Regents-GRA Eminent Scholar and Professor of Bioinformatics and Computational Biology Computational Systems Biology Laboratory (CSBL) Director Institute of Bioinformatics (IOB) Office: A108A Life Sciences Contact Phone Number: 542-9779 Fax Number: 542-9751 E-mail: xyn@bmb.uga.edu Additional Information / Lab Page

Research Interests

Our group's research and development center around the following areas:

• 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.

• Cancer Computational and Systems Biology: We are interested in developing computational and analysis techniques in support of (a) identification of biomarkers for a number of human cancers, detetable through imaging, analysis of serum/urine samples, (b) understanding the relationships between (computationally identifiable) genomic features and cancer formation and development, and (c) cancer epigenomic studies. Our work involves microarray gene expression data analyses, comparative genome analyses and analyses of other experimental data.

• 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.

Selected Recent Publications

• 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.



• J. Huang, P. Dam, J.P. Gogarten, Ying Xu, Chlamydiae-Related Genes in Plant Pectin Biosynthesis", submitted, 2007.



• Q Liu, H Liu, P Wan, X. Ye and Ying Xu, Tracing the origins of oncogenes: a systematic study, submitted to BMC Genomics, 2007.



• H. Wu, F Mao, Ying Xu, "On Application of Directons to Prediction of Orthologous Genes for Prokaryotes", submitted, 2007.



• G. Li, D. Che, Ying Xu, A universal operon predictor for prokaryotic genomes, submitted to JBCB, 2007.



• JT Guo and Ying Xu, Towards modeling of amyloid fibril structures, Frontiers in Biosciences, 2007 (in press).



• Qi Liu, Y Zhang, X. Ye, Ying Xu, Clustering of RNA secondary structures using a novel similarity metric, Journal of Biomolecular Structure and Dynamics, 2007 (in press).



• 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, 2007 (in press).



• X Qi, G. Li S. Li, Ying Xu, Sorting genome by translocations, insertions and deletions, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2007 (to appear).



• HQ Liu, S. Dalton, Ying Xu, Transcriptional Profiling of Definitive Endoderm Derived from Human Embryonic Stem Cells, Proceedings of CSB2007, 79 - 81, 2007.



• P Wang, Ying Xu, Systematic Discovery of Intronic Motifs Governing Splicing, submitted, 2007.



• 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, 2007 (in press).



• 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.



• 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 .



• 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, 2007 (in press).



• Z. Chen and Ying Xu, A statistical inter-residue contact energy for membrane proteins, submitted to Proteins, 2006.



• F. Mao, H. Wu, V Olman, Ying Xu, HCG: a database for hierarchical classification of functionally equivalent genes in prokaryotes, submitted, 2006.



• 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", submitted, 2006.



• G. Li, X. Deng, Ying Xu, A polynomial time approximation scheme for embedding a hypergraph in a cycle, submitted to ACM Transactions on Algorithms, 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.



• Y. Song, J. Guo, K, Ellrott, Ying Xu, and L Cai, "Efficient algorithms for protein threading via tree decomposition", submitted.



• 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.



• H. Wu, F. Mao, Z. Su, V Olman, Ying Xu, Prediction of functional modules based on gene distributions in microbial genomes, Genome Informatics , vol 16, pp. 247 - 259, 2005.



• 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.



• W. Gao, Y. Liu, C S. Giometti, L. Wu, X. Liu, T. Yan, Stanek, D. Xu, MW. Fields, Ying Xu, and J. Zhou, "A prohibitin-like protein of Shewanella oneidensis MR-1 is involved in iron homeostasis and oxidative damage protection", submitted, 2005.



• C. Chen, G Li, Z. Li, Ying Xu, On connected [g, f+1]-factors in graphs, Combinatorica, 25(4), 393--405, 2005.



• G Li, X. Wang, X Qi, B. Zhu, Ying Xu, A Linear-time Algorithm for computing the translocation distance between signed genomes", Theoretical Computer Science, 2005 (in press).



• 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.



• B. Yan, Y. Qu, F. Mao, V Olman, Ying Xu, PRIME: A Mass Spectrum Data Mining Tool for De Novo Sequencing and PTMs Identification, Journal of Computer Science and Technology (by invitation) 20(4); 483 - 490, 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.