朱浩｜南方医科大学｜学者主页

2026

Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

Jie Lin, Yujian Wen, Ji Tang, Xuecong Zhang, Huanlin Zhang, Hao Zhu

eLife

DOI

2026

Author response: Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

Jie Lin, Yujian Wen, Ji Tang, Xuecong Zhang, Huanlin Zhang, Hao Zhu

DOI

2026

Substantial unannotated noncoding transcripts in tumors may transcriptionally regulate cancer-related genes

Sha He, Wei Xiong, Jianping Huo, Jie Lin, Jianming Li, Hao Zhu

BMC Biology

DOI

2026

Stress triggers global histone synthesis in the liver

Shreenidhi Rajkumar, Lavanya Vumma, J. Naidoo, Min Zhu, Ishrat Durdana, Sri Vidhya Chandrasekar, Caiden J. Golder, Harsh Goar, W. Kicinski, Rico Gamuyao, Yu-Dong Wei, Hao Zhu, Suraj J. Patel, Joseph A. Ready, M. Buszczak, Joshua J. Gruber

bioRxiv

DOI

2026

Multiplexed lipid nanoparticle barcoding reveals tissue-dynamic kinetic insights and enriched cellular tropism in hepatic zones

Stephen Moore, Xi-Zhen Lian, Amogh Vaidya, Sumanta Chatterjee, Julien Santelli, Ye-Hui Sun, L. Farbiak, Hao Zhu, D. Siegwart

Nature Communications

DOI

2026

Niche-dependent epistasis within the cancer genome shapes metastatic fitness

Xi-Yu Liu, Le He, Min Zhao, Samantha M. Golomb, Wei-Mei Ma, Xin-Rui Yang, Emilija Aleksandrovic, H. Borges, Kevin M. Dean, Lei Wang, Gary C. Hon, Dai-Lin Gan, Hao Zhu, Jun Li, Lin Xu, Si-Yuan Zhang

bioRxiv

DOI

2026

Interorganelle competition for linoleic acid underlies steatotic liver pathology

Chuanhai Zhang, Dengbao Yang, Hiroyuki Suzuki, Gonçalo Dias Do Vale, Jing-Xuan Chen, Amogh Vaidya, K. Melikov, Alexandra Swisher, Jingjing Wang, Mengchen Ye, Jin Zhou, Qi-Yu Zeng, Meijuan Bai, Mei-Jung Lin, Jeon Lee, Hao Zhu, D. Siegwart, Y. Hoshida, Jeffrey G. McDonald, Xing Zeng

bioRxiv

DOI

2026

Engineered protein circuits for cancer therapy

Andrew C. Lu, Lukas Moeller, Stephen Moore, K. Ho, Victoria R. Tobin, Albert Qiang, E. Zhang, Zhijie Li, Mengmeng Wang, Shiyu Xia, Mark W. Budde, H. Larson, A. A. Diaz, Bo Gu, J. M. Linton, L. Klock, M. J. Flynn, Q. Igomu, Xiao-Jing J. Gao, D. Siegwart, Hao Zhu, M. Elowitz

bioRxiv

DOI

2026

Interpretable AI model reveals spatial codes of cell recruitment in tissues.

Jia Yao, Ji Seon Shim, Kelly Wong, James Zhu, Yun-He Liu, Sung Wook Kang, Kelli A. McCord, Bryan M. Burt, Jong-Min Choi, Claire Lee, I. C. Lubo Julio, L. M. Solis Soto, Sharia D. Hernandez, Karen Colbert Maresso, Yang Liu, Yi-Bo Dai, Tian Chu, Wei Lu, Khaja B. Khan, Paul F. Mansfield, Hee-Jin Jang, William H. Hudson, Tao Yue, Bing Zhang, Chang-Wei Li, Ling-Hua Wang, Hao Zhu, Hyun-Sung Lee, Tao Wang

Nature Biomedical Engineering

DOI

2026

The liver compensates for zonal loss of glucose 6-phosphatase to prevent glycogen storage disease

R. Liang, Ling Cai, Phong T. Nguyen, Sherwin Kelekar, Margaret B Cervantes, Trevor S. Tippetts, Eric Chen, R. Ribas, Alison M. Ryan, Janice Y. Chou, Ramon C. Sun, Hao Zhu, Ralph J. Deberardinis

bioRxiv

DOI

2026

Somatic genomics as a discovery engine for biomedicine.

Simon F. Brunner, I. Martincorena, Greg Mannino, C. Fox, Michael R. Stratton, Jacob R. Rubens, P. J. Campbell, Hao Zhu

Cell

DOI

2025

Population Size Differences Can Lead to Biases in Phylogenetic Inference and Introgression Detection in the Presence of Purifying Selection

Chong He, Meng‐Yun Chen, Hao Zhu

Systematic Biology

DOI

2025

A medium throughput approach for single cell copy number variation sequencing towards efficient application in clinics

Guanchuan Lin, Mengchang Xu, Caiming Chen, Bin Peng, Zhanying Dong, Xuewen Zhou, Jinyu Gao, Jie Yu, Bei Jia, Chen Luo, Rui Hua, Changtai Xiao, Liyao Mai, Yulong Zhang, Yuanqiao He, Yali Song, Sadie L. Marjani, Xingguang Luο, Weimin Zhang, Mei Zhong, Song Quan, Sherman M. Weissman, Xin Hong, Hao Zhu, Paul Kwong Hang Tam, Xinghua Pan

Journal of Advanced Research

DOI

2025

How Everything Is Connected to Everything Else – Population‐Specific Connections between Adaptive Evolution, Disease Susceptibility, and Drug Responsiveness

Ji Tang, Hao Zhu

Advanced Genetics

DOI

2025

Somatic loss-of-function mutations in CIDEB reduce hepatic steatosis by increasing lipolysis and fatty acid oxidation

Qi-Yu Zeng, Satish Patel, Xun Wang, Meng-Hsiung Hsieh, Zhijie Li, Xiongzhao Ren, Jingjing Wang, Dohun Kim, Shili Li, X. Gu, Greg Mannino, Gianna Maggiore, Xiangyi Fang, Lin Li, Min Zhu, Mengmeng Wang, Boyuan Li, Amaey Bellary, Koini Lim, Zhetuo Qi, Pushpa m pushpa, M. O. Mandour, V. Saudek, Tripti Sharma, Yu Zhang, Gerta Hoxhaj, Prashant Mishra, P. Gopal, Peter Campbell, Matthew Hoare, David B. Savage, Hao Zhu

Journal of Hepatology

DOI

2025

Spatial regulation of glucose and lipid metabolism by hepatic insulin signaling

Baiyu He, Kyle D. Copps, O. Stöhr, Bei-Bei Liu, Songhua Hu, Shakchhi Joshi, M. Haigis, M. F. White, Hao Zhu, Rong-Ya Tao

Cell Metabolism

DOI

2025

Hepatic zonation determines tumorigenic potential of mutant β-catenin

A. Raven, K. Gilroy, Hu Jin, Joseph A. Waldron, Holly Leslie, June Munro, Holly Hall, Rachel A. Ridgway, Catriona A. Ford, D. Gulhan, Nikola Vlahov, Megan L. Mills, A. Hartley, Eve Anderson, S. Bryson, Nathalie Sphyris, Miryam Müller, S. May, Barbara Cadden, Colin Nixon, S. Waddell, Rachel V. Guest, L. Boulter, Nick Barker, H. Clevers, Hao Zhu, Johanna Ivaska, D. Strathdee, Crispin J Miller, N. Jamieson, Martin Bushell, Peter J. Park, T. G. Bird, O. Sansom

Nature

DOI

2025

Hepatocyte-specific CLSTN3B ablation impairs lipid droplet maturation and alleviates diet-induced steatohepatitis in mice

Chuanhai Zhang, Dengbao Yang, Hiroyuki Suzuki, Jing-Xuan Chen, Jingjing Wang, Mengchen Ye, Jin Zhou, Qi-Yu Zeng, Meijuan Bai, Mei-Jung Lin, Jeon Lee, Hao Zhu, Y. Hoshida, Xing Zeng

bioRxiv

DOI

2025

The origin of hepatocellular carcinoma depends on metabolic zonation

Jason Guo, Roger Liang, Andrew Chung, Zhijie Li, Boyuan Li, E. Chen, Lin Li, Jingjing Wang, Meng-Hsiung Hsieh, Ivy Xiangyi Fang, Benjamin R. Kroger, Yun-Guan Wang, Min Zhu, Xiongzhao Ren, Greg Mannino, Yuemeng Jia, Yonglong Wei, Stephen Moore, D. Siegwart, Stephen S. Chung, Zixi Wang, Tripti Sharma, Suman Komjeti, Yi Han, P. Gopal, Guanghua Xiao, Tao Wang, Hao Zhu

Science

DOI

2025

Chemoprevention of hepatocellular carcinoma using N-acetylgalactosamine-conjugated siRNAs

Gianna Maggiore, Meng-Hsiung Hsieh, Amaey Bellary, P. Gopal, Lin Li, Jason Guo, D. Hsiehchen, Tulin Dadali, Wendy J. Broom, Martin Maier, Hao Zhu

Disease Models & Mechanisms

DOI

2025

Somatic TYK2 activating mutations in tumor-infiltrating T cells promote anti-cancer immunity

Zhijie Li, Meng-Hsiung Hsieh, A. Arutyunova, J. Evans, Tao Liu, A. Lawson, P. Nicola, Gerda Kildisiute, Heather E. Machado, Ahmad Al Kawam, Rui Wang, Qi-Yu Zeng, Ni-Si Jiang, Xun-Zhang Wang, Greg Mannino, Xiongzhao Ren, Xiangyi Fang, Tripti Sharma, Suman Komjeti, D. Hsiehchen, Scott Hayton, Simon F. Brunner, I. Martincorena, P. J. Campbell, Hao Zhu

bioRxiv

DOI

2025

An Interpretable Multi-instance Learner Decodes Cellular Recruitment from Spatially Resolved Transcriptomics

Jia Yao, Ji Seon Shim, Kelly Wong, James Zhu, Yun-He Liu, Sung Wook Kang, K. Burt, Jong-Min Choi, Claire Lee, I. Julio, Luisa Maren Solis Soto, Sharia D. Hernandez, K. Colbert, Wei Lu, Khaja B. Khan, Paul F. Mansfield, Hee-Jin Jang, Tao Yue, Chang-Wei Li, Hao Zhu, Ling-Hua Wang, Hyun-Sung Lee, Tao Wang

bioRxiv

DOI

2024

工业大麻miR156基因家族在NaHCO3胁迫下的表达模式及生物信息学分析

曹焜，孙宇峰，张晓艳，赵越，边境，朱浩，王盼，韩承伟，孙凯旋，王晓楠

《中国麻业科学》

2024

工业大麻类受体激酶基因家族生物信息学分析

曹焜，孙宇峰，赵越，朱浩，王盼，孙凯旋，王晓楠

《黑龙江科学》

2024

Evolutionary Nonindependence Between Human piRNAs and Their Potential Target Sites in Protein-Coding Genes

Chong He, Hao Zhu

Journal of Molecular Evolution

DOI

2024

Human-specific protein-coding and lncRNA genes cast sex-biased genes in the brain and their relationships with brain diseases

Sha He, Xuecong Zhang, Hao Zhu

Biology of Sex Differences

DOI

2024

Cancer mutations rewire the RNA methylation specificity of METTL3-METTL14

Chi Zhang, Robyn L Scott, Luiza Tunes, Meng-Hsiung Hsieh, Ping Wang, Ashwani Kumar, Brijesh B Khadgi, Yen-Yu Yang, Katelyn A. Doxtader Lacy, E. Herrell, Xunzhi Zhang, Bret M. Evers, Yin-Sheng Wang, Chao Xing, Hao Zhu, Yunsun Nam

Science Advances

DOI

2024

PKD1 mutant clones within cirrhotic livers inhibit steatohepatitis without promoting cancer

Min Zhu, Yunguan Wang, Tianshi Lu, Jason Guo, Lin Li, Meng-Hsiung Hsieh, P. Gopal, Yi Han, Naoto Fujiwara, Darren P. Wallace, A. S. Yu, Xiangyi Fang, Crystal Ransom, Sara Verschleisser, D. Hsiehchen, Y. Hoshida, Amit G. Singal, A. Yopp, Tao Wang, Hao Zhu

Cell Metabolism

DOI

2024

Tryptophan fuels MYC-dependent liver tumorigenesis through indole 3-pyruvate synthesis

Niranjan Venkateswaran, Roy Garcia, M. Lafita-Navarro, Yi-Heng Hao, Lizbeth Perez-Castro, Pedro A. S. Nogueira, Ashley Solmonson, I. Mender, Jessica A. Kilgore, Shun Fang, I. N. Brown, Li Li, Emily Parks, Igor Lopes dos Santos, Mahima Bhaskar, Jiwoong Kim, Yuemeng Jia, Andrew Lemoff, Nick V. Grishin, Lisa Kinch, Lin Xu, N. Williams, J. W. Shay, R. DeBerardinis, Hao Zhu, Maralice Conacci-Sorrell

Nature Communications

DOI

2024

De novo and Salvage Purine Synthesis Pathways Across Tissues and Tumors

Diem H. Tran, Dohun Kim, Rushendhiran Kesavan, Harrison Brown, Trishna Dey, Mona H Soflaee, Hieu S Vu, Alpaslan Tasdogan, Jason Guo, Divya Bezwada, Houssam Al-Saad, F. Cai, Ashley Solmonson, Halie Rion, Rawand Chabatya, Salma Merchant, N. J. Manales, V. Tcheuyap, Megan Mulkey, Thomas P. Mathews, J. Brugarolas, Sean J. Morrison, Hao Zhu, R. DeBerardinis, Gerta Hoxhaj

Cell

DOI

2024

Metabolic inflexibility promotes mitochondrial health during liver regeneration

Xun Wang, Cameron J. Menezes, Yuemeng Jia, Yi Xiao, Siva Sai Krishna Venigalla, Feng Cai, Meng-Hsiung Hsieh, Wen Gu, Li-Ming Du, J. Sudderth, Dohun Kim, Spencer D. Shelton, Claire B Llamas, Yu-Hsuan Lin, Min Zhu, Salma Merchant, Divya Bezwada, Sherwin Kelekar, L. Zacharias, Thomas P. Mathews, Gerta Hoxhaj, R. M. Wynn, U. Tambar, R. DeBerardinis, Hao Zhu, Prashant Mishra

Science

DOI

2024

A non-canonical role for a small nucleolar RNA in ribosome biogenesis and senescence

Yujing Cheng, Si-Wen Wang, He Zhang, Jong-Sun Lee, Chun-Yang Ni, Jason Guo, Eric X. Chen, Shen-Ming Wang, Asha Acharya, T. Chang, M. Buszczak, Hao Zhu, J. Mendell

Cell

DOI

2024

LIFR regulates cholesterol-driven bidirectional hepatocyte-neutrophil cross-talk to promote liver regeneration

Yalan Deng, Zilong Zhao, Marisela Sheldon, Yang Zhao, Hong-Qi Teng, Consuelo Martinez, Jie Zhang, Chun-Ru Lin, Yutong Sun, Fan Yao, Michael A. Curran, Hao Zhu, Li Ma

Nature Metabolism

DOI

2023

工业大麻转录组学研究进展

李紫薇，李洪超，王晓楠，赵越，曹焜，王盼，朱浩，肖湘

《中国麻业科学》

2023

大口黑鲈鳃响应热胁迫的转录组和DNA甲基化分析

朱浩

《苏州大学》

2023

Author Response: Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

Jie Lin, Yujian Wen, Ji Tang, Xuecong Zhang, Huanlin Zhang, Hao Zhu

DOI

2023

Reviewer #1 (Public Review): Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

Jie Lin, Yujian Wen, Ji Tang, Xuecong Zhang, Huanlin Zhang, Hao Zhu

DOI

2023

Pan-glioma analyses reveal species- and tumor-specific regulation of neuron-glioma synapse genes by lncRNAs

Wei Xiong, Xuecong Zhang, Bin Peng, Hao Zhu, Lijin Huang, Sha He

Frontiers in Genetics

DOI

2023

Reviewer #2 (Public Review): Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

Jie Lin, Yujian Wen, Ji Tang, Xuecong Zhang, Huanlin Zhang, Hao Zhu

DOI

2023

Applying causal discovery to single-cell analyses using CausalCell

Yujian Wen, Jielong Huang, Hai Zhang, Shuhui Guo, Yehezqel Elyahu, Alon Monsonego, Yanqing Ding, Hao Zhu

eLife

DOI

2023

PopTradeOff: A database for exploring population-specificity of adaptive evolution, disease susceptibility, and drug responsiveness

Ji Tang, Huanlin Zhang, Huanlin Zhang, Hai Zhang, Hai Zhang, Hao Zhu

Computational and Structural Biotechnology Journal

DOI

2023

Positive selection of somatically mutated clones identifies adaptive pathways in metabolic liver disease

Zixi Wang, Shijia Zhu, Yuemeng Jia, Yunguan Wang, Naoto Kubota, N. Fujiwara, Ruth Gordillo, Cheryl M. Lewis, Min Zhu, Tripti Sharma, Lin Li, Qi-Yu Zeng, Yu-Hsuan Lin, Meng-Hsiung Hsieh, P. Gopal, Tao Wang, Matt Hoare, P. Campbell, Y. Hoshida, Hao Zhu

bioRxiv

DOI

2023

In vivo screening identifies SPP2, a secreted factor that negatively regulates liver regeneration

Yu-Hsuan Lin, Qi-Yu Zeng, Yuemeng Jia, Zixi Wang, Lin Li, Meng-Hsiung Hsieh, Qiang Cheng, C. Pagani, Nicholas Livingston, Jeon Lee, Yu Zhang, Tripti Sharma, D. Siegwart, Dean Yimlamai, Benjamin Levi, Hao Zhu

Hepatology

DOI

2023

LIFR recruits HGF-producing neutrophils to promote liver injury repair and regeneration

Yalan Deng, Zilong Zhao, Marisela Sheldon, Yang Zhao, Hong-Qi Teng, Consuelo Martinez, Jie Zhang, Chun-Ru Lin, Yutong Sun, Fan Yao, Hao Zhu, Li Ma

bioRxiv

DOI

2023

Exploiting liver metabolism for tissue-specific cancer targeting

Zixi Wang, Hao Zhu

Nature Cancer

DOI

2023

Deep-Learning-Based Hepatic Ploidy Quantification Using H&E Histopathology Images

Zhuoyu Wen, Yu-Hsuan Lin, Shidan Wang, N. Fujiwara, Ruichen Rong, Kevin W. Jin, Dong-Han M. Yang, Bo Yao, Shengjie Yang, Tao Wang, Yang Xie, Y. Hoshida, Hao Zhu, G. Xiao

Genes

DOI

2022

Analysis of ancient and modern horse genomes reveals the critical impact of lncRNA-mediated epigenetic regulation on horse domestication

Baoyan Xu, Guixian Yang, Baowei Jiao, Hao Zhu

Frontiers in Genetics

DOI

2022

Uncovering the extensive trade-off between adaptive evolution and disease susceptibility

Ji Tang, Maosheng Huang, Sha He, Junxiang Zeng, Hao Zhu

Cell Reports

DOI

2022

Author response: Applying causal discovery to single-cell analyses using CausalCell

Yujian Wen, Jielong Huang, Shuhui Guo, Yehezqel Elyahu, Alon Monsonego, Hai Zhang, Yan-qing Ding, Hao Zhu

DOI

2022

Rab13 Sustains Breast Cancer Stem Cells by Supporting Tumor–Stroma Cross-talk

Hui Wang, Haibo Xu, Wei Chen, Mei Cheng, Li Zou, Qin Yang, Chi Bun Chan, Hao Zhu, Ceshi Chen, Jianyun Nie, Baowei Jiao

Cancer Research

DOI

2022

Fasim-LongTarget enables fast and accurate genome-wide lncRNA/DNA binding prediction

Yujian Wen, Yijin Wu, Baoyan Xu, Jie Lin, Hao Zhu

Computational and Structural Biotechnology Journal

DOI

2022

Arid1a loss potentiates pancreatic β-cell regeneration through activation of EGF signaling.

Cemre Celen, J. Chuang, Shunli Shen, Lin Li, Gianna Maggiore, Yuemeng Jia, Xin-Yi Luo, A. Moore, Yunguan Wang, Jordan E. Otto, Clayton K. Collings, Zixi Wang, Xu-Xu Sun, I. Nassour, Jiyoung Park, Alexandra L. Ghaben, Tao Wang, Sam C. Wang, P. Scherer, C. Kadoch, Hao Zhu

Cell Reports

DOI

2022

Image-based quantification of histological features as a function of spatial location using the Tissue Positioning System

Ruichen Rong, Yonglong Wei, Lin Li, Tao Wang, Hao Zhu, G. Xiao, Yunguan Wang

bioRxiv

DOI

2022

IGFBP2 expressing midlobular hepatocytes preferentially contribute to liver homeostasis and regeneration

Yu-Hsuan Lin, Yonglong Wei, Qi-Yu Zeng, Yunguan Wang, C. Pagani, Lin Li, Min Zhu, Zixi Wang, Meng-Hsiung Hsieh, Natasha Corbitt, Yu Zhang, Tripti Sharma, Tao Wang, Hao Zhu

bioRxiv

DOI

2022

In vivo CRISPR screening identifies BAZ2 chromatin remodelers as druggable regulators of mammalian liver regeneration

Yuemeng Jia, Lin Li, Yu-Hsuan Lin, P. Gopal, Shunli Shen, Ke-Jin Zhou, Xueliang Yu, Tripti Sharma, Yu Zhang, D. Siegwart, J. Ready, Hao Zhu

Cell Stem Cell

DOI

2021

siRNAs Targeting Mouse-Specific lncRNA AA388235 Induce Human Tumor Cell Pyroptosis/Apoptosis

Yanru Chen, Wan-Ying Feng, Yuan-Xiong Cheng, Hao Zhu, Hong-Juan Liu, Yi Gao, Weijie Zhou

Frontiers in Oncology

DOI

2021

Elucidate growth control mechanisms using reconstructed spatiotemporal distributions of signaling events

Hao Zhu

Computational and Structural Biotechnology Journal

DOI

2021

Liver homeostasis is maintained by midlobular zone 2 hepatocytes

Yonglong Wei, Yunguan Wang, Yuemeng Jia, Lin Li, J. Yoon, Shu-Yuan Zhang, Zixi Wang, Yu Zhang, Min Zhu, Tripti Sharma, Yu-Hsuan Lin, Meng-Hsiung Hsieh, J. Albrecht, P. Le, C. Rosen, Tao Wang, Hao Zhu

Science

DOI

2021

A Malignant Case of Arrested Development: Cancer Cell Dormancy Mimics Embryonic Diapause.

Yu-Hsuan Lin, Hao Zhu

Cancer Cell

DOI

2021

Overcoming Expressional Drop-outs in Lineage Reconstruction from Single-Cell RNA-Sequencing Data.

Tianshi Lu, Seongoh Park, James Zhu, Yunguan Wang, Xiao-Wei Zhan, Xinlei Wang, Li Wang, Hao Zhu, Tao Wang

Cell Reports

DOI

2021

A targetable LIFR−NF-κB−LCN2 axis controls liver tumorigenesis and vulnerability to ferroptosis

Fan Yao, Yalan Deng, Yang Zhao, Ying Mei, Yilei Zhang, Xiaoguang Liu, Consuelo Martinez, Xiao-Hua Su, R. Rosato, Hong-Qi Teng, Q. Hang, Shannon Yap, Da-Hu Chen, Yu-Meng Wang, M. Chen, Mutian Zhang, Han Liang, D. Xie, Xin Chen, Hao Zhu, Jenny C. Chang, M. You, Yutong Sun, Bo-Yi Gan, Li Ma

Nature Communications

DOI

2021

Genetic and Cellular Contributions to Liver Regeneration.

R. Liang, Yu-Hsuan Lin, Hao Zhu

Cold Spring Harbor Perspectives in Biology

DOI

2020

Extended transcriptome analysis reveals genome-wide lncRNA-mediated epigenetic dysregulation in colorectal cancer

Sha He, Juanzhi Chen, Huan Gao, Guixian Yang, Feixiang Zhang, Yan-qing Ding, Hao Zhu

Computational and Structural Biotechnology Journal

DOI

2020

“Mice With Increased Numbers of Polyploid Hepatocytes Maintain Regenerative Capacity But Develop Fewer Hepatocellular Carcinomas Following Chronic Liver Injury”

Yu-Hsuan Lin, Shu-Yuan Zhang, Min Zhu, Tianshi Lu, Kenian Chen, Zhuoyu Wen, Shidan Wang, G. Xiao, Danni Luo, Yuemeng Jia, Lin Li, Malcolm P. MacConmara, Y. Hoshida, A. Singal, A. Yopp, Tao Wang, Hao Zhu

Gastroenterology

DOI

2020

Immune Checkpoint Inhibition is Safe and Effective for Liver Cancer Prevention in a Mouse Model of Hepatocellular Carcinoma

A. Chung, Marcel Mettlen, Debolina Ganguly, Tianshi Lu, Tao Wang, R. Brekken, D. Hsiehchen, Hao Zhu

Cancer Prevention Research

DOI

2020

Dual ARID1A/ARID1B loss leads to rapid carcinogenesis and disruptive redistribution of BAF complexes

Zixi Wang, Kenian Chen, Yuemeng Jia, J. Chuang, Xu-Xu Sun, Yu-Hsuan Lin, Cemre Celen, Lin Li, Fang Huang, Xin Liu, D. Castrillon, Tao Wang, Hao Zhu

Nature Cancer

DOI

2020

Uncovering biological factors that regulate hepatocellular carcinoma growth using patient derived xenograft assays

Min Zhu, Lin Li, Tianshi Lu, Hyesun Yoo, Ji Zhu, P. Gopal, Sam C. Wang, Matthew R Porempka, N. Rich, S. Kagan, M. Odewole, Veronica Renteria, A. Waljee, Tao Wang, A. Singal, A. Yopp, Hao Zhu

Hepatology

DOI

2019

Pipelines for cross-species and genome-wide prediction of long noncoding RNA binding

Jie Lin, Yujian Wen, Sha He, Xiaoxue Yang, Hai Zhang, Hao Zhu

Nature Protocols

DOI

2019

The origins and functions of hepatic polyploidy

Shu-Yuan Zhang, Yu-Hsuan Lin, Branden D. Tarlow, Hao Zhu

Cell Cycle

DOI

2019

Mitotic regulators and the SHP2-MAPK pathway promote IR endocytosis and feedback regulation of insulin signaling

E. Choi, S. Kikuchi, Hai-Shan Gao, Karolina Brodzik, I. Nassour, A. Yopp, A. Singal, Hao Zhu, Hong-Tao Yu

Nature Communications

DOI

2019

Arid1a loss drives non-alcoholic steatohepatitis in mice via epigenetic dysregulation of hepatic lipogenesis and fatty acid oxidation

A. Moore, Lin-Wei Wu, J. Chuang, Xu-Xu Sun, Xin-Yi Luo, P. Gopal, Lin Li, Cemre Celen, M. Zimmer, Hao Zhu

Hepatology

DOI

2019

Somatic mutations increase hepatic clonal fitness and regeneration in chronic liver disease

Min Zhu, Tianshi Lu, Yuemeng Jia, Xin Luo, P. Gopal, Lin Li, M. Odewole, Veronica Renteria, A. Singal, Younghoon Jang, K. Ge, Sam C. Wang, M. Sorouri, Justin R. Parekh, Malcolm P. MacConmara, Adam C. Yopp, Tao Wang, Hao Zhu

Cell

DOI

2018

人类与小鼠同源lncRNA基因及其表观遗传调控靶基因分析

蒋洋洋，朱浩，张海

《南方医科大学学报》

2018

COPCOP: A Novel Algorithm and Parallel Optimization Framework for Co-Evolutionary Domain Detection

Xiaoyu Zhang, Xiangke Liao, Hao Zhu, Kenli Li, Benyun Shi, Shaoliang Peng

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2018

LncRNA MIR100HG promotes cell proliferation in triple-negative breast cancer through triplex formation with p27 loci

Shaowei Wang, Ke Hao, Honglei Zhang, Yujie Ma, Lei Ao, Li Zou, Qin Yang, Hao Zhu, Jianyun Nie, Chunlian Wu, Baowei Jiao

Cell Death and Disease

DOI

2018

The polyploid state plays a tumor suppressive role in the liver

Shu-Yuan Zhang, Ke-Jin Zhou, Xin-Yi Luo, Lin Li, Ho-Chou Tu, A. Sehgal, Liem H. Nguyen, Yu Zhang, P. Gopal, Branden D. Tarlow, D. Siegwart, Hao Zhu

Developmental Cell

DOI

2018

Cytokinesis and the Hippo Pathway: New Molecular Links Between Intimate Partners.

Shu-Yuan Zhang, Hao Zhu

Gastroenterology

DOI

2018

Abstract A52: Arid1a exerts context-dependent oncogenic and tumor suppressor functions in liver cancer

Xu-Xu Sun, Sam C. Wang, Shu-Yuan Zhang, Hao Zhu

DOI

2018

Dendrimer‐Based Lipid Nanoparticles Deliver Therapeutic FAH mRNA to Normalize Liver Function and Extend Survival in a Mouse Model of Hepatorenal Tyrosinemia Type I

Qiang Cheng, Tuo Wei, Yuemeng Jia, L. Farbiak, Ke-Jin Zhou, Shu-Yuan Zhang, Yonglong Wei, Hao Zhu, D. Siegwart

Advances in Materials

DOI

2018

倍数体状態は肝臓における腫瘍抑制の役割を果たす【Powered by NICT】

Shu-Yuan Zhang, Ke-Jin Zhou, Xin-Yi Luo, Lin Li, Ho-Chou Tu, Sehgal Alfica, H. Liem, Yu Zhang, Gopal Purva, D. T. Branden, J. S. Daniel, Hao Zhu

2018

SWI/SNF component ARID1A restrains pancreatic neoplasia formation

Sam C. Wang, I. Nassour, Shu Xiao, Shu-Yuan Zhang, Xin-Yi Luo, Jeon Lee, Lin Li, Xu-Xu Sun, Liem H. Nguyen, J. Chuang, Lan Peng, S. Daigle, Jeanne Shen, Hao Zhu

Gut

DOI

2017

A novel algorithm for detecting co-evolutionary domains in protein and nucleotide sequences

Xiaoyu Zhang, Xiangke Liao, Hao Zhu, Kenli Li, Benyun Shi, Shaoliang Peng

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2017

Arid1a has context-dependent oncogenic and tumor suppressor functions in liver cancer

Xu-Xu Sun, Sam C. Wang, Yonglong Wei, Xin-Yi Luo, Yuemeng Jia, Lin Li, P. Gopal, Min Zhu, I. Nassour, J. Chuang, Thomas Maples, Cemre Celen, Liem H. Nguyen, Lin-Wei Wu, Shunjun Fu, Weiping Li, L. Hui, Feng Tian, Yuan Ji, Shu-Yuan Zhang, M. Sorouri, T. Hwang, L. Letzig, Laura P. James, Zixi Wang, A. Yopp, A. Singal, Hao Zhu

Cancer Cell

DOI

2017

Defining Hepatocellular Carcinoma Subtypes and Treatment Responses in Patient-Derived Tumorgrafts

Hao Zhu, A. Waljee, A. Singal, A. Yopp, D. Siegwart

2017

Knockdown of Anillin Actin Binding Protein Blocks Cytokinesis in Hepatocytes and Reduces Liver Tumor Development in Mice without Affecting Regeneration

Shu-Yuan Zhang, Liem H. Nguyen, Ke-Jin Zhou, Ho-Chou Tu, A. Sehgal, I. Nassour, Lin Li, P. Gopal, Joshua Goodman, A. Singal, A. Yopp, Yu Zhang, D. Siegwart, Hao Zhu

Gastroenterology

DOI

2016

LongMan:一个哺乳类直系同源长链非编码RNA数据库

杨小雪，张海，贺莎，林杰，朱浩

《南方医科大学学报》

2016

LncRNA/DNA binding analysis reveals losses and gains and lineage specificity of genomic imprinting in mammals

Haihua Liu, Xiaoxiao Shang, Hao Zhu

Bioinformatics

DOI

2016

The spatiotemporal order of signaling events unveils the logic of development signaling

Hao Zhu, Markus R. Owen, Yanlan Mao

Bioinformatics

DOI

2016

Abstract PR07: Precise let-7 expression levels balance organ regeneration against tumor suppression

Liem H. Nguyen, Lin-Wei Wu, Hao Zhu

DOI

2016

Modular degradable dendrimers enable small RNAs to extend survival in an aggressive liver cancer model

Ke-Jin Zhou, Liem H. Nguyen, Jason B. Miller, Yunfeng Yan, P. Kos, Hu Xiong, Lin Li, Jing Hao, Jonathan T Minnig, Hao Zhu, D. Siegwart

Proceedings of the National Academy of Sciences of the United States of America

DOI

2016

Abstract PR02: The SWI/SNF component Arid1a regulates regenerative capacity and carcinogenesis in a dose-dependent fashion

Xu-Xu Sun, Sam C. Wang, Thomas Maples, Lin Li, Liem H. Nguyen, J. Chuang, M. Sorouri, Shu-Yuan Zhang, Lin-Wei Wu, Cemre Celen, Hao Zhu

DOI

2016

Suppression of the SWI/SNF component Arid1a promotes mammalian regeneration

Xu-Xu Sun, J. Chuang, M. Kanchwala, Lin-Wei Wu, Cemre Celen, Lin Li, Han-Quan Liang, Shu-Yuan Zhang, Thomas Maples, Liem H. Nguyen, Sam C. Wang, R. Signer, M. Sorouri, I. Nassour, Xin Liu, Jian Xu, Meng Wu, Yong Zhao, Yi-Chun Kuo, Zhong Wang, Chao Xing, Hao Zhu

Cell Stem Cell

DOI

2016

Non-viral CRISPR/Cas gene editing in vitro and in vivo enabled by synthetic nanoparticle co-delivery of Cas9 mRNA and sgRNA

Jason B. Miller, Shu-Yuan Zhang, P. Kos, Hu Xiong, Ke-Jin Zhou, Sofya S. Perelman, Hao Zhu, D. Siegwart

Angewandte Chemie

DOI

2016

Abstract B43: Dose and context-dependent roles for Arid1a in liver tumorigenesis

Xu-Xu Sun, Sam C. Wang, Liem H. Nguyen, Hao Zhu

DOI

2015

A simple feature construction method for predicting upstream/downstream signal flow in human protein-protein interaction networks

Suyu Mei, Hao Zhu

Scientific Reports

DOI

2015

Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways

Suyu Mei, Hao Zhu

BMC Bioinformatics

DOI

2015

Robustness of cell cycle control and flexible orders of signaling events

Hao Zhu, Yanlan Mao

Scientific Reports

DOI

2015

A novel one-class SVM based negative data sampling method for reconstructing proteome-wide HTLV-human protein interaction networks

Suyu Mei, Hao Zhu

Scientific Reports

DOI

2015

Cutting short the path to murine liver cancer models

Shu-Yuan Zhang, Sam Wang, Hao Zhu

Hepatology

DOI

2015

Lin28 and let-7 in cell metabolism and cancer.

Liem H. Nguyen, Hao Zhu

Translational Pediatrics

DOI

2015

Author response: Precise let-7 expression levels balance organ regeneration against tumor suppression

Lin-Wei Wu, Liem H. Nguyen, Ke-Jin Zhou, T. D. de Soysa, Lin Li, Jason B. Miller, Jian-Min Tian, Joseph Locker, Shu-Yuan Zhang, Gen Shinoda, Marc T. Seligson, Lauren R. Zeitels, Asha Acharya, Sam C. Wang, J. Mendell, Xiao-Shun He, Jinsuke Nishino, S. Morrison, D. Siegwart, George Q. Daley, Ng Shyh-Chang, Hao Zhu

DOI

2015

Hepatic Arterial Infusion of Low-Density Lipoprotein Docosahexaenoic Acid Nanoparticles Selectively Disrupts Redox Balance in Hepatoma cells and Reduces Growth of Orthotopic Liver Tumors in Rats

Xiaodong Wen, Lacy Reynolds, Rohit S. Mulik, S. Kim, Tim Van Treuren, Liem H. Nguyen, Hao Zhu, I. Corbin

Gastroenterology

DOI

2014

AdaBoost Based Multi-Instance Transfer Learning for Predicting Proteome-Wide Interactions between Salmonella and Human Proteins

Suyu Mei, Hao Zhu

PLoS ONE

DOI

2014

LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis

Sha He, Hai Zhang, Haihua Liu, Hao Zhu

Bioinformatics

DOI

2014

Computational reconstruction of proteome-wide protein interaction networks between HTLV retroviruses and Homo sapiens

Suyu Mei, Hao Zhu

BMC Bioinformatics

DOI

2014

TALEN mediated somatic mutagenesis in murine models of cancer

Shu-Yuan Zhang, Lin Li, S. Kendrick, R. Gerard, Hao Zhu

Cancer Research

DOI

2014

Lin28b is sufficient to drive liver cancer and necessary for its maintenance in murine models

Liem H. Nguyen, D. Robinton, Marc T. Seligson, Lin-Wei Wu, Lin Li, D. Rakheja, S. Comerford, Saleh M. Ramezani, Xian-Kai Sun, M. S. Parikh, E. H. Yang, John T. Powers, Gen Shinoda, Samar P. Shah, R. Hammer, G. Daley, Hao Zhu

Cancer Cell

DOI

2013

E2F1调控细胞周期时程补偿机制的定量研究

刘文音，朱浩

《南方医科大学学报》

2013

ANRIL/CDKN2B-AS shows two-stage clade-specific evolution and becomes conserved after transposon insertions in simians

Sha He, Weiling Gu, Yize Li, Hao Zhu

BMC Evolutionary Biology

DOI

2013

Damped propagation of cell polarization explains distinct PCP phenotypes of epithelial patterning

Hao Zhu, Markus R. Owen

Scientific Reports

DOI

2013

Hippo pathway genes developed varied exon numbers and coevolved functional domains in metazoans for species specific growth control

Henan Zhu, Ziwei Zhou, Ziwei Zhou, Daxi Wang, Wenyin Liu, Hao Zhu, Hao Zhu

BMC Evolutionary Biology

DOI

2011

跨学科培养生物医学研究生

何沭蓉，朱浩，常军武

《学位与研究生教育》，No. 7

下载原文

2011

The sequence, structure and evolutionary features of HOTAIR in mammals

Sha He, Shiping Liu, Hao Zhu

BMC Evolutionary Biology

DOI

2010

Spatiotemporally modulated Vestigial gradient by Wingless signaling adaptively regulates cell division for precise wing size control

Hao Zhu

Journal of Theoretical Biology

DOI

2006

施旺细胞发育及其调控的信号通路

朱浩，丁文龙

《解剖科学进展》

精选作品

期刊论文

Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

Author response: Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

Substantial unannotated noncoding transcripts in tumors may transcriptionally regulate cancer-related genes

Stress triggers global histone synthesis in the liver

Multiplexed lipid nanoparticle barcoding reveals tissue-dynamic kinetic insights and enriched cellular tropism in hepatic zones

Niche-dependent epistasis within the cancer genome shapes metastatic fitness

Interorganelle competition for linoleic acid underlies steatotic liver pathology

Engineered protein circuits for cancer therapy

Interpretable AI model reveals spatial codes of cell recruitment in tissues.

The liver compensates for zonal loss of glucose 6-phosphatase to prevent glycogen storage disease

Somatic genomics as a discovery engine for biomedicine.

Population Size Differences Can Lead to Biases in Phylogenetic Inference and Introgression Detection in the Presence of Purifying Selection

A medium throughput approach for single cell copy number variation sequencing towards efficient application in clinics

How Everything Is Connected to Everything Else – Population‐Specific Connections between Adaptive Evolution, Disease Susceptibility, and Drug Responsiveness

Somatic loss-of-function mutations in CIDEB reduce hepatic steatosis by increasing lipolysis and fatty acid oxidation

Spatial regulation of glucose and lipid metabolism by hepatic insulin signaling

Hepatic zonation determines tumorigenic potential of mutant β-catenin

Hepatocyte-specific CLSTN3B ablation impairs lipid droplet maturation and alleviates diet-induced steatohepatitis in mice

The origin of hepatocellular carcinoma depends on metabolic zonation

Chemoprevention of hepatocellular carcinoma using N-acetylgalactosamine-conjugated siRNAs

Somatic TYK2 activating mutations in tumor-infiltrating T cells promote anti-cancer immunity

An Interpretable Multi-instance Learner Decodes Cellular Recruitment from Spatially Resolved Transcriptomics

工业大麻miR156基因家族在NaHCO3胁迫下的表达模式及生物信息学分析

工业大麻类受体激酶基因家族生物信息学分析

Evolutionary Nonindependence Between Human piRNAs and Their Potential Target Sites in Protein-Coding Genes

Human-specific protein-coding and lncRNA genes cast sex-biased genes in the brain and their relationships with brain diseases

Cancer mutations rewire the RNA methylation specificity of METTL3-METTL14

PKD1 mutant clones within cirrhotic livers inhibit steatohepatitis without promoting cancer

Tryptophan fuels MYC-dependent liver tumorigenesis through indole 3-pyruvate synthesis

De novo and Salvage Purine Synthesis Pathways Across Tissues and Tumors

Metabolic inflexibility promotes mitochondrial health during liver regeneration

A non-canonical role for a small nucleolar RNA in ribosome biogenesis and senescence

LIFR regulates cholesterol-driven bidirectional hepatocyte-neutrophil cross-talk to promote liver regeneration

工业大麻转录组学研究进展

大口黑鲈鳃响应热胁迫的转录组和DNA甲基化分析

Author Response: Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

Reviewer #1 (Public Review): Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

Pan-glioma analyses reveal species- and tumor-specific regulation of neuron-glioma synapse genes by lncRNAs

Reviewer #2 (Public Review): Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

Applying causal discovery to single-cell analyses using CausalCell

PopTradeOff: A database for exploring population-specificity of adaptive evolution, disease susceptibility, and drug responsiveness

Positive selection of somatically mutated clones identifies adaptive pathways in metabolic liver disease

In vivo screening identifies SPP2, a secreted factor that negatively regulates liver regeneration

LIFR recruits HGF-producing neutrophils to promote liver injury repair and regeneration

Exploiting liver metabolism for tissue-specific cancer targeting

Deep-Learning-Based Hepatic Ploidy Quantification Using H&E Histopathology Images

Analysis of ancient and modern horse genomes reveals the critical impact of lncRNA-mediated epigenetic regulation on horse domestication

Uncovering the extensive trade-off between adaptive evolution and disease susceptibility

Author response: Applying causal discovery to single-cell analyses using CausalCell

Rab13 Sustains Breast Cancer Stem Cells by Supporting Tumor–Stroma Cross-talk

Fasim-LongTarget enables fast and accurate genome-wide lncRNA/DNA binding prediction

Arid1a loss potentiates pancreatic β-cell regeneration through activation of EGF signaling.

Image-based quantification of histological features as a function of spatial location using the Tissue Positioning System

IGFBP2 expressing midlobular hepatocytes preferentially contribute to liver homeostasis and regeneration

In vivo CRISPR screening identifies BAZ2 chromatin remodelers as druggable regulators of mammalian liver regeneration

siRNAs Targeting Mouse-Specific lncRNA AA388235 Induce Human Tumor Cell Pyroptosis/Apoptosis

Elucidate growth control mechanisms using reconstructed spatiotemporal distributions of signaling events

Liver homeostasis is maintained by midlobular zone 2 hepatocytes

A Malignant Case of Arrested Development: Cancer Cell Dormancy Mimics Embryonic Diapause.

Overcoming Expressional Drop-outs in Lineage Reconstruction from Single-Cell RNA-Sequencing Data.

A targetable LIFR−NF-κB−LCN2 axis controls liver tumorigenesis and vulnerability to ferroptosis

Genetic and Cellular Contributions to Liver Regeneration.

Extended transcriptome analysis reveals genome-wide lncRNA-mediated epigenetic dysregulation in colorectal cancer

“Mice With Increased Numbers of Polyploid Hepatocytes Maintain Regenerative Capacity But Develop Fewer Hepatocellular Carcinomas Following Chronic Liver Injury”

Immune Checkpoint Inhibition is Safe and Effective for Liver Cancer Prevention in a Mouse Model of Hepatocellular Carcinoma

Dual ARID1A/ARID1B loss leads to rapid carcinogenesis and disruptive redistribution of BAF complexes

Uncovering biological factors that regulate hepatocellular carcinoma growth using patient derived xenograft assays

Pipelines for cross-species and genome-wide prediction of long noncoding RNA binding

The origins and functions of hepatic polyploidy

Mitotic regulators and the SHP2-MAPK pathway promote IR endocytosis and feedback regulation of insulin signaling

Arid1a loss drives non-alcoholic steatohepatitis in mice via epigenetic dysregulation of hepatic lipogenesis and fatty acid oxidation

Somatic mutations increase hepatic clonal fitness and regeneration in chronic liver disease

人类与小鼠同源lncRNA基因及其表观遗传调控靶基因分析

COPCOP: A Novel Algorithm and Parallel Optimization Framework for Co-Evolutionary Domain Detection

LncRNA MIR100HG promotes cell proliferation in triple-negative breast cancer through triplex formation with p27 loci

The polyploid state plays a tumor suppressive role in the liver

Cytokinesis and the Hippo Pathway: New Molecular Links Between Intimate Partners.

Abstract A52: Arid1a exerts context-dependent oncogenic and tumor suppressor functions in liver cancer