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 or Objective-C / Cocoa. 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).

Professional experience

  • Assistant research scientist / group leader , Computational Systems Biology Laboratory, University of Georgia, Athens, GA, 2013.4 - present
  • Group leader of microbial & biofuel group, Computational Systems Biology Laboratory, University of Georgia, Athens, GA, 2012.8 - present
  • Postdoctoral research associate, Computational Systems Biology Laboratory, University of Georgia, Athens, GA, 2008.9 - 2013.3
  • Graduate research assistant, Center for Bioinformatics, Peking University, Beijing, China, 2003.9 - 2008.7
  • Intern as software developer, Exoweb Ltd., Beijing, China, 2005.4 - 2005.6 and 2007.4 - 2007.8
  • Teaching Assistant of biostatistics for > 200 undergraduates in biology and medicine, Peking University, Beijing, China, 2005.2 - 2005.6
  • Activity Director of class graduation multimedia CD, Lanzhou University, Beijing, China, 2003.3 - 2003.6
* indicates co-first author

Published / prepared papers

  1. Qin Ma, Xizeng Mao, Fengfeng Zhou, Mark Schell, Ying Xu. Genomic Location is Information: Towards Complete Assignment of Metabolic Pathways by Bacterial Genes. In preparation, 2013.
  2. Xizeng Mao, Mirko Basen, Zheng Ruan, Xin Chen, Lauren Regan, Mike Adams and Ying Xu. iCbescii: a genome-scale construction of Caldicellulosiruptor bescii DSM 6725 metabolic network. In preparation, 2013.
  3. Xizeng Mao*, Victor Olman*, Chi Zhang*, Qin Ma, Tian Yuan, Zheng Chang, Henry Schwartz, Ying Xu. Elucidaion of sub-operonic transcription units in E. coli based on gene-expression data. In preparation, 2013.
  4. Xizeng Mao*, Qin Ma*, Bingqiang Liu, Zheng Chang, Chuan Zhou, Ying Xu. Revisiting Operons: An Analysis of the Landscape of Transcriptional Units in E. coli. In preparation, 2013.
  5. Chuan Zhou*, Qin Ma*, Xizeng Mao*, Yanbin Yin, Ying Xu. Insights into Biofuel Production through Comparative Genomic Analysis of Clostridium Genomes. Be submitted, 2013.
  6. Xizeng Mao*, Qin Ma*, Chuan Zhou*, Xin Chen, Hanyuan Zhang, Jincai Yang, Fenglou Mao, Wei Lai, Ying Xu. DOOR 2.0: presenting operons and their functions through dynamic and integrated views. Nucleic Acids Research, 1–6. doi:10.1093/nar/gkt1048
  7. Kun Xu, Xizeng Mao, Minesh Mehta, Juan Cui, Fei Ji, Chi Zhang, Fenglou Mao, Ying Xu. A Systems Biology Approach to Elucidation of How Cancer Cells Avoid Acidosis. PLoS ONE, 2013, 8(8): e71177. doi:10.1371/journal.pone.0071177.
  8. Xizeng Mao*, Xin Chen*, Yu Zhang and Ying Xu. CINPER: an interactive knowledge-based web platform for automated construction of biological pathways for prokaryotes. PLoS One, 2012, 7(12): e51252. doi:10.1371/journal.pone.0051252. Web server
  9. 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, doi:10.1093/nar/gks605.
  10. Yanbin Yin*, Xizeng Mao*, Jincai Yang, Xin Chen, Ying Xu. dbCAN: An HMM-based DataBase for Carbohydrate-active enzyme ANnotation. NAR Web Server Issue, 2012, July, 40 (Web Server issue), W445-51. Web server.
  11. Juan Cui*, Xizeng Mao*, Ying Xu. The Need for Survival Drives Cancer to Have Increasingly Faster Cell Cycles. Journal of Molecular Cell Biology, 2012, 4(3): 174-176.
  12. 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.
  13. 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.
  14. Xizeng Mao*, Yu Zhang*, and Ying Xu. 2011. SEAS: SEED-based Enrichment Analysis System for Prokaryotes. PLoS ONE 6(7): e22556. Download.
  15. 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
  16. 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.
  17. 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.
  18. Chuanyun Li, Xizeng Mao, Liping Wei. Genes and (Common) Pathways Underlying Drug Addiction. PLoS Computational Biology 2008. Vol. 4, No. 1, e2. (Cited by 100, Google Scholar, Jun. 20, 2013)
  19. 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 89 Google Scholar, Jun. 20, 2013)
  20. 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.
  21. 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
  22. 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.
  23. 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.
  24. 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 166, Google Scholar, Jun. 20, 2013)

Book / Books chapters

  1. Fenglou Mao, Xizeng Mao, Yanbin Yin. Three R chapters in Essential Computing Skills for Biologists. Higher Education Press of China & World Scientific Press. In preparation, 2012.
  2. 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.

Invited/contributed talks

  • Reconstruction of whole-genome metabolic network for Caldicellulosiruptor bescii DSM 6725. DOE BESC FY13 Retreat. Chattanooga, TX. 2013.7.
  • iCbescii: a genome-scale construction of . DOE BESC FY13 Enabling Characterization Workshop. Golden, Colorado. 2012.12
  • 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 21st, 2005

Conference posters

  • Mao X *, Ma Q *, Zhou C *, Chen X, Zhang H, Lai W, Xu Y. DOOR 2 - An Integrated View of Operons with Alternative TUs, Transcriptionally Regulatory Elements. DOE BESC 7th Retreat. Chattanooga, TX. 2013.
  • Mao X, Basen M, Ruan Z, Chen X, Lai W, Adam M, Xu Y. Reconstruction of whole-genome metabolic network for Caldicellulosiruptor bescii DSM 6725. DOE BESC 7th Retreat. Chattanooga, TX. 2013.
  • Mao X, Zhang H., Yin Y. and Xu Y. The Percentage of Bacterial Genes on Leading versus Lagging Strands is Influenced by Multiple Balancing Forces. DOE BESC 6th Retreat.. Chattanooga, TX. 2012.
  • Yin, Y., Mao, X., Yang, JC, Chen, X. and Xu, Y. dbCAN: a web resource and database for CAZy annotation. DOE BESC 6th Retreat.. Chattanooga, TX. 2012.

Academic activities

Education and Teaching

Education:

Teaching:

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

Honors, awards and certificates

Honors and Awards:

  • 2008, Excellent Graduate, Peking University, Beijing, China
  • 2008, May 4th Medal of Peking University, Beijing, China
  • 2007, 4thChina 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