Chair, Associate Professor
Web site: Digital Biology Laboratory Office address:
Department of Computer Science, Bioinformatics
201 Engineering Building West, University of Missouri Office phone:
(573) 882-7064 Fax:
Protein structure prediction, high-throughput biological data analyses, computational proteomics, in silico studies of plant, microbes, and neural systems.
The research focus of Digital Biology Laboratory (DBL) is Bioinformatics and Computational Biology. We are interested in various topics including protein structure prediction, high-throughput biological data analyses, computational proteomics, and in silico studies of plant and microbes.
Protein Structure Prediction and Modeling: We are interested in developing effective computational methods for protein structure prediction and modeling. Our research in this area includes protein structure comparison, protein secondary structure prediction, protein fold recognition (threading), mini-threading, NMR protein structure determination, and structure-based function prediction.
High-throughput Biological Data Analyses: We are interested in developing novel computational techniques for analyzing large-scale biological data, including genomic sequence, gene expression, protein-protein interaction, sub-cellular localization, and phenotypic data. The analyses are used for experimental design (e.g. microarray primer design) and predictions of gene function and biological pathway.
Computational Proteomics: We are interested in developing new computational methods for protein identification through analyzing mass spectrometry data, including mass fingerprinting and MS/MS data.
Application of Bioinformatics Methods in Biological Systems: We are interested in applying various computational methods/tools and available experimental data to study the evolution, protein structure and function, gene regulation and biological pathway through collaboration with experimentalists. Our main target systems are plants (especially Arabidopsis and soybean), bacteria (especially Rhizobium and Synechococcus), viruses (especially SARS and flu virus), and yeast (Saccharomyces cerevisia).
- In Press-
Martin Hajduch, Ganesh Kumar Agrawal, Jill E. Casteel, Trupti Joshi, Zhao Song, Mingyi Zhou, Huachun Wang, Dong Xu, Jay J. Thelen. Systems Analysis of Seed Filling in Arabidopsis: Using General Linear Modeling to Assess Concordance of Transcript and Protein Expression. Plant Physiology. In Press.
- Jingfen Zhang, Qingguo Wang, Bogdan Barz, Zhiquan He, Ioan Kosztin, Yi Shang, and Dong Xu. "MUFOLD: A New Solution for Protein 3D Structure Prediction." Proteins: Structure, Function, and Bioinformatics, in press.
- Yong Wang, Ruisheng Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, Luonan Chen. Inferring Gene Regulatory Networks from Genetical Genomics data. In "Computational Methodologies in Gene Regulatory Networks". In Press.
- Dongyu Zhao, Yan Wang, Di Luo, Xiaohu Shi, Liupu Wang, Dong Xu, Jun Yu, Yanchun Liang. PMirP: A pre-microRNA prediction method based on structure-sequence hybrid features. Artificial Intelligence in Medicine. In Press
Trupti Joshi, Zhe Yan, Marc Libault, Dong-Hoon Jeong, Sunhee Park, Pamela J Green, D Janine Sherrier, Andrew Farmer, Greg May, Blake C Meyers, Dong Xu and Gary Stacey. Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics, 11(Suppl 1):S14, 2010.
- Zheng Wang, Marc Libault, Trupti Joshi, Babu Valliyodan, Henry Nguyen, Dong Xu, Gary Stacey, and Jianlin Cheng. SoyDB: A Knowledge Database of Soybean Transcription Factors, BMC: Plant Biology 2010, 10:14.
- Jeremy Schmutz, Steven B. Cannon, Jessica Schlueter, Jianxin Ma, Therese Mitros, William Nelson, David L. Hyten, Qijian Song, Jay J. Thelen, Jianlin Cheng, Dong Xu, Uffe Hellsten, Gregory D. May, Yeisoo Yu, Tetsuya Sakurai, Taishi Umezawa, Madan K. Bhattacharyya, Devinder Sandhu, Babu Valliyodan, Erika Lindquist, Myron Peto, David Grant, Shengqiang Shu, David Goodstein, Kerrie Barry, Montona Futrell-Griggs, Brian Abernathy, Jianchang Du, Zhixi Tian, Liucun Zhu, Navdeep Gill, Trupti Joshi, Marc Libault, Anand Sethuraman, Xue-Cheng Zhang, Kazuo Shinozaki, Henry T. Nguyen, Rod A. Wing, Perry Cregan, James Specht, Jane Grimwood, Dan Rokhsar, Gary Stacey, Randy C. Shoemaker and Scott A. Jackson. Genome Sequence of the Palaeopolyploid Soybean . Nature. 463:178-83, 2010.
Guan Ning Lin, Zheng Wang, Dong Xu, and Jianlin Cheng. Sequence-based prediction of protein folding rates using contacts, secondary structures and support vector machines. Proceeding of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2009), Washington DC, USA, pp. 3-8, 2009.
- Marc Libault , Trupti Joshi , Vagner A. Benedito , Dong Xu , Michael K. Udvardi , and Gary Stacey. Legume transcription factor genes; what makes legumes so special?. Plant Physiology 151:991-1001, 2009.
- Marc Libault, Trupti Joshi, Kaori Takahashi, Andrea Hurley-Sommer, Kari Puricelli, Sean Blake, Richard E. Finger, Christopher G. Taylor, Dong Xu, Henry Nguyen, Gary Stacey. Large scale analysis of soybean regulatory gene expression identifies a Myb gene involved in soybean nodule development. Plant Physiology 151:1207-1220, 2009.
- Gyan Prakash Srivastava, Trupti Joshi, Zhao Song, Chao Zhang, Guan Ning Lin, Ping Li, Andy Ross, Mihail Popescu, Jingdong Liu, Jing Qiu, and Dong Xu, "GO-based Gene Function and Network Characterization", in, "Ontology-Based Data Mining in Biomedical Research", Mihail Popescu and Dong Xu eds. Artech House, Norwood, MA, USA. 83-111, 2009.
- Mihail Popescu and Dong Xu, "Mapping Genes to Biological Pathways Using Ontological Fuzzy Rule Systems", Mihail Popescu and Dong Xu eds. Artech House, Norwood, MA, USA. 113-132, 2009.
- Dong Xu. Computational Methods for Protein Sequence Comparison and Search. In: Current Protocols in Protein Science, edited by J. E. Coligan, B. M. Dunn, H. L. Ploegh, D. W. Speicher, and P. T. Wingfield. John Wiley & Sons, New York. 56:2.1.1-2.1.27, UNIT 2.1, 2009.
- Zhao Song, Luonan Chen, and Dong Xu. Confidence Assessment for Protein Identification by Using Peptide-Mass Fingerprinting Data. Proteomics, 9(11):3090-3099, 2009.