Selected Publications

Full list of publications on Google Scholar and PubMed

(*Contributed equally; ✉Corresponding author)

	Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease. Hongbo Liu, Tomohito Doke, Dong Guo, Xin Sheng, Ziyuan Ma, Joseph Park, Ha My T. Vy, Girish N. Nadkarni, Amin Abedini, Zhen Miao, Matthew Palmer, Benjamin F. Voight, Hongzhe Li, Christopher D. Brown, Marylyn D. Ritchie, Yan Shu, Katalin Susztak✉. Nature Genetics (2022) Highlighed by: Nature Genetics \| Kidney International \| Penn Medicine \| BioArt
	Dnmt3a and Dnmt3b-Decommissioned Fetal Enhancers are Linked to Kidney Disease. Yuting Guan, Hongbo Liu, Ziyuan Ma, Szu-Yuan Li, Jihwan Park, Xin Sheng, Katalin Susztak✉. Journal of the American Society of Nephrology** (2020)
	The MS-lincRNA landscape reveals a novel lincRNA BCLIN25 that contributes to tumorigenesis by upregulating ERBB2 expression via epigenetic modification and RNA–RNA interactions in breast cancer. Shouping Xu, Hongbo Liu*, Lin Wan, Weijia Zhang, Qin Wang, Shumei Zhang, Shipeng Shang, Yan Zhang✉, Da Pang✉. Cell Death & Disease (2019)
	DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database. Yichun Xiong, Yanjun Wei, Yue Gu, Shumei Zhang, Jie Lyu, Bin Zhang, Chuangeng Chen, Jiang Zhu, Yihan Wang, Hongbo Liu✉, Yan Zhang✉. Nucleic Acids Research* (2017)
	Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes. Hongbo Liu✉, Xiaojuan Liu, Shumei Zhang, Jie Lv, Song Li, Shipeng Shang, Shanshan Jia, Yanjun Wei, Fang Wang, Jianzhong Su, Qiong Wu, Yan Zhang✉. Nucleic Acids Research* (2016)
	SEA: a super-enhancer archive. Yanjun Wei, Shumei Zhang, Shipeng Shang, Bin Zhang, Song Li, Xinyu Wang, Fang Wang, Jianzhong Su, Qiong Wu, Hongbo Liu✉, Yan Zhang✉. Nucleic Acids Research* (2016)
	Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features. Jie Lv, Hongbo Liu*, Zhijun Huang, Jianzhong Su, Hongjuan He, Youcheng Xiu, Yan Zhang, Qiong Wu✉. Nucleic Acids Research (2013)
	DiseaseMeth: a human disease methylation database. Jie Lv, Hongbo Liu*, Jianzhong Su, Xueting Wu, Hui Liu, Boyan Li, Xue Xiao, Fang Wang, Qiong Wu✉, Yan Zhang✉ Nucleic Acids Research (2012)
	QDMR: a quantitative method for identification of differentially methylated regions by entropy. Yan Zhang✉, Hongbo Liu*, Jie Lv, Xue Xiao, Jiang Zhu, Xiaojuan Liu, Jianzhong Su, Xia Li, Qiong Wu, Fang Wang, Ying Cui Nucleic Acids Research (2011)
	HHMD: the human histone modification database. Yan Zhang✉, Jie Lv, Hongbo Liu, Jiang Zhu, Jianzhong Su, Qiong Wu, Yunfeng Qi, Fang Wang, Xia Li✉ Nucleic Acids Research* (2010)
	ACSS2 gene variants determine kidney disease risk by controlling de novo lipogenesis in kidney tubules. Dhanunjay Mukhi, Lingzhi Li, Hongbo Liu, Tomohito Doke, Lakshmi P Kolligundla, Eunji Ha, Konstantin A Klötzer, Amin Abedini, Sarmistha Mukherjee, Junnan Wu, Poonam Dhillon, Hailong Hu, Dongyin Guan, Katsuhiko Funai, Kahealani Uehara, Paul M Titchenell, Joseph A Baur, Kathryn E Wellen, Katalin Susztak✉. The Journal of Clinical Investigation (2023)
	Transcriptome-and proteome-wide association studies nominate determinants of kidney function and damage. Pascal Schlosser✉, Jingning Zhang, Hongbo Liu, Aditya L Surapaneni, Eugene P Rhee, Dan E Arking, Bing Yu, Eric Boerwinkle, Paul A Welling, Nilanjan Chatterjee, Katalin Susztak, Josef Coresh, Morgan E Grams. Genome Biology (2023)
	DNA methylation markers for kidney function and progression of diabetic kidney disease. Kelly Yichen Li, Claudia Ha Ting Tam, Hongbo Liu, Samantha Day, Cadmon King Poo Lim, Wing Yee So, Chuiguo Huang, Guozhi Jiang, Mai Shi, Heung Man Lee, TRANSCEND Consortium, Hui-yao Lan, Cheuk-Chun Szeto, Robert L Hanson, Robert G Nelson, Katalin Susztak, Juliana CN Chan, Kevin Y Yip✉, Ronald CW Ma✉. Nature Communications (2023)
	Systematic integrated analysis of genetic and epigenetic variation in diabetic kidney disease. Xin Sheng, Chengxiang Qiu, Hongbo Liu, Caroline Gluck, Jesse Y Hsu, Jiang He, Chi-yuan Hsu, Daohang Sha, Matthew R Weir, Tamara Isakova, Dominic Raj, Hernan Rincon-Choles, Harold I Feldman, Raymond Townsend, Hongzhe Li, Katalin Susztak✉. Proceedings of the National Academy of Sciences (2021)
	Renal Histologic Analysis Provides Complementary Information to Kidney Function Measurement for Patients with Early Diabetic or Hypertensive Disease. Ghazal Z Quinn, Amin Abedini, Hongbo Liu, Ziyuan Ma, Andrew Cucchiara, Andrea Havasi, Jon Hill, Matthew B Palmer, Katalin Susztak✉. Journal of the American Society of Nephrology (2021)
	Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets. Zhen Miao, Michael S Balzer, Ziyuan Ma, Hongbo Liu, Junnan Wu, Rojesh Shrestha, Tamas Aranyi, Amy Kwan, Ayano Kondo, Marco Pontoglio, Junhyong Kim, Mingyao Li, Klaus H Kaestner, Katalin Susztak✉. Nature Communications* (2021)
	Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments. Xin Sheng, Yuting Guan, Ziyuan Ma, Junnan Wu, Hongbo Liu, Chengxiang Qiu, Steven Vitale, Zhen Miao, Matthew J Seasock, Matthew Palmer, Myung K Shin, Kevin L Duffin, Steven S Pullen, Todd L Edwards, Jacklyn N Hellwege, Adriana M Hung, Mingyao Li, Benjamin F Voight, Thomas M Coffman, Christopher D Brown, Katalin Susztak✉. Nature Genetics (2021)

	Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease. Hongbo Liu, Tomohito Doke, Dong Guo, Xin Sheng, Ziyuan Ma, Joseph Park, Ha My T. Vy, Girish N. Nadkarni, Amin Abedini, Zhen Miao, Matthew Palmer, Benjamin F. Voight, Hongzhe Li, Christopher D. Brown, Marylyn D. Ritchie, Yan Shu, Katalin Susztak✉. Nature Genetics (2022) Highlighed by: Nature Genetics \| Kidney International \| Penn Medicine \| BioArt
	Dnmt3a and Dnmt3b-Decommissioned Fetal Enhancers are Linked to Kidney Disease. Yuting Guan, Hongbo Liu, Ziyuan Ma, Szu-Yuan Li, Jihwan Park, Xin Sheng, Katalin Susztak✉. Journal of the American Society of Nephrology** (2020)
	The MS-lincRNA landscape reveals a novel lincRNA BCLIN25 that contributes to tumorigenesis by upregulating ERBB2 expression via epigenetic modification and RNA–RNA interactions in breast cancer. Shouping Xu, Hongbo Liu*, Lin Wan, Weijia Zhang, Qin Wang, Shumei Zhang, Shipeng Shang, Yan Zhang✉, Da Pang✉. Cell Death & Disease (2019)
	DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database. Yichun Xiong, Yanjun Wei, Yue Gu, Shumei Zhang, Jie Lyu, Bin Zhang, Chuangeng Chen, Jiang Zhu, Yihan Wang, Hongbo Liu✉, Yan Zhang✉. Nucleic Acids Research* (2017)
	Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes. Hongbo Liu✉, Xiaojuan Liu, Shumei Zhang, Jie Lv, Song Li, Shipeng Shang, Shanshan Jia, Yanjun Wei, Fang Wang, Jianzhong Su, Qiong Wu, Yan Zhang✉. Nucleic Acids Research* (2016)
	SEA: a super-enhancer archive. Yanjun Wei, Shumei Zhang, Shipeng Shang, Bin Zhang, Song Li, Xinyu Wang, Fang Wang, Jianzhong Su, Qiong Wu, Hongbo Liu✉, Yan Zhang✉. Nucleic Acids Research* (2016)
	Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features. Jie Lv, Hongbo Liu*, Zhijun Huang, Jianzhong Su, Hongjuan He, Youcheng Xiu, Yan Zhang, Qiong Wu✉. Nucleic Acids Research (2013)
	DiseaseMeth: a human disease methylation database. Jie Lv, Hongbo Liu*, Jianzhong Su, Xueting Wu, Hui Liu, Boyan Li, Xue Xiao, Fang Wang, Qiong Wu✉, Yan Zhang✉ Nucleic Acids Research (2012)
	QDMR: a quantitative method for identification of differentially methylated regions by entropy. Yan Zhang✉, Hongbo Liu*, Jie Lv, Xue Xiao, Jiang Zhu, Xiaojuan Liu, Jianzhong Su, Xia Li, Qiong Wu, Fang Wang, Ying Cui Nucleic Acids Research (2011)
	HHMD: the human histone modification database. Yan Zhang✉, Jie Lv, Hongbo Liu, Jiang Zhu, Jianzhong Su, Qiong Wu, Yunfeng Qi, Fang Wang, Xia Li✉ Nucleic Acids Research* (2010)
	ACSS2 gene variants determine kidney disease risk by controlling de novo lipogenesis in kidney tubules. Dhanunjay Mukhi, Lingzhi Li, Hongbo Liu, Tomohito Doke, Lakshmi P Kolligundla, Eunji Ha, Konstantin A Klötzer, Amin Abedini, Sarmistha Mukherjee, Junnan Wu, Poonam Dhillon, Hailong Hu, Dongyin Guan, Katsuhiko Funai, Kahealani Uehara, Paul M Titchenell, Joseph A Baur, Kathryn E Wellen, Katalin Susztak✉. The Journal of Clinical Investigation (2023)
	Transcriptome-and proteome-wide association studies nominate determinants of kidney function and damage. Pascal Schlosser✉, Jingning Zhang, Hongbo Liu, Aditya L Surapaneni, Eugene P Rhee, Dan E Arking, Bing Yu, Eric Boerwinkle, Paul A Welling, Nilanjan Chatterjee, Katalin Susztak, Josef Coresh, Morgan E Grams. Genome Biology (2023)
	DNA methylation markers for kidney function and progression of diabetic kidney disease. Kelly Yichen Li, Claudia Ha Ting Tam, Hongbo Liu, Samantha Day, Cadmon King Poo Lim, Wing Yee So, Chuiguo Huang, Guozhi Jiang, Mai Shi, Heung Man Lee, TRANSCEND Consortium, Hui-yao Lan, Cheuk-Chun Szeto, Robert L Hanson, Robert G Nelson, Katalin Susztak, Juliana CN Chan, Kevin Y Yip✉, Ronald CW Ma✉. Nature Communications (2023)
	Systematic integrated analysis of genetic and epigenetic variation in diabetic kidney disease. Xin Sheng, Chengxiang Qiu, Hongbo Liu, Caroline Gluck, Jesse Y Hsu, Jiang He, Chi-yuan Hsu, Daohang Sha, Matthew R Weir, Tamara Isakova, Dominic Raj, Hernan Rincon-Choles, Harold I Feldman, Raymond Townsend, Hongzhe Li, Katalin Susztak✉. Proceedings of the National Academy of Sciences (2021)
	Renal Histologic Analysis Provides Complementary Information to Kidney Function Measurement for Patients with Early Diabetic or Hypertensive Disease. Ghazal Z Quinn, Amin Abedini, Hongbo Liu, Ziyuan Ma, Andrew Cucchiara, Andrea Havasi, Jon Hill, Matthew B Palmer, Katalin Susztak✉. Journal of the American Society of Nephrology (2021)
	Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets. Zhen Miao, Michael S Balzer, Ziyuan Ma, Hongbo Liu, Junnan Wu, Rojesh Shrestha, Tamas Aranyi, Amy Kwan, Ayano Kondo, Marco Pontoglio, Junhyong Kim, Mingyao Li, Klaus H Kaestner, Katalin Susztak✉. Nature Communications* (2021)
	Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments. Xin Sheng, Yuting Guan, Ziyuan Ma, Junnan Wu, Hongbo Liu, Chengxiang Qiu, Steven Vitale, Zhen Miao, Matthew J Seasock, Matthew Palmer, Myung K Shin, Kevin L Duffin, Steven S Pullen, Todd L Edwards, Jacklyn N Hellwege, Adriana M Hung, Mingyao Li, Benjamin F Voight, Thomas M Coffman, Christopher D Brown, Katalin Susztak✉. Nature Genetics (2021)