About个人简介
Shanjun Deng邓善俊
Associate Professor · School of Life Sciences, Sun Yat-sen University副教授 · 中山大学 生命科学学院
Shanjun Deng, born in 1994 in Foshan, Guangdong, is currently an Associate Professor and a doctoral supervisor at the School of Life Sciences, Sun Yat-sen University, in the group of Prof. Xionglei He (Dean of the School of Life Sciences). He received his B.S. in Biological Sciences (Science Experimental Class) from China Agricultural University in 2015 and his Ph.D. in Biochemistry and Molecular Biology from Sun Yat-sen University in 2021, and was a postdoctoral fellow at Sun Yat-sen University from 2022 to 2024.
Our research mainly focuses on molecular evolution and phylogenetics, using molecular similarity as a clue to explore the evolutionary processes of living systems at different levels, with the goal of making developmental biology more quantitative and theoretical. Specifically:
- Cell lineage tracing and cell population dynamics: we have built high-resolution lineage-tracing systems (SMALT) in yeast, fruit fly and zebrafish, and will extend them to mammals such as mouse to map the cell lineage of complex multicellular organisms.
- Quantification and theorization of developmental biology: transferring the quantitative algorithms and theories of species-tree analysis to cell-lineage research, establishing standardized cell-population measurements and building a "digital-twin embryo" AI model.
- Evolution of complex and neural-related traits: combining comparative genomics and phylogenetics to dissect the molecular mechanisms, cellular basis and spatial distribution of complex traits (e.g., sleep, intelligence, neurological disorders) within the framework of the species tree.
In recent years, as first or corresponding author, we have published multiple high-impact papers in Nature, Nature Methods, National Science Review and other leading international journals, and lead or participate in multiple projects, including key R&D programs of the Ministry of Science and Technology and key, general and young-scientist projects of the National Natural Science Foundation of China.
邓善俊，1994 年生于广东佛山，现任中山大学生命科学学院副教授、博士生导师，任职于贺雄雷教授团队（生命科学学院院长）。2015 年本科毕业于中国农业大学生物科学（理科实验班），2021 年于中山大学获生物化学与分子生物学博士学位，2022–2024 年在中山大学从事博士后研究。
研究方向主要聚焦分子进化与系统发育学，以分子层面的相似性为线索，探究生命系统在不同层级的演化进程，致力于推动发育生物学的计量化与理论化。具体包括：
- 细胞谱系示踪与细胞群体动态：我们已在酵母、果蝇、斑马鱼中构建高分辨率的细胞谱系追踪系统（SMALT），未来将拓展至小鼠等哺乳动物，绘制复杂多细胞生物的细胞谱系图谱。
- 发育生物学的计量化与理论化：将物种树分析中的定量算法与理论迁移至细胞谱系研究，建立标准化的细胞群体计量范式，并构建“数字孪生胚胎”人工智能模型。
- 复杂性状与神经相关性状的演化：结合比较基因组学与系统发育学，在物种树框架下解析睡眠、智力、神经性疾病等复杂性状的分子机制、细胞基础及其空间分布模式。
近年来，以第一或通讯作者在 Nature、Nature Methods、National Science Review 等国际顶尖期刊发表多篇高影响力论文，并主持/参与多项科技部重点研发项目、国自然重点项目、面上项目、青年科学基金等。
Research研究方向
Publication文章
LATEST 5
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A comprehensive single-cell atlas of monoallelic expression across various tissues in zebrafish
Using reciprocal crosses between divergent zebrafish strains, whole-genome sequencing and single-cell RNA sequencing, we build a single-cell atlas of allelic expression across 50,819 cells and 37 cell types, identifying 738 monoallelically expressed (MAE) genes and revealing that MAE is widespread and dynamic during vertebrate development and contributes to tissue specialization.
本文结合遗传距离较远的斑马鱼品系正反交、全基因组测序与单细胞 RNA 测序，在 50,819 个细胞、37 种细胞类型中构建了等位基因表达图谱，鉴定出 738 个单等位表达（MAE）基因，揭示 MAE 在脊椎动物发育中广泛而动态，并参与组织特化与调控多样性。
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Polyclonal-to-monoclonal transition in colorectal precancerous evolution
Cited by 71被引 71Using base-editor DNA barcoding to build single-cell phylogenies in mouse intestinal tumour models and validating them in human sporadic colorectal polyps, we find that precancerous lesions are often founded polyclonally by multiple lineages and support a 'polyclonal-to-monoclonal transition' model in which monoclonal lesions represent a later stage.
本文利用碱基编辑器 DNA 条形码在小鼠肠肿瘤模型中绘制单细胞系统发育树，并在人类散发性结直肠息肉中加以验证，发现癌前病灶常由多个谱系多克隆奠基，并支持“多克隆向单克隆转变”的模型，其中单克隆病灶代表更晚期的阶段。
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Variation in cancer risk between organs can not be explained by the degree of somatic clonal expansion
Cited by 7被引 7Quantifying somatic clonal expansion across nine human organs, we find that its degree varies among organs but is consistent among individuals and is not significantly correlated with lifetime cancer risk, suggesting that somatic clonal expansion in normal tissues is an evolutionary process distinct from carcinogenesis.
本文定量评估了九种人体器官的体细胞克隆扩增程度，发现其因器官而异、在个体间一致，且与终生癌症风险并无显著相关，提示正常组织中的体细胞克隆扩增是与癌变不同的一种独立演化过程。
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A statistical method for quantifying progenitor cells reveals incipient cell fate commitments
Cited by 18被引 18We propose TarCA, a statistical method that quantifies progenitor cells without progenitor-specific markers by computing the coalescent probability of two randomly sampled cells in the cell phylogenetic tree; it is validated in nematode, fruit fly and mouse data and used to identify lineage-specific upregulated genes and incipient cell fate commitments in mouse embryos.
本文提出无需祖细胞特异标志物的统计方法 TarCA，通过细胞系统发育树计算同一组织内两随机细胞的溯祖概率来估计祖细胞数目，并在线虫、果蝇和小鼠数据中得到验证，进而识别出小鼠胚胎发育中的谱系特异上调基因与早期细胞命运决定。
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Tree of life at two levels: from species to cell
Cited by 2被引 2This perspective parallels species trees with cell trees, reviews recent progress in reconstructing the developmental cell tree of complex multicellular organisms using somatic mutations and cell-tree-based population-genetic modelling, and anticipates the convergence of evolutionary biology with molecular, cellular and developmental biology.
本文以物种树类比细胞树，综述了利用体细胞突变重建复杂多细胞生物发育细胞树的最新进展及基于细胞树的群体遗传建模，并展望生态与演化生物学同分子、细胞与发育生物学的融合。
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News新闻
LATEST 5
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2024-10-31
Nature | Hu Zheng, He Xionglei and He Zhen labs reveal a new evolutionary model of early tumour transition from polyclonal to monoclonalNature | 胡政/贺雄雷/何真团队揭示早期肿瘤从多克隆至单克隆转变的演化新模式
Understanding the early mechanisms of tumour development is crucial for early prevention and treatment. The traditional…理解肿瘤的早期发生机制，对实现肿瘤的早期预防和治疗至关重要。传统的 Nowell 克隆演化理论认为，肿瘤是由一个发生致癌突变的单一细胞引起，经过不断的细胞扩增和筛选，最终形成恶性肿瘤。这一理论强调肿瘤具有“单克隆起源”，即肿瘤由一个细胞起源…
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2024-05-24
Advanced Biotechnology | He lab at Sun Yat-sen University uses a new quantitative method to explore the link between somatic clonal expansion and cancer riskAdvanced Biotechnology | 中山大学贺雄雷教授团队采用定量评估新方法探究体细胞克隆扩增与癌症风险的相关性
Somatic clonal expansion is an important form of cell proliferation in multicellular organisms and has long been conside…体细胞克隆扩增是多细胞生物体内细胞增殖的一种重要形式，长期以来被认为与癌症的发生和发展密切相关。尤其是在血液系统中，驱动突变导致的克隆扩增被视为白血病等血液系统肿瘤发生的重要标志。癌症的本质是细胞的失控增殖，而体细胞克隆扩增也具备增殖的表现…
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2024-02-23
Nature Methods | He lab at Sun Yat-sen University proposes a statistical method to quantify progenitor cells, revealing incipient cell fate commitmentsNat Methods | 中山大学贺雄雷团队提出一种量化祖细胞的统计方法，揭示了早期细胞命运的承诺
Quantifying the number of progenitor cells in an organ, tissue or cell population is crucial for understanding the devel…对一个器官、组织或细胞群中祖细胞的数量进行量化，对于理解多细胞生物的发育和体内平衡至关重要。以前的研究依赖于在祖细胞中特异性表达的标记基因。然而，这种策略常常因缺乏理想的标记而受阻。
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2023-10-31
Science Bulletin | The tree of life at two levels: from species to cellScience Bulletin | 两种尺度的生命之树：从物种到细胞
All species on Earth originate from a common ancestor. Their evolutionary history can be represented as a tree-like stru…所有生物种类均源自一个共同的祖先。它们的进化历史可以被呈现为一种树状结构，也即所谓的物种树。在这颗树上，根代表着这个共同的祖先，分支则代表了过去的物种分化事件，而叶子则代表了现代的各个物种。
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2021-12-19
National Science Review | New result from Sun Yat-sen University: 99.9% similarity — mutation signatures trace the natural host of SARS-CoV-2National Science Review | 中山大学最新成果：99.9%相似性！突变特征追溯新冠病毒的自然宿主
Since the outbreak of COVID-19, the origin of SARS-CoV-2 has been debated, one main reason being that RaTG13, the closes…自 COVID-19 爆发以来 SARS-CoV-2 的起源一直争论不休，其中一个主要原因是迄今为止发现与 SARS-CoV-2 最接近的近亲 RaTG13，与 SARS-CoV-2 只有 96.1% 的核苷酸相似性。而本世纪爆发的前两次冠…
Software软件
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LEAPLEAP ↗
A phylogeny-based computational framework that infers the transcriptional states of unobserved internal nodes from cell phylogenies via lineage-specific upregulated genes (LUGs), integrating lineage tracing with scRNA-seq to reconstruct ancestral transcriptomes and build lineage-resolved cell atlases.基于系统发育的计算框架：利用谱系特异性上调基因（LUGs），从细胞系统发育树推断未观测内部节点的转录状态；结合谱系追踪与单细胞 RNA 测序重建祖先转录组，支持构建谱系分辨的细胞图谱。
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LEAP_webLEAP_web ↗
Interactive in-browser visualization of 30 zebrafish cell lineage trees: nodes are coloured by cell type, with smooth zoom/pan, flexible cell selection and live cell-type composition charts. Live demo: https://shadowdeng1994.github.io/LEAP_web/30 个斑马鱼细胞谱系树的交互式网页可视化：节点按细胞类型着色，支持平滑缩放/平移、多种方式选择细胞，并实时显示所选细胞的类型组成。在线使用：https://shadowdeng1994.github.io/LEAP_web/
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TarCA.betaTarCA.beta ↗
Beta version of TarCA (targeting coalescent analysis): estimates the progenitor number (Np) of any defined tissue or cell population from its cell phylogeny via the average coalescent rate at its monophyletic clades, independent of pre-set markers; rewritten for higher computational efficiency.TarCA（靶向溯祖分析）测试版：基于细胞系统发育树估计任意组织或细胞群体的祖细胞数目（Np）——计算目标组织单系进化枝上的平均溯祖速率并取倒数，无需预设标记；为提升计算效率而重写的紧凑实现。
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NpDynamicNpDynamic ↗
Data and code for the Np dynamic reconstruction in Drosophila melanogaster with SMALT, quantifying the longitudinal dynamics of actively dividing parental cells (Np) during organ development, and informing symmetric vs. asymmetric division balance and a sigmoid organ-growth model.利用 SMALT 对黑腹果蝇进行 Np（活跃分裂的祖先细胞数目）动态重建的数据与代码：刻画各器官发育过程中 Np 的纵向动态，进而揭示细胞分裂的对称/不对称平衡与器官生长的sigmoid 规律。
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SarsMutSignatureSarsMutSignature ↗
Data and R scripts for analysing the SARS-CoV-2 mutation signature: comparing public viral genomes to infer the pre-outbreak mutation spectrum, which is 99.9% identical to that of RaTG13, suggesting they shared almost the same host environment before the outbreak.分析 SARS-CoV-2 突变特征的数据与 R 脚本：比较公开病毒基因组，推断病毒在疫情前积累的突变谱，发现其与 RaTG13 的突变谱高达 99.9% 一致，提示二者在疫情前共享几乎相同的宿主环境。
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FreeDrawInRFreeDrawInR ↗
A small R toolbox for free-form vector drawing directly as ggplot2 layers — trace outlines from PNG images, build geometric shapes (circle, ellipse, fan, rounded rectangle, smooth paths), transform coordinates, apply ready-made themes, and compose everything into a single ggplot2 plot.FreeDrawInR 是一个把自由绘制直接变成 ggplot2 图层的 R 工具箱，用于制作示意图、插图和图表：支持从 PNG 图像描摹轮廓、构建圆/椭圆/扇形/圆角矩形/平滑路径等几何形状、平移缩放旋转坐标系、套用现成主题，并拼装成一张完整的 ggplot2 图。
Photos照片
Contact联系我们
- Email邮箱 dengshj8@mail.sysu.edu.cn
- Address联系地址 6F, He Danqing Hall, Sun Yat-sen University, No.135 Xingang West Road, Haizhu District, Guangzhou, Guangdong, China中国广东省广州市海珠区新港西路 135 号中山大学贺丹青堂 6 楼
- Postcode邮编 510275
- Lab homepage实验室主页 rjsci.com/zh/lab/10156-hexionglei