代表论文:
# 同等贡献,* 通讯作者
A lineage-resolved cartography of microRNA promoter activity in C. elegans empowers multidimensional developmental analysis.
Xu W#, Liu J#, Qi H#, 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 (1-23).
─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, 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, Fan D, Qi H, Cong Y, Du Z*. Cell Systems. 2022 Aug 17;13(8):615-630.
─系统揭示胚胎在遗传干扰条件下具备自适应和自组织能力以应对细胞异常,在细胞水平增强发育稳固性。
A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis.
Ma X#, Zhao Z#, Xiao L#, 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 by a News & Views article in Nature Methods. https://doi.org/10.1038/s41592-021-01219-y
被Genomics Proteomics & Bioinformatics杂志评选为“2021年度中国生物信息学十大进展”
─绘制转录因子单细胞4D蛋白动态表达图谱,初步揭示细胞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#, Fan R#, 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及其多种发育动态变化基本模式及意义。
Multivariable regulation of gene expression plasticity in metazoans.
Xiao L#, Zhao Z#, He F*, Du Z*. Open Biology. 2019 Dec;9(12):190150 (1-16).
─揭示了顺式作用元件和组蛋白修饰调控基因表达的可塑性。
Systems properties and spatiotemporal regulation of cell position variability during embryogenesis.
Li X#, 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。
Trans-splicing enhances translational efficiency in C. elegans.
Yang YF#, Zhang X#, Ma X#, Zhao T#, Sun Q, Huan Q, Wu S, Du Z*, Qian W*. Genome Research. 2017 Sep;27(9):1525-1535.
─揭示mRNA反式剪接增强蛋白翻译效率。
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。
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.
─揭示泛素化蛋白降解促进细胞分化状态转变。
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。
Systematic quantification of developmental phenotypes at single-cell resolution during embryogenesis.
Moore JL, Du Z, Bao Z*. Development. 2013 Aug;140(15):3266-74.
─建立线虫胚胎发育单细胞表型定量分析方法。
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.
─预测G4 DNA是一类广谱性调控基因转录的结构性元件。
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.
─预测转录起始位点下游G4 DNA结构元件促进基因转录。
其他论文:
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#, 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.
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.
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.
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.
Advanced technologies for genomic analysis in farm animals and its application for QTL mapping.
Hu X, Gao Y, Feng C, Liu Q, Wang X, Du Z, Wang Q, Li N*. Genetica. 2009 Jun;136(2):371-86.
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:
更新时间:2024-04