15. 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^*. Nat Commun. 2024 Mar 30;15(1):2783 (1-23).   

14. Spatiotemporal analysis of mRNA-protein relationships enhances transcriptome-based developmental inference.
Fan D, Cong Y, Liu J, Zhang H, Du Z^*. Cell Rep. 2024 Mar 26;43(3):113928 (1-23).   

13. 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.   

12. 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.   
Highlighted by a News & Views article in Nature Methods. https://doi.org/10.1038/s41592-021-01219-y

11. 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).   

10. 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).   

9. 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.   

8. 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.   

7. 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.   

6. 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.   

5. 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.   

4. 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.   

3. Systematic quantification of developmental phenotypes at single-cell resolution during embryogenesis.
Moore JL, Du Z, Bao Z^*. Development. 2013 Aug;140(15):3266-74.   

2. 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.   

1. 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.   

14. 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.

13. 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.

12. 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.

11. 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.

10. 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.

9. 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.

8. 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.

7. 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.

6. A semi-local neighborhood-based framework for probabilistic cell lineage tracing. Santella A, Du Z, Bao Z^*. BMC Bioinformatics. 2014 Jun 25;15:217.

5. 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.

4. 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.

3. 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.

2. 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.

1. 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.