Wang Lab

Tissue Regeneration and Bioinformatics, GIBH

Journal Publications (# co-first author, * corresponding author)

Selected Publications


Gene regulatory networks controlling vertebrate retinal regeneration

Gene regulatory networks controlling vertebrate retinal regeneration


Hoang T#, Wang J#, Boyd P, Wang F, Santiago C, Jiang L, Yoo S, Lahne M, Todd LJ, Jia M, Saez C, Keuthan C, Palazzo I, Squires N, Campbell WA, Rajaii F, Payail T, Trinh V, Kim DW, Wang G, Campbell LJ, Ash J, Fischer AJ, Hyde DR*, Qian J*, Blackshaw S*.

Science 2020, 370(6519): eabb8598.
ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration

ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration


Wang J#, Zibetti C#, Shang P, Sripathi SR, Zhang P, Cano M, Hoang T, Xia S, Ji H, Merbs S, Zack D, Handa JT, Sinha D, Blackshaw S*, Qian J*.

Nature Communications 2018, 9(1): 1-13.
Lhx2 specifically expressed in HSCs promotes liver regeneration and inhibits liver fibrosis

Lhx2 specifically expressed in HSCs promotes liver regeneration and inhibits liver fibrosis


Tao J#, Wu Z#, Liang Y#, Wang J#, Tang M#, Huang S, Jiang F, Zhou G, Guo L, Yuan S*, Li Y*, Wang J*.

Hepatology 2025, 82(3):683-701.
ScReNI: Single-cell Regulatory Network Inference Through Integrating scRNA-seq and scATAC-seq Data

ScReNI: Single-cell Regulatory Network Inference Through Integrating scRNA-seq and scATAC-seq Data


Xu X#, Liang Y#, Tang M#, Wang J, Wang X, Li Y*, Wang J*.

Genomics, Proteomics & Bioinformatics 2025, 23(4):qzaf060.
CACIMAR: cross-species analysis of cell identities, markers, regulations, and interactions using single-cell RNA sequencing data

CACIMAR: cross-species analysis of cell identities, markers, regulations, and interactions using single-cell RNA sequencing data


Jiang J#, Li J#, Huang S, Jiang F, Liang Y, Xu X*, Wang J*.

Briefings in Bioinformatics 2024, 25(4): bbae283.

More Publications


  1. Tao J, Wang J*. Reply: Considerations on the specific role of LHX2 in the process of hepatic stellate cells regulating hepatocyte function. Hepatology 2025, 82(5): E134-E135.
  2. Xu Z, Zhou L, Wang J, Cho H, Cao Y, Shi L, Wu S, Xie Y, Qian J, Duh EJ*. Nrf2 Deficiency in Müller Cells Exacerbates Pathological Neovascularization in Ischemic Retinopathy. Arteriosclerosis, Thrombosis, and Vascular Biology 2025, 45(11):e544-e562.
  3. Li Y#, Wang J#, Zhou L#, Gu W#, Qin L, Peng D, Li S, Zheng D, Wu Q, Long Y, Yao Y, Lin S, Sun M, Zhang X, Wang J, Liu P, Kong X*, Li P*. DNMT1 inhibition reprograms T cells to NK-like cells with potent antitumor activity. Science Immunology 2025, 10(105): eadm8251.
  4. Fu Y#, Jiang F#, Zhang X, Pan Y, Xu R, Liang X, Wu X, Li X, Lin K, Shi R, Zhang X, Ferrandon D, Liu J, Pei D, Wang J*, Wang T*. Perturbation of METTL1-mediated tRNA N7- methylguanosine modification induces senescence and aging. Nature Communications 2024, 15(1): 1-21.
  5. Jiang J#, Lyu P#, Li J#, Huang S, Tao J, Blackshaw S, Qian J, Wang J*. IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles. iScience 2022, 25(11): 105359.
  6. Sun D#, Gan X#, Liu L#, Yang Y#, Ding D, Li W, Jiang J, Ding W, Zhao L, Hou G, Yu J, Wang J*, Yang F*, Yuan S*, Zhou W*. DNA hypermethylation modification promotes the development of hepatocellular carcinoma by depressing the tumor suppressor gene ZNF334. Cell Death & Disease 2022, 13(5): 446.
  7. Xin Y#, Lyu P#, Jiang J, Zhou F, Wang J, Blackshaw S, Qian J*. LRLoop: a method to predict feedback loops in cell–cell communication. Bioinformatics 2022, 38(17): 4117-4126.
  8. Datta S, Cano M, Satyanarayana G, Liu T, Wang L, Wang J, Cheng J, Itoh K, Sharma A, Bhutto I, Kannan R, Qian J, Sinha D, Handa JT*. Mitophagy initiates retrograde mitochondrial-nuclear signaling to guide retinal pigment cell heterogeneity. Autophagy 2022, 19(3): 1-18.
  9. Ma D, Zhan D, Fu Y, Wei S, Lal B, Wang J, Li Y, Lopez-Bertoni H, Yalcin F, Dzaye O, Eberhart CG, Laterra J, Wilson MA, Ying M, Xia S*. Mutant IDH1 promotes phagocytic function of microglia/macrophages in gliomas by downregulating ICAM1. Cancer Letters 2021, 517: 35-45.
  10. Wang L, Kaya KD, Kim S, Brooks MJ, Wang J, Xin Y, Qian J, Swaroop A, Handa JT*. Retinal pigment epithelium transcriptome analysis in chronic smoking reveals a suppressed innate immune response and activation of differentiation pathways. Free Radical Biology and Medicine 2020, 156: 176-189.
  11. Kallman A, Capowski EE, Wang J, Kaushik AM, Jansen AD, Edwards KL, Chen L, Berlinicke CA, Phillips MJ, Pierce EA, Qian J, Wang TH, Gamm DM*, Zack DJ*. Investigating cone photoreceptor development using patient-derived NRL null retinal organoids. Communications biology 2020, 3(1): 1-13.
  12. Wei S, Wang J, Oyinlade O, Ma D, Wang S, Kratz L, Lal B, Xu Q, Liu S, Shah S, Zhang H, Li Y, Quinones-Hinojosa A, Zhu H, Chen L, Qian J, Xia S*. Heterozygous IDH1R132H/WT created by “single base editing” inhibits human astroglial cell growth by downregulating YAP. Oncogene 2018, 37(38): 5160–5174.
  13. Newman EA, Kim DW, Wan J, Wang J, Qian J, Blackshaw S*. Foxd1 is required for terminal differentiation of anterior hypothalamic neuronal subtypes. Developmental Biology 2018, 439(2): 102-111.
  14. Yuan S#, Wang J#*, Yang Y, Zhang J, Liu H, Xiao J, Xu Q, Huang X, Xiang B, Zhu S, Li L*, Liu J*, Liu L*, Zhou W*. The prediction of clinical outcome in hepatocellular carcinoma based on a six-gene metastasis signature. Clinical Cancer Research 2017, 23(1): 289-297.
  15. Han X, Wang J, Wang J, Liu S, Hu J, Zhu H, Qian J*. ScaPD: a database for human scaffold proteins. BMC Bioinformatics 2017, 18(11): 87-91.
  16. Yuan S#, Wang J#, Yang F#, Tao Q#, Zhang J, Wang L, Yang Y, Liu H, Wang Z, Xu Q, Fan J, Liu L*, Sun S* and Zhou W*. Lhx2 specifically expressed in HSCs promotes liver regeneration and inhibits liver fibrosis. Hepatology 2016, 63(2): 499-511.
  17. Wang J, Xia S, Arand B, Zhu H, Machiraju R, Huang K, Ji H, Qian J*. Single-cell co-expression analysis reveals distinct functional modules, co-regulation mechanisms and clinical outcomes. PLOS Computational Biology 2016, 12(4): e1004892.
  18. Yuan X#, Wang J#, Tang X, Li Y, Xia P*, Gao X*. Berberine ameliorates nonalcoholic fatty liver disease by a global modulation of hepatic mRNA and lncRNA expression profiles. Journal of Translational Medicine 2015, 13(1): 1-11.
  19. Zhang M, Wang J, Jiang J, Zhan X, Ling Y, Lu Z, Guo J, Gao X*. Von Hippel-Lindau disease type 2 in a Chinese family with a VHL p. W88X truncation. Endocrine 2015, 48(1): 83-88.
  20. Yuan S#, Tao Q#, Wang J#, Yang F#, Liu L, Wang L, Zhang J, Yang Y, Liu H, Wang F, Sun S*, Zhou W*. Antisense long noncoding RNA PCNA-AS1 promotes tumor growth by regulating proliferating cell nuclear antigen in hepatocellular carcinoma. Cancer Letters 2014, 349(1): 87-94.
  21. Wang J, Wang Y, Wang Z*, Liu L*, Zhu XG*, Ma X*. Synchronization of cytoplasmic and transferred mitochondrial ribosomal protein gene expression in land plants is linked to telo-box motif enrichment. BMC Evolutionary Biology 2011, 11(1): 1-15.

In Review and Preparation

  • An Integrated Single-Cell Atlas Reveals Hepatic Stellate Cell Heterogeneity and Spatiotemporal Dynamics after Liver Injury.

  • scRetinaDB: A Comprehensive Database of Single-Cell and Spatial Omics from Cross-Species Retinas.