ArticleImmunity2013
Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design.
Article in Immunity, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers.
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Who cites it
139 citing papers in PubMed, 256 citations in OpenAlex.
- Long-term follow up of human T-cell responses to conserved HIV-1 regions elicited by DNA/simian adenovirus/MVA vaccine regimens.PloS one · 2017Trial
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- Design of an immunogen containing multidimensionally conserved and immunogenic parts of the HIV proteome.PLoS computational biology · 2026Article
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- Forecasting drug resistant HIV protease evolution.PLoS computational biology · 2026Article
- Mechanism for evolution of diverse autologous antibodies upon broadly neutralizing antibody therapy of people with HIV.Cell reports · 2025Article
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- A binary trait model reveals the fitness effects of HIV-1 escape from T cell responses.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Perturbational Decomposition Analysis for Quantum Ising Model with Weak Transverse Fields.Entropy (Basel, Switzerland) · 2024Article
- Efficient epistasis inference via higher-order covariance matrix factorization.bioRxiv : the preprint server for biology · 2024Article
- A binary trait model reveals the fitness effects of HIV-1 escape from T cell responses.bioRxiv : the preprint server for biology · 2024Article
- Deep-learning-based design of synthetic orthologs of SH3 signaling domains.Cell systems · 2024Article
- Polymorphic residues in HLA-B that mediate HIV control distinctly modulate peptide interactions with both TCR and KIR molecules.Structure (London, England : 1993) · 2024Article
- Functional effects of mutations in proteins can be predicted and interpreted by guided selection of sequence covariation information.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Inference of annealed protein fitness landscapes with AnnealDCA.PLoS computational biology · 2024Article
- Changing selection on amino acid substitutions in Gag protein between major HIV-1 subtypes.Virus evolution · 2024Article
79 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
A prophylactic or therapeutic vaccine offers the best hope to curb the HIV-AIDS epidemic gripping sub-Saharan Africa, but it remains elusive. A major challenge is the extreme viral sequence variability among strains. Systematic means to guide immunogen design for highly variable pathogens like HIV are not available. Using computational models, we have developed an approach to translate available viral sequence data into quantitative landscapes of viral fitness as a function of the amino acid sequences of its constituent proteins. Predictions emerging from our computationally defined landscapes for the proteins of HIV-1 clade B Gag were positively tested against new in vitro fitness measurements and were consistent with previously defined in vitro measurements and clinical observations. These landscapes chart the peaks and valleys of viral fitness as protein sequences change and inform the design of immunogens and therapies that can target regions of the virus most vulnerable to selection pressure.
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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.