ArticleProceedings of the National Academy of Sciences of the United States of America2010
Maximum entropy models for antibody diversity.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 134 papers.
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134 citing papers in PubMed.
- Discovering interpretable low-dimensional dynamics using maximum entropy.Physical review. E · 2026Article
- Profiling adaptive immunity: A quantitative framework for immune repertoire dynamics and clinical diagnostics.Fundamental research · 2026Article
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- Spontaneous switching in a protein signalling array reveals near-critical cooperativity.Nature physics · 2026Article
- Minimax entropy: The statistical physics of optimal models.Physical review. E · 2025Article
- Statistical physics of large-scale neural activity with loops.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- High-fidelity in silico generation and augmentation of TCR repertoire data using generative adversarial networks.Scientific reports · 2025Article
- Dynamical theory of complex systems with two-way micro-macro causation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Density estimation for ordinal biological sequences and its applications.Physical review. E · 2024Article
- Physical modeling of embryonic transcriptomes identifies collective modes of gene expression.bioRxiv : the preprint server for biology · 2024Article
- Valence and interactions in judicial voting.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2024Article
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- Steering and controlling evolution - from bioengineering to fighting pathogens.Nature reviews. Genetics · 2023Review
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- An integrated approach to the characterization of immune repertoires using AIMS: An Automated Immune Molecule Separator.PLoS computational biology · 2023Article
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- Universality of Form: The Case of Retinal Cone Photoreceptor Mosaics.Entropy (Basel, Switzerland) · 2023Article
- Inferring Cultural Landscapes with the Inverse Ising Model.Entropy (Basel, Switzerland) · 2023Article
- HCV E1 influences the fitness landscape of E2 and may enhance escape from E2-specific antibodies.Virus evolution · 2023Article
74 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Recognition of pathogens relies on families of proteins showing great diversity. Here we construct maximum entropy models of the sequence repertoire, building on recent experiments that provide a nearly exhaustive sampling of the IgM sequences in zebrafish. These models are based solely on pairwise correlations between residue positions but correctly capture the higher order statistical properties of the repertoire. By exploiting the interpretation of these models as statistical physics problems, we make several predictions for the collective properties of the sequence ensemble: The distribution of sequences obeys Zipf's law, the repertoire decomposes into several clusters, and there is a massive restriction of diversity because of the correlations. These predictions are completely inconsistent with models in which amino acid substitutions are made independently at each site and are in good agreement with the data. Our results suggest that antibody diversity is not limited by the sequences encoded in the genome and may reflect rapid adaptation to antigenic challenges. This approach should be applicable to the study of the global properties of other protein families.
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