Selected Publications

[19] 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

[18] 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

[17] 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

[16] C. Wu# & J. Huang*. Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns. BMC Genomics, 2024. HTTP  PDF

[15] 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

[14] Z. Zhang & J. Huang*. Cellular deconvolution with continuous transitions. Nature Computational Science, 2023. (News & views)  HTTP  PDF

[13] 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

[12] 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

[11] 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

[10] 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

[9] 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

[8] 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

[7] 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

[6] 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

[5] 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

[4] 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

[3] J. Huang, E. Marco, L. Pinello, G.-C. Yuan*. Predicting chromatin organization using histone marks. Genome Biology, 2015.  HTTP  PDF

[2] 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

[1] 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

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More Publications

[12] 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

[11] 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

[10] 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

[9] 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

[8] 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

[7] 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

[6] 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

[5] 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

[4] 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

[3] 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

[2] 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

[1] 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