Hongbo Liu (刘洪波)

hongbo919@gmail.com & hongbo.liu@pennmedicine.upenn.edu

My major research is focused on the design and application of bioinformatics algorithms to elucidate global epigenetic dynamics and regulatory mechanisms in normal development and diseases such as cancer and chronic kidney disease. Since starting bioinformatics research in early 2007, we have published more than 20 peer-reviewed papers in high profile journals including Nucleic Acids Research, Development, Database, Scientific Reports, Genes, Genomics and Briefings in bioinformatics.

My Citations @ Google Scholar

EDUCATION

Ph.D. in Biomedical engineering, Harbin Institute of Technology, October 2015
Major Area: Bioinformatics and Epigenomics
Thesis: Identification and characterization of novel DNA methylation markers in embryonic stem cells based on information entropy (Advisor: Prof. Qiong Wu)
M.A. in Biomedical engineering, Harbin Medical University, July 2010
Major Area: Bioinformatics and Epigenomics
Thesis: QDMR: A quantitative method for identification of differentially methylated regions (DMR) by entropy (Advisor: Prof. Yan Zhang)
B.A. in Information and Computing Science, Qufu Normal University, July 2007
 

WORK EXPERIENCE

Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
Postdoctoral Fellow, July 2018 - present

Center for Epigenetics, Van Andel Research Institute, Grand Rapids, USA
Postdoctoral Fellow, August 2016 - June 2018

College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
Associate Professor, September 2015 - July 2016
Assistant Professor, September 2010 - August 2015

Teaching Assistant, July 2007 - August 2010
 

AWARDS & FELLOWSHIPS

National scholarship for doctoral students, awarded by Ministry of Education of The People's Republic of China (2014)
Outstanding master degree graduates in Heilongjiang Province, awarded by Colleges and Universities Committee of Heilongjiang Province, Heilongjiang Province Office of Education (2010)

RESEARCH INTERESTS

Ø  Development of bioinformatics algorithms for integration and analysis of large sequencing data
Ø  Identification and characterization of epigenetic regulatory elements based on epigenome data
Ø  Exploration of abnormal epigenetic regulatory networks and their roles in human cancers
Ø  Epigenetic dynamics during development and their association with stem cell pluripotency
 

SOFTWARE, DATABASES, & RESOURCES

Ø  Software for DNA methylome analysis (SMART, QDMR, CpG_MPs, and EpiDiff)
Ø  Software for histone modification analysis (QDCMR, and QBioDiff)

Ø  Databases for epigenome research (SEA, DevMouse, DiseaseMeth, MetaImprint and HHMD)
Ø  Resources for methylation marks (human MethyMark, and mouse MethyMark)
 

SELECTED SCIENTIFIC PUBLICATIONS

2017

  1. Xiong Y, Wei Y, Gu Y, Zhang S, Lyu J, Zhang B, Chen C, Zhu J, Wang Y, Liu H * et al: DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database. Nucleic Acids Research 2017, 45(D1):Publishing.(Corresponding author)

2016

  1. Liu H *, Liu X, Zhang S, Lv J, Li S, Shang S, Jia S, Wei Y, Wang F, Su J et al: Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell-type-specific hypomethylation in regulation of cell identify genes. Nucleic Acids Research 2016, 44(1):75-94.(First and Corresponding author)
  2. Wei Y, Zhang S, Shang S, Zhang B, Wang X, Li S, Liu H *, Zhang Y *: SEA: a comprehensive Super-Enhancer Archive. Nucleic Acids Research 2016, 44(D1):D172-179.(Corresponding author)
  3. Liu H, Li S, Wang X, Zhu J, Wei Y, Wang Y, Wen Y, Wang L, Huang Y, Zhang B et al: DNA methylation dynamics: identification and functional annotation. Brief Funct Genomics 2016.(First and Corresponding author)
  4. Liu H, Lyu J, Liu H, Gao Y, Guo J, He H, Han Z, Zhang Y, Wu Q *: Computational identification of putative lincRNAs in mouse embryonic stem cell. Scientific reports 2016, 6:34892. (Co-first author)
  5. Wen Y, Wei Y, Zhang S, Li S, Liu H, Wang F, Zhao Y, Zhang D, Zhang Y *: Cell subpopulation deconvolution reveals breast cancer heterogeneity based on DNA methylation signature. Briefings in bioinformatics 2016.
  6. Wang Y, Zhang J, Xiao X, Liu H, Wang F, Li S, Wen Y, Wei Y, Su J, Zhang Y * et al: The identification of age-associated cancer markers by an integrative analysis of dynamic DNA methylation changes. Scientific reports 2016, 6:22722.
  7. Li W, Liu H, Yu M, Zhang X, Zhang Y, Liu H, Wilson JX, Huang G *: Folic Acid Alters Methylation Profile of JAK-STAT and Long-Term Depression Signaling Pathways in Alzheimer's Disease Models. Molecular neurobiology 2016, 53(9):6548-6556.

2010-2015

  1. Lv J, Liu H, Yu S, Liu H, Cui W, Gao Y, Zheng T, Qin G, Guo J, Zeng T et al: Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development. Molecular genetics and genomics : MGG 2015, 290(2):685-697. (Co-first author)
  2. Zhang C, Zhao H, Li J, Liu H, Wang F, Wei Y, Su J, Zhang D, Liu T, Zhang Y: The identification of specific methylation patterns across different cancers. PLoS One 2015, 10(3):e0120361.
  3. Liu, H., Zhu, R., Lv, J., He, H., Yang, L., Huang, Z., Su, J., Zhang, Y., Yu, S. and Wu, Q. (2014) DevMouse, the mouse developmental methylome database and analysis tools. Database : the journal of biological databases and curation, 2014, bat084.(First author)
  4. Lv, J., Huang, Z., Liu, H., Liu, H., Cui, W., Li, B., He, H., Guo, J., Liu, Q., Zhang, Y. et al. (2014) Identification and characterization of long intergenic non-coding RNAs related to mouse liver development. Molecular genetics and genomics : MGG. (Co-first author)
  5. Wei, Y., Su, J., Liu, H., Lv, J., Wang, F., Yan, H., Wen, Y., Liu, H., Wu, Q. and Zhang, Y.(2014) MetaImprint: an information repository of mammalian imprinted genes. Development, 141, 2516-2523.
  6. Cai, J., Yang, L., He, H.J., Xu, T., Liu, H.B., Wu, Q., Ma, Y., Liu, Q.H. and Nie, M.H. (2014) Antioxidant capacity responsible for a hypocholesterolemia is independent of dietary cholesterol in adult rats fed rice protein. Gene, 533, 57-66.
  7. Liu, H., Chen, Y., Lv, J., Zhu, R., Su, J., Liu, X., Zhang, Y. and Wu, Q. (2013) Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes. Scientific reports, 3, 2576.(First author)
  8. Lv, J., Liu, H., Huang, Z., Su, J., He, H., Xiu, Y., Zhang, Y. and Wu, Q. (2013) Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features. Nucleic Acids Res, 41, 10044-10061.(Co-first author)
  9. Lv, J., Cui, W., Liu, H., He, H., Xiu, Y., Guo, J., Liu, Q., Zeng, T., Chen, Y., Zhang, Y. et al. (2013) Identification and Characterization of Long Non-Coding RNAs Related to Mouse Embryonic Brain Development from Available Transcriptomic Data. PLoS ONE, 8, e71152.(Co-first author)
  10. Wang, F., Zhang, S., Wen, Y., Wei, Y., Yan, H., Liu, H., Su, J., Zhang, Y. and Che, J. (2013) Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model. Briefings in bioinformatics.
  11. Su, J., Yan, H., Wei, Y., Liu, H., Wang, F., Lv, J., Wu, Q. and Zhang, Y. (2013) CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. Nucleic Acids Res, 41, e4.
  12. Xiao, X., Li, Z., Liu, H., Su, J., Wang, F., Wu, X., Wu, Q. and Zhang, Y. (2013) Genome-wide identification of Polycomb target genes in human embryonic stem cells. Gene, 518, 425-430.
  13. Wu, X., Liu, H., Liu, H., Su, J., Lv, J., Cui, Y., Wang, F. and Zhang, Y. (2013) Z curve theory-based analysis of the dynamic nature of nucleosome positioning in Saccharomyces cerevisiae. Gene, 530, 8-18.
  14. Lv, J., Liu, H., Su, J., Wu, X., Li, B., Xiao, X., Wang, F., Wu, Q. and Zhang, Y. (2012) DiseaseMeth: a human disease methylation database. Nucleic Acids Res, 40, D1030-1035.(Co-first author)
  15. Su, J., Shao, X., Liu, H., Liu, S., Wu, Q. and Zhang, Y. (2012) Genome-wide dynamic changes of DNA methylation of repetitive elements in human embryonic stem cells and fetal fibroblasts. Genomics, 99, 10-17..
  16. Su, J., Qi, Y., Liu, S., Wu, X., Lv, J., Liu, H., Zhang, R. and Zhang, Y. (2012) Revealing epigenetic patterns in gene regulation through integrative analysis of epigenetic interaction network. Mol Biol Rep, 39, 1701-1712
  17. Zhang, Y., Liu, H., Lv, J., Xiao, X., Zhu, J., Liu, X., Su, J., Li, X., Wu, Q., Wang, F. et al. (2011) QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Res, 39, e58. (Co-first author)
  18. Liu, H., Su, J., Li, J., Liu, H., Lv, J., Li, B., Qiao, H. and Zhang, Y. (2011) Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network. BMC Syst Biol, 5, 158.
  19. Zhang, Y., Lv, J., Liu, H., Zhu, J., Su, J., Wu, Q., Qi, Y., Wang, F. and Li, X. (2010) HHMD: the human histone modification database. Nucleic Acids Res, 38, D149-154.(Co-first author)
  20. Su, J., Zhang, Y., Lv, J., Liu, H., Tang, X., Wang, F., Qi, Y., Feng, Y. and Li, X. (2010) CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes. Nucleic Acids Res, 38, e6.
  21. Lv, J., Qiao, H., Liu, H., Wu, X., Zhu, J., Su, J., Wang, F., Cui, Y. and Zhang, Y. (2010) Discovering cooperative relationships of chromatin modifications in human T cells based on a proposed closeness measure. PLoS ONE, 5, e14219.
  22. Lv, J., Su, J., Wang, F., Qi, Y., Liu, H. and Zhang, Y. (2010) Detecting novel hypermethylated genes in breast cancer benefiting from feature selection. Comput Biol Med, 40, 159-167.

FULL LIST OF PUBLICATIONS

                                   

VISITORS