ArticleJournal of clinical bioinformatics2013
Automated analysis of immunoglobulin genes from high-throughput sequencing: life without a template.
Article in Journal of clinical bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
7 citing papers in PubMed, 11 citations in OpenAlex.
- Mutational patterns along different evolution paths of follicular lymphoma.Frontiers in oncology · 2022Article
- Longitudinal analysis of the peripheral B cell repertoire reveals unique effects of immunization with a new influenza virus strain.Genome medicine · 2015Article
- Assigning and visualizing germline genes in antibody repertoires.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2015Article
- Article
- Old questions, new tools: does next-generation sequencing hold the key to unraveling intestinal B-cell responses?Mucosal immunology · 2015Review
- Modeling the T cell immune response: a fascinating challenge.Journal of pharmacokinetics and pharmacodynamics · 2014Review
- Immunoglobulin class-switched B cells form an active immune axis between CNS and periphery in multiple sclerosis.Science translational medicine · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundImmunoglobulin (that is, antibody) and T cell receptor genes are created through somatic gene rearrangement from gene segment libraries. Immunoglobulin genes are further diversified by somatic hypermutation and selection during the immune response. Studying the repertoires of these genes yields valuable insights into immune system function in infections, aging, autoimmune diseases and cancers. The introduction of high throughput sequencing has generated unprecedented amounts of repertoire and mutation data from immunoglobulin genes. However, common analysis programs are not appropriate for pre-processing and analyzing these data due to the lack of a template or reference for the whole gene.
resultsWe present here the automated analysis pipeline we created for this purpose, which integrates various software packages of our own development and others', and demonstrate its performance.
conclusionsOur analysis pipeline presented here is highly modular, and makes it possible to analyze the data resulting from high-throughput sequencing of immunoglobulin genes, in spite of the lack of a template gene. An executable version of the Automation program (and its source code) is freely available for downloading from our website: http://immsilico2.lnx.biu.ac.il/Software.html.
Identifiers
What OpenQuestion holds
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.