ArticlemAbs
The antibody mining toolbox: an open source tool for the rapid analysis of antibody repertoires.
Article in mAbs. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 42 citations in OpenAlex.
- Direct selection of functional fluorescent-protein antibody fusions by yeast display.PloS one · 2023Article
- B-cell receptor repertoire sequencing: Deeper digging into the mechanisms and clinical aspects of immune-mediated diseases.iScience · 2022Review
- Broad and ultra-potent cross-clade neutralization of HIV-1 by a vaccine-induced CD4 binding site bovine antibody.Cell reports. Medicine · 2022Article
- A single donor is sufficient to produce a highly functional in vitro antibody library.Communications biology · 2021Article
- Intrathecal B-cell activation in LGI1 antibody encephalitis.Neurology(R) neuroimmunology & neuroinflammation · 2020Article
- Cross-Reactive and Lineage-Specific Single Domain Antibodies against Influenza B Hemagglutinin.Antibodies (Basel, Switzerland) · 2019Article
- Current trends in biomarker discovery and analysis tools for traumatic brain injury.Journal of biological engineering · 2019Review
- Coupling Brain Perfusion Screens and Next Generation Sequencing to Identify Blood-Brain Barrier Binding Antibodies.AIChE journal. American Institute of Chemical Engineers · 2018Article
- Selection of phage-displayed accessible recombinant targeted antibodies (SPARTA): methodology and applications.JCI insight · 2018Article
- Massively Parallel Sequencing of Peritoneal and Splenic B Cell Repertoires Highlights Unique Properties of B-1 Cell Antibodies.Journal of immunology (Baltimore, Md. : 1950) · 2018Article
- Integrating high-throughput screening and sequencing for monoclonal antibody discovery and engineering.Immunology · 2018Review
- Analyzing Immunoglobulin Repertoires.Frontiers in immunology · 2018Review
- Many Routes to an Antibody Heavy-Chain CDR3: Necessary, Yet Insufficient, for Specific Binding.Frontiers in immunology · 2018Article
- Next-Generation Sequencing of Antibody Display Repertoires.Frontiers in immunology · 2018Review
- The dynamics of immunoglobulin V-gene usage and clonotype expansion in mice after prime and boost immunizations as analyzed by NGS.Human vaccines & immunotherapeutics · 2017Article
- VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.BMC bioinformatics · 2017Article
- A Haystack Heuristic for Autoimmune Disease Biomarker Discovery Using Next-Gen Immune Repertoire Sequencing Data.Scientific reports · 2017Article
- Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity.Nature communications · 2016Article
- B cell repertoire expansion occurs in meningeal ectopic lymphoid tissue.JCI insight · 2016Article
- Ligand-targeted theranostic nanomedicines against cancer.Journal of controlled release : official journal of the Controlled Release Society · 2016Review
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
Abstract
In vitro selection has been an essential tool in the development of recombinant antibodies against various antigen targets. Deep sequencing has recently been gaining ground as an alternative and valuable method to analyze such antibody selections. The analysis provides a novel and extremely detailed view of selected antibody populations, and allows the identification of specific antibodies using only sequencing data, potentially eliminating the need for expensive and laborious low-throughput screening methods such as enzyme-linked immunosorbant assay. The high cost and the need for bioinformatics experts and powerful computer clusters, however, have limited the general use of deep sequencing in antibody selections. Here, we describe the AbMining ToolBox, an open source software package for the straightforward analysis of antibody libraries sequenced by the three main next generation sequencing platforms (454, Ion Torrent, MiSeq). The ToolBox is able to identify heavy chain CDR3s as effectively as more computationally intense software, and can be easily adapted to analyze other portions of antibody variable genes, as well as the selection outputs of libraries based on different scaffolds. The software runs on all common operating systems (Microsoft Windows, Mac OS X, Linux), on standard personal computers, and sequence analysis of 1-2 million reads can be accomplished in 10-15 min, a fraction of the time of competing software. Use of the ToolBox will allow the average researcher to incorporate deep sequence analysis into routine selections from antibody display libraries.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.