Publications
CSBL Publications:

in press
 2005 2004 2003 2002 2001 2000
  • B Yan, G.T. Zhou, V Olman, P Wang and Ying Xu, A point process model for rapid identification of post-translational modifications in proteins, Proceedings of the PSB'06, 2006 (in press).
  • C. Liu, Y. Song, B Yan, Ying Xu, L. Cai, Fast De Novo sequencing and spectral alignment via tree decomposition, Proceedings of PSB'06, 2006 (in press).
  • Z. Chen and Ying Xu, Structure prediction on helical transmembrane proteins at two length scales, Jounral of Bioinformatics and Computational Biology (by invitation), 2006 (to appear).
  • X. Ji and Ying Xu, "A C library for stochastic ranking evolution strategy for parameter estimation", Bioinformatics, 2005 (to appear).
  • H. Wu, F. Mao, Z. Su, V Olman, Ying Xu, Prediction of functional modules based on gene distributions in microbial genomes, Proceedings of the 16th International Conference on Genome Informatics , 2005 (in press).
  • 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 (vols I and II), Y. Xu, D. Xu and J. Liang (eds), Springer, 2005 (to appear).
  • Z. Chen and Ying Xu, Energetics and Stability of Transmembrane Helix Packing: A Replica-exchange Simulation with a Knowledge-based Helix-lipid Potential, Proteins (in press), 2005.
  • Y Song, C Liu, X Huang, R Malmberg, Ying Xu, and L. Cai, Efficient Parameterized Algorithm for Biopolymer Structural-Sequence Alignment, Proceedings of WABI, 2005 (in press).
  • P. Wang, B. Yan, J. Guo, C. Hicks, Ying Xu, Structural genomics analysis of alternative splicing and its application in modeling structures of alternatively spliced variants, PNAS (to appear), 2005.
  • J. Guo and Ying Xu, Computational approaches to amyloid beta fibril core structures, Methods in Enzymology, vol 309, 2005 (to appear). 2005.
  • 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", PNAS, 2005 (to appear).
  • C. Chen, G Li, Z. Li, Ying Xu, On connected [g, f+1]-factors in graphs, Combinatorica, 2005 (in press).
  • 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).
  • J. Xu, M Li, and Ying Xu, Protein threading by linear programming: theoretical analysis and computational results, Journal of Combinatorial Optimization , 2004 (in press).

Top
2005
 2004 2003 2002 2001 2000

Top 2005
2004
 2003 2002 2001 2000
  • X. Chen, Z. Su, Ying Xu and T Jiang, "Computational Prediction of Operons in Synechococcus sp WH8102", Proceedings of 15th International Conference on Genome Informatics, pp 211 - 222, 2004 (Best paper award of GIW04).2004.
  • 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
  • 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.
  • V. Olman, H. Peng, Z. Su, Ying Xu, Mapping of microbial pathways through constrained mapping of orthologous genes, Proceedings of The IEEE Computational Systems Bionformatics Conference (CSB'04), pp 363 - 370, 2004.
  • B. Yan, C. Pan, R. Heittich, V Olman, Ying Xu, "Separation of ion types in tandem mass spectrometry data interpretation -a graph-theoretic approach", Proceedings of The IEEE Computational Systems Bionformatics Conference (CSB'04), pp. 236 - 244, 2004.
  • Guo, J-T.; R. Wetzel and Ying Xu, Computational modeling of Abeta amyloid fibril. PROTEINS, 7(2):357-364, 2004.
  • Y. Zou, Z. Yang, IG Minko, H. Ma, SM Shell, Y, QU, Ying Xu, NE. Geacintov and RS Lloyd, "DNA damage recognition of nucleotide excission repair protein UvrB". Biochemistry, 43 : 4196 - 4205, 2004
  • Gupta, V. Peterson, C.B. Dice, L. Uchiki, T. Guo, J-T. Xu, Y. Hettich, R. Dealwis, C. "Sml1p Protein is a Dimer in Solution: Characterization of Denaturation and Renaturation of Recombinant Sml1p", Biochemistry, 2004, 43(26):8568-8578.
  • Guo, J-T. Ellrott, K. Chung, WJ. Xu, D. Passovets, S. Xu, Y. "PROSPECT-PSPP: An Automatic Computational Pipeline for Protein Structure Prediction", Nucleic Acids Res., 2004, 32:W522-5.
  • Tiquia SM, Wu L, Chong SC, Passovets S, Xu D, Xu Y, Zhou J.Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques. 36(4):664-70,2004
  • 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):961-9, 2004.
  • Qu,Y. Guo,J-T. Olman,V. and Xu,Y. "Protein Structure Prediction Using Sparse Dipolar Coupling Data", Nucleic Acids Res., 32(2):551-561, 2004.
  • Williams, A. Portelius, E. Kheterpal, I. Guo, J-T. Cook, K. Xu, Y. Wetzel, R. Mapping Abeta Amyloid Fibril Secondary Structure Using Scanning proline Mutagenesis J. Mol. Biol.335:833-842, 2004.
  • Y. Qu, J-T. Guo, V. Olman, and Y. Xu, "Protein Fold Recognition Through Application of Residual Dipolar Coupling Data",  Proceedings of the 9th Pacific Symposium on Biocomputing (PSB), 9:459-470, 2004
Top 2005 2004
2003
 2002 2001 2000
  • Z. Su, A. Dam, X. Chen, V Olman, T. Jiang, B. Palenik, and Ying Xu, Computational Inference of Regulatory Pathways in Microbes: an application to the construction of phosphorus assimilation pathways in Synechococcus WH8102, Proceedings of 14th International Conference on Genome Informatics  pp:3-13,Universal Academy Publishing, 2003.
  • ZZ. Chen, T Jiang, G. Lin, R. Rizzi, Z. Wen, D. Xu, Ying Xu, More reliable protein NMR peak assignment via improved algorithm for 2-interval scheduling, Proceedings of the 11th European Symposium on Algorithms, 580-592, 2003.
  • D. Xu, V. Olman, L. Wang, and Ying Xu, "EXCAVATOR: a computer program for gene expression data analysis", Nucleic Acid Research, 31(19), 5582-5589, 2003.
  • D. Kim, D. Xu, J-T. Guo, K. Ellrott, Ying Xu, "PROSPECT II: protein structure prediction program for genome-scale application", Protein Engineering, 16(9), 641-650, 2003
  • V. Olman, D. Xu, and Ying Xu, CUBIC: Identification of Regulatory Binding Sites through Data Clustering, Journal of Bioinformatics and Computational Biology, 1(1), 21-40, 2003.
  • C. Secrest, L. Hauser, F. Larimer, D Thompson, A Beliaev, J. Zhou, Ying Xu, and Xu, A computational study of Shewanella oneidensis MR-1: Discovering the role of hypothetical proteins, OMICS, 7: 177-192, 2003.
  • Y. Chen, Y Liu, K.M. Goldstein, J. M. Becker, Ying Xu, D. Xu, A computational study on yeast signal transduction pathway for amino acid transport, Applied Genomics and Proteomics, 2(1), 43-50, 2003.
  • J. Xu, M Li, D. Kim and Ying Xu, RAPTOR: rapid protein threading by operations research techniques, Journal of Bioinformatics and Computational Biology, 1(1), pp95-118, 2003.
  • D. Xu, P. Dam, D. Kim, M. Shah, E. Uberbacher, and Ying Xu, Characterization of Protein Structrue and Function at Genome-scale using a Computational Prediction Pipeline, accepted to appear in Genetic Engineering: Principles and Methods , Vol 32, Jane Setlow (Ed.), Plenum Press, 2003.
  • V Olman, D Xu, and Ying Xu, "Solving data clustering problem as a string search problem", Proceedings of Conference on Statistical Data Mining and Knowledge Discovery (ed by Hamparsum Bozdogan), Chapman & Hall/CRC, 417-434, 2003.
  • M. Shah, S. Passovets, D. Kim, K. Ellrott, L. Wang, I. Vokler, P. Locascio, D. Xu, Ying Xu, A Computational Pipeline for Protein Structure Prediction and Analysis at Genome Scale, Proceedings of IEEE Conference on Bioinformatics and Biotechnology, 3-10, IEEE/CS Press, 2003 (An expanded journal version is published in Bioinformatics ,19(15):1985-1996, 2003).
  • Y Chen, T Joshi, Ying Xu, and D Xu, Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data, Proceedings of the IEEE Conference on Bioinformatics and Biotechnology, 18-25, IEEE/CS Press, 2003.
  • G. Lin, D. Xu, Z. Chen, G. Lin, and T. Jiang, and Ying Xu, "Computational assignments of protein backbone NMR peaks by efficient bounding and filtering", Journal of Bioinformatics and Computational Biology, 1(2), 387-410, 2003.
  • V. Olman, D. Xu and Ying Xu, "Identification of Regulatory Binding-sites using Minimum Spanning Trees", Proceedings of the 7th Pacific Symposium on Biocomputing (PSB), pp 327 - 338, 2003.
  • Y Li, J Yu, D Liu, W Yan, R Xu and Ying Xu, "Design of Zeolite Frameworks with Defined Pore Geometry through Constrained Assembly of Atoms", Chem Mater, 15, 2780-2785, 2003. 
  • J. Xu, M Li, G. Lin, D. Kim, and Ying Xu, Protein Structure Prediction by linear programming, Proceedings of The 7th Pacific Symposium on Biocomputing (PSB) , pp 264- 275 2003.
  • J-T. Guo, D. Kim,. D Xu, and Ying Xu, "Improving the Performance of DomainParser for Structural Domain Partition using Neural Network", Nucleic Acids Research, 31(3), 944-952, 2003.
  • H. Sun, M LI and Ying Xu, Molvie: an interactive visalization enviroment for molecular structures, Computer Methods and Programs in Biomedicine, vol 71, 85-90, 2003.
Top 2005 2004 2003
2002
 2001 2000
  • Z. Liu and Ying Xu, "Adaptive support vector classification", Proceedings of the Second Conference on Hybrid Intelligent Systems (edited by A. Abraham), IOS Press, pp 702-711, 2002.
  • G. Heffelfinger, A. Martino, A. Gorin, Ying Xu, et al., "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling", OMICS, 6(4), 305-330, 2002.
  • Z. Chen, T. Jiang, G. Lin, J. Wen, D. Xu, Ying Xu, "Approximation algorithms for NMR Spectral Peak Assignments, Proceedings of The Second Workshop on Algorithms in Bioinformatics (WABI), Lecture Notes in Computer Science 2452:82-96, 2002.
  • MV. Buchanan, FW Larimer, HS Wiley, S. Kennel, TJ Squier, JM Ramsey, KD Rodland, GB Hurst, RD. Smith, Ying Xu, D. Dixon, MJ Doktycs, S. Colson, and R. Gesteland, “Genomes to Life Center for Molecular and Cellular Systems”: a research program for identification and characterization of protein complexes, (by invitation), 6(4), 287-304, 2002.
  • G. Lin, D. Xu, Z. Chen, G. Lin, and T. Jiang, and Ying Xu, "A Branch and Bound Algorithm for assignment of protein backbone NMR peaks", Proceedings of First IEEE Bioinformatics Conference, pp. 165 - 174, August 2002.
  • G. Lin, Z. Chen, T. Jiang, J. Wen, J. Xu, Ying Xu, Approximation Algorithms for NMR Spectral Peak Assignment, Theoretical Computer Science, 299:211-229, 2002.
  • D. Xu, G. Li, J. Zhou, and Ying Xu, "PRIMEGENS: A Computer Program for Robust and Efficient Design of Gene-Specific Targets on Microarrays", Bioinformatics, 18(11):1432-1437, 2002.
  • Ying Xu, V. Olman, and D. Xu, Clustering Gene Expression Data Using a Graph-Theoretic Approach: An Application of Minimum Spanning Tree, Bioinformatics, Vol 18 (4), 526 - 535, 2002.
  • Ying Xu, D. Xu, D. Kim, V. Olman, J. Razumovskaya, and T. Jiang, Automated Assignment of Backbone NMR Peaks using Constrained Bipartite Matching, IEEE Computing in Science and Engineering vol 4 (1), pp 50-62, Jan. 2002.
  • Ying Xu, D. Xu and V. Olman, "A practical method for interpretation of threading scores: an application of neural networks", Statistica Sinica Special issue on Bioinformatics, 12, 159 - 177, 2002.
Top 2005 2004 2003 2002
2001
 2000
  • D. Xu and Ying Xu, "Computational Studies of Protein Structure and Function using Threading Program PROSPECT", In Protein Structure Prediction: Bioinformatic Approach (eds by Igor Tsigelny), International University Line (IUL) Publishers, by invitation, 2001.
  • D. Xu, O. Crawford, P. LoCascio, and Ying Xu, "Application of PROSPECT in CASP4: characterizing protein structures with new folds", Proteins: Structure, Function, Genetics special issue on CASP4, Suppl 5, 140 - 148, 2001.
  • Ying Xu, V Olman and D. Xu, “Minimum Spanning Trees for Gene-Expression Data Clustering”, The Twelfth International Conference on Genomics Informatics, pp. 24 – 33, 2001, Tokyo, Japan.
  • Dong Xu, Kunnumal Baburaj, Cynthia B. Peterson, and Ying Xu. A Model for the Three-Dimensional Structure of Vitronectin: Predictions for the Multi-Domain Protein from Threading and Docking. Proteins: Structure, Function, and Genetics. 44:312-320. 2001.
Top 2005 2004 2003 2002 2001
2000
  • Ying Xu, Dong Xu, and Harold N. Gabow. Protein Domain Decomposition using a Graph-Theoretic Approach. Bioinformatics. 16:1091-1104. 2000.
  • Ying Xu, Dong Xu. Oakley H. Crawford, and J. Ralph Einstein. "A computational method for NMR-constrained protein threading." Journal of Computational Biology. 7:449-467. 2000.
  • Ying Xu and Dong Xu. Protein threading using PROSPECT: Design and evaluation.Proteins: Structure, Function, and Genetics. 40:343-354. 2000.
  • Dong Xu, Ying Xu, Gary Li, and Jizhong Zhou. A Computer Program for Generating Gene-Specific Fragments for Microarrays. In Currents in Computational Molecular Biology, edited by S. Miyano, R. Shamir and T. Takagi. Universal Academy Press, Inc. Tokyo, Japan. Pages 3-4. 2000.
  • Dong Xu, Ying Xu, and Edward C. Uberbacher. Computational tools for protein modeling. Current Protein and Peptide Science. 1:1-21. 2000.
  • Dong Xu and Ying Xu. Protein tertiary structure prediction. 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. Volume 1, pages 2.7.1-2.7.17. 2000.
  • Dong Xu and Ying Xu. Protein Databases on the Internet. 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. Volume 1, pages 2.6.1-2.6.15. 2000.
  • Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein, and Engin Serpersu. Protein structure determination using protein threading and sparse NMR data. In: The Fourth Annual International Conference on Computational Molecular Biology, edited by R. Shamir, S. Miyano, S. Istrail, P. Pevzner, and M. Waterman. Pages 299-307, ACM, Tokyo, Japan. 2000. 
  • Dong Xu, Michael A. Unseren, Ying Xu, and Edward C. Uberbacher. Protein fold recognition at the secondary structure level. Bioinformatics. 16:257-68, 2000.

   


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