ArticleBioinformatics (Oxford, England)2010
SoDA2: a Hidden Markov Model approach for identification of immunoglobulin rearrangements.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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46 citing papers in PubMed, 75 citations in OpenAlex.
- Decoding adaptive immunity: advanced strategies in T and B cell repertoire analysis.Journal of translational medicine · 2026Review
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- An unbiased comparison of immunoglobulin sequence aligners.Briefings in bioinformatics · 2024Article
- T-cell repertoire diversity: friend or foe for protective antitumor response?Journal of experimental & clinical cancer research : CR · 2022Review
- Antibody repertoire sequencing analysis.Acta biochimica et biophysica Sinica · 2022Review
- Selective Recognition of Carbohydrate Antigens by Germline Antibodies Isolated from AID Knockout Mice.Journal of the American Chemical Society · 2022Article
- Plasma cell immunoglobulin heavy chain repertoire dynamics before and after tetanus booster vaccination.Immunogenetics · 2021Article
- Deep generative selection models of T and B cell receptor repertoires with soNNia.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Alignment free identification of clones in B cell receptor repertoires.Nucleic acids research · 2021Article
- The Bayesian optimist's guide to adaptive immune receptor repertoire analysis.Immunological reviews · 2018Review
- Unbiased quantification of immunoglobulin diversity at the DNA level with VDJ-seq.Nature protocols · 2018Article
- HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data.BMC bioinformatics · 2017Article
- Pentavalent HIV-1 vaccine protects against simian-human immunodeficiency virus challenge.Nature communications · 2017Article
- Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data.Journal of immunology (Baltimore, Md. : 1950) · 2017Article
- Genetic and structural analyses of affinity maturation in the humoral response to HIV-1.Immunological reviews · 2017Review
- VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.BMC bioinformatics · 2016Article
- Amino Acid Changes in the HIV-1 gp41 Membrane Proximal Region Control Virus Neutralization Sensitivity.EBioMedicine · 2016Article
- Likelihood-Based Inference of B Cell Clonal Families.PLoS computational biology · 2016Article
- Envelope-specific B-cell populations in African green monkeys chronically infected with simian immunodeficiency virus.Nature communications · 2016Article
- repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data.Bioinformatics (Oxford, England) · 2016Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationThe inference of pre-mutation immunoglobulin (Ig) rearrangements is essential in the study of the antibody repertoires produced in response to infection, in B-cell neoplasms and in autoimmune disease. Often, there are several rearrangements that are nearly equivalent as candidates for a given Ig gene, but have different consequences in an analysis. Our aim in this article is to develop a probabilistic model of the rearrangement process and a Bayesian method for estimating posterior probabilities for the comparison of multiple plausible rearrangements.
resultsWe have developed SoDA2, which is based on a Hidden Markov Model and used to compute the posterior probabilities of candidate rearrangements and to find those with the highest values among them. We validated the software on a set of simulated data, a set of clonally related sequences, and a group of randomly selected Ig heavy chains from Genbank. In most tests, SoDA2 performed better than other available software for the task. Furthermore, the output format has been redesigned, in part, to facilitate comparison of multiple solutions. AVAILABILITY: SoDA2 is available online at https://hippocrates.duhs.duke.edu/soda. Simulated sequences are available upon request.
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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.