Xiaowei Zhang

All Publications

• Efficient generation of epitope-targetedde novoantibodies with Germinal. bioRxiv : the preprint server for biology Mille-Fragoso, L. S., Wang, J. N., Driscoll, C. L., Dai, H., Widatalla, T., Zhang, X., Hie, B. L., Gao, X. J. 2025

  Abstract

  Obtaining novel antibodies against specific protein targets is a widely important yet experimentally laborious process. Meanwhile, computational methods for antibody design have been limited by low success rates that currently require resource-intensive screening. Here, we introduce Germinal, a broadly enabling generative framework that designs antibodies against specific epitopes with nanomolar binding affinities while requiring only low-n experimental testing. Our method co-optimizes antibody structure and sequence by integrating a structure predictor with an antibody-specific protein language model to perform de novo design of functional complementarity-determining regions (CDRs) onto a user-specified structural framework. When tested against four diverse protein targets, Germinal achieved an experimental success rate of 4-22% across all targets, testing only 43-101 designs for each antigen. Validated nanobodies also exhibited robust expression in mammalian cells and nanomolar binding affinities. We provide open-source code and full computational and experimental protocols to facilitate wide adoption. Germinal represents a milestone in efficient, epitope-targeted de novo antibody design, with notable implications for the development of molecular tools and therapeutics.

  View details for DOI 10.1101/2025.09.19.677421

  View details for PubMedID 41040335

• Enabling RNA-compatible synthetic receptors through RNA editing NATURE REVIEWS MOLECULAR CELL BIOLOGY Zhang, X., Mille-Fragoso, L. S. 2025

  View details for DOI 10.1038/s41580-025-00863-y

  View details for Web of Science ID 001492301400001

  View details for PubMedID 40399645

  View details for PubMedCentralID 12019813

• Post-transcriptional modular synthetic receptors. Nature chemical biology Zhang, X., Mille-Fragoso, L. S., Kaseniit, K. E., Lee, A. P., Zhang, M., Call, C. C., Hu, Y., Xie, Y., Gao, X. J. 2025

  Abstract

  Inspired by the power of transcriptional synthetic receptors and hoping to complement them to expand the toolbox for cell engineering, we establish LIDAR (Ligand-Induced Dimerization-Activating RNA editing), a modular post-transcriptional synthetic receptor platform that harnesses RNA editing by adenosine deaminases acting on RNA. LIDAR is compatible with various receptor architectures in different cellular contexts and enables the sensing of diverse ligands and the production of functional outputs. Furthermore, LIDAR can sense orthogonal signals in the same cell and produce synthetic spatial patterns, potentially enabling the programming of complex multicellular behaviors. Lastly, LIDAR is compatible with compact encoding and can be delivered as synthetic mRNA. Thus, LIDAR expands the family of synthetic receptors, holding the promise to empower basic research and therapeutic applications.

  View details for DOI 10.1038/s41589-025-01872-w

  View details for PubMedID 40155716

  View details for PubMedCentralID 9041813

• Sensitive bacterial Vm sensors revealed the excitability of bacterial Vm and its role in antibiotic tolerance. Proceedings of the National Academy of Sciences of the United States of America Jin, X., Zhang, X., Ding, X., Tian, T., Tseng, C. K., Luo, X., Chen, X., Lo, C. J., Leake, M. C., Bai, F. 2023; 120 (3): e2208348120

  Abstract

  As an important free energy source, the membrane voltage (Vm) regulates many essential physiological processes in bacteria. However, in comparison with eukaryotic cells, knowledge of bacterial electrophysiology is very limited. Here, we developed a set of novel genetically encoded bacterial Vm sensors which allow single-cell recording of bacterial Vm dynamics in live cells with high temporal resolution. Using these new sensors, we reveal the electrically "excitable" and "resting" states of bacterial cells dependent on their metabolic status. In the electrically excitable state, frequent hyperpolarization spikes in bacterial Vm are observed, which are regulated by Na+/K+ ratio of the medium and facilitate increased antibiotic tolerance. In the electrically resting state, bacterial Vm displays significant cell-to-cell heterogeneity and is linked to the cell fate after antibiotic treatment. Our findings demonstrate the potential of our newly developed voltage sensors to reveal the underpinning connections between bacterial Vm and antibiotic tolerance.

  View details for DOI 10.1073/pnas.2208348120

  View details for PubMedID 36623202

• Multiplexed genome regulation in vivo with hyper-efficient Cas12a. Nature cell biology Guo, L. Y., Bian, J., Davis, A. E., Liu, P., Kempton, H. R., Zhang, X., Chemparathy, A., Gu, B., Lin, X., Rane, D. A., Xu, X., Jamiolkowski, R. M., Hu, Y., Wang, S., Qi, L. S. 2022

  Abstract

  Multiplexed modulation of endogenous genes is crucial for sophisticated gene therapy and cell engineering. CRISPR-Cas12a systems enable versatile multiple-genomic-loci targeting by processing numerous CRISPR RNAs (crRNAs) from a single transcript; however, their low efficiency has hindered in vivo applications. Through structure-guided protein engineering, we developed a hyper-efficient Lachnospiraceae bacterium Cas12a variant, termed hyperCas12a, with its catalytically dead version hyperdCas12a showing significantly enhanced efficacy for gene activation, particularly at low concentrations of crRNA. We demonstrate that hyperdCas12a has comparable off-target effects compared with the wild-type system and exhibits enhanced activity for gene editing and repression. Delivery of the hyperdCas12a activator and a single crRNA array simultaneously activating the endogenous Oct4, Sox2 and Klf4 genes in the retina of post-natal mice alters the differentiation of retinal progenitor cells. The hyperCas12a system offers a versatile in vivo tool for a broad range of gene-modulation and gene-therapy applications.

  View details for DOI 10.1038/s41556-022-00870-7

  View details for PubMedID 35414015

• Membraneless organelles formed by liquid-liquid phase separation increase bacterial fitness. Science advances Jin, X., Lee, J. E., Schaefer, C., Luo, X., Wollman, A. J., Payne-Dwyer, A. L., Tian, T., Zhang, X., Chen, X., Li, Y., McLeish, T. C., Leake, M. C., Bai, F. 2021; 7 (43): eabh2929

  Abstract

  [Figure: see text].

  View details for DOI 10.1126/sciadv.abh2929

  View details for PubMedID 34669478

  View details for PubMedCentralID PMC8528417