Functional Genomics of Embryogenesis
Multidimensional Regulation of Gene Expression and Cell Differentiation
Cellular Robustness and Plasticity of Embryogenesis

2003-2008 Ph.D. Thesis, China Agricultural University, Beijing, China. Laboratory of Dr. Ning Li. Subject: Regulatory Genomics of G4 DNA Motifs

2008-2009 Postdoctoral Researcher, Albert Einstein College of Medicine, New York, U.S.A. Laboratory of Dr. Carl Schildkraut. Subject: Single-molecule Analysis of DNA Replication Dynamics During Cell Differentiation

2009-2014 Postdoctoral Researcher, Memorial Sloan Kettering Cancer Center, New York, U.S.A. Laboratory of Dr. Zhirong Bao, Subject: Systems Biology of Animal Development Using Live imaging-based Phenotype Analysis

* Corresponding Author

Multivariable regulation of gene expression plasticity in metazoans.

Xiao L#, Zhao Z#, He F*, Du Z*.

Open Biol. 2019 Dec;9(12):190150.

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).

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 Rep. 2019 Jan 8;26(2):313-321.e7.

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

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 Res. 2017 Sep;27(9):1525-1535.
 
Digital Development: A database of C. elegans cell lineage differentiation with lineage phenotypes, cell-specific gene functions and a multiscale model.
Santella A, Kovacevic I, Herndon L Hall D, Du Z*, Bao Z*. 
Nucleic Acids Res. 2016 Jan 4;44(D1):D781-5.
 
The Regulatory Landscape of lineage differentiation in a metazoan embryo.
Du Z*, Santella A, He F, Shah PK, Kamikawa Y, Bao Z*.
Dev. Cell. 2015 2015 Sep 14;34(5):592-607. (Free Featured Article)
 
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*
Dev. Cell. 2015 Jul 6;34(1):108-18. Recommend by F1000
 
E3 ubiquitin ligases promote progression of differentiation during C. elegans embryogenesis.
Du Z, He F, Yu Z, Bowerman B, Bao Z*.
Dev. Biol. 2015 Feb 15;398(2):267-79.
 
De novo inference of systems-level mechanistic models of development from live imaging-based phenotype analysis.
Du Z, Stantella A., He F., Tiongson M, Bao Z*.
Cell. 2014 Jan 16;156(1-2):359-72.
 
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 inCaenorhabditis 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. Recommend by F1000

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*.
Mol. Cell. Biol. 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 Res. 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 Res. 2008 Feb;18(2):233-41. (Highlighted on Cover)

Understanding embryogenesis at the systems-level, using C. elegans as a model

已指导学生

樊蓉  博士研究生  071008-发育生物学  

李小雨  硕士研究生  085238-生物工程  

肖龙  博士研究生  071008-发育生物学  

徐伟娜  博士研究生  071008-发育生物学  

寇雅慧  硕士研究生  071008-发育生物学  

赵志广  博士研究生  0710J3-生物信息学  

范渡长江  博士研究生  0710J3-生物信息学  

张昊烨  硕士研究生  071009-细胞生物学  

现指导学生

丛俞林  博士研究生  071008-发育生物学  

周子欣  博士研究生  071008-发育生物学  

孙小涵  硕士研究生  071007-遗传学  

刘瑾仪  博士研究生  071008-发育生物学  

杨淼泠  博士研究生  071008-发育生物学  

白宇川  博士研究生  071008-发育生物学