Portrait of Zhou-Geng Xu

Zhou-Geng Xu

徐洲更

Postdoctoral Fellow, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Jia-Wei Wang Lab

B.S. in Agronomy, Zhejiang A&F University; Ph.D., University of Chinese Academy of Sciences. Research focuses on plant single-cell sequencing and cross-species cell-atlas construction. Work has been published in Cell, Nature Communications, Nature Plants, Nature Methods, Science, and other journals, and was selected among the 2024 Top 10 Advances in Life Sciences in China.

He was selected for the CAS Special Research Assistant Program and the National Funded Postdoctoral Researcher Program (Category B), and received the 2025 Postdoctoral Research Performance Evaluation Grant (First Tier).

xuzhougeng@163.com xuzhougeng 0000-0001-7682-3482 Google Scholar 洲更的第二大脑

Experience

  • 2012–2016   Zhejiang A&F University — B.S. in Agronomy
  • 2016–2023   CAS Center for Excellence in Molecular Plant Sciences — Ph.D. in Genetics
  • July 2023–present — CAS Center for Excellence in Molecular Plant Sciences, Postdoctoral Fellow

Skills

  • Plant single-cell omics: scRNA-seq / snRNA-seq, ATAC-seq, cross-species cell atlases
  • Comparative genomics and gene-regulatory-network analysis
  • Linux scientific computing: servers, Shell, R, Python
  • Research software: desktop and web tool development
  • Connecting large language models to literature, analysis, and research workflows

AI4S (AI for Science)

He builds AI into research workflows, and independently designed three research-oriented AI tools:

  • Wisp Science: an open-source, local-first desktop AI workbench for research — search literature, run Python and R, query scientific databases, and keep analysis and manuscripts in the same project. github.com/xuzhougeng/wisp-science
  • CiteBox: an AI literature manager and reading assistant for searching, organizing, and understanding scientific papers. github.com/xuzhougeng/citebox
  • WispTerm: an AI-driven command-line terminal that keeps natural language and Shell in one workflow. github.com/xuzhougeng/wispterm

Science Communication & Teaching

Since 2016 he has written bioinformatics tutorials covering Linux, transcriptomics, genome assembly, comparative genomics, and single-cell analysis. His blog 徐洲更的第二大脑 has more than 290 posts and over 2 million reads across the web. The early series Introduction to Transcriptomics has been widely republished and is a common entry path in China. Tutorials have also appeared on influential Chinese bioinformatics public accounts. On Zhihu he runs the column “hoptop的生信笔记” (2,000+ followers). Hands-on courses on Bilibili have about 100,000 views.

Publications

2026

  1. Zhou-Geng Xu, G. Qin. LLM-assisted development of Rust for high-performance bioinformatics software: practices, workflows, and boundaries. Genomics Communications 3, e018 (2026). https://doi.org/10.48130/gcomm-0026-0018
  2. Song Wang, Li-Ying Ma, Zhou-Geng Xu, et al. Molecular mechanism underlying regulation of chalcone synthase by chalcone isomerase-like protein. Nature Communications 17, 3992 (2026). https://doi.org/10.1038/s41467-026-70563-4
  3. Xiang-Ru Meng, Qian-Qian Wang, Shang-Li Zhu, Jia-Li Wang, Chen-Ze Qi, Jiao Yu, Yu Zhang, Zhou-Geng Xu, et al. Unravelling the predominant genetic paths for asexual reproduction in Kalanchoe. Nature Plants 12, 369–385 (2026). https://doi.org/10.1038/s41477-025-02214-3

2025

  1. Xin Ming, Mu-Chun Wan, Zheng-Da Zhang, Hao-Chen Xue, Ya-Qi Wu, Zhou-Geng Xu, Heng Lian, Meng-Ting Yuan, Yan-Xia Mai, Ying-Xiong Hu, Ke Liu, Jian Gao, Qiao-Lin Shao, D. Blaine Marchant, Brad Nelms, Virginia Walbot & Jia-Wei Wang. FX-Cell: a method for single-cell RNA sequencing on difficult-to-digest and cryopreserved plant samples. Nature Methods, 2025. https://doi.org/10.1038/s41592-025-02900-2
  2. Shipeng Guo, Yanshuang Jiang, Jieya Zou, Mei Lu, Daxue Li, Qian Zhang, Weiwei Li, Lina Mao, Shengchun Liu, Zhougeng Xu, et al. GPSAdb 2.0: an expanded atlas of gene-perturbation transcriptomes with enhanced tools for regulatory gene discovery. Nucleic Acids Research, 2025. https://doi.org/10.1093/nar/gkaf1077
  3. Xiaofan Lu, Kailai Li, Zongcheng Li, Anqi Lin, Long Zhao, Rongfang Shen, Zhougeng Xu, Jianing Gao, et al. FigureYa: A Standardized Visualization Framework for Enhancing Biomedical Data Interpretation and Research Efficiency. iMetaMed. https://doi.org/10.1002/imm3.70005
  4. Hao-Chen Xue, Zhou-Geng Xu, Yu-Jie Liu, et al. A Unified Cell Atlas of Vascular Plants Reveals Cell-Type Foundational Genes and Accelerates Gene Discovery. Cell, 2025. https://doi.org/10.1016/j.cell.2025.07.036

2024

  1. Dong Zhai, Lu-Yi Zhang, Ling-Zi Li, Zhou-Geng Xu, et al. Reciprocal Conversion between Annual and Polycarpic Perennial Flowering Behavior in the Brassicaceae. Cell, 2024. https://doi.org/10.1016/j.cell.2024.04.047
  2. Chuan-Miao Zhou, Jian-Xu Li, Tian-Qi Zhang, Zhou-Geng Xu, et al. The Structure of B-ARR Reveals the Molecular Basis of Transcriptional Activation by Cytokinin. PNAS, 2024. https://doi.org/10.1073/pnas.2319335121
  3. Haibao Tang, Vivek Krishnakumar, Xiaofei Zeng, Zhougeng Xu, et al. JCVI: A Versatile Toolkit for Comparative Genomics Analysis. iMeta. https://doi.org/10.1002/imt2.211

2023

  1. L. Wang, M.-C. Wan, R.-Y. Liao, J. Xu, Z.-G. Xu, et al. The maturation and aging trajectory of Marchantia polymorpha at single-cell resolution. Developmental Cell, 2023.
  2. Hong-Bo Tang, Juan Wang, Long Wang, Guan-Dong Shang, Zhou-Geng Xu, et al. Anisotropic cell growth at the leaf base promotes age-related changes in leaf shape in Arabidopsis thaliana. The Plant Cell, 2023. https://doi.org/10.1093/plcell/koad031
  3. Ling-Zi Li, Zhou-Geng Xu, Tian-Guang Chang, et al. Common evolutionary trajectory of short life-cycle in Brassicaceae ruderal weeds. Nature Communications 14, 290 (2023). https://doi.org/10.1038/s41467-023-35966-7

2022

  1. Shipeng Guo, Zhougeng Xu, Xiangjun Dong, et al. GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets. Nucleic Acids Research, 2022. https://doi.org/10.1093/nar/gkac1066
  2. Chen-Yi Li, Lei Yang, Yan Liu, Zhou-Geng Xu, et al. The Sage Genome Provides Insight into the Evolutionary Dynamics of Diterpene Biosynthesis Gene Cluster in Plants. Cell Reports, 2022. https://doi.org/10.1016/j.celrep.2022.111236
  3. Guan-Dong Shang, Zhou-Geng Xu, M.-C. Wan, et al. FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data. BMC Genomics 23, 272 (2022). https://doi.org/10.1186/s12864-022-08506-8
  4. Jian Gao, Ke Zhang, Ying-Juan Cheng, Sha Yu, Guan-Dong Shang, Fu-Xiang Wang, Lian-Yu Wu, Zhou-Geng Xu, et al. A Robust Mechanism for Resetting Juvenility during Each Generation in Arabidopsis. Nature Plants 8(3):257–268 (2022). https://doi.org/10.1038/s41477-022-01110-4
  5. L.-Y. Wu, G.-D. Shang, F.-X. Wang, J. Gao, M.-C. Wan, Z.-G. Xu, and J.-W. Wang. Dynamic chromatin state profiling reveals regulatory roles of auxin and cytokinin in shoot regeneration. Developmental Cell, 2022.

2021

  1. Kun Huang, Xue-Xue Wu, Chen-Lu Fang, Z.-G. Xu, et al. Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA. Science, 2021. https://www.science.org/doi/10.1126/science.abj9184
  2. Yu-Jin Cheng, Guan-Dong Shang, Z.-G. Xu, et al. Cell division in the shoot apical meristem is a trigger for miR156 decline and vegetative phase transition in Arabidopsis. PNAS 118 (2021). https://doi.org/10.1073/pnas.2115667118
  3. Fu-Xiang Wang, Guan-Dong Shang, Lian-Yu Wu, Yan-Xia Mai, Jian Gao, Zhou-Geng Xu, Jia-Wei Wang. Protocol for assaying chromatin accessibility using ATAC-seq in plants. STAR Protocols 2(1):100289 (2021). https://doi.org/10.1016/j.xpro.2020.100289

2020

  1. Bin-Bin Ye, Guan-Dong Shang, Yu Pan, Zhou-Geng Xu, et al. AP2/ERF Transcription Factors Integrate Age and Wound Signals for Root Regeneration. The Plant Cell 32(1):226–241 (2020). https://doi.org/10.1105/tpc.19.00378
  2. Fu-Xiang Wang, Guan-Dong Shang, Lian-Yu Wu, Zhou-Geng Xu, et al. Chromatin Accessibility Dynamics and a Hierarchical Transcriptional Regulatory Network Structure for Plant Somatic Embryogenesis. Developmental Cell 54(6):742–757.e8 (2020). https://doi.org/10.1016/j.devcel.2020.07.003

2019

  1. Tian-Qi Zhang, Zhou-Geng Xu, Guan-Dong Shang, Jia-Wei Wang. A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root. Molecular Plant 12(5):648–660 (2019). https://doi.org/10.1016/j.molp.2019.04.004