Research Topics
Species | Zheng YuanSummaryAffiliation: University of Queensland Country: Australia Publications
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Detail Information
Publications
Prediction of protein solvent accessibility using support vector machinesZheng Yuan
Institute for Molecular Bioscience and ARC Special Centre for Functional and Applied Genomics, The University of Queensland, Brisbane, Australia
Proteins 48:566-70. 2002..In addition, our results further suggest that this system may be combined with other prediction methods to achieve more reliable results, and that the Support Vector Machine method is a very useful tool for biological sequence analysis...- Predicting the solvent accessibility of transmembrane residues from protein sequenceZheng Yuan
Institute for Molecular Bioscience and ARC Centre in Bioinformatics, The University of Queensland, St Lucia, 4072, Australia
J Proteome Res 5:1063-70. 2006..This approach can be used to annotate the membrane proteins in proteomes to provide extra structural and functional information... - Better prediction of protein contact number using a support vector regression analysis of amino acid sequenceZheng Yuan
Institute for Molecular Bioscience, ARC Centre in Bioinformatics, The University of Queensland, St Lucia, 4072, Australia
BMC Bioinformatics 6:248. 2005..In this study, we provide a more accurate contact number prediction method from protein primary sequence... - Prediction of protein B-factor profilesZheng Yuan
Institute for Molecular Bioscience and ARC Centre in Bioinformatics, The University of Queensland, St Lucia, Australia
Proteins 58:905-12. 2005..flexible). For almost all predicted B-factor thresholds, prediction accuracies (percent of correctly predicted residues) are greater than 70%. These results exceed the best results of other sequence-based prediction methods... - Prediction of protein accessible surface areas by support vector regressionZheng Yuan
Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, St Lucia, Australia
Proteins 57:558-64. 2004..7 A(2) and median absolute error is 36.31 A(2)). Our work suggests that the SVR approach can be directly applied to the ASA prediction where data preclassification has been used... - SVMtm: support vector machines to predict transmembrane segmentsZheng Yuan
ARC Centre in Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, 4072, Australia
J Comput Chem 25:632-6. 2004..This method can be used to complement current transmembrane helix prediction methods and can be used for consensus analysis of entire proteomes. The predictor is located at http://genet.imb.uq.edu.au/predictors/SVMtm... - Computational differentiation of N-terminal signal peptides and transmembrane helicesZheng Yuan
ARC Centre in Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4066, Australia
Biochem Biophys Res Commun 312:1278-83. 2003..85). The method can be used to complement current transmembrane protein prediction and signal peptide prediction methods to improve their prediction accuracies... - Quantifying the relationship of protein burying depth and sequenceZheng Yuan
Institute for Molecular Bioscience and ARC Centre in Bioinformatics, The University of Queensland, Brisbane, Australia
Proteins 70:509-16. 2008..The methods used to estimate the sequence-depth functions are expected to become more useful in the investigation of protein structures and folding mechanism... - Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structureJiangning Song
Advanced Computational Modelling Centre, The University of Queensland, Brisbane, QLD 4072, Australia
Bioinformatics 23:3147-54. 2007..Therefore, there is a great need to develop computational methods capable of accurately predicting disulfide connectivity patterns in proteins that could have potentially important applications... - Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structuresMikael Boden
School of Information Technology and Electrical Engineering, The University of Queensland, QLD 4072, St Lucia, Australia
BMC Bioinformatics 7:68. 2006..e. assigning probabilities to the conformational states of a residue. We train our methods using data derived from high-quality NMR models... - MemO: a consensus approach to the annotation of a protein's membrane organizationMelissa J Davis
Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, St. Lucia, 4072, Australia
In Silico Biol 6:387-99. 2006.... - Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure informationJiangning Song
Advanced Computational Modelling Centre, The University of Queensland, Brisbane QLD 4072, Australia
BMC Bioinformatics 7:124. 2006..Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function... - Prediction of Golgi Type II membrane proteins based on their transmembrane domainsZheng Yuan
Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, University of Queensland, St Lucia, 4072, Australia
Bioinformatics 18:1109-15. 2002..3% or 85.2%, respectively on our redundancy-reduced data sets. AVAILABILITY: See http://microarray.imb.uq.edu.au/golgi/.. - Exploiting structural and topological information to improve prediction of RNA-protein binding sitesStefan R Maetschke
Institute for Molecular Bioscience, University of Queensland, QLD 4072, Australia
BMC Bioinformatics 10:341. 2009..Particularly, different geometrical and network topological properties of protein structures are evaluated to improve interface residue prediction accuracy... - tonB3 is required for normal twitching motility and extracellular assembly of type IV piliBixing Huang
Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
J Bacteriol 186:4387-9. 2004..Three mutants with Tn5-B21 insertion in tonB3 (PA0406) of Pseudomonas aeruginosa exhibited defective twitching motility and reduced assembly of extracellular pili. These defects could be complemented with wild-type tonB3... - The mouse secretome: functional classification of the proteins secreted into the extracellular environmentSean M Grimmond
Institute for Molecular Bioscience and ARC Special Research Centre for Functional and Applied Genomics, University of Queensland, St Lucia 4072, Australia
Genome Res 13:1350-9. 2003..To highlight the utility of this information, we discuss the CUB domain-containing protein family... - Determining a maximum-tolerated schedule of a cytotoxic agentThomas M Braun
Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, USA
Biometrics 61:335-43. 2005.... - Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and ArabidopsisXiaoxing Li
Shanghai Jiao Tong University Shanghai Institutes for Biological Sciences Pennsylvania State University Joint Center for Life Sciences, Shanghai Jiao Tong University, Shanghai, People s Republic of China, 200240
Plant Physiol 141:1167-84. 2006..In addition, similar expression patterns suggest functional conservation between some rice bHLH genes and their close Arabidopsis homologs... - Flexibility analysis of enzyme active sites by crystallographic temperature factorsZheng Yuan
National Laboratory of Biomacromolecules, Institute of Biophysics, Academia Sinica, Beijing 100101, China
Protein Eng 16:109-14. 2003.... - Mouse proteome analysisAlexander Kanapin
EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
Genome Res 13:1335-44. 2003..The analysis of the membrane organization within the transcriptome of multiple eukaryotes provides valuable statistics about the distribution of secretory and transmembrane proteins.. - Combining multiple biomarker models in logistic regressionZheng Yuan
Eli Lilly and Company, Indianapolis, Indiana 46285, USA
Biometrics 64:431-9. 2008..Simulation studies are performed to assess the finite-sample properties of the proposed model-combining method. It is illustrated with an application to data from an immunohistochemical study in prostate cancer... - The rice tapetum degeneration retardation gene is required for tapetum degradation and anther developmentNa Li
Shanghai Jiao Tong University-Shanghai Institutes for Biological Sciences-Pensylvania State University Joint Center for Life Sciences, Shanghai 200240, China
Plant Cell 18:2999-3014. 2006..These results indicate that TDR is a key component of the molecular network regulating rice tapetum development and degeneration... - Comparing the small sample performance of several variance estimators under competing risksThomas M Braun
Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
Stat Med 26:1170-80. 2007..All but one of the martingale theory-based estimators tend to perform poorly in small samples, tending to either overestimate or underestimate the empirical variance in samples of fewer than 100 subjects... - Distribution of 19 major virulence genes in Legionella pneumophila serogroup 1 isolates from patients and water in Queensland, AustraliaBixing Huang
Public Health Microbiology Laboratory, Queensland Health Scientific Services, Coopers Plains, QLD 4108, Australia
J Med Microbiol 55:993-7. 2006..It was found that a PCR detection test strategy with lvh and rtxA as pathogenesis markers would be useful for determining the infection potential of an isolate... - Inhibition of GABA shunt enzymes' activity by 4-hydroxybenzaldehyde derivativesYun-Hai Tao
Institute of Materia Medica, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, China
Bioorg Med Chem Lett 16:592-5. 2006..This suggested that the presence of the benzene ring may be accepted by the active site of both enzymes, HBA and HBM may be considered as lead compounds to design novel GABA-T inhibitors...