Academic Interest
- Bioinformatics
- High-throughput genome sequencing data analysis: ChIP-seq and RNA-seq
- Transcription start site prediction on non-CpG related promoters
- The study of miRNAs and their targets
- Recombination hotspots characteristics analysis
- Microarray data analysis, especially using classification or clustering methods
- Pathway networks related analysis
- Machine Learning & Pattern Recognition
- Classification methods with feature selection and their applications
- Determining the number of clusters while clustering
- Multi-objective optimization methods
Education
-
2005.8-2011.6 PH.D. Candidate
Department of Automation, Tsinghua University
Bioinformatics Division, Tsinghua National Laboratory for Information Science & Technology
Advisor: Xuegong Zhang -
2001.8-2005.7 Undergraduate Student
Department of Control Science and Engineering, Harbin Institute of Technology
Major in Automation, B.E. awarded in July, 2005 -
1998.8-2001.7 Senior Middle School Student
Nankai Middle School, Chongqing
Experience
- Academic Experience
- 2012.01 Poster exhibitor at The Tenth Asia Pacific Bioinformatics Conference (APBC-2012), Melbourne, Australia.
- 2011.04 Participant of the Sequence Mapping and Assembly Assessment Project (SMAAP) Workshop for RGASP3 project, Barcelona, Spain.
- 2010.12 Oral speaker of the 21st International Conference on Genome Informatics (GIW-2010), Hangzhou, China
- 2010.10 Speaker of the 4th Chinese Conference on Bioinformatics & Systems Biology, (CCBSB-2010), Hangzhou, China.
- 2010.09-2011.01 Teaching Assistant of Fundamental Pattern Recognition, undergraduate student course, 2010 autumn.
- 2010.06 Poster exhibitor in the international workshop IScIDE-2010, Harbin, China.
- 2010.02 Speaker for Tsinghua-PICB bioinformatics workshop 2010, Beijing, China.
- 2009.09-2010.01 Teaching Assistant of Fundamental Pattern Recognition, undergraduate student course, 2009 autumn.
- 2009.02-2010.07 Member of Tsinghua Team for SEQC (MAQC-III) project.
- 2009.01 Volunteer for APBC2009, Beijing, China.
- 2008.10 Attendee of the Third National Bioinformatics & Systems Biology Conference, Wuhan, China
- 2008.09-2009.09 Executive Leader for one of the Tsinghua Student Research Training (SRT) project.
- 2008.09-2009.01 Teaching Assistant of Fundamental Pattern Recognition, undergraduate student course, 2008 autumn.
- 2007.10 Student of DAAD Summer School 2007, Shanghai.
- 2007.08 Attendee of the Computational Systems Bioinformatics Conference (CSB2007), San Diego, California.
- 2007.07-2007.08 Management Assistant & Teaching Assistant of Graduate Summer School on Bioinformatics of China (GSSBC'07).
- 2006.07-2011.05 Administrators of Lab Computational Server (Linux Cluster) and Web Server.
- 2005.09-2011.06 Research Assistant of Prof. Xuegong Zhang, Bioinformatics Division, TNLIST.
- 2004.09-2005.06 Research Member for Joint Project of Signal Detection Laboratory, HIT and Information Technology Academe, CASIC.
- 2004.06-2004.07 Intern Student in CASIC, Beijing.
- Other Experience
- 2009.03-2009.06 Participant in Tsinghua the 4th Excelerrate Career Coaching Program, 2009.
- 2008.10 Half-distance Marathon Runner, 2008 Beijing International Marathon, Beijing.
- 2008.10 Winner of the 4th aigo Chess Competition: Peking VS Tsinghua, the 1st World Mind Sports Games Series, 2008, Beijing.
- 2008.08-2008.09 Teaching Assistant of Integrated Training Courses for New Graduate Students, Dep. of Automation, 2008.
- 2008.06-2008.08 Social Practice at Wuxi Hanshen Electric Co., Ltd.
- 2008.06-2008.08 Branch Leader of Tsinghua Social Practice Team, 2008.
- 2007.04-2008.02 Vice President of Graduate Student Union, Department of Automation, Tsinghua University.
- 2006.10 Half-distance Marathon Runner, 2006 Beijing International Marathon, Beijing.
- 2006.09-2007.09 Monitor of Graduate Student Class, Department of Automation, Tsinghua University.
- 2006.09-2007.04 Minister of Culture & Life Ministry, Graduate Student Union, Department of Automation, Tsinghua University.
- 2005.09-2006.09 Member of Culture & Life Ministry, Graduate Student Union, Department of Automation, Tsinghua University.
Honors and Awards
- Laboratory-building Contribution Award, Bioinformatics Division, TNLIST, 2011
- Second Class of Laboratory-building Contribution Award for Students, Tsinghua University, 2011
- First Class (Toshiba) Scholarship, Tsinghua University, 2010
- Outstanding Individual in Social Practice, Tsinghua University, 2008
- Excellent Cadre of Communist Youth League (CYL), Tsinghua University, 2008
- Third Class of Laboratory-building Contribution Award for Students, Tsinghua University, 2008
- Excellent Social Work Scholarship for Graduate Students, Tsinghua University, 2007
- Excellent Cadre of Communist Youth League (CYL), Tsinghua University, 2007
- First Class Aerospace Changfeng Scholarship, 2004
- Meritorious Winner in Mathematical Contest in Modeling, COMAP, 2004 (MCM2004)
- First Class Award of China Undergraduate Mathematical Contest in Modeling (CUMCM), HeiLongJiang, 2003
- Delta Science & Technology Scholarship, 2003
- First Class Award (twice) and Third-Class Award (twice) of Disciplinary Knowledge Contest in Harbin Institute of Technology, 2002-2004
- PetroChina Scholarship, 2002
- First Class Scholarship (4 times) and Second Class Scholarship (twice), Harbin Institute of Technology, 2001-2004
- Second Class Award of National Olympic Contest on Mathematics for Middle School Students, 2000
- Second Class Award of National Olympic Contest on Physics for Middle School Students, 2000
Publications
- Xi Wang and Xuegong Zhang. (2011) Pinpointing Transcription Factor Binding Sites from ChIP-seq Data with SeqSite. BMC Systems Biology, 5(Suppl 2):S3 [Abstract][PDF][SeqSite]
- Chao Ye, Linxi Liu, Xi Wang, Xuegong Zhang. (2011) Observations on potential novel transcripts from RNA-Seq data. Front. Electr. Electron. Eng. China, 6(2): 275-282. [Abstract] [PDF]
- Likun Wang, Xiaowo Wang, Xi Wang, Yanchun Liang, Xuegong Zhang. (2011) Observations on novel splice junctions from RNA sequencing data. Biochemical and Biophysical Research Communications, 409(2): 299-303. [PubMed] [FullText] [SeqSaw]
- Zhengpeng Wu*, Xi Wang* and Xuegong Zhang. (2011) Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq. Bioinformatics, 27(4): 502-508. [PubMed] [Abstract] [FullText] [Suppl.Data] (*Equal contributors)
- Xi Wang*, Zhengpeng Wu*, Xuegong Zhang. (2010) Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq. Journal of Bioinformatics and Computational Biology: 8(Suppl.1): 177-192. (*Equal contributors) [PubMed] [Abstract] [Fulltext] [Slides]
- Xi Wang, Xuegong Zhang. (2010) A model-based approach to identifying adjacent transcription-factor binding sites from ChIP-Seq data. The 4th Chinese Conference on Bioinformatics & Systems Biology, Hangzhou, China, 7-9 October 2010. [CCBSB-4]
- Xi Wang, Zhengpeng Wu, Xuegong Zhang. (2010) Inferring isoform abundance from RNA-Seq data in consideration of the non-uniform read distribution. Sino-foreign-interchange Workshop on Intelligence Science and Intelligent Data Engineering in Harbin, China, June 3-5, 2010. [IScIDE-2010]
- WANG Xi, WANG Xiao-Wo, WANG Li-Kun, FENG Zhi-Xing, ZHANG Xue-Gong. (2010) A review on the processing and analysis of next-generation RNA-seq data. (in Chinese) Progress in Biochemistry and Biophysics: 37(8): 834~846. [Abstract][Fulltext]
- Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang and Xuegong Zhang. (2009) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics. 26(1): 136-138. [PubMed] [Fulltext][Reprint] [DEGseq@Bioconductor] [DEGseq]
- Yunfei Pei*, Xi Wang*, Xuegong Zhang. (2009) Predicting the fate of microRNA target genes based on sequence features. Journal of Theoretical Biology. 261(1): 17-22. (*Equal contributors) [PubMed] [Fulltext]
- Yunfei Pei, Xi Wang, Xuegong Zhang. (2009) The microRNAs' effects on the expression of target genes at mRNA and protein levels. The Seventh Asia Pacific Bioinformatics Conference. Beijing, China, 13-16 January 2009. (Poster) [APBC2009]
- Xi Wang*, Sanghamitra Bandyopadhyay*, Zhenyu Xuan, Xiaoyue Zhao, Michael Q.Zhang and Xuegong Zhang. (2007) Prediction of Transcription Start Sites Based on Feature Selection Using AMOSA. Computational Systems Bioinformatics Conference 2007, 6: 183-193. (*Equal contributors) [PubMed] [eProceeding] [FullText]
- Chen, Z., Wang, X., He, M. (2005) Optimized model and simulation for QPS in theme parks. Journal of Harbin Institute of Technology. 37, 1261-1263. [Abstract] [FullText]
Resources
- Xi Wang's Network Resource List in related fields. (updated: Sep 26, 2010) [Links]
- Xi Wang and Xuegong Zhang. SeqSite: pinpointing transcription factor binding sites from ChIP-seq data (2011) [SeqSite]
- Xi Wang. Methods in Processing and Analyzing the Next-Generation High-Throughput RNA-seq and ChIP-seq Data (2011) (Ph.D. Dissertation; in Chinese) [PDF]
- Likun Wang, Xiaowo Wang, Xi Wang, Yanchun Liang and Xuegong Zhang. SeqSaw: Short Spliced Sequence Mapping Tool (2011) [SeqSaw][Comments]
- Likun Wang and Xi Wang. DEGseq: Identify Differentially Expressed Genes from RNA-seq data (2009) [DEGseq@Bioconductor]
- Xi Wang. A Brief Summary of Next-Generation DNA Sequencing. (2008) [PDF]
Summary
Xi Wang received his B.E. degree in Automation from Harbin Institute of Technology. He was granted his Ph.D. degree in 2011 from MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Tsinghua National Laboratory of Information Science and Technology (TNLIST) and Department of Automation, Tsinghua University. His research interest includes machine leaning methods, data mining for bioinformatics, DNA sequence analysis and ChIP-seq/RNA-seq data analysis.
