Selected Publications 
S. Luo#, M Zhu#, L. Lin#, J. Xie, S. Lin, Y Chen, J. Zhu, J. Huang*. DECA: harnessing interpretable transformer model for cellular deconvolution of chromatin accessibility profile. Briefings in Bioinformatics, 2025.HTTP PDF
Z. Zhang#, R. Tang#, M Zhu#, Z. Zhu, J. Zhu, H Li, M. Tong, N. Li, J. Huang*. Deciphering cell states and the cellular ecosystem to improve risk stratification in acute myeloid leukemia. Briefings in Bioinformatics, 2025. HTTP PDF
Lin H#, Ye X, Chen W, Hong D, Liu L, Chen F, Sun N, Ye K, Hong J, Zhang Y, Lu F, Li L, Huang J*. Modular organization of enhancer network provides transcriptional robustness in mammalian development. Nucleic Acids Research, 2025. HTTP PDF
C. Wu# & J. Huang*. Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns. BMC Genomics, 2024. HTTP PDF
M. Tong#*, S Luo#, L Gu#, W Yang, Z Zhang, C Liang, H huang, Y Lin, J. Huang*. SIMarker: Cellular similarity detection and its application to diagnosis and prognosis of liver cancer. Computers in Biology and Medicine, 2024. HTTP PDF
Z. Zhang & J. Huang*. Cellular deconvolution with continuous transitions. Nature Computational Science, 2023. (News & views) HTTP PDF
D. Hong#, H. Lin#, L. Liu, M. Shu, J. Dai, F. Lu, M. Tong, J. Huang*. Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis. Briefings in Bioinformatics, 2023. HTTP PDF
M. Tong#*, Y Lin#, W Yang, J Song, Z Zhang, J Xie, J Tian, S Luo, C Liang, J Huang* and R Yu*. Prioritizing prognostic-associated subpopulations and individualized recurrence risk signatures from single-cell transcriptomes of colorectal cancer. Briefings in Bioinformatics, 2023. HTTP PDF
M. Shu#, D. Hong#, H. Lin, J. Zhang, Z. Luo, Y. Du, Z. Sun, M. Yin, Y. Yin, L. Liu, S. Bao, Z. Liu, F. Lu*, J. Huang*, J. Dai*. Single-cell chromatin accessibility identifies enhancer networks driving gene expression during spinal cord development. Developmental Cell, 2022. HTTP PDF
Z. Wang#, T. Wang#, D. Hong#, B. Dong#, Y. Wang, H. Huang, W. Zhang, B. Lian, B. Ji, H. Shi, M. Qu, X. Gao, D. Li, C. Collins, G. Wei, C. Xu*, H. J. Lee*, J. Huang*, J. Li*. Single-cell transcriptional regulation and genetic evolution of neuroendocrine prostate cancer. iScience, 2022. HTTP PDF
C. Wu, F. Chen, D. Hong, M. Zhu, M. Tong, J. Huang*. Enhancer in control of gene regulation: from new technology to new mechanism. Journal of Xiamen University (Natural Science), 2022. HTTP PDF
Y. Kai#, B. E. Li#, M. Zhu#, G. Y. Li, F. Chen, Y. Han, H. J. Cha, S. H. Orkin, W. Cai*, J. Huang*, G.-C. Yuan*. Mapping the evolving landscape of super-enhancers during cell differentiation. Genome Biology, 2021. HTTP PDF
W. Cai#, J. Huang#, Q. Zhu, B. Li, D. Seruggia, P. Zhou, M. Nguyen, Y. Fujiwara, H. Xie, Z. Yang, D. Hong, P. Ren, J. Xu, W. Pu, G.-C. Yuan* and S. H. Orkin*. Enhancer-dependence of cell-type-specific gene expression increases with developmental age. PNAS, 2020. HTTP PDF
J. Huang#, K. Li#, W. Cai, X. Liu, Y. Zhang, S. H. Orkin, J. Xu*, G.-C. Yuan*. Dissecting super-enhancer hierarchy based on chromatin interactions. Nature Communications, 2018. HTTP PDF
E. Marco#, W. Meuleman#, J. Huang#, K. Glass, L. Pinello, J. Wang, M. Kellis*, G.-C. Yuan*. Multi-scale chromatin state annotation using a hierarchical hidden Markov model. Nature Communications, 2017. HTTP PDF
J. Huang#, X. Liu#, D. Li#, Z. Shao#, H. Cao, Y. Zhang, E. Trompouki, T. V. Bowman, L. I. Zon, G.-C. Yuan, S. H. Orkin*, J. Xu*. Dynamic control of enhancer repertoires drives lineage and stage-specific transcription during hematopoiesis. Developmental Cell, 2016. HTTP PDF
J. Huang, E. Marco, L. Pinello, G.-C. Yuan*. Predicting chromatin organization using histone marks. Genome Biology, 2015. HTTP PDF
J. Huang, C. Niu, C. D.Green, L. Yang, H. Mei*, J.-D. J. Han*. Systematic prediction of pharmacodynamic drug-drug interactions through protein-protein-interaction network. PLoS Computational Biology, 2013. HTTP PDF
J. Huang, Y. Liu, W. Zhang, H. Yu and J.-D. J. Han*. eResponseNet: a package prioritizing candidate disease genes through cellular pathways. Bioinformatics, 2011. HTTP PDF
更多论文 More Publications
Y. Li#, X. He#, X. Lu, Z. Gong, Q. Li, L. Zhang, R. Yang, C. Wu, J. Huang, J. Ding, Y. He, W. Liu, C. Chen, B. Cao, D. Zhou, Y. Shi, J. Chen, C. Wang, S. Zhang, J. Zhang, J. Ye, H. You*. METTL3 acetylation impedes cancer metastasis via fine-tuning its nuclear and cytosolic functions. Nature Communications, 2022. HTTP PDF
Z. Gong#, A. Li#, J. Ding, Q. Li, L. Zhang, Y. Li, Z. Meng, F. Chen, J. Huang, D. Zhou, R. Hu, J. Ye, W. Liu, H. You*. OTUD7B Deubiquitinates LSD1 to Govern Its Binding Partner Specificity, Homeostasis, and Breast Cancer Metastasis. Advanced Science. 2021. HTTP PDF
N. Cizmecioglu, J. Huang, E. Keskin, X. Wang, I. Esen, F. Chen, S. H. Orkin. Arid4b is critical for mouse embryonic stem cell differentiation towards mesoderm and endoderm, linking epigenetics to pluripotency exit. J Biol Chem. 2020. HTTP PDF
T. Fei#, W. Li#, J. Peng#, T. Xiao, C-H. Chen, A. Wu, J. Huang, C. Zang, X. S. Liu*, M. Brown*. Deciphering essential cistromes using genome-wide CRISPR screens. PNAS, 2019. HTTP PDF
S. Beyaz#, J. Kim#, L. Pinello#, Y. Hu, M. A. Kerenyi, P. P. Das, R. A. Barnitz, M. E. Xifaras, R. Dogum, J. Huang, W. N. Haining, O. Yifoulmaz, G.-C. Yuan, S. H. Orkin*, F. Winau*. The histone demethylase UTX regulates the linge-specific epigenetic program of invariant natural killer T cells. Nature Immunology. 2017. HTTP PDF
J. H-R. Hsu, B. Hubbell-Engler, G. O. Adelmant, J. Huang, C. E. Joyce, F. Vazquez, B. A. Weir, P. Montgomery, A. O. Giacomelli, J. A. Perry, J. J. Trowbridge, Y. Fujiwara, G. S.Cowley, H. Xie, W. Kim, W. C. Hahn, J. A. Marto, S. H. Orkin*. Prmt1-mediated translation regulation is a crucial vulnerability of cancer. Cancer Research. 2017. HTTP PDF
S. Luc, J. Huang, J. McEldoon, E. Somuncular, D. Li, C. Rhodes, S. Mamoor, S. Hou, J. Xu, S. H. Orkin*. Bcl11a-deficiency causes hematopoietic stem cell defects with an aging-like phenotype. Cell Reports, 2016. HTTP PDF
H. Xie, C. Peng, J. Huang, B. Li, W. Kim, E. Smith, Y. Fujiwara, J. Qi, G. Cheloni, P. P. Das, M. Nguyen, S. Li, J. E. Bradner, S. H. Orkin*. Chronic myelogenous leukemia initiating cells require Polycomb group protein EZH2. Cancer Discovery, 2016. HTTP PDF
J. Xu#, Z. Shao#, D. Li, H. Xie, W. Kim, J. Huang, J. E. Taylor, L. Pinello, K. Glass, J. D. Jaffe, G.-C. Yuan, S. H. Orkin*. Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions. Molecular Cell, 2015. HTTP PDF
H. Luo, P. Zhang, H. Huang, J. Huang, E. Kao, L. Shi, L. He and L. Yang*. DDI-CPI, a server that predicts drug-drug interactions through implementing the chemical-protein interactome. Nucleic Acids Research, 2014. HTTP PDF
B. Zhou#, L. Yang#, S. Li, J. Huang, H. Chen, L. Hou, J. Wang, C. D. Green, Z. Yan, X. Huang, M. Kaeberlein, L. Zhu, H. Xiao, Y. Liu, and J-D. J. Han*. Midlife gene expressions identify modulators of aging through dietary interventions. PNAS, 2012. HTTP PDF
T. Mao, M. Shao, Y. Qiu, J. Huang, Y. Zhang, B. Song, Q. Wang, L. Jiang, Y. Liu, J-D J. Han, P. Cao, J Li, X. Gao, L. Rui, L. Qi, W. Li and, Y. Liu*. PKA phosphorylation couples hepatic inositol-requiring enzyme 1α to glucagon signaling in glucose metabolism. PNAS, 2011. HTTP PDF
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