徐洲更的头像

徐洲更

中国科学院分子植物科学卓越创新中心（CEMPS）博士后（王佳伟研究组）

浙江农林大学农学学士学位，中国科学院大学博士学位。主要研究方向为植物单细胞测序与跨物种细胞图谱构建。研究成果发表于 Cell、Nature Communications、Nature Plants、Nature Methods、Science 等国内外重要学术期刊，相关成果入选 2024 年度"中国生命科学十大进展"。

入选"中国科学院特别研究助理资助项目"和"国家资助博士后研究人员计划（B档）"，并获得 2025 年度博士后科研业绩评估考核资助（一档）。

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

经历

  • 2012-2016   浙江农林大学 — 农学学士学位
  • 2016-2023   中国科学院分子植物科学卓越创新中心 — 遗传学博士学位
  • 2023 年 7 月至今 — 中国科学院分子植物科学卓越创新中心，博士后

专业技能

  • 植物单细胞组学：scRNA-seq / snRNA-seq、ATAC-seq、跨物种细胞图谱
  • 比较基因组与基因调控网络分析
  • Linux 科研计算：服务器环境、Shell、R、Python
  • 科研软件：桌面与 Web 工具开发
  • 把大模型接到文献、分析和科研工作流里

AI4S（AI for Science）

将人工智能与科研工作流深度结合，独立设计并开发了三款面向科研的 AI 工具：

  • AI 科研工作台 Wisp Science：开源、本地优先的桌面 AI 科研工作台，检索文献、运行 Python 与 R、查询科学数据库，把分析与稿件留在同一项目中。github.com/xuzhougeng/wisp-science
  • 智能文献管理工具 CiteBox：基于 AI 的文献管理与阅读助手，帮助检索、整理与理解科研文献。github.com/xuzhougeng/citebox
  • 智能终端 WispTerm：AI 驱动的命令行终端，让自然语言与 Shell 操作在同一工作流里完成。github.com/xuzhougeng/wispterm

科普与教学

自 2016 年起持续撰写生物信息学教程，覆盖 Linux、转录组、基因组组装、比较基因组与单细胞分析。个人博客徐洲更的第二大脑累计 290 余篇，全网阅读超过 200 万；早期《转录组入门》系列被多个专栏转载，成为国内常见的入门路径之一。教程也曾在生信领域内较有影响的公众号等平台发布，并在知乎开设专栏「hoptop的生信笔记」（两千余关注）。B 站同步录制操作课，累计播放约 10 万次。

发表论文

2026

  1. 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
  2. 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