Ying Xu, Ph.D. Department of Biochemistry and Molecular Biology A110, Life Science Building 120 Green Street University of Georgia Athens, GA 30602-7229   Phone: 706-542-9779 (CSBL) Phone: 706-542-7783 (IOB) Fax: 706-542-9751/7782 Email: xyn bmb.uga.edu           xyn csbl.bmb.uga.edu

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POSITION

Regents-GRA Eminent Scholar and Professor of bioinformatics and computational biology Computational Systems Biology Laboratory (CSBL) Dept. of Biochemistry and Molecular Biology University of Georgia, Athens

Director Institute of Bioinformatics (IOB) University of Georgia Athens, GA 30602-7229 Phone: 706-542-7783

RESEARCH INTERESTS

Our group's research and development center around the following areas:
• Cancer Computational and Systems Biology: We are interested in developing integrated computational and omic techniques for (a) identification of biomarkers for a number of human cancers, detetable through analyses of serum/urine samples, and (b) understanding the relationships between molecular signatures and cancer formation & development. Our work involves microarray gene expression data generation and analyses, comparative genome analyses and analyses of other experimental data.
• Computational Study of Plant Cell-wall Synthesis Genes and Pathways : We are interested in developing computational prediction and analysis techniques for inference of genes involved in cell wall synthesis in plants and regulatory elements of these genes & their relevant biochemical pathways. Our work currently involves prediction and analyses of protein-protein interactins relevant to cell wall synthesis, prediction of Golgi-residing proteins, bi-clustering analyses of microarray gene expression data and co-evolutionary analyses of cell-wall synthesis genes.
• Study of Microbial Genome Structure and Application to Pathway & Network Inference: We are interested in understanding both the micro- and macro-structures of microbial genomes through computational studies and experimental validation, and in understanding why microbial genomes are organized the way they are. We are also interested applying the knowledge and information gained through such studies to prediction of pathways and networks in microbes.

• Computational Methods for Protein Structure Prediction and Modeling: We are interested in developing effective computational methods for protein fold recognition, protein structure prediction and modeling, and protein complex prediction; and applying these tools to solve real structural biology problems. We are also interested in developing hybrid methods for protein structure solution using information from derived from  computational tools and partial experimental data, including NMR and X-ray crystallograpohic data. 

Our research work is currently sponsored by NSF, DOE, NIH, Georgia Research Alliance, Georgia Cancer Coalition and the University of Georgia. In addition, our work had been generously supported by Oak Ridge National Lab and Pacific Northwest National Lab.

BIOSKETCH

Here is my biosketch (2008-2009).

IN MEMORY OF THE 5-12-2008 SICHUAN EARTHQUAKE VICTIMS!

Pictures selected from 100 Moments to Remember -- Sichuan Earthquake

SELECTED PUBLICATIONS IN THE PAST FIVE YEARS

• Ying Xu, "Computational Challenges in Deciphering Genomic Structures of Bacteria", Journal of Computer Science and Technology, 2009 (invited review).
• F. Mao, Y. Yin, FF. Zhou, WC Chou, C. Zhou, H Chen and Ying Xu, "pDAWG: an integrated database for plant cell-wall genes", Bioenergy Research, 2009 (in press).
• X Gu, J Glushka, Y Yin, Ying Xu, T Denny, J Smith, Y Jiang and M Bar-Peled, "Identification of UDP-4-keto-pentose/UDP-xylose synthase: a member of the 4,6-dehydratase & decarboxylase family in the devastating plant pathogenic bacterium Ralstonia solanacearum str. GMI1000", submitted to JBC, 2009.
• G Wang, F Zhou, V Olamn, F. Li and Ying Xu, "Prediction of pathogenicity islands in Escherichia coli O157:H7 using genomic barcode", submitted, 2009.
• H Shen, YB Yin, F. Chen, Ying Xu and RA Dixon, "The bioinformatics baseline analysis of the NAC genes for plant cell wall development in bioenergy production", Bioenergy Research, 2009 (in press).
• X Ren, Y Li, Q Pan, J Yu, R Xu, Ying Xu, An Open-Framework Germanate with 30-Ring Channels Built from Ge7 and Ge9 Clusters, Journal of American Society of Chemistry, 2009 (online now).
• Y Wang, J Cui, W Du, C Zhang, F Mao, J Wang, Y Sun, C Zhou, Y Liang, F Li, Ying Xu, "DMarker: A Bio-Marker Inference System for Human Diseases based on Microarray Gene Expression Data, submitted, 2009.
• L L. Escamilla-Trevino, H Shen, R Uppalapati, T Ray, Y Tang, T Hernandez, Y Yin, Ying Xu, and R A. Dixon, "Functional Characterization of two Cinnamoyl CoA Reductase (CCR) Genes for lignin modification in Switchgrass (Panicum virgatum)", New Phytologist, 2009 (online now).
• X. Mao and Ying Xu, "In silico reconstruction of osmoregulation network in Synechococcus sp. WH8102", submitted, 2009.
• C. Zhou, YB Yin, P. Dam, Ying Xu, "Identification of novel genes involved in plant cell wall biosynthesis by protein-protein interaction data", submitted to New Phytologist, 2009.
• G. Li, B. Liu, Ying Xu, "Accurate Recognition of cis Regulatory Motifs with the Correct Lengths in Prokaryotic Genomes", Nucleic Acids Research, 2009 (in press).
• YB Yin, H Chen, M. Hahn, D. Mohnen, Ying Xu, "Plant galacturonosyltransferase (GAUT) related genes have a different origin than the other glycosyltransferase family 8 genes and may be anciently acquired from Cyanobacteria", submitted, 2009.
• TT. Tran, F Zhou, S Marshburn, M Stead, S Kushner, and Ying Xu, "De novo computational prediction of small non-coding RNA genes", Bioinformatics, 2009 (in press).
• C. Gervais, T Wurst, D Landau, Ying Xu, "Application of the Wang-Landau Algorithm to the Dimerization of Glycophorin A", Journal of Physical Chemistry (in press), 2009.
• G. Li, Q. Ma, H. Tang, Ying Xu, "A close-to-optimum bi-clustering algorithm for microarray gene expression data", Nucleic Acids Research (online now), 2009.
• B. Liu, F Zhou, Ying Xu and X. Zhang, Functional genomic analyses of a novel bacteriophage GVE2 from a deep-sea thermophile, Research in Microbiology, 160, 166 - 171, 2009.
• W. Zhou, B. Schuttler, Z. Hao, Ying Xu, "Cellulose hydrolysis in evolving substrate morphologies I: a general modeling formalism", Biotechnology and Bioengineering (online now), 2009.
• W. Zhou, Z. Hao, Ying Xu, and B. Schuttler, "Cellulose hydrolysis in evolving substrate morphologies II: numerical results and analysis", Biotechnology and Bioengineering, 2009 (online now).
• Q Liu, H Liu, P Wan, X. Ye and Ying Xu, Analyses of Domains and Domain Fusions in Human Oncogenes , BMC Bioinformatics , 10, 88 - 103, 2009.
• Y Yin and Ying Xu, "The cellulose synthase superfamily in fully sequenced plants and algae", BMC Plant Biology, 2009 (online now).
• G. Li, X Deng and Ying Xu, A polynomial time approximation scheme for embedding hypergraph in a cycle, ACM Transactions on Algorithms , 5(2), pp 20 - , 2009.
• Y. Chen, F. Zhou, G. Li, and Ying Xu, MUST: a system for identification of miniature inverted repeats transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi, Gene, 436: 1-7, 2009.
• F. Zhou and Ying Xu, RepPop: a database for repetitive elements in Populus trichocarpa, BMC Genomics, 10, 14 - , 2009.
• G. Li, D. Che, Ying Xu, "A universal operon predictor for prokaryotic genomes", Journal of Binformatics and Computational Biology, 7(1), 19 - 38, 2009.
• F. Mao, P. Dam, J. Chou, V Olman, and Ying Xu, "DOOR: a database for praokaryotic operons", Nucleic Acids Research vol 37(1), D459 - 463, 2009.
• V Olman, F. Mao, H Wu, Ying Xu, "A parallel clustering algorithm for very large data sets", IEEE/ACM Transaction on Computational Biology and Bioinformatics, 6(2), 344 - 352, 2009.
• J. Li, L. Li, J. Liang, P. Chen, J. Yu, Ying Xu, RR. Xu, "Template-Designed Synthesis of Open-Framework Zinc Phosphites with Extra-Large 24-Ring Channels", Crystal Growth and Design, 8(7), 2318-2323, 2008 (my second computational chemistry paper!).
• F Zhou, V Olman, Ying Xu, "Barcodes for genomes", BMC Bioinformatics , 9(1), 546- , 2008.
• F Zhou, Y Chen, G Li, Ying Xu, "A novel active MITE, Chunjie, inserted safely into an operon in Geobacter uraniireducens Rf4", Genetics, 179: 2291-2297, 2008.
• F Zhou, V Olman, Ying Xu, "Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea", BMC Genomics, 9:36, 2008.
• J Cui, Q. Liu, D. Puett, Ying Xu, "Computational prediction of human proteins that can be secreted into bloodstream", Bioinformatics, 24, 2370 - 2375, 2008
• C. Liu, Y. Song, B. Yan, Ying Xu, and L. Cai "Fast de novo peptide sequencing and spectral alignment via tree decomposition", International Journal of Computational Science, Special Issue on Bioinformatics and Computational Biology, 2008 (in press).
• H. Wu, F Mao, Ying Xu, "On Application of Directons to Prediction of Orthologous Genes for Prokaryotes", Computational Biology and Chemistry, 32, 176 - 184, 2008.
• Qi Liu, Y Zhang, X. Ye, Ying Xu, "Clustering of RNA secondary structures using a novel similarity metric", Journal of Biomolecular Structure and Dynamics, 25(6), 685-696, 2008.
• F. Zhou, T Tran, Ying Xu, "Nezha: a novel active miniature inverted repeat transposable element in cyanobacteria", Biochemical and Biophysical Research Communication, 365, 790 - 794, 2008.
• JT Guo and Ying Xu, "Towards modeling of amyloid fibril structures", Frontiers in Biosciences, 13:4039-4050, 2008.
• X Qi, G. Li S. Li, Ying Xu, "Sorting genome by translocations, insertions and deletions", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 99, 1- , 2008.
• Qi Liu, V Olman, H Liu, X Ye, Ying Xu, "RNACluster : an integrated tool for RNA secondary structure comparison and clustering", Journal of Computational Chemistry, 29(9), 1517 - 1526, 2008.
• Z. Liu, JT Guo, T Li, Ying Xu, "Structure-based recognition of binding sites of transcription factors using an efficient protein-DNA docking approach", Proteins: structure, function and bioinformatics, 72, 1114 - 1124, 2008.
• H. Wu, F. Mao, V Olman, Ying Xu, "Hierarchical Classification of Functionally Equivalent Genes in Prokaryotes", Nucleic Acids Research, 35, 2125 - 2140, 2007.
• JT Guo, JW Jaromczyk, Ying Xu, "Analysis of Chameleon Sequences and Their Implications in Biological Processes", Proteins: structure, function and bioinformatics, 67(3):548-58, 2007.
• G. Li, J Lu, V. Olman, Ying Xu, "A Highly Sensitive Algorithm for Identification of cis Regulatory Elements: from cliques to high information content analysis", Journal of Bioinformatics and Computational Biology, 2007, 5(4), 817-838.
• Z. Su, V Olman and Ying Xu, "Computational prediction of Pho Regulons in Cyanobacteria", BMC Genomics, vol 8, 156 - 167, 2007.
• P. Dam, V Olman, K. Harris, Z. Su, Ying Xu, "Operon prediction using both genome-specific and general genome information", Nucleic Acids Research, 35:288 - 298, 2007.
• T.T. Tran, P. Dam, H. Wu, Z. Su, F. Poole, M Adams, G.T. Zhou, and Ying Xu, "Operon prediction in Pyrococcus furiosus", Nucleic Acids Research , 35:69 - 78, 2007.
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• AB McLean, KA D'Amour, KL Jones, M Krishnamoorthy, MJ Kulik, DM Reynolds, AM Sheppard, H Liu, Ying Xu, "EE Baetge and S Dalton, Activin A efficiently specifies definitive endoderm from human embryonic stem cells only when PI3K signaling is suppressed", Stem Cell , 25:29 - 38, 2007.
• G Li, Z Liu, J Guo, Ying Xu, "An Algorithm for Simultaneous Backbone Threading and Side-Chain Packing", Algorithmica, 48(4), 329 - 342, 2007.
• L. Cai, Y Qu, Z Yang, Ying Xu and Y Zou, "Structural Characterization of Human RPA Sequential Binding to Single-Stranded DNA Using Model ssDNA as a Molecular Ruler", Biochemistry, 46(28):8226-33, 2007.
• M Jiang, Ying Xu, B. Zhu, "The Discrete Frechet Distance and Its Application to Protein Structure-Structure Alignment", Proceedings of Asia-Pacific Bioinformatics Conference, pp 131 - 141, 2007. An expanded version will appear in Journal of Binformatics and Computational Biology .
• K Petritis, L.J. Kangas, B Yan, E.F. Strittmatter, M. Monroe, W. Qian, J. N. Adkins, RJ. Moore, Ying Xu, MS. Lipton, DG. Camp II, and RD. Smith, "Improved artificial neural network based peptide elution time prediction in reversed-phase liquid chromatography by incorporating peptide sequence information", Analytical Chemistry, 78 (14), 5026 - 39, 2006, 2006.
• F Zhou, Y Xue, X Yao, Ying Xu, "A general user interface for prediction servers of proteins' post-translational modification sites", Nature Protocols, 1(3):1318 - 1321, 2006.
• C. Liu, B. Yan, Y. Song, Ying Xu and L. Cai, "Blind Post-Translational Modification Identification by Combining Peptide Sequence Tag Generation and Database Search", Bioinformatics, vol 22(14), pp 307 - 313, 2006.
• K.L. Mayer, Y. Qu, S. Bansal, P.D. Leblond, F.E. Jenny, Jr., P.S. Brereton, M.W.W. Adams, Ying. Xu, and J.H. Prestegard, "Structure determination of a new protein from backbone-centered NMR data and NMR-assisted structure prediction", Proteins: structure, function and bioinformatics, 65(2), 480 - 489, 2006.
• C. Hicks, V. Olman, P. Wang and Ying Xu, Gene expression data analysis in subtypes of ovarian cancer using maximum covariance analysis, Journal of Bioinformatics and Computational Biology, 4(5), 999 - 1014, 2006.
• Y Xue, F Zhou, C Fu, Ying Xu and X. Yao, "SUMOsp: a web server for sumoylation site prediction", Nucleic Acids Research, Vol 34: W254 - W257, 2006.
• D. Che, G Li, F. Mao, H Wu, and Ying Xu, "Detecting uber-operons in prokaryotic genomes", Nucleic Acids Research, 34(8), 2418 - 2427, 2006.
• F. Zhou, Y. Xue, X. Yao and Ying Xu, "CSS-Palm: Palmitoylation site prediction with a clustering and scoring strategy", Bioinformatics , 22(7), 894 - 896, 2006.
• Z. Chen and Ying Xu, Energetics and Stability of Transmembrane Helix Packing: A Replica-exchange Simulation with a Knowledge-based Helix-lipid Potential, Proteins: structure, function and bioinformatics, 62 (2): 539 - 552, 2006.
• Z. Chen and Ying Xu, Structure prediction on helical transmembrane proteins at two length scales, Jounral of Bioinformatics and Computational Biology (by invitation), vol 4(2), 317-333, 2006.
• Ying Xu, Z. Liu, L. Cai and D. Xu, Protein Structure Prediction by Protein Threading, a chapter in Computational Methods for Protein Structure Prediction and Modeling, I, II , Y. Xu, D. Xu and J. Liang (eds), vol 2, pp. 389 - 430 2006.
• JT. Guo, C. Hall, Ying Xu and R. Wetzel, Modeling Protein Aggregate Assembly and Structure, a chapter in Computational Methods for Protein Structure Prediction and Modeling, I, II , Y. Xu, D. Xu and J. Liang (eds), vol 1, pp. 279 - 318, 2006.
• F. Mao, Z. Su, V. Olman, P. Dam, Z. Liu, Ying Xu, "Mapping of orthologous genes in the context of biological pathways: an application of integer programming", Proc Natl Acad Sci USA, 103 (1): 129-134, 2006.
• X. Ji and Ying Xu, "A C library for stochastic ranking evolution strategy for parameter estimation", Bioinformatics, 22: 124-126, 2006.
• Z. Su, P. Dam, F. Mao, V. Olman, I. Paulsen, B. Palenik and Ying Xu, Computational inference and experimental validation of nitrogen assimilation regulatory networks in cyanobacterium Synechococcus sp. WH8102, Nucleic Acids Research 34(3), 1050 - 1065, 2006.
• JT. Guo and Ying Xu, Computational approaches to amyloid beta fibril core structures, Methods in Enzymology, vol 412:300-314, 2006.
• Y. Song, C. Liu, X. Huang, R. Malmberg, Ying Xu, and L. Cai, "Efficient parameterized algorithm for biopolymer structure-sequence alignment", Lecture Notes in Bioinforamtics 3692, pp. 376-388, 2005. An expanded version appeared in ACM Transactions on Computational Biology and Bioinformatics, 3(4):423-432, 2006.
• P. Wang, B. Yan, JT. Guo, C. Hicks, Ying Xu, Structural genomics analysis of alternative splicing and its application in modeling structures of alternatively spliced variants, Proc Natl Acad Sci USA, pp 18920 - 18925, 102 (52), 2005.
• J. Huang, Ying Xu, J.P. Gogarten, Ancient Lateral Gene Transfer Marks the Opisthokont, Molecular Biology and Evolution, vol 22(11), 2142 - 2146, 2005.
• Z. Su, F. Mao, V. Olman and Ying Xu, Comparative genomics analyses of ntcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis, Nucleic Acids Research, vol 33(16): 5156 - 5171, 2005.
• H. Wu, Z. Su, F. Mao, V Olamn, Ying Xu, "Prediction of functional modules through comparative genome analysis and application of gene ontology", Nucleic Acids Research , 33:2822-2837, 2005.
• JS Sharp, JT Guo, T. Uchiki, Ying Xu, C. Dealwis, R. Hettich, "Application of Photochemical Surface Mapping of C14S Sml1p to Constrained Computational Modeling", Analytical Biochemistry, 340(2):201-12. 2005.
• B. Yan, C. Pan, V. Olman, R. Hettich, Ying Xu, A graph-theoretic approach to separation of b- and y- ions in tandem mass spectra, Bioinformatics, Vol 21: 563-574, 2005.
• Z. Liu, D. Chen, H. Bensmail, Ying Xu, "Gene Expression Data Clustering with Kernel Principal Component Analysis", Journal of Bioinformatics and Computational Biology, vol 3(2), 303-316, 2005.
• Z. Liu, F. Mao, JT Guo, B Yan, Ying Xu, "Quantitative Validation of Protein-DNA Interaction using an Optimized Knowlege-based Potential", Nucleic Acids Research Vol 32:2, pp546-558, 2005.
• J. Huang, Z. Su, Ying Xu, "The Evolution of Phosphonate Degradation Pathways", Journal of Molecular Evolution, vol 61: 682-690, 2005.
• T. Fridman, J. Razumovskaya, N. Verberkmoes, Ying Xu, The probability distribution for a random match between an experimental - theoretical spectral pair in tandem mass spectrometry, Journal of Bioinformatics and Computational Biology, vol 3(2), 455-476, 2005.
• J. Wen, Z. Chen, R. Rizzi, D. Xu, G. Lin, Ying Xu, T. Jiang, "An improved approximation algorithm for 2-interval scheduling and NMR spectral peak assignment, Journal of Computational Biology 12 (2): 129-146, 2005.
• X. Chen, Z. Su, Ying Xu and T Jiang, "Computational Prediction of Operons in Synechococcus sp WH8102", Genome Informatics, pp 211 - 222, 2004 (Best paper award of GIW04).
• P. Dam, Z. Su, V Olman, Ying Xu, In silico construction of the carbon fixation pathway in Synechococcus sp. WH8102, Journal of Biological Systems, vol. 12, pp.97-125, 2004.
• J. Xu, M Li, and Ying Xu, Protein threading by linear programming: theoretical analysis and computational results, Journal of Combinatorial Optimization , 8:403-418, 2004.
• Y Zou, Z Yang, IG. Minko, H Ma, SM. Shell, Y Qu, Ying Xu, N E. Geacintov, and R. S Lloyd, DNA Damage Recognition of Nucleotide Excision Repair Protein UvrB, Biochemistry, 43 : 4196 - 4205, 2004.
• SM Tiquia, L Wu, S Passovets, D Xu, Ying Xu, and J Zhou, "Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples", Biotechnique, 36(4), 664 - 670, 2004.
• JT Guo, K Ellrott, W J Chung, D Xu, S Passovets and Ying Xu, PROSPECT-PSPP: An Automatic Computational Pipeline for Protein Structure Prediction, Nucleic Acids Research, Vol 32, W1 - W4, 2004.
• X. Chen, Z. Su, P. Dam, B. Palenik, Ying Xu, and T. Jiang, Operon prediction by comparative genomics: an application to the Synechococcus WH8102 genome, Nucleic Acids Research, Vol32 (7), 2147 - 2157, 2004.
• JT Guo, R. Wetzel, Ying Xu. "Molecular Modeling of the Core of Abeta Amyloid Fibrils", Proteins:Structure, Function and Bioinformatics , 57(2), 357-364, 2004.
• A. Williams, E. Portelius, I. Kheterpal, JT Guo, K. Cook, Ying Xu, R. Wetzel, "Mapping Abeta Amyloid Fibril Secondary Structure Using Scanning proline Mutagenesis", Journal of Mol. Biol. , 335, 833-842, 2004.
• Y. Qu, JT. Guo, V. Olman, and Ying Xu, "Protein fold recognition using residual dipolar coupling data, Nucleic Acids Research 32(2), 551-561, 2004.
• Jane Razumovskaya, Victor Olman, Dong Xu, Ed Uberbacher, Ying Xu, A Computational Method for Assessing Peptide-Identification Reliability in Tandem Mass Spectrometry Analysis with SEQUEST, Proteomics, 4(4), 961 - 969, 2004.
• V. Gupta, CB. Peterson, L. Dice, T. Uchiki, JT. Guo, Ying Xu, R. Hettich, C. Dealwis, "Sml1p Protein is a Dimer in Solution: Characterization of Denaturation and Renaturation of Recombinant Sml1p", Biochemistry, 43(26), 8586 - 8578, 2004.

A FEW EARLIER PAPERS (with citation information)

• Ying Xu and D. Xu, "Protein Threading using PROSPECT: Design and Evaluation", Proteins: Structure, Function, and Genetics, 40:343- 354, 2000.
• Ying Xu, D Xu and EC Uberbacher, "An Efficient Computational Method for Globally Optimal Threading", J Comput Biol. 5(3):597-614, 1998.
• Ying Xu and EC Uberbacher, "Automated Gene Identification in Large-Scale Genomic Sequences", J Comput Biol., 4(3):325-38, 1997.
• EC Uberbacher, Ying Xu, RJ Mural, "Discovering and understanding genes in human DNA sequence using GRAIL", Methods Enzymol., 266:259-81, 1996.
• Ying Xu, RJ Mural, M. Shah, EC Uberbacher, "Recognizing exons in genomic sequence using GRAIL II", Genet Eng., 16:241-53, 1994.
• Ying Xu, J. Einstein, RJ Mural and EC Uberbacher, "An improved system for exon recognition and gene modeling in human DNA sequences", Proc Int Conf Intell Syst Mol Biol., 2:376-84, 1994.
• Ying Xu, RJ Mural and EC Uberbacher, "Constructing gene models from accurately predicted exons: an application of dynamic programming", Bioinformatics (CABIOS), 10:613-623, 1994.




• J. Guan and Ying Xu, "An Algorithm for Linear Realization of Finite Automata", Acta Scientiarum Naturalium Universitatis Jilinensis, Vol. 1, pp. 119-126, 1985. (my first research paper).

BOOKS

• Current Topics in Computational Molecular Biology, T. Jiang, Ying Xu, Michael Zhang (eds), the MIT Press (and co-published by Tsinghua Univ. Press in China), 2002.

• Microbial Functional Genomics, J. Zhou, D. Thompson, Ying Xu, and J. Tiedje, John Wiley and Sons, 2004.

• Computational Methods for Protein Structure Prediction and Modeling, I and II , Ying Xu, D. Xu and J Liang, Springer, 2006.

• Computational Methods for Understanding Archaeal and Bacterial Genomes, Ying Xu and J. Peter Gogarten, Imperial College Press, 2008.

TEACHING

"Computational Methods in Bioinformatics" (UGA/BCMB8210) (course organizer; team teaching), Fall 2004, 2005, 2006, 2007, 2008.

"Genomics and Bioinformatics" (UGA/BCMB3600) (with M Adams and C Glover), Spring 2004, 2005, 2006, 2007, 2008, 2009.

"Advanced computational methods in bioinformatics" (UTK/LS695) (with D Xu, V Olman, and D Kim), Fall 2002.

LECTURE NOTES

"Solving Biological Problems Computationally"

"An introduction to bioinformatics -- a talk given to high school students"

"How to give a 'good' research talk, with a bit of bioinformatics flavor"

"How to write a 'good' research paper in an interdisciplinary field" (coming soon)

LINKS

• Our lab Computational Systems Biology Laboratory
  
• Department of Biochemistry and Molecular Biology
  
• Institute of Bioinformatics
  
• University of Georgia
  
• Georgia Research Alliance
  
• Georgia Cancer Coalition
  

WORK EXPERIENCE

• ChangJiang (Cheung Kong) Chair Professor (two months/year appointment), College of Computer Science and Technology, Jilin University, China, 2009 -
• Director, Institute of Bioinformatics, University of Georgia, 2004 -
• Adjunct Professor, Computer Science Department (2004 - ), Statistics Department (2006 - ), University of Georgia,
• Regents-GRA Eminent Scholar and Professor, Biochemistry and Molecular Biology Department, University of Georgia, 2003 -- 
• Distinguished visiting scientist, Computational Biology Institute, Oak Ridge National Laboratory, 2003 -- .
  
• Senior Staff Scientist/Group Leader (and earlier titles: staff scientist, research associate), Protein Informatics Group, Divisions of Life Sciences and Computer Science & Mathematics, Oak Ridge National Laboratory, Oak Ridge, TN, 1993 - 2003.
• Visiting Assistant Professor, Mathematics and Computer Sciences Department, Colorado School of Mines, Golden, CO, 1991 - 1993.
• Teaching/Research Assistant, Computer Science Department, Univ. of Colorado, Boulder, CO, 1986 - 1991.

EDUCATION

• Ph.D., Computer Science Dept., Univ. of Colorado at Boulder (research focus: combinatorial optimization, graph/matroid algorithm design and analysis)
• M.S., Computer Science Dept., Jilin Univ., China (research focus: expert system design, linear automata theory)
• B.S., Computer Science Dept., Jilin Univ., China (senior project: natural language processing)

UGA/CSBL --

The people (research scientists, postdocs, grad/under-grad students & staff) we have at CSBL are really a fun group to work with! Here is a picture we recently (Sept 2004) took after a group lunch

2009 SPRING PICNIC

"Group picture 1"

"Group picture 2"

"Group picture 3"

BIOINFORMATICS CONFERENCES

• International Bioinformatics Workshop (IBW2009), Suzhou, China, June 19-21, 2009.
• International Bioinformatics Workshop (IBW2008), Kunming, China, June 7-9, 2008.
• The Fifth International Bioinformatics Workshop (IBW2007) , Weihai, China, June 24-26, 2007.

FAMILY

A photo of my family: my wife, son Tony and myself (May 2004 on vacation in Taiwan).

Tony (Summer 2005) recently became quite interested in chess and swimming.

A photo we took during vacation in Changchun, China (June 2005) with my mom, dad, wife, son and myself

A photo of Hu-Niu, our family dog (2005).

HOBBIES

A fan of             and       .