Weichaun Yu

Summary

Affiliation: Clear Water Bay
Country: China

Publications

  1. ncbi request reprint Detecting and aligning peaks in mass spectrometry data with applications to MALDI
    Weichuan Yu
    Department of Molecular Biophysics and Biochemistry, Yale University, Suite 503, 300 George Street, New Haven, CT 06520, USA
    Comput Biol Chem 30:27-38. 2006
  2. pmc Using microPET imaging in quantitative verification of the acupuncture effect in ischemia stroke treatment
    Huafeng Liu
    State Key Laboratory of Modern Optical Instrumentation, Department of Optical Engineering, Zhejiang University, Hangzhou, Zhejiang, China
    Sci Rep 3:1070. 2013
  3. pmc The complete compositional epistasis detection in genome-wide association studies
    Xiang Wan
    Department of Computer Science and Institute of Theoretical and Computational Study, Hong Kong Baptist University, Hong Kong, China
    BMC Genet 14:7. 2013
  4. pmc Identifying main effects and epistatic interactions from large-scale SNP data via adaptive group Lasso
    Can Yang
    Laboratory for Bioinformatics and Computational Biology, Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, PR China
    BMC Bioinformatics 11:S18. 2010
  5. pmc A hidden two-locus disease association pattern in genome-wide association studies
    Can Yang
    Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong
    BMC Bioinformatics 12:156. 2011
  6. pmc Motif-All: discovering all phosphorylation motifs
    Zengyou He
    School of Software, Dalian University of Technology, Dalian, China
    BMC Bioinformatics 12:S22. 2011
  7. pmc Score regularization for peptide identification
    Zengyou He
    School of Software, Dalian University of Technology, Dalian, China
    BMC Bioinformatics 12:S2. 2011
  8. pmc The choice of null distributions for detecting gene-gene interactions in genome-wide association studies
    Can Yang
    Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong
    BMC Bioinformatics 12:S26. 2011
  9. pmc Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis
    Chao Yang
    Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, PR China
    BMC Bioinformatics 10:4. 2009
  10. pmc MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study
    Xiang Wan
    Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong, PR China
    BMC Bioinformatics 10:13. 2009

Detail Information

Publications24

  1. ncbi request reprint Detecting and aligning peaks in mass spectrometry data with applications to MALDI
    Weichuan Yu
    Department of Molecular Biophysics and Biochemistry, Yale University, Suite 503, 300 George Street, New Haven, CT 06520, USA
    Comput Biol Chem 30:27-38. 2006
    ..Additional comparisons also demonstrate that our method has a similar performance as the hierarchical clustering method, although the implementations of these methods are different...
  2. pmc Using microPET imaging in quantitative verification of the acupuncture effect in ischemia stroke treatment
    Huafeng Liu
    State Key Laboratory of Modern Optical Instrumentation, Department of Optical Engineering, Zhejiang University, Hangzhou, Zhejiang, China
    Sci Rep 3:1070. 2013
    ..Statistical tests also confirmed that acupuncture was more effective than random stimulus in improving the metabolic recovery after stroke...
  3. pmc The complete compositional epistasis detection in genome-wide association studies
    Xiang Wan
    Department of Computer Science and Institute of Theoretical and Computational Study, Hong Kong Baptist University, Hong Kong, China
    BMC Genet 14:7. 2013
    ..However, due to the high computational cost involved, most methods focus on specific epistasis models, making the potential loss of power when the underlying epistasis models are not examined in these analyses...
  4. pmc Identifying main effects and epistatic interactions from large-scale SNP data via adaptive group Lasso
    Can Yang
    Laboratory for Bioinformatics and Computational Biology, Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, PR China
    BMC Bioinformatics 11:S18. 2010
    ..For the analysis of high throughput data, the main difficulty is that the number of SNPs far exceeds the number of samples. This difficulty is amplified when identifying interactions...
  5. pmc A hidden two-locus disease association pattern in genome-wide association studies
    Can Yang
    Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong
    BMC Bioinformatics 12:156. 2011
    ..This phenomenon is due to the existence of unfaithfulness: the marginal effects of correlated SNPs do not express their significant joint effects faithfully due to the correlation cancelation...
  6. pmc Motif-All: discovering all phosphorylation motifs
    Zengyou He
    School of Software, Dalian University of Technology, Dalian, China
    BMC Bioinformatics 12:S22. 2011
    ..To date, people have gathered large amounts of phosphorylation data, making it possible to perform substrate-driven motif discovery using data mining techniques...
  7. pmc Score regularization for peptide identification
    Zengyou He
    School of Software, Dalian University of Technology, Dalian, China
    BMC Bioinformatics 12:S2. 2011
    ..Thus, it is critical to develop new post-processing techniques that can distinguish true identifications from false identifications effectively...
  8. pmc The choice of null distributions for detecting gene-gene interactions in genome-wide association studies
    Can Yang
    Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong
    BMC Bioinformatics 12:S26. 2011
    ..In the third stage, the significance of the identified interaction patterns is evaluated by hypothesis testing...
  9. pmc Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis
    Chao Yang
    Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, PR China
    BMC Bioinformatics 10:4. 2009
    ..The main objective of this paper is to provide such a survey and to compare the performance of single spectrum based peak detection methods...
  10. pmc MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study
    Xiang Wan
    Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong, PR China
    BMC Bioinformatics 10:13. 2009
    ....
  11. pmc Semi-supervised protein subcellular localization
    Qian Xu
    Program of Bioengineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
    BMC Bioinformatics 10:S47. 2009
    ..However, in real world cases, it is laborious, expensive and time-consuming to experimentally determine the subcellular localization of a protein and prepare instances of labeled data...
  12. ncbi request reprint Improving mass spectrometry peak detection using multiple peak alignment results
    Weichaun Yu
    Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
    J Proteome Res 7:123-9. 2008
    ..Consequently, the discovery of cancer biomarkers also benefits from this improvement. Source code and additional data are available at: http://www.ece.ust.hk/ approximately eeyu/mspeak.htm...
  13. ncbi request reprint A new protocol of analyzing isotope-coded affinity tag data from high-resolution LC-MS spectrometry
    Weichuan Yu
    Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
    Comput Biol Chem 31:215-21. 2007
    ..Compared with current approaches that choose peaks with high intensity values for tandem MS/MS scanning, the new protocol can improve the scanning efficiency and accuracy...
  14. ncbi request reprint Multiple peak alignment in sequential data analysis: a scale-space-based approach
    Weichuan Yu
    Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Sai Kung, Kowloon, Hong Kong
    IEEE/ACM Trans Comput Biol Bioinform 3:208-19. 2006
    ..e., a candidate is considered either as a peak or as a nonpeak) with a quantitative scoring measure-based approach (i.e., we assign to each candidate a possibility of being a peak)...
  15. pmc BOOST: A fast approach to detecting gene-gene interactions in genome-wide case-control studies
    Xiang Wan
    Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, China
    Am J Hum Genet 87:325-40. 2010
    ..We believe that our method can serve as a computationally and statistically useful tool in the coming era of large-scale interaction mapping in genome-wide case-control studies...
  16. doi request reprint Optimization-based peptide mass fingerprinting for protein mixture identification
    Zengyou He
    Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong
    J Comput Biol 17:221-35. 2010
    ....
  17. doi request reprint A regularized method for peptide quantification
    Chao Yang
    Laboratory for Bioinformatics and Computational Biology, Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
    J Proteome Res 9:2705-12. 2010
    ..A suggestion about parameter selection is given based on the discussion of variance and bias. Matlab source codes and detailed experimental results are available at http://bioinformatics.ust.hk/PeptideQuant/peptidequant.htm...
  18. doi request reprint Predictive rule inference for epistatic interaction detection in genome-wide association studies
    Xiang Wan
    Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
    Bioinformatics 26:30-7. 2010
    ..In this work, we propose a novel learning approach (SNPRuler) based on the predictive rule inference to find disease-associated epistatic interactions...
  19. doi request reprint Improving peptide identification with single-stage mass spectrum peaks
    Zengyou He
    Laboratory for Bioinformatics and Computational Biology, Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
    Bioinformatics 25:2969-74. 2009
    ..To address this issue, we like to improve peptide identification by using additional information from other data sources...
  20. doi request reprint SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies
    Can Yang
    Laboratory for Bioinformatics and Computational Biology, Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
    Bioinformatics 25:504-11. 2009
    ..Hence, it is desirable to develop an effective method to search epistatic interactions in genome-wide scale...
  21. doi request reprint Peak bagging for peptide mass fingerprinting
    Zengyou He
    Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
    Bioinformatics 24:1293-9. 2008
    ..Thus, it is desirable to develop PMF-based algorithm with higher protein identification accuracy to facilitate proteome research...
  22. ncbi request reprint MALDI-MS data analysis for disease biomarker discovery
    Weichuan Yu
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
    Methods Mol Biol 328:199-216. 2006
    ..After that, we show some application examples using an ovarian sera cancer dataset. Finally, we discuss the limitations of current approaches and possible future research directions...
  23. ncbi request reprint Towards pointwise motion tracking in echocardiographic image sequences--comparing the reliability of different features for speckle tracking
    Weichuan Yu
    Department of Molecular Biophysics and Biochemistry, Yale University, 300 George Street, Suite 503, New Haven, CT 06511, USA
    Med Image Anal 10:495-508. 2006
    ..g., larger than 2% compression). The use of a band-passed filtered feature does not result in significant improvement in tracking...
  24. ncbi request reprint Combinative multi-scale level set framework for echocardiographic image segmentation
    Ning Lin
    Department of Electrical Engineering, Yale University, BML 322, PO Box 208042, New Haven, CT 06520 8042, USA
    Med Image Anal 7:529-37. 2003
    ..This constraint functions similar to a traditional shape prior. Experimental results validate this combinative framework...