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title: "Curriculum Vitae" slug: "en/vitae" disable_comments: true

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# Hong Zheng

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Education  |   Publications  |   Presentations  |   Research experience  |   Other work  |   Teaching Experience  |   Awards  |   Skills

Contact Information


Research Interests

Cancer genomics | Precision medicine | Multi-omics data integration | RNASeq | Methylation profiling

Professional appointments

  • 2017-present
    Postdoctoral researcher, Gevaert Lab, Center for Biomedical Informatics Research, Stanford University
## Education
  • 2012 ~ 2016, Ph.D. The University of Hong Kong
    • Department of Clinical Oncology, School of Medicine
    • Study field: cancer genomics
    • Supervisor: Prof. Maria Li Lung
    • Thesis title: Identification of Genetic Susceptibility Genes and Characterization of Somatic Mutations in Nasopharyngeal Carcinoma
  • 2006 ~ 2010, Bachelor of Engineering, Xi'an Jiaotong University
    • Study field: Biomedical Engineering
    • Final project: Profiling of small RNAs derived from two rice viruses in defense response in infected rice
    • Graduated with Distinguished Graduate Student Award

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## Publications
  • Original Articles

    • Zheng H, Brennan K, Hernaez M, Gevaert O, Benchmark of lncRNA Quantification for RNA-Seq of Cancer Samples, bioRxiv preprint,, 2018 Jan, under review in Nucleic Acid Research
    • Qiu Y, Zheng H, Gevaert O, A deep learning framework for imputing missing values in genomic data, bioRxiv preprint, doi:
    • Lin W, Yip YL, Jia L, Deng W, Zheng H, Dai W, et al, Establishment and characterization of new tumor xenografts and cancer cell lines from EBV-positive nasopharyngeal carcinoma, Nat Commun. 2018 Nov 7
    • Bakr S, Gevaert O, Echegaray S, Ayers K, Zhou M, Shafiq M, Zheng H, Benson J, Zhang W, Leung A, Kadoch M, Shrager J, Quon A, Rubin D, Plevritis S, Napel S, A Radiogenomic Dataset of Non-Small Cell Lung Cancer, Sci Data. 2018 Oct 16;5:180202
    • Dai W, Ko JMY, Choi SSA, Yu Z, Ning L, Zheng H et al. Whole-exome sequencing reveals critical genes underlying metastasis in esophageal squamous cell carcinoma. J Pathol. 2017 Aug;242(4):500-510
    • Zheng H*, Dai W*, Cheung AKL*, Ko JMY, Whole-exome sequencing identifies multiple loss-of-function mutations of NF-κB pathway regulators in nasopharyngeal carcinoma, Proc Natl Acad Sci U S A. 2016, 113(40):11283–11288 *contributed equally
    • Dai W*, Zheng H*, Cheung AKL, Tang CS, Ko JMY, Wong BWY, et al. Whole-exome sequencing identifies MST1R as a genetic susceptibility gene in nasopharyngeal carcinoma. Proc Natl Acad Sci U S A. 2016, 113(12):3317-3322. *contributed equally
    • Dai W, Cheung AKL, Ko JM, Cheng Y, Zheng H, Ngan RK, Ng WT, Lee AW, Yau CC, Lee VH et al: Comparative methylome analysis in solid tumors reveals aberrant methylation at chromosome 6p in nasopharyngeal carcinoma. Cancer Med. 2015, 4(7):1079-1090.
    • Wu J, Yang Z, Wang Y, Zheng L, Ye R, Ji Y, Zhao S, Ji S, Liu R, Xu L, Zheng H et al: Viral-inducible Argonaute18 confers broad-spectrum virus resistance in rice by sequestering a host microRNA. eLife. 2015, 4.
    • Jiang L, Qian D, Zheng H, Meng LY, Chen J, Le WJ, Zhou T, Zhou YJ, Wei CH, Li Y: RNA-dependent RNA polymerase 6 of rice (Oryza sativa) plays role in host defense against negative-strand RNA virus, Rice stripe virus. Virus Res. 2012, 163(2):512-519.
    • Du P, Wu J, Zhang J, Zhao S, Zheng H, Gao G, Wei L, Li Y: Viral infection induces expression of novel phased microRNAs from conserved cellular microRNA precursors. PLoS Pathog. 2011, 7(8):e1002176.
  • Reviews

    • Dai W, Zheng H, Cheung AKL, Lung ML. Genetic and epigenetic landscape of nasopharyngeal carcinoma. Chin Clin Oncol. 2016, 5(2):16.

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## Presentations
  • 2018 Poster presentation at AACR Annual Meeting, Chicago, April 14-18, Benchmark of lncRNA Quantification for RNA-Seq of Cancer Samples
  • 2016 Invited talk at Nasopharyngeal Carcinoma Gordon Research Conference, Hong Kong, June 26 - July 1, Identification of genetic susceptibility genes in nasopharyngeal carcinoma by next-generation sequencing
  • 2016 Poster presentation at AACR Annual Meeting, New Orleans, April 16-20, Whole-exome sequencing identifies NF-κB pathway regulators frequently mutated in nasopharyngeal carcinoma
  • 2016 Presentation at NPC AoE General Meeting, The University of Hong Kong, August 27, Whole-exome sequencing of NPC xenografts and human tumors
  • 2016 Presentation at departmental postgraduate seminar, August 20, Genetic and genomic characterization of nasopharyngeal carcinoma, received best presentation award
  • 2015 Poster presentation at AACR Annual Meeting, Philadelphia, April 18-22, Unraveling the genetic basis of nasopharyngeal carcinoma using next-generation sequencing approaches
  • 2015 Presentation at Joint NPC AoE and TBRS Thematic meeting, The University of Hong Kong, September 5, Whole-Exome sequencing analysis identifies the landscape of somatic mutations in NPC
  • 2014 Poster presentation at 19th Research Postgraduate Symposium, Li Ka Shing Faculty of Medicine, The University of Hong Kong, December 10-11, Whole-exome sequencing of nasopharyngeal carcinoma
  • 2014 Presentation at NPC AoE Genetics and Genomics Thematic Meeting, The University of Hong Kong, September 29, Whole-exome sequencing of NPC
  • 2013 Presentation at NPC AoE General Meeting, The University of Hong Kong, August 31, Whole-exome sequencing of nasopharyngeal cancer

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## Research experience
  • 2017-present, Stanford University
    Postdoctoral researcher at Gevaert Lab, Stanford Center for Biomedical Informatics Research, School of Medicine, Stanford University. My research focuses on integration of multi-omics datasets in biomedical research.

    • DNA methylation profiling in cancers. I’m working on developing a framework to model DNA methylation from bisulfite sequencing of cancer samples, aiming to identify genes or non-coding regions that are epigenetically-regulated in cancers and reveal epigenetically distinct cancer subtypes.
    • Long noncoding RNAs in cancer. I’m exploring the expression pattern of long noncoding RNAs in cancer samples and integrating with other omics data such as DNA methylation to identify regulatory lncRNAs in cancer.
    • Module network analysis of single-cell RNA sequencing datasets. I’m developing a module network analysis framework based on AMARETTO that aims to capture major biological pathways driving cell type evolution and tumor subtype classification from single-cell RNA sequencing datasets in cancer.
  • 2012-2016, The University of Hong Kong
    Ph.D. candidate in the lab of Prof. Maria Li Lung, Department of Clinical Oncology, studying the genetic and genomic basis of nasopharyngeal carcinoma (NPC). Established the pipeline for analysis of multi-omics datasets, including whole-exome sequencing (WES), targeted sequencing and RNASeq. Worked collaboratively on several projects.

    • Genetic susceptibility study of NPC. WES and targeted sequencing were used to examine blood samples of cancer cases and controls to identify genes or pathways associated with disease risk.
    • Characterization of somatic mutations of NPC tumors. Paired tumor and blood samples were sequenced to characterize the mutation landscape and signatures in NPC tumors and to identify significantly mutated genes and pathways. Apart from data analysis, I also did wet-lab mutation validation.
    • Expression profiling of NPC tumors. Paired tumor and non-tumor samples were examined with RNASeq to characterize the expression profiles, alternative splicing, and fusion events in tumors.
    • DNA methylome profiling of NPC tumors. Helped in the analysis of DNA methylome data using HumanMethylation450 BeadArray to study the methylation patterns in NPC tumors.
  • 2010-2012, Peking University
    Worked at the State Key Laboratory of Protein and Plant Gene Research, studying plant pathogens and host defense responses, particularly the role of small RNAs and host microRNAs in the defense response of Oryza sativa against two rice viruses. Conducted both bench-top experiments and data analysis.

    • Constructed small RNA libraries from rice infected by viruses for Solexa/Illumina high throughput sequencing
    • Analyzed the small RNASeq data to investigate the profile of small RNAs and host microRNAs

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## Other work
  • 2017-present Board member, Chinese Life-science Postdocs and Students CLIPSS, Stanford University
  • 2016-2017 Bioinformatic Consultant, Prenetics Limited, Hong Kong
    Developed next-generation sequencing (NGS) product and set up the analysis pipeline for sequencing data
  • 2010-present Science writer of Scientific Guokr
  • 2014 Organized One Youth Talk at HK, The University of Hong Kong, October 5
  • 2014 Invited talk, One Youth Talk at HK, City University of Hong Kong, April 13, DNA sequencing, genetic testing and risk prediction

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## Teaching Experience - 2018 Mentor, Stanford Canary CREST Program - 2018 Instructor, Principles of Cancer Systems Biology (CBIO 243), DNA methylation analysis, Stanford University - 2011 Teaching assistant, New Thinkings of Life Science, School of Life Sciences, Peking University - 2011 Teaching assistant, Molecular Virology, School of Life Sciences, Peking University

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## Awards
  • 2017 Summer Institutes Scholarship, Department of Biostatistics, University of Washington
  • 2016 Y S and Christabel Lung Postgraduate Scholarship, The University of Hong Kong
  • 2012-2016 Postgraduate Scholarship, The University of Hong Kong
  • 2011 Excellent Academic Performance Scholarship, Peking University
  • 2011 Dupont Scholarship, Peking University
  • 2007-2010 Cyrus Tang Scholarship
  • 2010 Distinguished Graduate Student Award, Xi’an Jiaotong University
  • 2007-2009 Distinguished Student Xi’an Jiaotong University
  • 2008-2010 Siyuan Scholarship, Xi’an Jiaotong University

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## Skills
  • Hands-on experiences in bioinformatics toolkits and programs. Intensive analysis and interpretation skills of multiple next-generation sequencing datasets
    • Whole-exome sequencing
    • Whole-genome sequencing
    • RNASeq, small RNAseq
    • ChIPSeq
    • Methylome data
    • Microarray data
  • Familiar with statistical methods, high-dimensional data analysis, and machine learning algorithms
  • Programming languages
    • R Professional working proficiency
    • Linux/Bash Professional working proficiency
    • Perl Professional working proficiency
    • Python Professional working proficiency
    • MATLAB Limited working proficiency
  • Experimental skills
    • DNA/RNA extraction
    • PCR and quantitative PCR
  • Languages
  • Chinese Mandrin Native
  • Cantonese Full professional proficiency
  • English Full professional proficiency
  • German Elementary proficiency

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