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Ying Xu

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Protein Folding

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Publications

TOP 3
Tran Thao T; Zhou Fengfeng; Marshburn Sarah; Stead Mark; Kushner Sidney R; Xu Ying
De novo computational prediction of non-coding RNA genes in prokaryotic genomes.
Zhou Wen; Schüttler Heinz-Bernd; Hao Zhiqian; Xu Ying
Cellulose hydrolysis in evolving substrate morphologies I: A general modeling formalism.
Zhou Wen; Hao Zhiqian; Xu Ying; Schüttler Heinz-Bernd
Cellulose hydrolysis in evolving substrate morphologies II: Numerical results and analysis.

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All Publications

2009: Tran Thao T; Zhou Fengfeng; Marshburn Sarah; Stead Mark; Kushner Sidney R; Xu Ying
De novo computational prediction of non-coding RNA genes in prokaryotic genomes.
Bioinformatics (Oxford, England) 2009;25(22):2897-905.
2009: Zhou Wen; Schüttler Heinz-Bernd; Hao Zhiqian; Xu Ying
Cellulose hydrolysis in evolving substrate morphologies I: A general modeling formalism.
Biotechnology and bioengineering 2009;104(2):261-74.
2009: Zhou Wen; Hao Zhiqian; Xu Ying; Schüttler Heinz-Bernd
Cellulose hydrolysis in evolving substrate morphologies II: Numerical results and analysis.
Biotechnology and bioengineering 2009;104(2):275-89.
2009: Kong Yingzhen; Zhou Gongke; Avci Utku; Gu Xiaogang; Jones Chelsea; Yin Yanbin; Xu Ying; Hahn Michael G
Two Poplar Glycosyltransferase Genes, PdGATL1.1 and PdGATL1.2, Are Functional Orthologs to PARVUS/AtGATL1 in Arabidopsis.
Molecular plant 2009;2(5):1040-50.
2009: Li Guojun; Ma Qin; Tang Haibao; Paterson Andrew H; Xu Ying
QUBIC: a qualitative biclustering algorithm for analyses of gene expression data.
Nucleic acids research 2009;37(15):e101.
2009: Gervais Claire; Wüst Thomas; Landau D P; Xu Ying
Application of the Wang-Landau algorithm to the dimerization of glycophorin A.
The Journal of chemical physics 2009;130(21):215106.
2009: Kataeva Irina A; Yang Sung-Jae; Dam Phuongan; Poole Farris L; Yin Yanbin; Zhou Fengfeng; Chou Wen-chi; Xu Ying; Goodwin Lynne; Sims David R; Detter John C; Hauser Loren J; Westpheling Janet; Adams Michael W W
Genome sequence of the anaerobic, thermophilic, and cellulolytic bacterium "Anaerocellum thermophilum" DSM 6725.
Journal of bacteriology 2009;191(11):3760-1.
2009: Shou Z; Xiao H; Xu Y; Wang Y; Yang Y; Jiang H; Chen J; Yamada K; Miyamoto K
SHARP-2 gene silencing by lentiviral-based short hairpin RNA interference prolonged rat kidney transplant recipients' survival time.
The Journal of international medical research 2009;37(3):766-78.
2009: Chen Yong; Zhou Fengfeng; Li Guojun; Xu Ying
MUST: a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi.
Gene 2009;436(1-2):1-7.
2009: Zhou Chan; Zhou Fengfeng; Xu Ying
Comparative analyses of distributions and functions of Z-DNA in Arabidopsis and rice.
Genomics 2009;93(4):383-91.
2009: Li Guojun; Che Dongsheng; Xu Ying
A universal operon predictor for prokaryotic genomes.
Journal of bioinformatics and computational biology 2009;7(1):19-38.
2009: Pan Wei-wei; Cao Li-xian; Yi Fa-ping; Xu Ying; Bu You-quan; Lai Guo-qi; Ma Yong-ping; Song Fang-zhou
[HPV caused pathological changes in genital system of mice]
Bing du xue bao = Chinese journal of virology / [bian ji, Bing du xue bao bian ji wei yuan hui] 2009;25(1):35-40.
2009: Mao Fenglou; Dam Phuongan; Chou Jacky; Olman Victor; Xu Ying
DOOR: a database for prokaryotic operons.
Nucleic acids research 2009;37(Database issue):D459-63.
2009: Yin Yanbin; Huang Jinling; Xu Ying
The cellulose synthase superfamily in fully sequenced plants and algae.
BMC plant biology 2009;9():99.
2009: Liu Qi; Huang Jinling; Liu Huiqing; Wan Ping; Ye Xiuzi; Xu Ying
Analyses of domains and domain fusions in human proto-oncogenes.
BMC bioinformatics 2009;10():88.
2009: Zhou Fengfeng; Xu Ying
RepPop: a database for repetitive elements in Populus trichocarpa.
BMC genomics 2009;10():14.
2008: Cui Juan; Liu Qi; Puett David; Xu Ying
Computational prediction of human proteins that can be secreted into the bloodstream.
Bioinformatics (Oxford, England) 2008;24(20):2370-5.
2008: Liu Zhijie; Guo Jun-Tao; Li Ting; Xu Ying
Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach.
Proteins 2008;72(4):1114-24.
2008: Chen Yong; Zhou Fengfeng; Li Guojun; Xu Ying
A recently active miniature inverted-repeat transposable element, Chunjie, inserted into an operon without disturbing the operon structure in Geobacter uraniireducens Rf4.
Genetics 2008;179(4):2291-7.
2008: Liu Qi; Olman V; Liu Huiqing; Ye Xiuzi; Qiu Shilun; Xu Ying
RNACluster: An integrated tool for RNA secondary structure comparison and clustering.
Journal of computational chemistry 2008;29(9):1517-26.
2008: Xu Ying; Markstein Peter
Computational Systems Bioinformatics Conference 2007. Introduction.
Journal of bioinformatics and computational biology 2008;6(3):v-vi.
2008: Ellrott Kyle; Guo Jun-Tao; Olman Victor; Xu Ying
Improving the performance of protein threading using insertion/deletion frequency arrays.
Journal of bioinformatics and computational biology 2008;6(3):585-602.
2008: Wu Hongwei; Mao Fenglou; Olman Victor; Xu Ying
On application of directons to functional classification of genes in prokaryotes.
Computational biology and chemistry 2008;32(3):176-84.
2008: Liu Qi; Zhang Yin; Xu Ying; Ye Xiuzi
Fuzzy kernel clustering of RNA secondary structure ensemble using a novel similarity metric.
Journal of biomolecular structure & dynamics 2008;25(6):685-96.
2008: Jiang Minghui; Xu Ying; Zhu Binhai
Protein structure-structure alignment with discrete Fréchet distance.
Journal of bioinformatics and computational biology 2008;6(1):51-64.
2008: Zhou Fengfeng; Tran Thao; Xu Ying
Nezha, a novel active miniature inverted-repeat transposable element in cyanobacteria.
Biochemical and biophysical research communications 2008;365(4):790-4.
2008: Zhou Fengfeng; Olman Victor; Xu Ying
Barcodes for genomes and applications.
BMC bioinformatics 2008;9():546.
2008: Guo Jun-tao; Xu Ying
Towards modeling of amyloid fibril structures.
Frontiers in bioscience : a journal and virtual library 2008;13():4039-50.
2008: Zhou Fengfeng; Olman Victor; Xu Ying
Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea.
BMC genomics 2008;9():36.
2008: Guo Jun-Tao; Ellrott Kyle; Xu Ying
A historical perspective of template-based protein structure prediction.
Methods in molecular biology (Clifton, N.J.) 2008;413():3-42.
2007: Li Guojun; Lu Jizhu; Olman Victor; Xu Ying
Prediction of cis-regulatory elements: from high-information content analysis to motif identification.
Journal of bioinformatics and computational biology 2007;5(4):817-38.
2007: Cai Lifeng; Roginskaya Marina; Qu Youxing; Yang Zhengguan; Xu Ying; Zou Yue
Structural characterization of human RPA sequential binding to single-stranded DNA using ssDNA as a molecular ruler.
Biochemistry 2007;46(28):8226-33.
2007: Guo Jun-Tao; Jaromczyk Jerzy W; Xu Ying
Analysis of chameleon sequences and their implications in biological processes.
Proteins 2007;67(3):548-58.
2007: McLean Amanda B; D'Amour Kevin A; Jones Karen L; Krishnamoorthy Malini; Kulik Michael J; Reynolds David M; Sheppard Alan M; Liu Huiqing; Xu Ying; Baetge Emmanuel E; Dalton Stephen
Activin a efficiently specifies definitive endoderm from human embryonic stem cells only when phosphatidylinositol 3-kinase signaling is suppressed.
Stem cells (Dayton, Ohio) 2007;25(1):29-38.
2007: Ellrott Kyle; Guo Jun-tao; Olman Victor; Xu Ying
Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays.
Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference 2007;6():335-42.
2007: Liu Huiqing; Dalton Stephen; Xu Ying
Transcriptional profiling of definitive endoderm derived from human embryonic stem cells.
Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference 2007;6():79-82.
2007: Su Zhengchang; Olman Victor; Xu Ying
Computational prediction of Pho regulons in cyanobacteria.
BMC genomics 2007;8():156.
2007: Wu Hongwei; Mao Fenglou; Olman Victor; Xu Ying
Hierarchical classification of functionally equivalent genes in prokaryotes.
Nucleic acids research 2007;35(7):2125-40.
2007: Dam Phuongan; Olman Victor; Harris Kyle; Su Zhengchang; Xu Ying
Operon prediction using both genome-specific and general genomic information.
Nucleic acids research 2007;35(1):288-98.
2007: Tran Thao T; Dam Phuongan; Su Zhengchang; Poole Farris L; Adams Michael W W; Zhou G Tong; Xu Ying
Operon prediction in Pyrococcus furiosus.
Nucleic acids research 2007;35(1):11-20.
2006: Mayer K L; Qu Y; Bansal S; LeBlond P D; Jenney F E; Brereton P S; Adams M W W; Xu Y; Prestegard J H
Structure determination of a new protein from backbone-centered NMR data and NMR-assisted structure prediction.
Proteins 2006;65(2):480-9.
2006: Olman Victor; Hicks Chindo; Wang Peng; Xu Ying
Gene expression data analysis in subtypes of ovarian cancer using covariance analysis.
Journal of bioinformatics and computational biology 2006;4(5):999-1014.
2006: Song Yinglei; Liu Chunmei; Huang Xiuzhen; Malmberg Russell L; Xu Ying; Cai Liming
Efficient parameterized algorithms for biopolymer structure-sequence alignment.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2006;3(4):423-32.
2006: Liu Chunmei; Yan Bo; Song Yinglei; Xu Ying; Cai Liming
Peptide sequence tag-based blind identification of post-translational modifications with point process model.
Bioinformatics (Oxford, England) 2006;22(14):e307-13.
2006: Xue Yu; Zhou Fengfeng; Fu Chuanhai; Xu Ying; Yao Xuebiao
SUMOsp: a web server for sumoylation site prediction.
Nucleic acids research 2006;34(Web Server issue):W254-7.
2006: Petritis Konstantinos; Kangas Lars J; Yan Bo; Monroe Matthew E; Strittmatter Eric F; Qian Wei-Jun; Adkins Joshua N; Moore Ronald J; Xu Ying; Lipton Mary S; Camp David G; Smith Richard D
Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information.
Analytical chemistry 2006;78(14):5026-39.
2006: Chen Zhong; Xu Ying
Structure prediction of helical transmembrane proteins at two length scales.
Journal of bioinformatics and computational biology 2006;4(2):317-33.
2006: Zhou Fengfeng; Xue Yu; Yao Xuebiao; Xu Ying
CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS).
Bioinformatics (Oxford, England) 2006;22(7):894-6.
2006: Chen Zhong; Xu Ying
Energetics and stability of transmembrane helix packing: a replica-exchange simulation with a knowledge-based membrane potential.
Proteins 2006;62(2):539-52.
2006: Mao Fenglou; Su Zhengchang; Olman Victor; Dam Phuongan; Liu Zhijie; Xu Ying
Mapping of orthologous genes in the context of biological pathways: An application of integer programming.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(1):129-34.
2006: Ji Xinglai; Xu Ying
libSRES: a C library for stochastic ranking evolution strategy for parameter estimation.
Bioinformatics (Oxford, England) 2006;22(1):124-6.
2006: Ellrott Kyle; Guo Jun-tao; Olman Victor; Xu Ying
A generalized threading model using integer programming that allows for secondary structure element deletion.
Genome informatics. International Conference on Genome Informatics 2006;17(2):248-58.
2006: Zhou Fengfeng; Xue Yu; Yao Xuebiao; Xu Ying
A general user interface for prediction servers of proteins' post-translational modification sites.
Nature protocols 2006;1(3):1318-21.
2006: Qi Xingqin; Li Guojun; Li Shuguang; Xu Ying
Sorting genomes by translocations and deletions.
Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference 2006;():157-66.
2006: Yan Bo; Zhou Tong; Wang Peng; Liu Zhijie; Emanuele Vincent A; Olman Victor; Xu Ying
A point-process model for rapid identification of post-translational modifications.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2006;():327-38.
2006: Liu Chunmei; Song Yinglei; Yan Bo; Xu Ying; Cai Liming
Fast de novo peptide sequencing and spectral alignment via tree decomposition.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2006;():255-66.
2006: Guo Jun-Tao; Xu Ying
Amyloid fibril structure modeling using protein threading and molecular dynamics simulations.
Methods in enzymology 2006;412():300-14.
2006: Che Dongsheng; Li Guojun; Mao Fenglou; Wu Hongwei; Xu Ying
Detecting uber-operons in prokaryotic genomes.
Nucleic acids research 2006;34(8):2418-27.
2006: Su Zhengchang; Mao Fenglou; Dam Phuongan; Wu Hongwei; Olman Victor; Paulsen Ian T; Palenik Brian; Xu Ying
Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102.
Nucleic acids research 2006;34(3):1050-65.
2005: Wang Peng; Yan Bo; Guo Jun-Tao; Hicks Chindo; Xu Ying
Structural genomics analysis of alternative splicing and application to isoform structure modeling.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(52):18920-5.
2005: Huang Jinling; Su Zhengchang; Xu Ying
The evolution of microbial phosphonate degradative pathways.
Journal of molecular evolution 2005;61(5):682-90.
2005: Huang Jinling; Xu Ying; Gogarten Johann Peter
The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic.
Molecular biology and evolution 2005;22(11):2142-6.
2005: Sharp Joshua S; Guo Jun-tao; Uchiki Tomoaki; Xu Ying; Dealwis Chris; Hettich Robert L
Photochemical surface mapping of C14S-Sml1p for constrained computational modeling of protein structure.
Analytical biochemistry 2005;340(2):201-12.
2005: Fridman Tema; Razumovskaya Jane; Verberkmoes Nathan; Hurst Greg; Protopopescu Vladimir; Xu Ying
The probability distribution for a random match between an experimental-theoretical spectral pair in tandem mass spectrometry.
Journal of bioinformatics and computational biology 2005;3(2):455-76.
2005: Liu Zhenqiu; Chen Dechang; Bensmail Halima; Xu Ying
Clustering gene expression data with kernel principal components.
Journal of bioinformatics and computational biology 2005;3(2):303-16.
2005: Chen Zhi-Zhong; Lin Guohui; Rizzi Romeo; Wen Jianjun; Xu Dong; Xu Ying; Jiang Tao
More reliable protein NMR peak assignment via improved 2-interval scheduling.
Journal of computational biology : a journal of computational molecular cell biology 2005;12(2):129-46.
2005: Yan Bo; Pan Chongle; Olman Victor N; Hettich Robert L; Xu Ying
A graph-theoretic approach for the separation of b and y ions in tandem mass spectra.
Bioinformatics (Oxford, England) 2005;21(5):563-74.
2005: Liu Zhenqiu; Chen Dechang; Xu Ying; Liu Jian
Logistic support vector machines and their application to gene expression data.
International journal of bioinformatics research and applications 2005;1(2):169-82.
2005: Wu Hongwei; Mao Fenglou; Su Zhengchang; Olman Victor; Xu Ying
Prediction of functional modules based on gene distributions in microbial genomes.
Genome informatics. International Conference on Genome Informatics 2005;16(2):247-59.
2005: Chen Zhong; Xu Ying
Multi-scale hierarchical structure prediction of helical transmembrane proteins.
Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference 2005;():203-7.
2005: Wu Hongwei; Mao Fenglou; Olman Victor; Xu Ying
Accurate prediction of orthologous gene groups in microbes.
Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference 2005;():73-9.
2005: Su Zhengchang; Olman Victor; Mao Fenglou; Xu Ying
Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis.
Nucleic acids research 2005;33(16):5156-71.
2005: Wu Hongwei; Su Zhengchang; Mao Fenglou; Olman Victor; Xu Ying
Prediction of functional modules based on comparative genome analysis and Gene Ontology application.
Nucleic acids research 2005;33(9):2822-37.
2005: Liu Zhijie; Mao Fenglou; Guo Jun-tao; Yan Bo; Wang Peng; Qu Youxing; Xu Ying
Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential.
Nucleic acids research 2005;33(2):546-58.
2004: Xu Dong; Xu Ying
Protein databases on the internet.
Current protocols in protein science / editorial board, John E. Coligan ... [et al.] 2004;Chapter 2():Unit 2.6.
2004: Xu Dong; Xu Ying
Protein databases on the internet.
Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] 2004;Chapter 19():Unit 19.4.
2004: Guo Jun-tao; Wetzel Ronald; Xu Ying
Molecular modeling of the core of Abeta amyloid fibrils.
Proteins 2004;57(2):357-64.
2004: Gupta Vibha; Peterson Cynthia B; Dice Lezlee T; Uchiki Tomoaki; Racca Joseph; Guo Jun-tao; Xu Ying; Hettich Robert; Zhao Xiaolan; Rothstein Rodney; Dealwis Chris G
Sml1p is a dimer in solution: characterization of denaturation and renaturation of recombinant Sml1p.
Biochemistry 2004;43(26):8568-78.
2004: Guo Jun-tao; Ellrott Kyle; Chung Won Jae; Xu Dong; Passovets Serguei; Xu Ying
PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction.
Nucleic acids research 2004;32(Web Server issue):W522-5.
2004: Tiquia Sonia M; Wu Liyou; Chong Song C; Passovets Sergei; Xu Dong; Xu Ying; Zhou Jizhong
Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples.
BioTechniques 2004;36(4):664-70, 672, 674-5.
2004: Zou Yue; Ma Huaxian; Minko Irina G; Shell Steven M; Yang Zhengguan; Qu Youxing; Xu Ying; Geacintov Nicholas E; Lloyd R Stephen
DNA damage recognition of mutated forms of UvrB proteins in nucleotide excision repair.
Biochemistry 2004;43(14):4196-205.
2004: Razumovskaya Jane; Olman Victor; Xu Dong; Uberbacher Edward C; VerBerkmoes Nathan C; Hettich Robert L; Xu Ying
A computational method for assessing peptide- identification reliability in tandem mass spectrometry analysis with SEQUEST.
Proteomics 2004;4(4):961-9.
2004: Williams Angela D; Portelius Erik; Kheterpal Indu; Guo Jun-tao; Cook Kelsey D; Xu Ying; Wetzel Ronald
Mapping abeta amyloid fibril secondary structure using scanning proline mutagenesis.
Journal of molecular biology 2004;335(3):833-42.
2004: Olman Victor; Peng Hanchuan; Su Zhengchang; Xu Ying
Mapping of microbial pathways through constrained mapping of orthologous genes.
Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference 2004;():363-70.
2004: Yan Bo; Pan Chongle; Olman Victor N; Hettich Robert L; Xu Ying
Separation of ion types in tandem mass spectrometry data interpretation -- a graph-theoretic approach.
Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference 2004;():236-44.
2004: Chen Xin; Su Zhengchang; Xu Ying; Jiang Tao
Computational prediction of operons in Synechococcus sp. WH8102.
Genome informatics. International Conference on Genome Informatics 2004;15(2):211-22.
2004: Chen X; Su Z; Dam P; Palenik B; Xu Y; Jiang T
Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome.
Nucleic acids research 2004;32(7):2147-57.
2004: Qu Y; Guo J T; Olman V; Xu Y
Protein fold recognition through application of residual dipolar coupling data.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2004;():459-70.
2004: Qu Youxing; Guo Jun-tao; Olman Victor; Xu Ying
Protein structure prediction using sparse dipolar coupling data.
Nucleic acids research 2004;32(2):551-61.
2003: Shah Manesh; Passovets Sergei; Kim Dongsup; Ellrott Kyle; Wang Li; Vokler Inna; LoCascio Philip; Xu Dong; Xu Ying
A computational pipeline for protein structure prediction and analysis at genome scale.
Bioinformatics (Oxford, England) 2003;19(15):1985-96.
2003: Xu Dong; Olman Victor; Wang Li; Xu Ying
EXCAVATOR: a computer program for efficiently mining gene expression data.
Nucleic acids research 2003;31(19):5582-9.
2003: Kim Dongsup; Xu Dong; Guo Jun-tao; Ellrott Kyle; Xu Ying
PROSPECT II: protein structure prediction program for genome-scale applications.
Protein engineering 2003;16(9):641-50.
2003: Lin Guohui; Xu Dong; Chen Zhi-Zhong; Jiang Tao; Wen Jianjun; Xu Ying
Computational assignment of protein backbone NMR peaks by efficient bounding and filtering.
Journal of bioinformatics and computational biology 2003;1(2):387-409.
2003: Sun Huandong; Li Ming; Xu Ying
MOLVIE: an interactive visualization environment for molecular structures.
Computer methods and programs in biomedicine 2003;71(1):85-90.
2003: Xu Jinbo; Li Ming; Kim Dongsup; Xu Ying
RAPTOR: optimal protein threading by linear programming.
Journal of bioinformatics and computational biology 2003;1(1):95-117.
2003: Olman Victor; Xu Dong; Xu Ying
CUBIC: identification of regulatory binding sites through data clustering.
Journal of bioinformatics and computational biology 2003;1(1):21-40.
2003: Guo Jun-tao; Xu Dong; Kim Dongsup; Xu Ying
Improving the performance of DomainParser for structural domain partition using neural network.
Nucleic acids research 2003;31(3):944-52.
2003: Su Zhengchang; Dam Phuongan; Chen Xin; Olman Victor; Jiang Tao; Palenik Brian; Xu Ying
Computational inference of regulatory pathways in microbes: an application to phosphorus assimilation pathways in Synechococcus sp. WH8102.
Genome informatics. International Conference on Genome Informatics 2003;14():3-13.
2003: Xu Dong; Kim Dongsup; Dam Phuongan; Shah Manesh; Uberbacher Edward C; Xu Ying
Characterization of protein structure and function at genome scale with a computational prediction pipeline.
Genetic engineering 2003;25():269-93.
2003: Yost Christal; Hauser Loren; Larimer Frank; Thompson Dorothea; Beliaev Alexander; Zhou Jizhong; Xu Ying; Xu Dong
A computational study of Shewanella oneidensis MR-1: structural prediction and functional inference of hypothetical proteins.
Omics : a journal of integrative biology 2003;7(2):177-91.
2003: Olman Victor; Xu Dong; Xu Ying
Identification of regulatory binding sites using minimum spanning trees.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2003;():327-38.
2003: Xu Jinbo; Li Ming; Lin Guohui; Kim Dongsup; Xu Ying
Protein threading by linear programming.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2003;():264-75.
2002: Xu Dong; Li Guangshan; Wu Liyou; Zhou Jizhong; Xu Ying
PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis.
Bioinformatics (Oxford, England) 2002;18(11):1432-7.
2002: Xu Ying; Olman Victor; Xu Dong
Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees.
Bioinformatics (Oxford, England) 2002;18(4):536-45.
2002: Lin Guohui; Xu Dong; Chen Zhi-Zhong; Jiang Tao; Wen Jianjun; Xu Ying
An efficient branch-and-bound algorithm for the assignment of protein backbone NMR peaks.
Proceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference 2002;1():165-74.
2002: Buchanan Michelle V; Larimer Frank W; Wiley H Steven; Kennel Steve J; Squier Thomas J; Ramsey J Michael; Rodland Karin D; Hurst Gregory B; Smith Richard D; Xu Ying; Dixon David; Doktycz Mitchel J; Colson Steve; Gesteland Ray; Giometti Carol; Young Malin; Giddings Michael
Genomes to Life "Center for Molecular and Cellular Systems": a research program for identification and characterization of protein complexes.
Omics : a journal of integrative biology 2002;6(4):287-303.
2002: Heffelfinger Grant S; Martino Anthony; Gorin Andrey; Xu Ying; Rintoul Mark D; Geist Al; Al-Hashimi Hashim M; Davidson George S; Faulon Jean Loup; Frink Laurie J; Haaland David M; Hart William E; Jakobsson Erik; Lane Todd; Li Ming; Locascio Phil; Olken Frank; Olman Victor; Palenik Brian; Plimpton Steven J; Roe Diana C; Samatova Nagiza F; Shah Manesh; Shoshoni Arie; Strauss Charlie E M; Thomas Edward V; Timlin Jerilyn A; Xu Dong
Carbon sequestration in Synechococcus Sp.: from molecular machines to hierarchical modeling.
Omics : a journal of integrative biology 2002;6(4):305-30.
2001: Xu D; Baburaj K; Peterson C B; Xu Y
Model for the three-dimensional structure of vitronectin: predictions for the multi-domain protein from threading and docking.
Proteins 2001;44(3):312-20.
2001: Xu D; Xu Y
Protein tertiary structure prediction.
Current protocols in protein science / editorial board, John E. Coligan ... [et al.] 2001;Chapter 2():Unit2.7.
2001: Xu D; Crawford O H; LoCascio P F; Xu Y
Application of PROSPECT in CASP4: characterizing protein structures with new folds.
Proteins 2001;Suppl 5():140-8.
2001: Xu Y; Olman V; Xu D
Minimum spanning trees for gene expression data clustering.
Genome informatics. International Conference on Genome Informatics 2001;12():24-33.
2000: Xu Y; Xu D; Gabow H N;
Protein domain decomposition using a graph-theoretic approach.
Bioinformatics (Oxford, England) 2000;16(12):1091-104.
2000: Xu Y; Xu D
Protein threading using PROSPECT: design and evaluation.
Proteins 2000;40(3):343-54.
2000: Xu D; Xu Y; Uberbacher E C
Computational tools for protein modeling.
Current protein & peptide science 2000;1(1):1-21.
2000: Xu D; Unseren M A; Xu Y; Uberbacher E C
Sequence-structure specificity of a knowledge based energy function at the secondary structure level.
Bioinformatics (Oxford, England) 2000;16(3):257-68.
2000: Xu Y; Xu D; Crawford O H; Einstein J R
A computational method for NMR-constrained protein threading.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(3-4):449-67.
1999: Xu Y; Xu D; Crawford O H; Einstein; Larimer F; Uberbacher E; Unseren M A; Zhang G
Protein threading by PROSPECT: a prediction experiment in CASP3.
Protein engineering 1999;12(11):899-907.
1999: Xu Y; Singer M A; Lindquist S
Maturation of the tyrosine kinase c-src as a kinase and as a substrate depends on the molecular chaperone Hsp90.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(1):109-14.
1998: Xu Y; Xu D; Uberbacher E C
An efficient computational method for globally optimal threading.
Journal of computational biology : a journal of computational molecular cell biology 1998;5(3):597-614.
1998: Uberbacher E C; Xu Y; Shah M B; Olman V; Parang M; Mural R J
An editing environment for DNA sequence analysis and annotation (extended abstract).
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1998;():217-27.
1997: Xu Y; Mural R J; Uberbacher E C
Inferring gene structures in genomic sequences using pattern recognition and expressed sequence tags.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1997;5():344-53.
1997: Xu Y; Uberbacher E C
Automated gene identification in large-scale genomic sequences.
Journal of computational biology : a journal of computational molecular cell biology 1997;4(3):325-38.
1996: Xu Y; Uberbacher E C
A polynomial-time algorithm for a class of protein threading problems.
Computer applications in the biosciences : CABIOS 1996;12(6):511-7.
1996: Matis S; Xu Y; Shah M; Guan X; Einstein J R; Mural R; Uberbacher E
Detection of RNA polymerase II promoters and polyadenylation sites in human DNA sequence.
Computers & chemistry 1996;20(1):135-40.
1996: Xu Y; Mural R J; Uberbacher E C
An iterative algorithm for correcting sequencing errors in DNA coding regions.
Journal of computational biology : a journal of computational molecular cell biology 1996;3(3):333-44.
1996: Xu Y; Uberbacher E C
Gene prediction by pattern recognition and homology search.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1996;4():241-51.
1996: Uberbacher E C; Xu Y; Mural R J
Discovering and understanding genes in human DNA sequence using GRAIL.
Methods in enzymology 1996;266():259-81.
1995: Xu Y; Mural R J; Uberbacher E C
Correcting sequencing errors in DNA coding regions using a dynamic programming approach.
Computer applications in the biosciences : CABIOS 1995;11(2):117-24.
1994: Xu Y; Mural R J; Uberbacher E C
Constructing gene models from accurately predicted exons: an application of dynamic programming.
Computer applications in the biosciences : CABIOS 1994;10(6):613-23.
1994: Xu Y; Mural R; Shah M; Uberbacher E
Recognizing exons in genomic sequence using GRAIL II.
Genetic engineering 1994;16():241-53.
1994: Xu Y; Einstein J R; Mural R J; Shah M; Uberbacher E C
An improved system for exon recognition and gene modeling in human DNA sequences.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1994;2():376-84.

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