Curriculum Vitae
Ximiao He
CAS Key Laboratory of Genome Sciences and Information
Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS)
No.7, Beitucheng West Road, Chaoyang District
Beijing 100029, P. R. China
Email: Hexm@big.ac.cn; HexiToFor@gmail.com
Telephone: 86-10-82995386 (Lab); 86-13520710124(Mobile)
RESEARCH INTEREST
l DNA methylation, CpG islands and cancer
l Alternative splicing in disease and development
l Evolution of new genes and comparative genomics
l Tools and web services for analysis of genomic/epigenomic data
EDUCATION Background
Ph.D. in Genomics, supervised by Dr. Jun Yu, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing, China (09/2004 – 02/2009)
Dissertation: Construction of Genome Databases (BGI-RIS, ChickVD and SilkDB) and Global Analysis of Human CpG Islands & MethyCancer
B.S. in Medical Informatics, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China (09/1997 – 07/2002)
Professional Experiences
l Working Experiences
07/2002–11/2004: Bioinformatics Department, Beijing Genomics Institute (BGI), Beijing
Position: Programmer; Database Group Leader
01/2002–05/2002: Statistics Information Center, Ministry of Health, P. R. China, Beijing
Position: Statistical Analysis of Health Information
11/2000–02/2001: Wuhan General Hospital of Air Force, Wuhan
Position: Intern
l Academic Experiences11/2006–present: Global Analysis of Human CpG Islands and DNA Methylation. An altered pattern of epigenetic modifications, such as DNA methylation, is central to many common human diseases, including cancer. In collaboration with Dr. Zhongsheng Sun’s lab, based on the sequencing and analysis of the clones from the CpG islands library, we aim to identify the CpG islands (CGIs) on the human whole genome and study the interplay between DNA methylation and cancer. In our study, 18,816 new CGI clones sequenced, combined with 26,565 clones from Sanger and UHN, are aligned to the human genome, and clustered into 18,240 distinct genomic loci. 8,967 representative CGI clones from CGI library and 830 CGIs from target genes were amplified, of which 9,223 CGI probes were successfully amplified for 9K CGI array spotting. GO and KEGG analysis of 361 differential CGI related genes from methylation profiling of Ges-1 and MGC-803 cell lines was performed. The results showed that the genes were involved in many vital biological processes including cellular component, molecular function and biological process.
11/2006–10/2007: MethyCancer: the database of human DNA methylation and cancer. Working with Ms. Suhua Chang, Mr. Jiajie Zhang, Ms. Qian Zhao and other colleagues, we developed a publicly accessible database for human DNA Methylation and Cancer (MethyCancer) to study interplay of DNA methylation, gene expression and cancer. MethyCancer hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer information from public resources, and the CpG Island (CGI) clones derived from our large-scale sequencing. Furthermore, a powerful search tool is developed to provide user-friendly access to all the data and data connections.
10/2006–present: Adaptive origination of type III antifreeze protein in Antarctic zoarcid fish. The remarkable diversity and distribution of antifreeze proteins (AFPs) suggests that the different types evolved recently in response to sea level glaciation occurring 1-2 million years ago in the Northern hemisphere and 10-30 million years ago in Antarctica. In collaboration with Mr. Cheng Deng from Dr. Liangbiao Chen’s lab, using Lycodichthys dearborni as model organism, we investigated the evolutionary mechanisms underlying AFPs (Type III) gene origination. Based on the phylogenetic and structural analysis of AFP III and sialic acid synthase (SAS), we proposed that AFP III gene originates from SAS gene. My major work includes assembly of the sequenced BACs, design of restriction enzymes, and analysis of comparative genomics.
12/2004–10/2006: Genome-wide detection of alternative splicing. Recent analyses of sequencing and microarray data have suggested that alternative splicing (AS) plays a major role in generation of proteomic diversity and cellular complexity in higher eukaryotic organisms. To study human alternative splicing, using the sequencing (EST/cDNA) and microarray data downloaded from public databases (NCBI, HASDB, ASD), I identified the AS events on the whole chromosomes. Sequences near the splice sites (SS) and AS sites (ASS) were analyzed respectively, focusing on GC contents and sequence patterns. I was also interested in relationship of AS and disease, and I involved the study of identification of a certain kind of deafness genes and proposed that the alternative splicing may play a critical role in the development of deafness.
03/2004–01/2005: Human Leukocyte Antigen (HLA) Matching Project. The complete HLA typing and matching systems including sample collection, personal information management, sequencing based HLA typing (SBT), HLA typing software, LIMS (Laboratory Information Management System), and web-based submission and query systems. I mainly involved in personal information management, SBT-HLA typing, and web-based submission and query systems.
08/2003–12/2004: SilkDB: a knowledgebase for silkworm biology and genomics. Working with Dr. Qingyou Xia, Dr. Jing Wang, Mr. Ruiqiang Li and other colleagues, we developed the Silkworm Knowledgebase (SilkDB), a webbased repository for the curation, integration and study of silkworm genetic and genomic data. SilkDB provides an integrated representation of genome-wide sequence assembly, cDNAs, clusters of expressed sequence tags (ESTs), transposable elements (TEs), mutants, single nucleotide polymorphisms (SNPs) and functional annotations of genes. I was in charge of the project, including SilkDB requirement analysis, design of the database and web pages, and part of data analysis.
06/2003–10/2004: ChickVD: a sequence variation database for the chicken genome. Working with Dr. Yong Zhang, Dr. Jing Wang and other colleagues, using the Red Jungle Fowl genome sequence as a reference, we identified 3.1 million non-redundant DNA sequence variants. To facilitate the application of our data to avian genetics and to provide a foundation for functional and evolutionary studies, we created the ‘Chicken Variation Database’ (ChickVD). I was in charge of the project.
03/2003–07/2003: Severe Acute Respiratory Syndrome (SARS) Research Project. When SARS broke out in Beijing, I participated the SARS Research Project. I involved in the information collection from the web and media, sampling from hospital in Hohhot, and analysis of SARS genomic sequence and the E protein.
07/2002–11/2004: BGI-RIS: Rice Information System at Beijing Genomics Institute. In order to facilitate the application of the rice genomic information and to provide a foundation for functional and evolutionary studies of other important cereal crops, working with Mr. Wenming Zhao, Dr. Jing Wang, Mr. Xiaobing Huang and other colleagues, we implemented our Rice Information System (BGI-RIS), the most up-to-date integrated information resource as well as a workbench for comparative genomic analysis. My major work includes requirement analysis, data analysis, design of database and web pages, and system test.
l International or National Meetings
1. International Workshop of Epigenetic Mechanism and Technology (Dec 12-14, 2007 Beijing, China)
2. Conference on Epigenetics by National Scientific Foundation (Oct 26-28, 2007 Yantai, China)
3. Annual Meeting of the Sino-European Project on SARS Diagnostics and Antivirals (SEPSDA) (Jun 17-19, 2005 Hangzhou, China)
4. The 5th Conference of Plant Genomics in China (Aug 19-22, 2004 Wuhan, China)
5. The 2nd Chinese Conference on Bioinformatics (Jun 28-30, 2002 Beijing, China)
6. Conference of Sino-UK Urban Health and Poverty Project(UHPP) (Mar 5-6, 2002 Beijing, China)
Honors
1. Outstanding Student Scholarship (Grade 1), CAS (Dec 2008)
2. ZHU-LI-Yuehua Scholarship, CAS (Sep 2008)
3. Excellent Research Article Award (Grade 3), BIG, CAS (Sep 2007)
4. Excellent Research Article Award (Grade 3), BIG, CAS (Sep 2005)
5. Excellent Graduation Paper, TJMC, HUST (Jun 2002)
6. Excellent Student Award, TJMC, HUST (1999 – 2001)
7. First Prize Scholarship, TJMC, HUST (1998)
Publications
First Author or Joint First Author
1. He X., Chang S., Zhang J., Zhao Q. et al., MethyCancer: the database of human DNA methylation and cancer, Nucleic Acids Res., 36 (2008) D836-41 PUBMED PDF
2. Wang J., Xia Q., He X. et al., SilkDB: a knowledgebase for silkworm biology and genomics, Nucleic Acids Res., 33 (2005) D399-402 PUBMED PDF
3. Wang J., He X. et al., ChickVD: a sequence variation database for the chicken genome, Nucleic Acids Res., 33 (2005) D438-41 PUBMED PDF
4. Zhao W., Wang J., He X., Huang X. et al., BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics, Nucleic Acids Res., 32 (2004) D377-82 PUBMED PDF
Others
5. Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P. et al., The Genomes of Oryza sativa: A History of Duplications, Plos Biology 3:2 (2005) 0001-0016 PUBMED PDF
6. Wong, G. K., Liu, B., Wang J., Zhang Y., Yang X. et al., A genetic variation map for chicken with2.8 million single-nucleotide polymorphisms, Nature 432(2004) 717-722 PUBMED PDF
7. Wu Q., Zhang Y., Lu H, Wang J., He X., et al., The E Protein Is a Multifunctional Membrane Protein of SARS-CoV, Genomics, Proteomics & Bioinformatics (GPB) 2003 1(2) 131-144 PUBMED PDF
Book Chapters
8. He X., Wang J. (2007) BGI-RIS V2: Rice Information System at the Beijing Genomics Institute. – Chapter 13 in: Methods in Molecular Biology, vol. 406: Plant Bioinformatics: methods and protocols (Edwards, David ed.) Humana Press Inc., Totawa, NJ. Pp275-300 PUBMED PDF
Posters
9. He X., Yang L., Xiang H., Zhao Q., Feng T., Chang S., Zhang J., Wang J., Sun Z., Yu J. Global Analysis of Human CpG Islands & MethyCancer, in Beijing Forum of Life Sciences, Beijing 2009 PPT
sKIlls
l Professional skills
Operating systems: Unix, Linux, Windows 2000/XP
Programming language: Perl, C/C++; Familiar with HTML, XML, Java and JavaScript.
Database management system: Oracle, MySQL
Statistics software/package: R, SAS; Familiar with MATLAB and SPSS.
Bioinformatics software/package: BLAST, BLAT, CLUSTALW, SIM4, Phred/Phrap/Consed, SOAP
High-throughput data analysis: genome assembly (EST, BAC, Chromosome), genome annotation (gene prediction, promotor, UTR and CDS), identification of alternative splicing, transcriptome profile (EST, RNA-seq, tiling array), DNA methylation analysis (prediction of DNA methylation status and CpG Islands, bisulfite genomic sequencing), gene functional analysis (GO, KEGG, and DAVID)
l Languages
Chinese: Native, Excellent
English: Fluent
German: Fair in Reading Ability
PROFESSIONAL SERVICE AND VOLUNTEER WORK
l City Volunteer for the Beijing Olympic and Paralympic Games (Jul 26 – Sep 28, 2008 Beijing, China)
l Membership of Letting Education Achieve Dreams (LEAD) (Mar 2007 – Present , Beijing, China)