RESEARCH INTEREST

Protein structure prediction, high-throughput biological data analyses, computational proteomics, in silico studies of plant, microbes, and neural systems.


RESEARCH

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).


Selected Publications

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.

Yi Shang, Qingguo Wang, Jingfen Zhang, Bogdan Barz, Rajkumar Bondugula, Ioan Kosztin, and Dong Xu. A New Computational Intelligent Approach to Protein Tertiary Structure Prediction, in "Advance in Computational Intelligence". Ed: Xin Yao. University of Science and Technology of China Press, 2008.

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.

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.

Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen, Zoran Obradovic, A. Keith Dunker, and Dong Xu. A New Machine Learning Approach for Protein Phosphorylation Site Prediction in Plants. Lecture Notes in Bioinformatics (LNBI 5462): Proceeding of the First International Conference on Bioinformatics and Computational Biology (BICoB), April 2009, New Orleans, USA, pp. 18-29.

Mingjie Chen, Brian P. Mooney, Martin Hajduch, Jill E. Casteel, Trupti Joshi, Mingyi Zhou, Dong Xu, Jay J. Thelen. System Analysis of An Arabidopsis Mutant Altered in de novo Fatty Acid Synthesis Reveals Diverse Changes in Seed Composition and Metabolic Regulation. Plant Physiology. 150:27-41, 2009.

Sandra Thibivilliers, Trupti Joshi, Kimberly B. Campbell, Brian Scheffler, Dong Xu, Bret Cooper, Henry T. Nguyen and Gary Stacey. Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection. BMC Plant Biology 2009, 9:46 (27 Apr 2009)

Laurent Brechenmacher, Joohyun Lee, Sherri Sachdev, Zhao Song, Tran Hong Nha Nguyen; Joshi Trupti, Beverly Dague, Nathan Oehrle, Marc Libault, Brian Mooney, Dong Xu, Bret Cooper, and Gary Stacey. Establishment of a Protein Reference Map for Soybean Root Hair Cells.Plant Physiology, February 2009, Vol. 149, pp. 670-682.

Guan Ning Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty, and Dong Xu, ComPhy: Prokaryotic Composite Distance Phylogenies Inferred from Whole-Genome Gene Sets. BMC Bioinformatics, 2009, 10(Suppl 1):S5.


2008-

Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen, and Dong Xu. P3DB: a plant protein phosphorylation database. Nucleic Acids Research, 37 (Database issue):D960-962, Epub 2009.

Chao Zhang, Trupti Joshi, Guan Ning Lin, Dong Xu. An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data. International Journal of Computational Biology and Drug Design, Volume 1, Number 3, 26 November 2008 , pp. 254-274(21).

Christopher A. Bottoms and Dong Xu "Wanted: Unique Names for Unique Atom Positions. PDB-Wide Analysis of Diastereotopic Atom Names of Small Molecules Containing Diphosphate", BMC Bioinformatics, 9 Suppl 9:S16, 2008.

Gyan P Srivastava, Juyuan Guo, Huidong Shi, and Dong Xu. PRIMEGENS-v2: Genome-wide primer design for analyzing DNA methylation patterns of CpG islands. Bioinformatics, 24(17):1837-42, 2008.

Robin Kramer and Dong Xu. Projecting Gene Expression Trajectories through Inducing Differential Equations from Microarray Time Series Experiments. Journal of VLSI Signal Processing Systems. 50(3):321-329, 2008.

Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen, and Dong Xu. P3DB: a plant protein phosphorylation database. Nucleic Acids Research, Advance Access published online on October 17, 2008.

Rajkumar Bondugula and Dong Xu. Combining Sequence and Structural Profiles for Protein Solvent Accessibility Prediction, Proceeding of the 7th Annual International Conference on Computational Systems Bioinformatics (CSB 2008), Stanford University, California, USA, pp. 195-200, 2008.

Gyan P. Srivastava, Jing Qiu, Dong Xu, Functional Annotation from Meta-Analysis of Microarray Datasets, Proceeding of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008), Philadelphia, Pennsylvania, USA, pp. 367-271, 2008.

Debjani Ghosh, Gyan P Srivastava, Dong Xu, and R. Michael Roberts. The Interaction between Stress-Activated Protein Kinase Interacting Protein 1 (SIN1/MAKPAP1) and poly(RC) Binding Protein-2(PCBP2): Potential Involvement In Counteracting Environmental Stress. Proceedings of National Academy of Sciences. 105 (33):11673-11678, 2008.

Dong Xu, James Keller, Mihail Popescu, and Rajkumar Bondugula. "Application of Fuzzy Logic in Bioinformatics", Imperial College Press, London, UK. 2008.

Lourdes Pena-Castillo, Murat Tasan, Chad L Myers, Hyunju Lee, Trupti Joshi, Chao Zhang, Yuanfang Guan, Michele Leone, Andrea Pagnani, Wan Kyu Kim, Chase Krumpelman, Weidong Tian, Guillaume Obozinski, Yanjun Qi, Sara Mostafavi, Guan Ning Lin, Gabriel F Berriz, Francis D Gibbons, Gert Lanckriet, Jian Qiu, Charles Grant, Zafer Barutcuoglu, David P Hill, David Warde-Farley, Chris Grouios, Debajyoti Ray, Judith A Blake, Minghua Deng, Michael I Jordan, William S Noble, Quaid Morris, Judith Klein-Seetharaman, Ziv Bar-Joseph, Ting Chen, Fengzhu Sun, Olga G Troyanskaya, Edward M Marcotte, Dong Xu, Timothy R Hughes, Frederick P Roth. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence, Genome Biology. 9(Suppl 1):S2 (27 June 2008).

Laurent Brechenmacher, Moon-Young Kim, Marisol Benitez, Min Li, Trupti Joshi, Bernarda Calla, Mei Phing Lee, Marc Libault, Lila O. Vodkin, Dong Xu, Suk-Ha Lee, Steven J. Clough, and Gary Stacey. Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. Molecular Plant-Microbe Interactions. Vol.21, No. 5, 631-645, 2008.

Trupti Joshi, Chao Zhang, Guan Ning Lin, Zhao Song, Dong Xu. GeneFAS: A tool for prediction of gene function using multiple sources of data. In "Genomics Protocols" volume of "Methods in Molecular Biology", the second edition, edited by Ramnath Elaswarapu and Michael P. Starkey. Humana Press, Totowa, New Jersey. Vol.439, 369-386, 2008.

Yu Chen and Dong Xu. Predicting Functional Modules Using Microarray and Protein Interaction Data. In: Analysis of Microarray Data, A Network-Based Approach, edited by F. Emmert-Streib and M. Dehmer. VILEY_VCH Verlag GmbH &Co. KGaA, Weinheim. 307-329, 2008.

Sum Kim, Meng Li, Henry H. Paik, Kenneth P. Nephew, Huidong Shi, Robin Kramer, Dong Xu, Tim H.-M. Huang. Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences. Pacific Symposium on Biocomputing, the Big Island of Hawaii, 13:315-326, January, 2008.