Overcoming immunological challenges limiting capsid-mediated gene therapy with machine learning
April 27, 2021
Frontiers in Immunology
A key hurdle to making adeno-associated virus (AAV) capsid mediated gene therapy broadly beneficial to all patients is overcoming pre-existing and therapy-induced immune responses to ...
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Generative AAV capsid diversification by latent interpolation
April 17, 2021
Preprint
Adeno-associated virus (AAV) capsids have shown clinical promise as delivery vectors for gene therapy. However, the high prevalence of pre-existing immunity against natural capsids poses ...
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Deep diversification of an AAV capsid protein by machine learning
February 11, 2021
Nature Biotechnology
Modern experimental technologies can assay large numbers of biological sequences, but engineered protein libraries rarely exceed the sequence diversity of natural protein families. Machine learning ...
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AdaLead: A simple and robust adaptive greedy search algorithm for sequence design
October 5, 2020
Preprint (arXiv) with code
Efficient design of biological sequences will have a great impact across many industrial and healthcare domains. However, discovering improved sequences requires solving a difficult optimization ...
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A primer on model-guided exploration of fitness landscapes for biological sequence design
October 4, 2020
Preprint (arXiv)
Machine learning methods are increasingly employed to address challenges faced by biologists. One area that will greatly benefit from this cross-pollination is the problem of ...
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Accurately quantifying transduction within barcoded AAV capsid libraries via tracking of single-molecule ID tags
April 28, 2020
ASGCT 2020
Multiplexed barcoded capsid libraries have emerged as a powerful tool for high-throughput AAV engineering. Barcoded studies facilitate the accurate measurement of tropism across multiple capsids ...
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Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design
November 9, 2019
Science
Adeno-associated virus (AAV) capsids can deliver transformative gene therapies, but our understanding of AAV biology remains incomplete. We generated the complete first-order AAV2 capsid fitness ...
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Challenges and opportunities of machine-guided capsid engineering for gene therapy
February 26, 2019
Gene and Cell Therapy Insights
Advances in DNA delivery will be crucial to the enablement of new gene therapies. Pioneering efforts in developing recombinant AdenoAssociated Virus (AAV) technology for gene ...
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