Publications (journals and conferences)

#co-first authors; * corresponding authors; lab members

  • Dunming Hua#, Ming Gu#, Xiao Zhang#, Yanyi Du#, Li Qi, Xiangjun Du, Zhidong Bai, Xiaopeng Zhu, Dechao Tian* (2024)
    DiffDomain enables identification of structurally reorganized topologically associating domains.
    Nature Communications. 15:502 [Link]

    • Early version presented at RECOMB 2022, RECOMB, LNCS, vol 13278. Springer, Cham [Link]
  • Bonnie Berger, Dechao Tian, Wei Vivian Li, Mohammed El-Kebir, Alexandru I. Tomescu, Ritambhara Singh, Niko Beerenwinkel, Yu Li, Christina Boucher, Ziv Bar-Joseph (2022)
    What are the keys to succeeding as a computational biologist in today’s research climate?
    Cell Systems. 13(10):781-785 [Link]
  • Jiahui Tan., Yutong Zhao, Cara Burns, Dechao Tian, Kun Zhao (2022)
    A novel network method MMVC for analysis of WGS data unveils high-resolution linkages in poliovirus clusters: application to polio eradication.
    Journal of Computational Biology (online) [Link]

    • Earlier version is selected as oral presentation at
      • MEEGID XV 2021: 15th International Conference on Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases
      • ICCABS-CANGS 2021
  • Dechao Tian#, Ruochi Zhang#,  Yang Zhang, Xiaopeng Zhu, Jian Ma* (2020)
    MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome.
    Genome Research. 30(2): 227–238. (SCI, IF=11.093) [Link]

  • Dechao Tian, Quanquan Gu*, Jian Ma* (2016)
    Identifying gene regulatory network rewiring using latent differential graphical models.
    Nucleic Acids Research. 44(17): e140. (SCI, IF=11.147) [Link]
  • Shihua Zhang#, Dechao Tian# , Ngoc-Hieu Tran, Kwok-Pui Choi,  Louxin Zhang (2014)
    Profiling human cell-type specific transcription factor regulatory networks.
    Nucleic Acids Research. 42(20): 12380-12387. (SCI, IF=11.147) [Link]
  • Dechao Tian, Kwok-Pui Choi (2013)
    Sharp bounds and normalization of Wiener-type indices.
    PLOS ONE. 8(11): e78448. (SCI, IF=2.776) [Link]
Collaboration papers

(visit Google Scholar for full list of papers)

  • Xiaopeng Zhu, Yang Zhang, Yuchuan Wang, Dechao Tian, Andrew S Belmont, Jason R Swedlow, Jian Ma (2022)
    Nucleome Browser: An integrative and multimodal data navigation platform for 4D Nucleome
    Nature Methods. 19(8):909-913
  • Yaqi Wang, Guoqin Mai, Min Zou, Haoyu Long, Yao-Qing Chen, LItao Sun, Dechao Tian,  Yang Zhao, Guozhi Jiang, Zicheng Cao, Xiangjun Du (2022)
    Heavy chain sequence-based classifier for the specificity of human antibodies
    Briefings in Bioinformatics. 23(1): bbab516
  • Qi L, Liu T, Gao Y, Tian D, Li Q, Su K, Tang W, Feng L, Liu Q. (2021)
    Effect of meteorological factors on the activity of influenza in Chongqing, China, 2012–2019.
    PLOS ONE. 16(2):e0246023 (SCI, IF=2.74)
  • Chen, L. Cheng C.Y., Choi H., Ikram M.K., Sabanayagam C., Tan G.S., Tian D. … & Wong T.T. (2016)
    Plasma metabonomic profiling of diabetic retinopathy.
    Diabetes. 65(4): 1099- 1108. (SCI, IF=7.199)
  • Koh V., Cheung C., Li X., Tian D., Wang J.J., Mitchell P., Cheng C.Y., and Wong T.T. (2016)
    Retinal vein occlusion in a multi-ethnic asian population: the singapore epidemiology of eye disease study.
    Ophthalmic Epidemiology. 23(1): 6-13. (SCI, IF=2.779)
  • Yam G.H.F., Yusoff N.Z.B.M., Kadaba A., Tian D., Myint H.H., Beuerman R.W., Zhou L., Mehta J.S. (2015)
    Ex vivo propagation of human corneal stromal “activated keratocytes” for tissue engineering.
    Cell Transplantation. 24(9): 1845-1861. (SCI, IF=3.477)
  • Chen L., Li J., Guo T., Ghosh S., Koh S.K., Tian D., …  & Zhou L. (2015)
    Global metabonomic and proteomic analysis of human conjunctival epithelial cells (IOBA-NHC) in response to hyperosmotic stress.
    Journal of Proteome Research. 14(9): 3982-3995. (SCI, IF=3.537)
  • Tong L., Zhou X., Jylha A., Aapola U., Liu D.N., Koh S.W., Tian D., … & Zhou L. (2015)
    Quantitation of 47 human tear proteins using high resolution multiple reaction monitoring (HR-MRM) based-mass spectrometry.
    Journal of Proteomics. 115: 36- 48. (SCI, IF=3.537)
  • Barathi V.A., Chaurasia S.S., Poidinger M., Koh S.K., Tian D., … & Zhou L. (2014)
    Involvement of GABA transporters in atropine-treated myopic retina as revealed by iTRAQ quantitative proteomics.
    Journal of Proteome Research. 13(11): 4647-4658. (SCI, IF=3.537)