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Publications

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2010

Chou WC, Ying YB, and Xu Y. GolgiP: prediction of Golgi resident proteins in plants. Bioinformatics, In press.
Zhou C, Yin Y, Dam P, Xu Y. Identification of novel proteins involved in plant cell-wall synthesis based on protein-protein interaction data. J Proteome Res, In press.
Zhang H, Wang P, Papangelopoulos N, Xu Y, Sette A, Bourne PE, Lund O, Ponomarenko J, Nielsen M, Peters B. Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules. PLoS One. 2010 Feb 17;5(2):e9272.
W. Zhou, Ying Xu, HB Schuttler, Cellulose Hydrolysis in Evolving Substrate Morphologies III: Time Scale Analysis, submitted to Journal of Biotechnology and Bioengineering, 2010.
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 2:209–216.
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 Enterohemorrhagic Escherichia coli O157:H7 using genomic barcodes", FEBS Lett. 2010 Jan 4;584(1):194-8.

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 non-coding RNA genes in prokaryotic genomes", Bioinformatics, 2009 Nov 15;25(22):2897-905.
C. Gervais, T Wurst, D Landau, Ying Xu, "Application of the Wang-Landau algorithm to the dimerization of glycophorin A", J Chem Phys. 2009 Jun 7;130(21):215106.
Li G, Ma Q, Tang H, Paterson AH, Xu Y, "QUBIC: a qualitative biclustering algorithm for analyses of gene expression data", Nucleic Acids Res. 2009 Aug;37(15):e101.
B. Liu, F Zhou, Ying Xu and X. Zhang, Genomic and proteomic characterization of a thermophilic Geobacillus bacteriophage GBSV1, 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", Biotechnol Bioeng. 2009 Oct 1;104(2):261-74.
W. Zhou, Z. Hao, Ying Xu, and B. Schuttler, "Cellulose hydrolysis in evolving substrate morphologies II: numerical results and analysis", Biotechnol Bioeng. 2009 Oct 1;104(2):275-89.
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.
T. Wust, DP, Landau, C Gervais and Ying Xu, Monte Carlo Simulations of protein models: at the interface between statistical physics and biology, Proceedings of the BIOMAT, 2009 (in press).
Y. Yin, J. Huang, and Ying Xu, The cellulose synthase superfamily in fully sequenced plants and algae, BMC Plant Biology 9:99, 2009.
Y. Yin, M. G. Hahn, I Gelineo-Albersheim, Ying Xu, D. Mohnen, Glycosyltransferases of Family (GT8), in Plant Cell Polysacharides: Biosysynthesis and Bioengineering: Annual Plant Review Series, Blackwell Publishing, 2009.
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 (JACS), 2009.
IA. Kataeva, SJ Yang, P Dam, FL Poole II, Y Yin, F Zhou, W Chou, Ying Xu, L Goodwin, DR. Sims, JC. Detter, LG. Hauser, J Westpheling and MWW. Adams, Genome Sequence of the Anaerobic, Thermophilic and Cellulolytic Bacterium Anaerocellum thermophilum DSM 6725, J Bacteriol. 2009 Jun;191(11):3760-1.
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.
F. Mao, P. Dam, J. Chou, V Olman, and Ying Xu, "DOOR: a database for prokaryotic operons", Nucleic Acids Research, 37(1), D459 - 463, 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.
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.
C. Zhou, F. Zhou, Ying Xu, Comparative analyses of distribution and function of Z-DNA in Arabidopsis and rice, Genomics, 93: 383- 391, 2009.
T. Wust, D. Landau, C Gervais, Ying Xu, Monte Carlo simulations of systems with complex landscapes, Computer Physics Communications, 180: 475-479, 2009.

2008

P Dam, F Mao, D Che, P Wan, T Tran, Ying Xu, "Computational elucidation of operons and uber-operons", a chapter in Computational Methods for Understanding Bacterial and Archaeal Genomes (eds, Y. Xu and JP. Gogarten), Imperial College Press, p. 233 - 258, 2008.
Z. Su, G. Li, Ying Xu, "Prediction of Regulons through Comparative Genome Analyses", a chapter in Computational Methods for Understanding Bacterial and Archaeal Genomes (eds, Y. Xu and JP. Gogarten), Imperial College Press, p. 259 - 280, 2008.
F Mao, P Dam, H Wu, I Chou, E Voit, Ying Xu, "Prediction of Biological Pathways through Data Mining and Information Fusion", a chapter in Computational Methods for Understanding Bacterial and Archaeal Genomes (eds, Y. Xu and JP. Gogarten), Imperial College Press, p. 281 - 314, 2008.
SR. Veflingstad, P Dam, Ying Xu, EO. Voit, "Microbial Pathway Models", a chapter in Computational Methods for Understanding Bacterial and Archaeal Genomes (eds, Y. Xu and JP. Gogarten), Imperial College Press, p. 315 - 344, 2008.
M Langille, F Zhou, Ying Xu, FS.L. Brinkman, "Mobile genetic elements and their predictions in prokaryotes", a chapter in Computational Methods for Understanding Bacterial and Archaeal Genomes (eds, Y. Xu and JP. Gogarten), Imperial College Press, p. 113 - 136, 2008.
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,9(1) 2008.
F Zhou, V Olman, Ying Xu, Barcodes for genomes and applications, BMC Bioinformatics, 9(1), 546 - , 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.
F. Zhou, Y. Chen, G. Li, and Ying Xu, "A recently active MITE, Chunjie, inserted into an operon without disturbing the operon structure in Geobacter uraniireducens Rf4", Genetics, 179: 2291-2297, 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, accepted, 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.
M. Jiang, Ying Xu, B Zhu, Protein structure-structure alignment with discrete Frechet distance, Journal of Bioinformatics and Computational Biology, 6(1), 51-64, 2008.
D. Che, G. Li, S. Jensen, J. Liu and Ying Xu, PFP: a new approach to phylogenetic footprinting in prokaryotic genomes, Proceedings of International Symposium on Bioinformatics Research and Applications, pp. 110-121, 2008.
JT Guo and Ying Xu, Towards modeling of amyloid fibril structures, Frontiers in Biosciences, 13, 4039-4050, 2008.
F. Zhou, V Olman, Ying Xu, Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea", BMC Genomics, 9:36, 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.
X Qi, G. Li S. Li, Ying Xu, Sorting genome by translocations, insertions and deletions, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol 99, 1 - , 2008.
K. Ellrott, JT Guo, V Olman, Ying Xu, IMPROVING THE PERFORMANCE OF PROTEIN THREADING USING INSERTION/DELETION FREQUENCY ARRAYS, Journal of Bioinformatics and Computational Biology, vol 6(3), 585 - 602, 2008 (expanded version of the CSB2007 conference proceedings paper).
Qi Liu, Y Zhang, X. Ye, Ying Xu, Fuzzy kernel clustering of RNA secondary structures using a novel similarity metric, Journal of Biomolecular Structure and Dynamics, 25(6), 685-696, 2008.
H. Wu, F Mao and Ying Xu, On Application of Directons to Prediction of Orthologous Genes for Prokaryotes, Journal of Computational Biology and Chemistry, 32, 176 - 184, 2008.
Z. Liu, J Guo, T. Li and Ying Xu, Structure-based recognition of binding sites of transcription factors using an efficient protein-DNA docking approach, Proteins, 72, 1114 - 1124, 2008.
Z. Chen and Ying Xu, Energetics and stability of transmembrane helix packing: a replica-exchange simulation with a knowledge-based membrane potential, Proteins, 2008 (to appear).

2007

H Liu, L Wong, and Ying Xu, "Survival prediction of patients based on microarray gene expression data analysis", a chapter in Knowledge Discovery in Bioinformatics: Techniques, Methods and Applications (eds: Y Pan and T Hu), John Wiley and Sons, 2007 (by invitation), p. 89 - 112.
J Guo and Ying Xu, "A historical perspective of protein structure prediction", chapter 1 in "Protein Structure Prediction" (eds Chris Bystroff and Mohammed Zaki), Humana Press, pp. 3 - 42, 2007.
K. Ellrott, JT Guo, V Olman, Ying Xu, IMPROVING THE PERFORMANCE OF PROTEIN THREADING USING INSERTION/DELETION FREQUENCY ARRAYS, Journal of Bioinformatics and Computational Biology, vol 6(3), 585 - 602, 2008 (expanded version of the CSB2007 conference proceedings paper).
HQ Liu, S. Dalton, Ying Xu, Transcriptional Profiling of Definitive Endoderm Derived from Human Embryonic Stem Cells, Proceedings of CSB2007, pp. 79 - 82, 2007.
K. Ellrott, JT Guo, V Olman, Ying Xu, Improvement in Protein Sequence Structure Alignment Using Insertion/Deletion Frequency Array, Proceedings of CSB2007, pp. 335 - 342, 2007.
Z. Su, V Olman, Ying Xu, Computational prediction of Pho regulons in Cyanobacteria, BMC Genomics, vol 8, pp. 156 - 167, 2007.
H Wu, F Mao, V Olman, and Ying Xu, An Algorithm for Hierarchical Classification of Prokaryotic Genes, Lecture Notes in Bioinformatics, vol 4463, pp 551 - 563, 2007.
D. Che, J. Zhao, L. Cai and Y. Xu. "Operon prediction in microbial genomes using decision tree approach", Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp. 135 - 142, 2007. An expanded version to appear in Journal International Journal of Information Technology and Intelligent Computing.
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.
P. Dam, V Olman, K. Harris, F. Mao, H. Wu, Z. Su, Ying Xu, Operon prediction using both genome-specific and general genome information, Nucleic Acids Research, 35:288 - 298, 2007.
AB McLean, KA D'Amour, KL Jones, M Krishnamoorthy, MJ Kulik, DM ReynoldsAM Sheppard, H Liu, Ying Xu, EE Baetge and S Dalton157i15 Activin A efficiently specifies definitive endoderm from human embryonic stem cells only when PI3K signaling is suppressed, Stem Cell, 25: 29 - 38 , 2007.
M Jiang, Ying Xu, B. Zhu, "The Discrete Fr?echet Distance and Its Application to Protein Structure-Structure Alignment", Proceedings of Asia-Pacific Bioinformatics Conference (APBC), pp 131 - 141, Imperial College Publishing, 2007.
H. Wu, F. Mao, V Olman, Ying Xu, Hierarchical Classification of Functionally Equivalent Genes, Nucleic Acids Research, 35: 2125 - 2140, 2007.
JT Guo, JW Jaromczyk, Ying Xu, Analysis of Chameleon Sequences and Their Implications in Biological Processes, Proteins, 67(3):548-58, 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 Yue Zou, Structural characterization of human RPA sequential binding to single-stranded DNA using ssDNA as a molecular ruler, Biochemistry, 46(28):8226-33, 2007.
G. Li, J Lu, V. Olman, Ying Xu, Highly Sensitive Algorithm for Identification of cis Regulatory Elements: from cliques to high information content analysis, Journal of Bioinformatics and Computational Biology, Vol 5(4), 817 - 838, 2007.

2006

B. H. Park, P. Dam, C Pan, Ying Xu, A. Geist, G. Heffelfinger and N.F. Samatova, In silico recognition of protein-protein interactions: theory and applications, book chapter in Advanced Data Mining Technologies in Bioinformatics, 248 - 268, 2006, Idea Group Publishing.
Ying Xu, Z. Liu, L. Cai and D. Xu, Protein Structure Prediction by Protein Threading, in Computational Methods for Protein Structure Prediction and Modeling (vols I and II), Y. Xu, D. Xu and J. Liang (eds), Springer, vol 2, 389 - 430, 2006.
J. Guo, C. Hall, Ying Xu, R. Wetzel, Modeling Protein Aggregate Assembly and Structure, in Computational Methods for Protein Structure Prediction and Modeling (vols I and II), Y. Xu, D. Xu and J. Liang (eds), Springer, vol 1, 279 - 318, 2006
D. Xu, J Liang and Ying Xu, Bioinformatics infrastructure and resources for protein structure/function characterization, in Computational Methods for Protein Structure Prediction and Modeling (vols I and II), Y. Xu, D. Xu and J. Liang (eds), Springer, vol. 2 pp. 595 - 616, 2006.
D. Xu and Ying Xu, Protein Structure Prediction as a Systems Problem, in Computational Methods for Protein Structure Prediction and Modeling (vols I and II), Y. Xu, D. Xu and J. Liang (eds), Springer, vol 2, pp 565 - 594, 2006.
G. Lin, D. Xu and Ying Xu, Computer Algorithms for Structural Informatics, in Computational Methods for Protein Structure Prediction and Modeling (vols I and II), Y. Xu, D. Xu and J. Liang (eds), Springer, vol 2, 629 - 654, 2006.
K Ellrott, J. Guo, V. Olman, and Ying Xu, A Generalized Threading model using Integer Programming that allows for Secondary Structure Element Deletion, Proceedings of GIW2006, pp 248 - 258, 2006.
V. A. Emanuele, V Olman, B Yan, Ying Xu, and GT Zhou, An approximate Bayesian detection scheme with applications to tandem mass spectrometry data analysis", Proceedings of 12th IEEE Digital Signal Processing Workshop, pp. 550 - 560, 2006.
X. Qi, S. Li, G. Li and Ying Xu, "Sorting genomes by translocations and deletions", Proceedings of CSB2006, pp. 157-166, 2006.
C. Liu, B. Yan, Y. Song, Ying Xu and L. Cai, "Tag-based blind Post Translational Modification identification with point process model", Bioinformatics, vol 22 (14), pp. 307-313, 2006.
R. Kramer, V. Olman, Ying Xu and D. Xu, "DigitalTree: an open source tool for displaying biological data in tree structure, Lecture Notes in Computer Science, vol 3992, 855-862, 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), pp 480 - 489, 2006.
D. Che, G Li, F. Mao, H Wu, and Ying Xu, "Detecting uber-operons in microbial genomes", Nucleic Acids Research, 34(8), 2418 - 2427, 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.
F. Zhou, Y. Xue, X. Yao and Ying Xu, "CSS-Palm: Palmitoylation site prediction with a clustering and scoring strategy", Bioinformatics, vol 22 (7), 894-896, 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, Analytical Chemistry, 78 (14), 5026 - 39, 2006.
C. Hicks, V. Olman, P. Wang and Ying Xu, Codifferential gene expression analysis in subtypes of ovarian cancer using maximum covariance analysis, Journal of Bioinformatics and Computational Biology, 4(5), 999 - 1014, 2006.
Z. Chen and Ying Xu, Structure prediction on helical transmembrane proteins at two length scales, Journal of Bioinformatics and Computational Biology, vol 4(2), 317-333, 2006.
X. Ji and Ying Xu, "A C library for stochastic ranking evolution strategy for parameter estimation", Bioinformatics, 22: 124 - 126, 2006.
F. Mao, Z. Su, V. Olman, P. Dam, Z. Liu and Ying Xu, Mapping of Orthologous Genes in the Context of Biological Pathways: an Application of Integer Programming, Proc Natl Acad Sci USA, 2006 103: 129-134.
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 PSB, pp. 327 - 338, 2006.
C. Liu, Y. Song, B Yan, Ying Xu, L. Cai, Fast De Novo Sequencing and Spectral Alignment via Tree Decomposition, Proceedings of PSB', pp 255 - 266, 2006.
Z. Su, P Dam, F Mao, V. Olman, B Palenik, I Paulsen 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.
Y Song, C Liu, X Huang, R Malmberg, Ying Xu, and L. Cai, Efficient Parameterized Algorithm for Biopolymer Structural-Sequence Alignment, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol 3(4), pp. 423 - 432, 2006 (an expanded version of the LNB paper).
J Guo and Ying Xu, "Computational approaches to amyloid beta fibril core structure" (by invitation), Methods in Enzymology, vol, 412:300-314, 2006.
A Williams, J Guo, E Portelius, I Kheterpal, I Huff, K Cook ,Ying Xu, and R Wetzel, Mapping Abeta Amyloid Fibril Secondary Structure Using Scanning proline Mutagenesis, Journal of Molecular Biology, 335, 833-842, 2004 (ranked as one of the top ten most cited articles in Alzheimer disease research by Nature Medicine, 2006).

2005

Y Song, C Liu, X Huang, R Malmberg, Ying Xu, and L. Cai, Efficient Parameterized Algorithm for Biopolymer Structural-Sequence Alignment, Lecture Notes in Bioinformatics, vol 3692, 376 - 388, 2005.
H. Wu, F. Mao, V Olman, Ying Xu, Prediction of functional modules based on gene distribution in microbial genomes, pp. 247 - 259, Genome Informatics, 2005.
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, 2005.
F. Mao, H. Wu, V. Olman, Ying Xu, Accurate Prediction of Orthologous Gene Groups in Microbes, Proceedings of CSB2005, pp. 73 - 79, 2005.
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, pp 18920 - 18925, 102 (52), Proc Natl Acad Sci USA, 2005.
Z. Chen and Ying Xu, Multi-Scale Hierarchical Structure Prediction of Helical Transmembrane Proteins, Proceedings of CSB2005, pp. 203 - 208, 2005.
J. Huang, Ying Xu, J.P. Gogarten, Ancient Lateral Gene Transfer Marks the Opisthokont, Molecular Biology and Evolution, 22(11), 2142 - 2146, 2005.
Z Su, V Olman, F Mao, and Ying Xu, Comparative genomics analyses of ntcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis, Nucleic Acids Research, 33 (16): 5156 - 5171, 2005.
C. Chen，G Li, Z. Li, Ying Xu, On connected [g, f+1]-factors in graphs, Combinatorica, 25(4), 393--405, 2005.
H. Wu, Z. Su, V Olman, Ying Xu, Prediction of functional modules through comparative genome analysis and application of gene ontology, Nucleic Acids Research, 33: 2822-2837, 2005.
B. Yan, C. Pan, V. Olman, B. Heittich, Ying Xu, A graph-theoretic approach to separation of b- and y-ions in tandem mass spectra", Bioinformatics, 21: 563-574, 2005.
J. Huang, Z. Su, Ying Xu, The Evolution of the Phosphonate Degradation Pathways, Journal of Molecular Evolution, vol 61: 682-690, 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, D. Chen, Ying Xu, Logistic Support Vector Machines and Their Application to Gene Expression Data, Journal of Bioinformatics Research and its Applications, vol 1:2, 169 - 180, 2005.
J. S. Sharp, J. Guo, T. Uchiki, Ying Xu, C. Dealwis, R. Hettich, "Photochemical Surface Mapping of C14S-Sml1p for Constrained Computational Modeling of Protein Structure", Journal of Analytical Biochemistry, 340(2):201-12. 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, 20(4): 483 - 490, 2005.
Z. Liu, F. Mao, J Guo, B Yan, Ying Xu, Quantitative Validation of Protein-DNA Interaction in Transcription Process: Distance-dependent Knowledge-based Potential Considering Multi-body Interaction, Nucleic Acids Research, 32:2, pp 546-558, 2005.
Z. Chen, GH Lin, R. Rizzi, D. Xu, Ying Xu, T. Jiang, "More reliable protein NMR peak assignment via improved 2-interval scheduling, Journal of Computational Biology, 12 (2): 129-146, 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 (in press), 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.
P. Dam, Z. Su, V Olman, Ying Xu, Computational reconstruction of the carbon fixation pathway in Synechococcus sp. WH8102 (extended abstract), Proceedings of International Conference on Bioinformatics and its Applications, pp. 37 - 46, 2005, World Scientific Publisher.

2004

Ying Xu, Computational Genome Annotation, in Microbial Functional Genomics (J Zhou, DK. Thompson, Y. Xu, JM Tiedje), pp. 41 - 66, Wiley-LISS, 2004.
Ying Xu, Computational Methods for Functional Prediction of Genes, in Microbial Functional Genomics (J Zhou, DK. Thompson, Y. Xu, JM Tiedje), pp. 113 - 140, Wiley-LISS, 2004.
Ying Xu, Microarray gene expression data analysis, in Microbial Functional Genomics (J Zhou, DK. Thompson, Y. Xu, JM Tiedje), pp. 177 - 206, Wiley-LISS, 2004.
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.
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.
V. Olman, H. Peng, Z. Su, Ying Xu, Mapping of microbial pathways through constrained mapping of orthologous, Proceedings of The IEEE Computational Systems Bioinformatics Conference (CSB'04), pp 363 - 370, 2004.
Y. Qu, J. Guo, V. Olman, and Ying Xu, Protein fold recognition through application of residual dipolar coupling data, Conference Proceedings of PSB, pp. 459 - 470, 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 (invited paper), 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.
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, Vol 32 (7), 2147 - 2157, 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.
Y. Qu, J. Guo, V. Olman, and Ying Xu, Protein fold recognition using residual dipolar coupling data, Nucleic Acids Research, 32(2), 551-561, 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.
V. Gupta, C. B. Peterson, L. Dice, T. Uchiki, J.T. Guo, Ying Xu, R. Hettich and C. Dealwis, "Sml1p protein is a dimer in solution: characterization of denaturation and renaturation of recombinant Sml1p", Biochemistry, 43(26), 8568 - 8578, 2004.
J. Guo, R. Wetzel and Ying Xu, Computational modeling of Abeta amyloid fibril, Proteins: Structure, Function and Bioinformatics, 57(2):357-364, 2004.
A Williams, J Guo, E Portelius, I Kheterpal, I Huff, K Cook ,Ying Xu, and R Wetzel, Mapping Abeta Amyloid Fibril Secondary Structure Using Scanning proline Mutagenesis, Journal of Molecular Biology, 335, 833-842, 2004 (ranked as one of the top ten most cited articles in Alzheimer disease research by Nature Medicine, 2006).
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.

2003

D. Xu, V. Olman, L. Wang, and Ying Xu, "EXCAVATOR: a computer program for gene expression data analysis", Nuclear Acid Research, 31(19), 5582-5589, 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, Bioinformatics, 19, 1985 - 1996, 2003.
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, Genome Informatics, pp 3- 13, Universal Academy Press Inc. 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 System on Algorithms, pp 580 - 592, 2003.
XD Liu, YH Xu, JH Yu, Y Li, W Zeng, C Chen, JY Li, WQ Pang, RR Xu, Ying Xu, Rational design and synthesis aided by data mining - microporus aluminophosphates with specific structure, Chemical Journal of Chinese Universities, 24(6), 949 - 952, 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 (BIBE), 3-10, IEEE Press, 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 (BIBE), pp 18-27, IEEE Press, 2003.
V. Olman, D. Xu, and Ying Xu, "A New Framework for Biological Data Clustering using Minimum Spanning Trees", Proceedings of The 7th Pacific Symposium on Biocomputing, pp. 324 - 335, 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, 264 - 375, 2003, World Scientific Publishing Co.
D. Kim, D. Xu, J. Guo, K. Ellrott, Ying Xu, "PROSPECT II: protein structure prediction program for genome-scale application", Protein Engineering, 16 (9), 641 - 650, 2003.
Z. Chen, G. Lin, and T. Jiang and Ying Xu, "Approximation Algorithms for NMR Protein Backbone Assignments", Theoretical Computer Science, 299:211-229, 2003.
C. Secrest, L. Hauser, F. Larimer, D Thompson, A Beliaev, J. Zhou, Ying Xu, and D. Xu, "A computational study of Shewanella oneidensis MR-1: Discovering the role of hypothetical proteins", OMICS, 7:177-192, 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.
H Sun, M Li, Ying Xu, Molvie: An Interactive Visualization Environment for Molecular Structures, Computer Methods and Programs in Biomedicine, vol 71, 85-90, 2003
D. Xu, P. Dam, D. Kim, M. Shah, E. Uberbacher, and Ying Xu, "Characterization of Protein Structure and Function at Genome-scale using a Computational Prediction Pipeline, Genetic Engineering: Methods and Principles, Jane Setlow (Ed.), Kluwer Academic/Plenum Publishers, New York. 269-293. 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. 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), 1 - 9, 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", Chemistry of Materials, 15, 2780 - 2785, 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.
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", Special IEEE Bioinformatics Conference Issue of Journal of Bioinformatics and Computational Biology (by invitation), 1(2), 387-410, 2003.

2002

Ying Xu and D. Xu, Protein structure prediction by protein threading and partial experimental data, in Current methods in Computational Molecular Biology (eds by T Jiang, Y Xu, MQ. Zhang), pp. 467 - 502, MIT Press, 2002.
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, pp 3 - 42, 2002.
Z. Liu and Ying Xu, Adaptive support vector classification, Proceedings of the Second Conference on Hybrid Intelligent Systems (edited by A. Abraham), pp. 702 - 711, IOS Press, Dec. 1-4, 2002.
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, (by invitation), pp. 417-434, 2002.
Z. Chen, T. Jiang, G. Lin, J. Wen, D. Ying Xu, "Approximation algorithms for NMR Spectral Peak Assignments, Lecture Notes in Computer Science, 2452:82-96, 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 (extended abstract)", Proceedings of First IEEE Bioinformatics Conference, pp. 165 - 174, August 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, D, Xu, "A Graph-theoretical Approach for Gene Expression Data Analysis: an application of minimum spanning trees", 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, 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.

2001

D. Xu, K. Baburaj, C. 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, Genetics, vol. 44: 312-320, 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 (by invitation), Suppl 5: 140 - 148, 2001.
Ying Xu, V Olman and D. Xu, "Minimum Spanning Trees for Gene-Expression Data Clustering", Genomics Informatics, pp. 24 - 33, 2001.

2000

Ying Xu, D. Xu, and H. N. Gabow, "Protein Domain Decomposition using a Graph-Theoretic Approach", Bioinformatics, vol 16 (12), 1091 - 1104, 2000.
Ying Xu, D. Xu, O. Crawford, J. R. Einstein, "A computational method for NMR-constrained protein threading", Journal of Computational Biology, 2000, Vol 7(3/4), 449 - 467, 2000 (invited).
Ying Xu and D. Xu, "Protein Threading using PROSPECT: design and evaluation", Protein: Structure, Function, Genetics, Vol 40, pp 343 - 354, 2000.
Ying Xu, D. Xu, O.H. Crawford, J. R. Einstein, and E. Serpersu, "Protein structure determination using protein threading and sparse NMR data", Proceedings of The Fourth Annual International Conference on Computational Molecular Biology, pp. 299 - 307, 2000.
D. Xu, Ying Xu, G. Li and J. Zhou, "A Computer Program for Generating Gene-Specific Fragments for Microarrays", Currents in Computational Molecular Biology (eds by S. Miyano, R. Shamir and T. Takagi), Universal Academy Press, pp. 2-3, 2000.
D. Xu, M. Unseren, Ying Xu, and E. C. Uberbacher, "Sequence-Structure Specificity of a Knowledge Based Energy Function at the Secondary Structure Level", Bioinformatics, Vol 16 (3), pp 257-268, 2000.

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