ArticlePLoS computational biology2016
Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- Priming of Multiple HIV Neutralizing B Cell Precursors in Humans.medRxiv : the preprint server for health sciences · 2026Article
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- Nucleotide context models outperform protein language models for predicting antibody affinity maturation.PLoS computational biology · 2025Article
- Nucleotide context models outperform protein language models for predicting antibody affinity maturation.bioRxiv : the preprint server for biology · 2025Article
- Improved Deep Learning Prediction of TCR-HLA Associations.Statistics in biosciences · 2025Article
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- A Sitewise Model of Natural Selection on Individual Antibodies via a Transformer-Encoder.Molecular biology and evolution · 2025Article
- Enhancing sequence alignment of adaptive immune receptors through multi-task deep learning.Nucleic acids research · 2025Article
- An engineered immunogen activates diverse HIV broadly neutralizing antibody precursors and promotes acquisition of improbable mutations.Science translational medicine · 2025Article
- An unbiased comparison of immunoglobulin sequence aligners.Briefings in bioinformatics · 2024Article
- Evaluating methods for B-cell clonal family assignment.bioRxiv : the preprint server for biology · 2024Article
- Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data.Briefings in bioinformatics · 2024Article
- Vaccine induction of CD4-mimicking HIV-1 broadly neutralizing antibody precursors in macaques.Cell · 2024Article
- Applying phylogenetic methods for species delimitation to distinguish B-cell clonal families.Frontiers in immunology · 2024Article
- IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data.Nucleic acids research · 2023Article
- VHH CDR-H3 conformation is determined by VH germline usage.Communications biology · 2023Article
- Germline-encoded specificities and the predictability of the B cell response.PLoS pathogens · 2023Article
23 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D, or J genes, or from an N-addition (a.k.a. non-templated insertion). Previous work has used simple parametric distributions to model transitions from state to state in a hidden Markov model (HMM) of VDJ recombination, and assumed that mutations occur via the same process across sites. However, codon frame and other effects have been observed to violate these parametric assumptions for such coding sequences, suggesting that a non-parametric approach to modeling the recombination process could be useful. In our paper, we find that indeed large modern data sets suggest a model using parameter-rich per-allele categorical distributions for HMM transition probabilities and per-allele-per-position mutation probabilities, and that using such a model for inference leads to significantly improved results. We present an accurate and efficient BCR sequence annotation software package using a novel HMM "factorization" strategy. This package, called partis (https://github.com/psathyrella/partis/), is built on a new general-purpose HMM compiler that can perform efficient inference given a simple text description of an HMM.
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