Publications

Yang H, Shan Z, Shang H, Jiang P, Li Y^#, Tu Q^#. 2024. From Understudied to Understood: Multi-Omics Analysis with MiniENCODE Exemplified by Zebrafish. bioRxiv 2024.01.06.573815. [bioRxiv | miniODP | GitHub ]
Chen M*, Wang N*, Yang H*, Liu D*, Gao Y, Duo L, Cui X, Hao F, Ye J, Gao F, Tu Q^#, Gui Y^#. 2023. Single-cell transcriptome analysis of the germ cells and somatic cells during mitotic quiescence stage in goats. FASEB J 37: e23244. [DOI]
Zhang W*, Wang Y*, Liu Y*, Liu C, Wang Y, He L, Cheng X, Peng Y, Xia L, Wu X, Wu J, Zhang Y, Sun L, Chen P, Li G, Tu Q, Liang J^#, Shang Y^#. 2023. NFIB facilitates replication licensing by acting as a genome organizer. Nat Commun 14: 5076. [DOI]
Du J*, Zheng L*, Gao P, Yang H, Yang W-J, Guo F, Liang R, Feng M, Wang Z, Zhang Z, Bai L, Bu Y, Xing S, Zheng W, Wang X, Quan L, Hu X, Wu H, Chen Z, Chen L, Wei K, Zhang Z, Zhu X, Zhang X, Tu Q, Zhao S-M^#, Lei X^#, Xiong J-W^#. 2022. A small-molecule cocktail promotes mammalian cardiomyocyte proliferation and heart regeneration. Cell Stem Cell 29: 545-558.e13. [DOI]
Zhao Z*, Zhang D*, Yang F*, Xu M, Zhao S, Pan T, Liu C, Liu Y, Wu Q, Tu Q, Zhou P, Li R, Kang J, Zhu L, Gao F, Wang Y^#, Xu Z^#. 2022. Evolutionarily conservative and non-conservative regulatory networks during primate interneuron development revealed by single-cell RNA and ATAC sequencing. Cell Res. [DOI]
Wang F*, Jia W*, Fan M*, Shao X*, Li Z, Liu Y, Ma Y, Li Y-X, Li R^#, Tu Q^#, Wang Y-L^#. 2021. Single-cell Immune Landscape of Human Recurrent Miscarriage. Genomics Proteomics Bioinformatics 19: 208–222. [DOI]
Li Y*, Liu Y*, Yang H, Zhang T, Naruse K^#, Tu Q^#. 2020. Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis. Genome Res 30: 924–937. [DOI | Website]
Li Y*, Yang H, Zhang H, Liu Y, Shang H, Zhao H, Zhang T, Tu Q^#. 2020. Decode-seq: a practical approach to improve differential gene expression analysis. Genome Biol 21: 66. [DOI | Website | GitHub]

Pre-Lab

Barsi JC*, Tu Q*, Calestani C, Davidson EH. 2015. Genome-wide assessment of differential effector gene use in embryogenesis. Development 142: 3892–3901. [ PDF | Website]
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. [ PDF | Website]
Tu Q, Cameron RA, Davidson EH. 2014. Quantitative developmental transcriptomes of the sea urchin Strongylocentrotus purpuratus. Dev Biol 385: 160-167. [ PDF | Website]
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. [ PDF | Website]
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. [ PDF | PNAS Feature Article| PNAS Comment | F1000 Comment]
Tu Q, Brown CT, Davidson EH, Oliveri P. 2006. Sea urchin Forkhead gene family: Phylogeny and embryonic expression. Dev Biol 300: 49-62. [ PDF ]
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.
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.
Tu Q, Tang H, Ding D. 2004. MedBlast: searching articles related to a biological sequence. Bioinformatics 20: 75-77.
Tu Q, Ding D. 2003. Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis. FEMS Microbiol Lett 221: 269-275.
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.
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.
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.
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.