Publications

Hang Yang, Zehui Wang, Zhaojun Shan, Hanqiao Shang, Puxuan Jiang, Yingshu Li, Qiang Tu (2026). miniODP: a reusable framework for building multi-omics resources in understudied organisms. bioRxiv.

Code Dataset DOI

Hanqiao Shang, Puxuan Jiang, Zehui Wang, Zhaojun Shan, Yuze Chen, Ting Zhang, Yingshu Li, Qiang Tu (2025). Tatdn2 is required for DNA repair to safeguard genome stability in primordial germ cells. Nucleic Acids Res, 53(22): gkaf1289.

DOI

Min Chen*, Nan Wang*, Hang Yang*, Dongjun Liu*, Yuan Gao, Lei Duo, Xiuhong Cui, Fei Hao, Jing Ye, Fei Gao, Qiang Tu, Yaoting Gui (2023). Single-Cell Transcriptome Analysis of the Germ Cells and Somatic Cells during Mitotic Quiescence Stage in Goats. FASEB J, 37(11): e23244.

DOI

Wenting Zhang*, Yue Wang*, Yongjie Liu*, Cuifang Liu, Yizhou Wang, Lin He, Xiao Cheng, Yani Peng, Lu Xia, Xiaodi Wu, Jiajing Wu, Yu Zhang, Luyang Sun, Ping Chen, Guohong Li, Qiang Tu, Jing Liang, Yongfeng Shang (2023). NFIB Facilitates Replication Licensing by Acting as a Genome Organizer. Nat Commun, 14(1): 5076.

DOI

Jianyong Du*, Lixia Zheng*, Peng Gao, Hang Yang, Wan-Jie Yang, Fusheng Guo, Ruqi Liang, Mengying Feng, Zihao Wang, Zongwang Zhang, Linlu Bai, Ye Bu, Shijia Xing, Wen Zheng, Xuelian Wang, Li Quan, Xinli Hu, Haosen Wu, Zhixing Chen, Liangyi Chen, Ke Wei, Zhe Zhang, Xiaojun Zhu, Xiaolin Zhang, Qiang Tu, Shi-Min Zhao, Xiaoguang Lei, Jing-Wei Xiong (2022). A Small-Molecule Cocktail Promotes Mammalian Cardiomyocyte Proliferation and Heart Regeneration. Cell Stem Cell, 29(4): 545-558.

DOI

Ziqi Zhao*, Dan Zhang*, Fuqiang Yang*, Mingrui Xu, Shaoli Zhao, Taotao Pan, Chuanyu Liu, Yongjie Liu, Qingfeng Wu, Qiang Tu, Ping Zhou, Rong Li, Jia Kang, Lan Zhu, Fei Gao, Yaqing Wang, Zhiheng Xu (2022). Evolutionarily Conservative and Non-Conservative Regulatory Networks during Primate Interneuron Development Revealed by Single-Cell RNA and ATAC Sequencing. Cell Res, 32(5): 425-436.

DOI

Feiyang Wang*, Wentong Jia*, Mengjie Fan*, Xuan Shao*, Zhilang Li, Yongjie Liu, Yeling Ma, Yu-Xia Li, Rong Li, Qiang Tu, Yan-Ling Wang (2021). Single-Cell Immune Landscape of Human Recurrent Miscarriage. Genomics Proteomics Bioinformatics, 19(2): 208-222.

DOI

Yingshu Li*, Yongjie Liu*, Hang Yang, Ting Zhang, Kiyoshi Naruse, Qiang Tu (2020). Dynamic Transcriptional and Chromatin Accessibility Landscape of Medaka Embryogenesis. Genome Res, 30(6): 924-937.

Dataset DOI

Yingshu Li, Hang Yang, Hujun Zhang, Yongjie Liu, Hanqiao Shang, Herong Zhao, Ting Zhang, Qiang Tu (2020). Decode-Seq: A Practical Approach to Improve Differential Gene Expression Analysis. Genome Biol, 21(1): 66.

Code Dataset DOI

Selected Prior Publications

  • Barsi JC*, Tu Q*, Calestani C, Davidson EH. 2015. Genome-wide assessment of differential effector gene use in embryogenesis. Development 142: 3892–3901. [DOI]
  • Barsi JC*, Tu Q*, Davidson EH. 2014. General approach for in vivo recovery of cell type-specific effector gene sets. Genome Res 24: 860–868. [DOI]
  • Tu Q, Cameron RA, Davidson EH. 2014. Quantitative developmental transcriptomes of the sea urchin Strongylocentrotus purpuratus. Dev Biol 385: 160-167. [DOI]
  • Tu Q, Cameron RA, Worley KC, Gibbs RA, Davidson EH. 2012. Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. Genome Res 22: 2079–2087. [DOI]
  • Oliveri P*, Tu Q*, Davidson EH. 2008. Global regulatory logic for specification of an embryonic cell lineage. Proc Natl Acad Sci USA 105: 5955-5962. [PNAS Comment | F1000 Comment | DOI]
  • Tu Q, Brown CT, Davidson EH, Oliveri P. 2006. Sea urchin Forkhead gene family: Phylogeny and embryonic expression. Dev Biol 300: 49-62. [DOI]
  • Howard-Ashby M, Materna SC, Brown CT, Tu Q, Oliveri P, Cameron RA, Davidson EH. 2006. High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution. Dev Biol 300: 27-34. [DOI]
  • Samanta MP, Tongprasit W, Istrail S, Cameron RA, Tu Q, Davidson EH, Stolc V. 2006. The transcriptome of the sea urchin embryo. Science 314: 960-962. [DOI]
  • Tu Q, Tang H, Ding D. 2004. MedBlast: searching articles related to a biological sequence. Bioinformatics 20: 75-77. [DOI]
  • Tu Q, Ding D. 2003. Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis. FEMS Microbiol Lett 221: 269-275. [DOI]
  • Tu Q, Yu L, Zhang P, Zhang M, Zhang H, Jiang J, Chen C, Zhao S. 2000. Cloning, characterization and mapping of the human ATP5E gene, identification of pseudogene ATP5EP1, and definition of the ATP5E motif. Biochem J 347: 17-21. [DOI]
  • Zheng L, Yu L, Tu Q, Zhang M, He H, Chen W, Gao J, Yu J, Wu Q, Zhao S. 2000. Cloning and mapping of human PKIB and PKIG, and comparison of tissue expression patterns of three members of the protein kinase inhibitor family, including PKIA. Biochem J 349: 403-407. [DOI]
  • Lang T, Yu L, Tu Q, Jiang J, Chen Z, Xin Y, Liu G, Zhao S. 2000. Molecular cloning, genomic organization, and mapping of PRKAG2, a heart abundant gamma2 subunit of 5’-AMP- activated protein kinase, to human chromosome 7q36. Genomics 70: 258-263. [DOI]
  • 屠强. 1997. 植物分类学工具软件 (PTT) 的设计. 安徽师大学报 (自然科学版) 20: 189-193.