Publications

Overcoming immunological challenges limiting capsid-mediated gene therapy with machine learning

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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Publications

Generative AAV capsid diversification by latent interpolation

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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Publications

Deep diversification of an AAV capsid protein by machine learning

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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Publications

AdaLead: A simple and robust adaptive greedy search algorithm for sequence design

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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Publications

A primer on model-guided exploration of fitness landscapes for biological sequence design

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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Publications

Accurately quantifying transduction within barcoded AAV capsid libraries via tracking of single-molecule ID tags

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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Publications

Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design

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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Publications

Challenges and opportunities of machine-guided capsid engineering for gene therapy

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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