf7bimxld7p7nfzce</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211108153006/https://fjfsdata01prod.blob.core.windows.net/articles/files/739179/pubmed-zip/.versions/1/.package-entries/fimmu-12-739179.pdf?sv=2018-03-28&amp;sr=b&amp;sig=2zroreKRGLOr5NQjPMq%2F0Q%2BrEXhsvk93C7lzr2cS%2FM4%3D&amp;se=2021-11-08T15%3A30%3A35Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fimmu-12-739179.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/10/60/1060d514d913203c6ceea28b6e6c5ff429b03e80.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fimmu.2021.739179"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8576399" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A recombinant antibody toolbox for Dictyostelium discoideum

Wanessa C. Lima, Philippe Hammel, Pierre Cosson
<span title="2020-04-10">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gl3hmlq4ebd3jcx3yuj2yfzivq" style="color: black;">BMC Research Notes</a> </i> &nbsp;
For the past 5 years, our laboratory has worked to promote an increased use of recombinant antibodies (rAbs) by academic laboratories.  ...  Following the cDNA synthesis reaction, the heavy (V H ) and light (V L ) variable domain sequences were amplified by PCR using degenerate primer sets (500 nM, Integrated DNA Technologies; Additional file  ...  (B) An scFv is made of the V H and V L variable chains joined by a peptide linker (GGGGSGGGGSGGGGS).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13104-020-05048-8">doi:10.1186/s13104-020-05048-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32276653">pmid:32276653</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xvy75honrfdwhkuz4jx2zb2nta">fatcat:xvy75honrfdwhkuz4jx2zb2nta</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200411074530/https://bmcresnotes.biomedcentral.com/track/pdf/10.1186/s13104-020-05048-8" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5e/cf/5ecf2db2e322f30bedd35fa9b9fbaa048e8f9665.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13104-020-05048-8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Knowledge-based antibody repertoire simulation, a novel allele detection tool evaluation and application [article]

Xiujia Yang, Yan Zhu, Huikun Zeng, Sen Chen, Junjie Guan, Qi-Long Wang, Chunhong Lan, Deqiang Sun, Xueqing Yu, Zhenhai Zhang
<span title="2021-07-02">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Here, we developed a tool to simulate repertoires by integrating the full spectrum features of an antibody repertoire such as germline gene usage, junctional modification, position-specific SHM and clonal  ...  Detailed knowledge of the diverse immunoglobulin germline genes is critical for the study of humoral immunity.  ...  All collected V allele sequences are outlined in Supplementary IgPdb, https://cgi.cse.unsw.edu.au/~ihmmune/IgPdb/information.php; VBASE2 22 , 5,6,19,[24][25][26][27][28][29]blic databases (IMGT/GENE-DB  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.07.01.450681">doi:10.1101/2021.07.01.450681</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mityo3d7g5g25izodenmfi3wiq">fatcat:mityo3d7g5g25izodenmfi3wiq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211020074443/https://www.biorxiv.org/content/biorxiv/early/2021/07/02/2021.07.01.450681.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3b/d3/3bd32b5bbf147843745e816736b73a3d7600824d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.07.01.450681"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>
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