Research interests

• Computational construction and modeling of biological pathway: I'm interested in (a) computational construction of biological pathways using comparative genomics techniques and functional relation prediction and (b) computational modeling of metabolic pathway for experimental design and hypothesis generation. I'm also interested in developing intuitive softwares and web servers to facilitate pathway construction and modeling. I have been focusing on bacterial pathways, and I recently start to be interested in understand the metabolism in human cancer.
• Development of intuitive bioinformatics software and web server: I'm interested in design and implementation of (a) intuitive interactive web server using the state-of-art web technologies (HTML / CSS / Javascript, jQuery / PHP, Python / MySQL, PostgreSQL, SQLite); and (b) intuitive standalone cross-platform console- or graphic- based softwares using C, C++ / Qt, Objective-C / Cocoa or C# / .NET. I have designed and implemented the six web servers / command line programs for pathway construction and enrichment analysis, and carbon-hydrate enzyme classfication knowledgebase (see SOFTWARES).

Published papers

1. Fengfeng Zhou, Xizeng Mao, Qin Ma, Mark Schell, Ying Xu. Genomic Location is Information: Towards Complete Assignment of Metabolic Pathways by Bacterial Genes. In preparation, 2012.
2. Xizeng Mao*, Victor Olman*, Qin Ma, Henry Schwartz, Bingqiang Liu, Zheng Chang, Ying Xu. Prediction and Analyses of the Landscape of Transcriptional Units in E. coli: Going Beyond Operons. In preparation, 2012.
3. Xizeng Mao^*, Xin Chen^*, Yu Zhang and Ying Xu. CINPER: an interactive knowledge-based web platform for automated construction of biological pathways for prokaryotes. BMC Bioinformatics, 2012 (under review). Web server
4. Xizeng Mao, Han Zhang, Yanbin Yin, and Ying Xu. The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces. Nucleic Acids Research, 2012 (under review).
5. Yanbin Yin*, Xizeng Mao*, Jincai Yang, Xin Chen, Ying Xu. dbCAN: An HMM-based DataBase for Carbohydrate-active enzyme ANnotation. Submitted NAR Web Server Issue, 2012. Web server.
6. Juan Cui*, Xizeng Mao*, Ying Xu. The Need for Survival Drives Cancer to Have Increasingly Faster Cell Cycles. Journal of Molecular Cell Biology, 2012 (to appear).
7. Kun Xu, Xizeng Mao, Minesh Mehta, Juan Cui, Chi Zhang, Ying Xu. A comparative study of gene-expression data of basal cell carcinoma and melanoma reveals new insights about the two cancers. PLoS ONE, 7(1): e30750, 2012.
8. Guojun Li*, Qin Ma*, Xizeng Mao, Xiaoran Zhu, Yanbin Yin, Ying Xu. Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes. Nucleic Acids Res, 2011, 1-9.
9. Xizeng Mao*, Yu Zhang*, and Ying Xu. 2011. SEAS: SEED-based Enrichment Analysis System for Prokaryotes. PLoS ONE 6(7): e22556. Download.
10. Chen Xie, Xizeng Mao, Jiaju Huang, Yang Ding, Jianmin Wu, Shan Dong, Lei Kong, Ge Gao, Chuan-Yun Li, Liping Wei. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucl. Acids Res. (2011) 39(suppl 2): W316-W322 doi:10.1093/nar/gkr483. Web server
11. Xizeng Mao, Victor Olman, Rhona Stuart, Ian Paulsen, Brian Palenik, and Ying Xu. 2010. Computational prediction of the osmoregulation network in Synechococcus sp. WH8102. BMC Genomics 11, no. 1: 291.
12. Chinese Human Liver Proteome Profiling Consortium. First Insight into the Human Liver Proteome from PROTEOME(SKY)-LIVER(Hu) 1.0, a Publicly Available Database. Journal of Proteome Research 2010 9 (1), 79-94.
13. Chuanyun Li, Xizeng Mao, Liping Wei. Genes and (Common) Pathways Underlying Drug Addiction. PLoS Computational Biology 2008. Vol. 4, No. 1, e2. (Cited by 57, Google Scholar, Jul. 30, 2011)
14. Jianmin Wu^*, Xizeng Mao.^*, Tao Cai, Jingchu Luo, Liping Wei. (2006) KOBAS server: a web-based platform for automated annotation and pathway identification. Nucleic Acids Res. 2006; 34:W720-W724. Web Server URL: http://kobas.cbi.pku.edu.cn. (Cited by 58 Google Scholar, Jul. 30, 2011)
15. Zhaotao Cai, Xizeng Mao, Songgang Li, Liping Wei. (2006) Genome comparison using Gene Ontology (GO) with statistical testing. BMC Bioinformatics. 2006 Aug 11;7:374.
16. Yonghui Shi, Shengwei Zhu, Xizeng Mao, Jianxun Feng, Yongmei Qin, Liang Zhang, Jing Cheng, Liping Wei, Zhiyong Wang, and Yuxian Zhu. Transcriptome Profiling, Molecular Biological, and Physiological Studies Reveal a Major Role for Ethylene in Cotton Fiber Cell Elongation. Plant Cell 18: 651-664
17. Xiaochun Lu, Huaqin Gong, Moli Huang, Sulan Bai, Yangbo He, Xizeng Mao, Zhi Geng, Songgang Li, Liping Wei, Jieshuai Yuwen, Zhihong Xu, Shunong Bai. Molecular analysis of early rice stamen development using organ-specific gene expression profiling. Plant Molecular Biology, 2006, 61:845-861.
18. Jianyong Wu, Junru Shen, Xizeng Mao, Kede Liu, Liping Wei, Pingwu Liu, and Guangsheng Yang. 2007. Isolation and analysis of differentially expressed genes in dominant genic male sterility (DGMS) Brassica napus L. using subtractive PCR and cDNA microarray. Plant Science 172, no. 2 (February): 204-211. doi:10.1016/j.plantsci.2006.08.010.
19. Xizeng Mao^*, Tao Cai^*, J.G. Olyarchuk. and Liping Wei. (2005) Automated Genome Annotation and Pathway Identification Using the KEGG Orthology (KO) As a Controlled Vocabulary, Bioinformatics, 21:3787-3793. (Cited by 123, Google Scholar, Jul. 30, 2011)

Book chapters

• Xizeng Mao, Fenglou Mao, Zhengchang Su, Yi Li and Ying Xu. (2012). Transcriptional Regulation Network in Cyanobacteria: a Comparative Genomic View. In Bacterial Gene Regulation and Transcriptional Networks. Editor: Madan Babu, Cambridge.

Professional activities

• Ph. D. thesis, Identification and Network Analysis of Biological Pathway, 2008, Peking University.
• Editorial services:
  • Review editor: Frontiers in Genomic Assay Technology, Frontiers in Bioinformatics and Computational Biology
• Program Committee Member:
  • IEEE International Conference on Bioinformatics and Bioengineering (BIBE): 2011
  • International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC/BIOINFORMATICS): 2011, 2012
  • ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB): 2011
  • International Conference on Intelligent Biology and Medicine (ICIBM): 2012
• Reviewers for journals:
  Bioinformatics, BMC Research Notes, Briefing in Bioinformatics, Journal of Biomedical Informatics, Journal of Biomedicine and Biotechnology, Journal of Bioinformatics and Computational Biology, Mathematical Biosciences, Nucleic Acids Research, PLoS Computational Biology, PloS One
• Reviewers for meetings:
  • ACM-BCB (ACM Conference on Bioinformatics, Computational Biology and Biomedicine): 2010, 2011
  • CSB (International Conference on Computational Systems Bioinformatics): 2009
  • IBW (International Bioinformatics Workshop): 2010
• Attended meetings: BESC retreat 2011, IBW 2006 and 2008, ICCSB 2006, Lindau Nobel Laureates Meetings 2007

Posters and talks

• Development and Application of Pathway Identification and Network Analysis Platform. Department of Biochemistry and Molecular Biology, University of Georgia, Athens, USA. Sep. 15th, 2008.
• Identification and Statistical Analysis of Biological Pathway Networks. Bole Forum of Graduate. College of Life Science, Peking University, Beijing. China. Jan 15, 2008
• Pathway Prediction and Mining Using KOBAS. College of Life Science, Chinese Normal University, beijing, China. May 20, 2007
• Pathway Prediction and Mining Using KOBAS. College of Life Science, Chinese Agriculture University, beijing, China. October, 2006
• The development and application of KOBAS in pathway analysis and prediction. College of Life Science, Peking University, Beijing, China. March, 2006
• Pathway-centered Computation. College of Life Science, Peking University, Beijing, China. September 21^st, 2005

Work experience

• 2008.9 - present, post-doctoral research associate, Computational Systems Biology Laboratory, University of Georgia, Athens, GA. Systems biology analysis and biological investigation of metabolic pathways and networks in cyanobacteria
• 2003.9 - 2008.7, Ph. D student, research assistant, Center for Bioinformatics, Peking University, Beijing, China.
  • Designed, developed and maintained KOBAS (KEGG-Orthology Based Annotation System) algorithm, KOBAS v1.0 and KOBAS Web Server
  • Analyzed experimental data from other wet labs, especially gene expression profile using KOBAS and other Bioinformatics tools
  • For more details, please refer to publication section above.
• 2007.7 - 2007.8, Intern as junior developer, Exoweb Ltd., Beijing, China. Maintained and improved City Weekend using Python / Django technologies.
  • Maintained and improved City Weekend v2.0, including bug fixes, new features clients required
  • Participated in developing web page and business logic for City Weekend v3.0
• 2007.4 - 2007.6, Intern as junior developer, Exoweb Ltd., Beijing, China. Participated the design and implementation of internal R&D project using Python / Twisted / SQLAlchemy (PostgreSQL, MySQL) / Jabber technologies
  • Designed basic framework based on Twisted, an famous asynchronous Python framework
  • Code refactoring using object pattern, to remove unless logic and make key logic more flexible
  • Integrated Jabber (a famous instant messaging framework) and Django (a famous rapid web development framework) into Twisted to enable accession from Jabber client and browser simultaneously
• 2005.4 - 2005.6, Intern as junior developer, Exoweb Ltd., Beijing, China. Participated in implementing Restaurateur web site.
  • Implemented business logic for information publishing of restaurateur vendors and contributors based on persistent object model in Zope / Plone
  • Implemented web page using HTML, CSS and Plone Template language
• 2005.2 - 2005.6, Teaching Assistant of biostatistics for > 200 undergraduates in biology and medicine, Peking University, Beijing, China.
  • Read over and comment homeworks with another teaching assistant
  • Answered questions from undergraduates
  • Participated in the problem design, monitoring and scoring of examinations
• 2003.3 - 2003.6, Activity Director of class graduation multimedia CD, Lanzhou University, Beijing, China.
  • Designed and implemented multimedia CD using Macromedia Authorware and video editing technologies, including clickable main page, resumes, electric album for sports activities and animation-style leaving messages for graduation.
  • Designed class logo using CorelDRAW, by blending double helix and 99, the date of class foundation, which were used in multimedia CD and class T-shirt

Education and Teaching

Education:

• Postdoc in Bioinformatics, CSBL, University of Georgia, USA, 2008.9 - present
• Ph.D. Bioinformatics, Center for Bioinformatics, Peking University, China, 2003.9 - 2008.7
• B.S.Biology, College of Life Sciences, Lanzhou University, China, 1999.9 - 2003.7

Teaching:

• 2005.2 - 2005.6, teaching assistant for biostatistics , Peking University, Beijing, China

Honors, awards and certificates

Honors and Awards:

• 2008, Excellent Graduate, Peking University, Beijing, China
• 2008, May 4th Medal of Peking University, Beijing, China
• 2007, 4^thChina Adolescents Science & Technology Innovation Award, China
• 2006 - 2007, Best Students Honor, Peking University, Beijing, China
• 2005 - 2006, Model of Best Students Honor, Peking University, Beijing, China
• 2005 - 2006, Donggangbo Scholarship, Peking University, Beijing, China
• 2004 - 2005, Best Students Honor, Peking University, Beijing, China
• 2004 - 2005, Yichang Lv Research Fund for Excellent Graduate, Peking Univerisity, Beijing, China
• 2004 - 2005, Fuqing Yang & Yangyuan Wang Scholarship, Peking University, Beijing, China
• 2000 - 2002, Scholarship, Lanzhou University, Lanzhou, Gansu Province, China

Certificates:

• 2002 CCNA (Cisco Certified Network Associate)
• 2001 NCRE-3 (National Computer Rank Exam, Level 3), China