代表论文：
# 同等贡献，* 通讯作者
Intracellular buffering enables developmental robustness after genome doubling in C. elegans embryos.
Yang M (杨淼泠)*, Bai Y, Wang Z, Du Z*
Cell Reports. 2026 Mar 2:117005.
Previewed in Cell Reports by Alexander Lessenger and Rebecca Heald: "Building life from a bigger blueprint: Embryogenesis in whole-organism tetraploids."
─揭示尺寸-功能精确耦合在维持大尺度基因组扰动下发育稳健性中的重要作用。
To see and to know: the power of live imaging in illuminating and decoding biological complexity.
Yang M (杨淼泠)*, Du Z*
Journal of Genetics and Genomics. 2026 Mar;53(3):361-380.
─看见"生命进行时"：活体成像赋能复杂生命解析的进展、挑战及展望。
Reaffirming the value of model organisms in training scientific minds.
Yang M (杨淼泠), Du Z*
Nature Cell Biology. 2025 Oct;27(10):1589-1591.
─探讨"简单"模式生物在科研思维塑造与人才培养中的独特价值。
知微与思序：探索复杂系统 (A journey into biological complexity: continuing the legacy of Doug and Bill).
杨淼泠, 杜茁*
遗传/Hereditas (Beijing). 2025 Dec;47(12):1377-1386.
─生命科学教学经典故事The Salvation of Doug与The Demise of Bill的现代续写。
A lineage-resolved cartography of microRNA promoter activity in C. elegans empowers multidimensional developmental analysis.
Xu W (徐伟娜)#, Liu J (刘瑾仪)#, Qi H (齐欢)#, Si R, Zhao Z, Tao Z, Bai Y, Hu S, Sun X, Cong Y, Zhang H, Fan D, Xiao L, Wang Y, Li Y*, Du Z*
Nature Communications. 2024 Mar 30;15(1):2783.
─揭示microRNA的胚胎发育4D表达及功能模式。
Spatiotemporal analysis of mRNA-protein relationships enhances transcriptome-based developmental inference.
Fan D (范渡长江), Cong Y, Liu J, Zhang H, Du Z*
Cell Reports. 2024 Mar 26;43(3):113928 (1-23).
─报导基于mRNA表达解析胚胎发育的局限性及应对策略。
Defect-buffering cellular plasticity increases robustness of metazoan embryogenesis.
Xiao L (肖龙), Fan D, Qi H, Cong Y, Du Z*
Cell Systems. 2022 Aug 17;13(8):615-630.
─系统揭示胚胎具备自适应和自组织能力以应对细胞异常，增强发育稳固性。
A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis.
Ma X (马雪华)#, Zhao Z (赵志广)#, Xiao L (肖龙)#, Xu W, Kou Y, Zhang Y, Wu G, Wang Y, Du Z*
Nature Methods. 2021 Aug;18(8):893-902.
封面文章
Highlighted in a Nature Methods News & Views by Aly Makhlouf and Marta Shahbazi: "The long and winding road of development: a coordinated song of transcription factors."
被Genomics Proteomics & Bioinformatics杂志评选为"2021年度中国生物信息学十大进展"。
─绘制转录因子的单细胞4D蛋白动态表达图谱，初步揭示命运图式建立及分化状态转变的调控规律。
Single-cell dynamics of chromatin activity during cell lineage differentiation in Caenorhabditis elegans embryos.
Zhao Z (赵志广)#, Fan R (樊蓉)#, Xu W, Kou Y, Wang Y, Ma X, Du Z*
Molecular Systems Biology. 2021 Apr;17(4):e10075 (1-24).
─在单细胞精度和基因组尺度解析染色质活性多种发育动态变化模式及意义。
Systems properties and spatiotemporal regulation of cell position variability during embryogenesis.
Li X (李小雨)#, Zhao Z, Xu W, Fan R, Xiao L, Ma X, Du Z*
Cell Reports. 2019 Jan 8;26(2):313-321.e7.
─揭示了细胞表型变异的发育时空特异性。
Digital development: a database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model.
Santella A, Kovacevic I, Herndon LA, Hall DH, Du Z*, Bao Z*
Nucleic Acids Research. 2016 Jan 4;44(D1):D781-5.
─构建细胞谱系分化的表型组学数据库。
The regulatory landscape of lineage differentiation in a metazoan embryo.
Du Z*, Santella A, He F, Shah PK, Kamikawa Y, Bao Z*
Developmental Cell. 2015 Sep 14;34(5):592-607.
─揭示进化保守必需基因对细胞谱系分化的多维度调控。
De novo inference of systems-level mechanistic models of development from live-imaging-based phenotype analysis.
Du Z, Santella A, He F, Tiongson M, Bao Z*
Cell. 2014 Jan 16;156(1-2):359-72.
─建立细胞发育命运解析方法，实现了高通量解析细胞命运抉择的调控模型。
其他论文：
Lactate shuttling links histone lactylation to adult hippocampal neurogenesis in mice.
Li Z, Liang Z, Qi H, Luo X, Wang M, Du Z, Guo W*
Developmental Cell. 2025 Apr 21;60(8):1182-1198.
Vacuolar H+-ATPase determines daughter cell fates through asymmetric segregation of the nucleosome remodeling and deacetylase complex.
Xie Z, Chai Y*, Zhu Z, Shen Z, Guo Z, Zhao Z, Xiao L, Du Z, Ou G, Li W*
Elife. 2024 Jul 12;12:RP89032.
Gene regulatory patterning codes in early cell fate specification of the C. elegans embryo.
Cole AG#, Hashimshony T#, Du Z, Yanai I*
Elife. 2024 Jan 29;12:RP87099.
Metabolic plasticity sustains the robustness of Caenorhabditis elegans embryogenesis.
Chen S, Su X, Zhu J, Xiao L, Cong Y, Yang L, Du Z, Huang X*
EMBO Reports. 2023 Dec 6;24(12):e57440.
Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat.
Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J*
Genome Biology. 2023 Jan 13;24(1):7.
Comparative proteome and cis-regulatory element analysis reveals specific molecular pathways conserved in dog and human brains.
Hong H#, Zhao Z (赵志广)#, Huang X, Guo C, Zhao H, Wang GD, Zhang YP, Zhao JP, Shi J, Wu QF, Jiang YH, Wang Y, Li LM, Du Z, Zhang YQ*, Xiong Y*
Mol Cell Proteomics. 2022 Aug;21(8):100261.
Dogs lacking Apolipoprotein E show advanced atherosclerosis leading to apparent clinical complications.
Zhao H#, Zhao J#, Wu D#, Sun Z#, Hua Y, Zheng M, Liu Y, Yang Q, Huang X, Li Y, Piao Y, Wang Y, Lam SM, Xu H, Shui G, Wang Y, Yao H, Lai L, Du Z, Mi J*, Liu E*, Ji X*, Zhang YQ*
Science China Life Science. 2022 Jul;65(7):1342-1356.
Multivariable regulation of gene expression plasticity in metazoans.
Xiao L (肖龙)#, Zhao Z (赵志广)#, He F*, Du Z*
Open Biology. 2019 Dec;9(12):190150 (1-16).
Lineage context switches the function of a C. elegans Pax6 homolog in determining a neuronal fate.
Brandt JP#, Rossillo M#, Du Z, Ichikawa D, Barnes K, Chen A, Noyes M, Bao Z, Ringstad N*
Development. 2019 Apr 15;146(8):dev168153.
mTOR regulates phase separation of PGL granules to modulate their autophagic degradation.
Zhang G, Wang Z, Du Z, Zhang H*
Cell. 2018 Sep 6;174(6):1492-1506.e22.
Trans-splicing enhances translational efficiency in C. elegans.
Yang YF#, Zhang X#, Ma X (马雪华)#, Zhao T#, Sun Q, Huan Q, Wu S, Du Z*, Qian W*
Genome Research. 2017 Sep;27(9):1525-1535.
E3 ubiquitin ligases promote progression of differentiation during C. elegans embryogenesis.
Du Z#, He F#, Yu Z, Bowerman B, Bao Z*
Developmental Biology. 2015 Feb 15;398(2):267-79.
POS-1 promotes endo-mesoderm development by inhibiting the cytoplasmic polyadenylation of neg-1 mRNA.
Elewa A, Shirayama M, Kaymak E, Harrison PF, Powell DR, Du Z, Chute CD, Woolf H, Yi D, Ishidate T, Srinivasan J, Bao Z, Beilharz TH, Ryder SP, Mello CC*
Developmental Cell. 2015 Jul 6;34(1):108-18.
A semi-local neighborhood-based framework for probabilistic cell lineage tracing.
Santella A, Du Z, Bao Z*
BMC Bioinformatics. 2014 Jun 25;15:217.
Systematic quantification of developmental phenotypes at single-cell resolution during embryogenesis.
Moore JL, Du Z, Bao Z*
Development. 2013 Aug;140(15):3266-74.
Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans.
Wu Y*, Ghitani A, Christensen R, Santella A, Du Z, Rondeau G, Bao Z, Colón-Ramos D, Shroff H
Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17708-13.
A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D.
Santella A, Du Z, Nowotschin S, Hadjantonakis AK, Bao Z*
BMC Bioinformatics. 2010 Nov 29;11:580.
Single-molecule analysis reveals changes in the DNA replication program for the POU5F1 locus upon human embryonic stem cell differentiation.
Schultz SS, Desbordes SC, Du Z, Kosiyatrakul S, Lipchina I, Studer L, Schildkraut CL*
Molecular and Cellular Biology. 2010 Sep;30(18):4521-34.
Genome-wide colonization of gene regulatory elements by G4 DNA motifs.
Du Z#, Zhao Y#, Li N*
Nucleic Acids Research. 2009 Nov;37(20):6784-98.
Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription.
Du Z#, Zhao Y#, Li N*
Genome Research. 2008 Feb;18(2):233-41.
Extensive selection for the enrichment of G4 DNA motifs in transcriptional regulatory regions of warm blooded animals.
Zhao Y#, Du Z#, Li N*
FEBS Letters. 2007 May 15;581(10):1951-6.
研究数据共享及可视化：
microRNA单细胞时空转录活性：https://dulab.genetics.ac.cn/scCAMERA/
进化保守基因的胚胎发育表型组：https://dulab.genetics.ac.cn/single-cell-phenomics/
转录因子单细胞蛋白动态表达图谱：http://dulab.genetics.ac.cn/TF-atlas/
单细胞染色质活性图谱：http://dulab.genetics.ac.cn/chromatin-landscape/
细胞表型变异图像及数据：http://dulab.genetics.ac.cn/data_sharing.html
发育必需基因敲降的细胞分化表型组：http://www.digital-development.org/
更新时间：2026年3月
