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Showing 1–15 of 15 results
Advanced filters: Author: Yujia A. Chan Clear advanced filters

  • ABMACT, an agent-based model of adoptive cell therapy, recapitulated cellular dynamics in two cancer preclinical models and showed that enhancing immune cell proliferation, cytotoxicity, and serial killing capacity is critical for optimal efficacy.

    • Yujia Wang
    • Stefano Casarin
    • Ken Chen
    ResearchOpen Access
    Communications Biology
    P: 1-20

  • Immune receptors regulate immune responses and are key cancer immunotherapy targets. Here, the authors designed helical concave scaffolds to bind convex sites in immune receptors, creating high-affinity protein binders for TGFβRII, CTLA-4, and PD-L1. Co-crystal structures confirmed their therapeutic potential.

    • Wei Yang
    • Derrick R. Hicks
    • David Baker
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-12

  • Conventional selections of AAV capsid libraries are inefficient at searching sequence space. Here the authors report ‘Fit4Function’, a generalizable ML approach for systematically engineering multi-trait AAV capsids, and use this to predict cross-species traits of peptide-modified AAV capsids.

    • Fatma-Elzahraa Eid
    • Albert T. Chen
    • Benjamin E. Deverman
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-14

  • Computationally designed genetically encoded proteins can be used to target surface proteins, thereby triggering endocytosis and subsequent intracellular degradation, activating signalling or increasing cellular uptake in specific tissues.

    • Buwei Huang
    • Mohamad Abedi
    • David Baker
    ResearchOpen Access
    Nature
    Volume: 638, P: 796-804

  • Qin, Pei and colleagues report that autophagy is induced early during somatic cell reprogramming into induced pluripotent stem cells. mTORC1 and autophagy control reprogramming efficiency by modulating mitochondrial architecture and p62 levels.

    • Yasong Wu
    • Yuan Li
    • Duanqing Pei
    Research
    Nature Cell Biology
    Volume: 17, P: 715-725

  • Despite an emerging role for cerebrovascular endothelial cells in a range of neurological pathologies, AAV vector development to date has focused on tools designed to target neurons or astrocytes. Here, Krolak et al. describe a specific variant of AAV (AAV-BI30), with high specificity and efficacy for transduction of endothelial cells across the central nervous system.

    • Trevor Krolak
    • Ken Y. Chan
    • Benjamin E. Deverman
    Research
    Nature Cardiovascular Research
    Volume: 1, P: 389-400

  • Training a deep neural network can be costly but training time is reduced when a pre-trained network can be adapted to different use cases. Ideally, only a small number of parameters needs to be changed in this process of fine-tuning, which can then be more easily distributed. In this Analysis, different methods of fine-tuning with only a small number of parameters are compared on a large set of natural language processing tasks.

    • Ning Ding
    • Yujia Qin
    • Maosong Sun
    ResearchOpen Access
    Nature Machine Intelligence
    Volume: 5, P: 220-235

  • Fatma-Elzahraa Eid et al. illustrate a principled approach for identifying biases that can inflate the performance of biological machine learning models. When applied to three biomedical prediction problems, they identify previously unrecognized biases and ultimately show that models are likely to learn primarily from data biases when there is insufficient learnable signal in the data.

    • Fatma-Elzahraa Eid
    • Haitham A. Elmarakeby
    • Kasper Lage
    ResearchOpen Access
    Communications Biology
    Volume: 4, P: 1-9

  • Combining crystallographic data, MD simulations, mutagenesis, lipid transfer and liposome binding assays, Lu et al. determine the mechanism of PA transfer between mitochondrial membranes, mediated by the Ups1/Mdm35 protein family. In particular, they describe role of the conformational change of the omega loop or α2 loop of Ups1 in the Ups1 PA transfer activity.

    • Jiuwei Lu
    • Chun Chan
    • Yujia Zhai
    ResearchOpen Access
    Communications Biology
    Volume: 3, P: 1-14