Senxin Zhang

Shanghai Normal University

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Xiaoqi Zheng

Meizhou City People's Hospital

Fei‐Long Meng

Center for Excellence in Molecular Cell Science

Leng-Siew Yeap

State Key Laboratory of Oncogene and Related Genes

Chaoyang Lian

State Key Laboratory of Oncogene and Related Genes

Chao Qiu

Jiangnan University

Haocheng Zhang

Zhengzhou University

Yanni Cai

Center for Excellence in Molecular Cell Science

Zhangfan Fu

Huashan Hospital

Tuantuan Gui

Chinese Academy of Medical Sciences & Peking Union Medical College

Yawen Zhou

State Key Laboratory of Electrical Insulation and Power Equipment

Cooperative Institutions

University of Chinese Academy of Sciences

Chinese Academy of Sciences

Shanghai Jiao Tong University

Center for Excellence in Molecular Cell Science

Fudan University

Peking University

Huashan Hospital

The Sixth People's Hospital of Shenyang

Zhengzhou University

Chinese Academy of Medical Sciences & Peking Union Medical College

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Mesoscale DNA feature in antibody-coding sequence facilitates somatic hypermutation

Cell (2023)

Yanyan Wang Senxin Zhang Xinrui Yang Joyce K. Hwang Chuanzong Zhan

Coding region

Activation-induced (cytidine) deaminase

Sequence motif

10.1016/j.cell.2023.03.030

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Citations (18)

B cell receptor signatures associated with strong and poor SARS-CoV-2 vaccine responses

Figshare (2022)

Ke Lin Yawen Zhou Jingwen Ai Y. Wang Senxin Zhang

Breakthrough infection of SARS-CoV-2 is a serious challenge, as increased infections were documented in fully-vaccinated individuals. Recipients with poor antibody response are highly vulnerable to reinfection, whereas those with strong antibody responses achieve sterilizing immunity. Thus far, biomarkers associated with levels of vaccine-elicited antibody response are still lacking. Here, we studied the antibody response of age- and gender-controlled healthy cohort, who received inactivated SARS-CoV-2 vaccines and profiled the B cell receptor repertoires in longitudinally consecutive samples. Upon vaccination, all vaccinated individuals displayed a convergent antibody response with shared common antibody clones and public neutralizing antibodies. Strikingly, poor vaccine-responders are distinguishable from strong vaccine-responders by a biased V-usage before vaccination and IgG to IgM mRNA ratio. These findings reveal molecular signatures associated with the different levels of vaccine-induced antibody response, which could be further developed into biomarkers for the design of vaccination strategies.

2019-20 coronavirus outbreak

10.6084/m9.figshare.18743686

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B cell receptor signatures associated with strong and poor SARS-CoV-2 vaccine responses

Emerging Microbes & Infections (2022)

Ke Lin Yawen Zhou Jingwen Ai Yan A. Wang Senxin Zhang

Antibody response

10.1080/22221751.2022.2030197

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Citations (9)

CellPatch: a Highly Efficient Foundation Model for Single-Cell Transcriptomics with Heuristic Patching

bioRxiv (Cold Spring Harbor Laboratory) (2024)

Hua‐Jun Wu Xiaoqi Zheng Zeyu Ma Hanwen Zhu Yufeng Yuan

The rapid advancement of foundation models has significantly enhanced the analysis of single-cell omics data, enabling researchers to gain deeper insights into the complex interactions between cells and genes across diverse tissues. However, existing foundation models often exhibit excessive complexity, hindering their practical utility for downstream tasks. Here, we present CellPatch, a lightweight foundation model that leverages the strengths of the cross-attention mechanism and patch tokenization to reduce model complexity while extracting efficient biological representations. Comprehensive evaluations conducted on single-cell RNA-sequencing datasets across multiple organs and tissue states demonstrate that CellPatch achieves state-of-the-art performance in downstream analytical tasks while maintaining ultra-low computational costs during both pretraining and finetuning phases. Moreover, the flexibility and scalability of CellPatch allow it to serve as a general framework that can be incorporated with other well established single-cell analysis software, thereby enhancing their performance through transfer learning on diverse downstream tasks.

Foundation (evidence)

10.1101/2024.11.15.623701

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Antibody repertoire sequencing analysis

Acta Biochimica et Biophysica Sinica (2022)

Senxin Zhang Tiange Yang Xiaojing Liu Jiyuan Yang Xiaoqi Zheng

High-throughput sequencing for B cell receptor (BCR) repertoire provides useful insights for the adaptive immune system. With the continuous development of the BCR-seq technology, many efforts have been made to develop methods for analyzing the ever-increasing BCR repertoire data. In this review, we comprehensively outline different BCR repertoire library preparation protocols and summarize three major steps of BCR-seq data analysis, i. e., V(D)J sequence annotation, clonal phylogenetic inference, and BCR repertoire profiling and mining. Different from other reviews in this field, we emphasize background intuition and the statistical principle of each method to help biologists better understand it. Finally, we discuss data mining problems for BCR-seq data and with a highlight on recently emerging multiple-sample analysis.

breakpoint cluster region

10.3724/abbs.2022062

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Citations (2)

C-to-G editing generates double-strand breaks causing deletion, transversion and translocation

Nature Cell Biology (2024)

Min Huang Yining Qin Yafang Shang Qian Hao Chuanzong Zhan

Transversion

Double strand

Non-homologous end joining

10.1038/s41556-023-01342-2

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Citations (20)

A high-throughput protocol for deamination of long single-stranded DNA and oligo pools containing complex sequences

STAR Protocols (2023)

Yanyan Wang Senxin Zhang Xiaoqi Zheng Leng-Siew Yeap Fei‐Long Meng

Cytidine deaminases as DNA mutators play important roles in immunity and genome stability. Here, we present a high-throughput protocol for deamination of long single-stranded (ss) DNA or oligo pools containing complex sequences. We describe steps for the preparation of both enzyme (activation-induced deaminase, AID) and ssDNA substrates, the deamination reaction, uracil-friendly amplification, and data analysis. This assay can be used to determine the intrinsic mutation profile of a single antibody gene or a pool of selected regions on genomic DNA. For complete details on the use and execution of this protocol, please refer to Wang et al. (2023).

Deamination

Activation-induced (cytidine) deaminase

Cytidine

genomic DNA

Uracil

10.1016/j.xpro.2023.102602

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Citations (2)