黄佳良｜厦门大学｜学者主页

2026

Towards efficient perturbation for the noncoding genome

Han Zhang, Shijie Luo, Xiaofeng Wang, Liquan Lin, Ruipu Liang, Chunge Zhong, Yunhan Zhang, Wenchang Zhao, Zhisong Chen, Xiaoya Liu, Yunyan Gao, Feng Chen, Ning Sun, Jialiang Huang, Fei Teng

Nature Communications

DOI

2026

xmuhuanglab/DeepDC: DeepDC v1.0.0

Han Zhang, Shijie Luo, Xiaofeng Wang, Liquan Lin, Ruipu Liang, Chunge Zhong, Yunhan Zhang, wenchang Zhang, Zhisong Chen, Xiaoya Liu, Gao Y, F N Chen, Ning Sun, Jialiang Huang, Fei Teng

Zenodo (CERN European Organization for Nuclear Research)

DOI

2026

Single‐cell analysis reveals cytotoxic and memory CD8 + T cells associated with prolonged survival in relapsed/refractory leukaemia patients after haplo+cord haematopoietic stem cell transplantation

Hua Li, Zheyang Zhang, Ming Zhu, Xiaofan Li, Jinxian Dai, Ping Chen, Fei Chen, Xianling Chen, Yiding Yang, Xiaohong Yuan, Ronghan Tang, Zhijuan Zhu, Hongli Lin, Ting Lin, Mengsha Tong, Tao Chen, Yuehua Chen, Jialiang Huang, Nainong Li

Clinical and Translational Medicine

DOI

2026

Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5

Xindong Wang, Xusheng Deng, Lu Qiu, Junjia Liu, Hengxiang Shen, Haoran Du, Weijie Li, Linxuan Song, Wenhui Deng, Xiaoning Dong, Yi Han, Benchao Liu, Jialiang Huang, Zengpeng Li, Yongyou Zhang

Nature Communications

DOI

2025

功能性增强子:概念、筛选与验证

林虹利，陈斐，黄佳良

《中国科学:生命科学》

2025

Benchmarking Perturbation Tools for the Noncoding Genome

Han Zhang, Shi-Jie Luo, Xiao-Feng Wang, Li-Quan Lin, Rui-Pu Liang, Chun-Ge Zhong, Yun-Han Zhang, Wen-Chang Zhao, Zhi-Song Chen, Xiao-Yan Liu, Feng Chen, Ning Sun, Jialiang Huang, T. Fei

bioRxiv

DOI

2025

Modular organization of enhancer network provides transcriptional robustness in mammalian development

Hongli Lin, Xinyu Ye, Wenyan Chen, Danni Hong, Lifang Liu, Feng Chen, Ning Sun, Keying Ye, Jizhou Hong, Ya-Lin Zhang, Fa-Long Lu, Lei Li, Jialiang Huang

Nucleic Acids Research

DOI

2025

Functional enhancers: concept, screening, and validation

Hongli Lin, Fei Chen, Jialiang Huang

Scientia Sinica Vitae

DOI

2025

Divergent combinations of enhancers encode spatial gene expression

Danni Hong, Muya Shu, Jiamao Liu, Lifang Liu, Hao Cheng, Ming Zhu, Yi Du, Bo Xu, Di Hu, Zhiyong Liu, Yannan Zhao, Jianwu Dai, Falong Lu, Jialiang Huang

Nature Communications

DOI

2025

Discovery of candidate functional non-coding mutations in acute myeloid leukemia using single-cell chromatin accessibility sequencing

Ming Zhu, Jiali Zhu, Zhijuan Zhu, Yiding Yang, Jinxian Dai, Hua Li, Nainong Li, Jialiang Huang

Communications Biology

DOI

2024

SIMarker: Cellular similarity detection and its application to diagnosis and prognosis of liver cancer

Mengsha Tong, Shi-Jie Luo, Lin Gu, Xinkang Wang, Zhe-Yang Zhang, Chen-Yu Liang, Hua-Ying Huang, Yu-Xiang Lin, Jialiang Huang

Comput. Biol. Medicine

DOI

2024

PhosMap: An ensemble bioinformatic platform to empower interactive analysis of quantitative phosphoproteomics

Mengsha Tong, Zan Liu, Jiaao Li, Xin Wei, Wenhao Shi, Chen-Yu Liang, Chun-Yu Yu, Rongting Huang, Yu-Xiang Lin, Xinkang Wang, Shun Wang, Yi Wang, Jialiang Huang, Yi-Ni Wang, Tingting Li, Jun Qin, Dong-Dong Zhan, Zhi-Liang Ji

Comput. Biol. Medicine

DOI

2024

Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns

Cheng-Yi Wu, Jialiang Huang

BMC Genomics

DOI

2024

DECA: harnessing interpretable transformer model for cellular deconvolution of chromatin accessibility profile

Shijie Luo, Ming Zhu, Liquan Lin, Jiajing Xie, Shihao Lin, Ying Chen, Jiali Zhu, Jialiang Huang

Briefings in Bioinformatics

DOI

2024

Deciphering cell states and the cellular ecosystem to improve risk stratification in acute myeloid leukemia

Zheyang Zhang, Ronghan Tang, Ming Zhu, Zhijuan Zhu, Jiali Zhu, Hua Li, Mengsha Tong, Nainong Li, Jialiang Huang

Briefings in Bioinformatics

DOI

2024

Single-Cell Multi-Omics Analysis Reveals Autologous Stem Cell Chemo-Mobilization with Etoposide +Cytarabine Plus G-CSF in Multiple Myeloma

Zhijuan Zhu, Jiali Zhu, Xiaofan Li, Ming Fang Zhu, Jinxian Dai, Jialiang Huang, Nainong Li

Blood

DOI

2024

Single-Cell Multi-Omics Reveals Immune Characteristics of T Cells in Patients with Relapsed/Refractory Leukemia after Haplo+Cord HSCT

Nainong Li, Hua Li, Zheyang Zhang, Mingming Zhu, Xiaofan Li, Ping Chen, Fei Chen, Xianling Chen, Yiding Yang, Xiaohong Yuan, Ronghan Tang, Zhijuan Zhu, Hongli Lin, Ting Lin, Mengsha Tong, Tao Chen, Chen Zhong, Jialiang Huang

Blood

DOI

2024

Epigenome-augmented eQTL-hotspots reveal genome-wide transcriptional programs in 36 human tissues

Huanhuan Liu, Qinwei Chen, Jintao Guo, Ying Zhou, Zhiyu You, Jun Ren, Yuanyuan Zeng, Jing Yang, Jialiang Huang, Qiyuan Li

Briefings in Bioinformatics

DOI

2023

Cellular deconvolution with continuous transitions

Zhe-Yang Zhang, Jialiang Huang

Nature Computational Science

DOI

2023

Prioritizing prognostic-associated subpopulations and individualized recurrence risk signatures from single-cell transcriptomes of colorectal cancer

Mengsha Tong, Yuxiang Lin, Wenxian Yang, Jinsheng Song, Zheyang Zhang, Jiajing Xie, Jingyi Tian, Shijie Luo, Chenyu Liang, Jialiang Huang, Rongshan Yu

Briefings in Bioinformatics

DOI

2023

High-precision mapping of nuclear pore-chromatin interactions reveals new principles of genome organization at the nuclear envelope

S. Tyagi, Juliana S. Capitanio, Jiawei Xu, F. Chen, Rahul Sharma, Jialiang Huang, M. Hetzer

bioRxiv

DOI

2022

增强子对基因表达的调控：从新技术到新机制

武成一，陈斐，洪丹妮，朱明，童梦莎，黄佳良

《厦门大学学报(自然科学版)》

2022

Integrated analysis of single-cell transcriptome of liver cancer and cirrhosis reveals cell lineage similarity and prognostic-associated subpopulations

Mengsha Tong, Shi-Jie Luo, Lin Gu, Zhe-Yang Zhang, Chenyu Liang, Jingyi Tian, Huaqiang Huang, Yu-Xiang Lin, Jialiang Huang

bioRxiv

DOI

2022

Single-Cell Multi-Omics Analysis Reveals the Role of CX3CR1+ GNLY+ CD8+ T Cells in Improving Survival of Patients with Relapse/Refractory Hematologic Malignancies after Haplo+Cord HSCT

Hua Li, Zhe-Yang Zhang, Ming Zhu, Xiao-Fan Li, Tao Chen, Yuanzhong Chen, Jialiang Huang, Nai-Nong Li

Blood

DOI

2022

Single-cell transcriptional regulation and genetic evolution of neuroendocrine prostate cancer

Zi-Wei Wang, Tao Wang, Danni Hong, B. Dong, Yan Wang, Hua-Qiang Huang, Wenhui Zhang, Bijun Lian, Boyao Ji, Haoqing Shi, Min Qu, Xu-Jie Gao, Dao-Feng Li, C. Collins, G. Wei, Chuan-Liang Xu, H. Lee, Jialiang Huang, Jing Li

iScience

DOI

2022

Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis

Danni Hong, Hongli Lin, Lifang Liu, Muya Shu, Jianwu Dai, Falong Lu, Mengsha Tong, Jialiang Huang

Briefings in Bioinformatics

DOI

2022

Single-cell chromatin accessibility identifies enhancer networks driving gene expression during spinal cord development in mouse.

Mu-Ya Shu, Danni Hong, Hongli Lin, Ji-Xiang Zhang, Zhengnan Luo, Yi Du, Zheng Sun, Man Yin, Yanyun Yin, Lifang Liu, Shi-Lai Bao, Zhi-Yong Liu, Fa-Long Lu, Jialiang Huang, Jianwu Dai

Developmental Cell

DOI

2022

METTL3 acetylation impedes cancer metastasis via fine-tuning its nuclear and cytosolic functions

Yuanpei Li, Xiaoniu He, Lu Xiao, Zhicheng Gong, Qing Li, Lei Zhang, Ronghui Yang, Chengyi Wu, Jialiang Huang, Jian‐cheng Ding, Yaohui He, Wen Liu, Ceshi Chen, Bin Cao, Dawang Zhou, Yufeng Shi, Juxiang Chen, Chuangui Wang, Shengping Zhang, Jian Zhang, Jing Ye, Han You

Nature Communications

DOI

2021

Mapping the evolving landscape of super-enhancers during cell differentiation

Yan Kai, Bin E. Li, Ming Zhu, Grace Y. Li, Fei Chen, Yingli Han, H. Cha, S. Orkin, Wenqing Cai, Jialiang Huang, Guo-Cheng Yuan

Genome Biology

DOI

2021

Arid4b physically interacts with Tfap2c in mouse embryonic stem cells

E. Keskin, Jialiang Huang, Nihal Terzi Çizmecioğlu

Turkish journal of biology = Turk biyoloji dergisi

DOI

2021

OTUD7B Deubiquitinates LSD1 to Govern Its Binding Partner Specificity, Homeostasis, and Breast Cancer Metastasis

Zhicheng Gong, Aicun Li, Jian‐cheng Ding, Qing Li, Lei Zhang, Yuanpei Li, Zhe Meng, Fei Chen, Jialiang Huang, Dawang Zhou, Ronggui Hu, Jing Ye, Wen Liu, Han You

Advanced Science

DOI

2020

Arid4b is critical for mouse embryonic stem cell differentiation towards mesoderm and endoderm, linking epigenetics to pluripotency exit.

Nihal Terzi Cizmecioglu, Jialiang Huang, E. Keskin, Xiao-Feng Wang, Idil Esen, Fei Chen, S. Orkin

Journal of Biological Chemistry

DOI

2020

Enhancer dependence of cell-type–specific gene expression increases with developmental age

Wenqing Cai, Jialiang Huang, Qian Zhu, Bin E. Li, Davide Seruggia, Pingzhu Zhou, Minh Nguyen, Yuko Fujiwara, Huafeng Xie, Zhenggang Yang, Danni Hong, Pengfei Ren, Jian Wei Xu, William T. Pu, Guo‐Cheng Yuan, Stuart H. Orkin

Proceedings of the National Academy of Sciences

DOI

2008

基于Petri网的基因调控网络建模与分析

黄佳良，郭红，孟春

《生物化学与生物物理进展》

2008

一种基于Petri网的代谢流分析方法

黄佳良，孟春，郭红

《计算机与应用化学》

精选作品

期刊论文

Towards efficient perturbation for the noncoding genome

xmuhuanglab/DeepDC: DeepDC v1.0.0

Single‐cell analysis reveals cytotoxic and memory CD8 + T cells associated with prolonged survival in relapsed/refractory leukaemia patients after haplo+cord haematopoietic stem cell transplantation

Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5

功能性增强子:概念、筛选与验证

Benchmarking Perturbation Tools for the Noncoding Genome

Modular organization of enhancer network provides transcriptional robustness in mammalian development

Functional enhancers: concept, screening, and validation

Divergent combinations of enhancers encode spatial gene expression

Discovery of candidate functional non-coding mutations in acute myeloid leukemia using single-cell chromatin accessibility sequencing

SIMarker: Cellular similarity detection and its application to diagnosis and prognosis of liver cancer

PhosMap: An ensemble bioinformatic platform to empower interactive analysis of quantitative phosphoproteomics

Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns

DECA: harnessing interpretable transformer model for cellular deconvolution of chromatin accessibility profile

Deciphering cell states and the cellular ecosystem to improve risk stratification in acute myeloid leukemia

Single-Cell Multi-Omics Analysis Reveals Autologous Stem Cell Chemo-Mobilization with Etoposide +Cytarabine Plus G-CSF in Multiple Myeloma

Single-Cell Multi-Omics Reveals Immune Characteristics of T Cells in Patients with Relapsed/Refractory Leukemia after Haplo+Cord HSCT

Epigenome-augmented eQTL-hotspots reveal genome-wide transcriptional programs in 36 human tissues

Cellular deconvolution with continuous transitions

Prioritizing prognostic-associated subpopulations and individualized recurrence risk signatures from single-cell transcriptomes of colorectal cancer

High-precision mapping of nuclear pore-chromatin interactions reveals new principles of genome organization at the nuclear envelope

增强子对基因表达的调控：从新技术到新机制

Integrated analysis of single-cell transcriptome of liver cancer and cirrhosis reveals cell lineage similarity and prognostic-associated subpopulations

Single-Cell Multi-Omics Analysis Reveals the Role of CX3CR1+ GNLY+ CD8+ T Cells in Improving Survival of Patients with Relapse/Refractory Hematologic Malignancies after Haplo+Cord HSCT

Single-cell transcriptional regulation and genetic evolution of neuroendocrine prostate cancer

Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis

Single-cell chromatin accessibility identifies enhancer networks driving gene expression during spinal cord development in mouse.

METTL3 acetylation impedes cancer metastasis via fine-tuning its nuclear and cytosolic functions

Mapping the evolving landscape of super-enhancers during cell differentiation

Arid4b physically interacts with Tfap2c in mouse embryonic stem cells

OTUD7B Deubiquitinates LSD1 to Govern Its Binding Partner Specificity, Homeostasis, and Breast Cancer Metastasis

Arid4b is critical for mouse embryonic stem cell differentiation towards mesoderm and endoderm, linking epigenetics to pluripotency exit.

Enhancer dependence of cell-type–specific gene expression increases with developmental age

基于Petri网的基因调控网络建模与分析

一种基于Petri网的代谢流分析方法

预印本

eScreen: a deep learning framework for functionally decoding the regulatory genome at single-nucleotide resolution

Chrombus-XMBD: A Graph Generative Model Predicting 3D-Genome, ab initio from Chromatin Features

The glycolysis/HIF-1α axis defines the inflammatory role of IL-4-primed 2 macrophages

Type 2 Immune Response Plays A Critical Role in Trained Immunity