Publications of Weichuan Yu

1 denotes student (e.g., C. Yang1), 2 denotes postdoc/RA (e.g., Z. He2), and 3 denotes former supervisor (e.g., H. Zhao3)

 

Books

1.      W. Yu.  Local Orientation Analysis in Images and Image Sequences Using Steerable Filters. Shaker Verlag, Aachen, Germany, February 2001,  ISBN 3-8265-8442-2.

2.      W. Yu, M. Zhang, L. Wang, and Y. Song,  Editors,  Proceedings of the 3rd International Conference on BioMedical Engineering and Informatics, Yantai University Press, China, 2010, ISBN 978-1-4244-6496-8.

     

 

      Book Chapters

B1.   W. Yu, B. Wu, T. Huang, X. Li, K. Williams, and H. Zhao3.  Statistical Methods In Proteomics. In Springer Handbook of Engineering Statistics (editor: H. Pham),  Springer-Verlag, London,  UK,  pp.623-638, 2006.

      B2.    W. Yu,  B. Wu, J. Liu, X. Li, K. Williams, and H. Zhao3. MALDI-MS Data Analysis for Disease Biomarker Discovery. In New and Emerging Proteomics Techniques (editors: D. Nedelkov and R. W. Nelson),  Humana Press Inc., Totowa,  New Jersey, USA, pp.199-216, 2006.

      B3.     N. Lin, W. Yu,  and J.S. Duncan3. Echocardiographic Image Analysis. In Medical Imaging Systems (editor: C.T. Leondes), World Scientific Publishing Company, New Jersey, USA, pp.89-108, 2005.

 

 

Refereed Journal papers

J57.   C. Zhang1, T. Liang, P. K.T. Mok, and W. Yu.  FPGA Implementation of the Coupled Filtering Method and the Affine Warping Method, IEEE Transactions on NanoBioscience, in press.

J56.   W. Jiang1 and W. Yu. Jointly determining significance levels of primary and replication studies by controlling the false discovery rate in two-stage genome-wide association studies, Statistical Methods

         in Medical Research, Published on January 8, 2017.  doi: 10.1177/0962280216687168

J55.   W. Jiang1 and W. Yu. Controlling the joint local false discovery rate is more powerful than meta-analysis methods in joint analysis of summary statistics from multiple genome-wide association studies, Bioinformatics, 33(4):500-507. Published on December 5, 2016. doi: 10.1093/bioinformatics/btw690.

J54.   F. Yu1, N. Li, and W. Yu. PIPI: PTM-Invariant Peptide Identification Using Coding Method, Journal of Proteome Research, 15(12):4423-4435, 2016. Published on October 17, 2016.  

J53.   W. Jiang1, J. Xue, and W. Yu. What is the probability of replicating a statistically significant association in Genome-Wide Association Studies, Briefings in Bioinformatics, published on 28 September 2016, DOI: https://doi.org/10.1093/bib/bbw091

J52.   X. Zhu, F. Yu1, Z. Yang, S. Liu, C. Dai, X. Lu, C. Liu, W. Yu*, and N. Li. Application of in planta chemical cross-linking in mass spectrometry¡Vbased analysis of the tertiary structure of a plant ATPase subunit, Proteomics, 16:1915-1927,2016.  (* co-corresponding author.  F. Yu1 is the co-first author).

J51.   F. Yu1, N. Li, and W. Yu. ECL: An Exhaustive Search Tool for the Identification of Cross-Linked Peptides Using Whole Database, BMC Bioinformatics, 17:217, 2016.

J50.   W. Jiang1 and W. Yu. Power Estimation and Sample Size Determination for Replication Studies of Genome-Wide Association Studies, BMC Genomics, 17(Suppl 1):3, 2016.  

J49.   G. Yang1, W. Jiang1, Q. Yang, and W. Yu. PBOOST: a GPU based tool for parallel permutation tests in genome-wide association studies. Bioinformatics, 31:1460-1462, 2015.

J48.   X. Zhou1, C. Yang, H. Zhao3, and W. Yu. Low-Rank Modeling and Its Applications in Image Analysis. ACM Computing Surveys, 47, 2, Article 36, 33 pages, 2014.

J47.  X. Zhou1, J. Liu, X. Wan, and W. Yu. Piecewise-constant and Low-rank Approximation for Identification of Recurrent Copy Number Variations. Bioinformatics, 30:1943-1949, 2014

J46.  Ch. Yang1, Z. He, and W. Yu. A Combinatorial Perspective of the Protein Inference Problem. IEEE/ACM Trans. Computational Biology and Bioinformatics, 10:1542-1547, 2013.

J45.  X. Wan, C. Yang, Q. Yang, H. Zhao3, and W. Yu. The Complete Compositional Epistasis Detection in Genome-wide Association Studies. BMC Genetics, 14:7, 2013. 

J44.  X. Zhou1, L. Sun, Y. Yu, W. Qiu, C. Lien, K. Shung, and W. Yu. Ultrasound Bio-Microscopic Image Segmentation for Evaluation of Zebrafish Cardiac Function. IEEE Trans. Ultrasonics, Ferroelectrics,

        and Frequency Control, 60:718-726,2013.

J43.   X. Wan2, C. Yang, Q. Yang, H. Zhao3, and W. Yu. HapBoost: A fast approach to boosting haplotype association analyses in genome-wide association studies. IEEE/ACM Trans. Computational Biology and Bioinformatics, 10:207-212, 2013.

J42.  H. Liu, X. Shen, H. Tang, J. Li, T. Xiang, and W. Yu. Using MicroPET Imaging in Quantitative Verification of the Acupuncture Effect in Ischemia Stroke Treatment. Scientific Reports, 3:1070, 2013

J41.   X. Zhou1, C. Yang1,  X. Wan2, H. Zhao3 and W. Yu. Multi-sample aCGH Data Analysis via Total Variation and Spectral Regularization. IEEE/ACM Trans. Computational Biology and Bioinformatics, 10:230-235, 2013.

J40.   T. Liang1, L. Yung1, and W. Yu. On Feature Motion Decorrelation in Ultrasound Speckle Tracking. IEEE Trans. Medical Imaging,32:435-448, 2013.

J39.  X. Zhou1, C. Yang1, and W. Yu. Moving Object Detection by Detecting Contiguous Outliers in the Low-Rank Representation. IEEE Trans. Pattern Analysis and Machine Intelligence,35:597-610, 2013.

J38.  Z. He2, R.Z. Qi, and W. Yu. Bioinformatic Analysis of Data Generated from MALDI Mass Spectrometry for Biomarker Discovery. Topics in Current Chemistry, 331:193-209, 2013.

J37.   Ch. Yang1, C. Yang1, Z. He, and W. Yu. Peptide Re-ranking with Protein-peptide Correspondence and Precursor Peak Intensity Information. IEEE/ACM Trans. Computational Biology and Bioinformatics, 9:1212-1219, 2012.

J36.   T. Huang, J. Wang, W. Yu and Z. He. Protein Inference: A Review. Briefings in Bioinformatics, 13:586-614, 2012.

J35.  X. Wan2, C. Yang1, and W. Yu. Comments on ¡§An empirical comparison of several recent epistatic interaction detection methods¡¨.  Bioinformatics, 28:145-146, 2012.  

J34.  C. Yang1, X. Zhou1, X. Wan2, Q. Yang, H. Xue, and W. Yu. Identifying Disease-associated SNP Clusters via Contiguous Outlier Detection. Bioinformatics, 27:2578-2585, 2011.  

J33.   C. Yang1, X. Wan2, Q. Yang, H. Xue, N. Tang, and W. Yu. A Hidden Two-locus Disease Association Pattern in Genome-wide Association Studies. BMC Bioinformatics, 12:156, 2011.

J32.   L. Yung1, C. Yang1, X. Wan2, and W. Yu. GBOOST: A GPU-Based Tool for Detecting Gene-Gene Interactions in Genome-Wide Case Control Studies. Bioinformatics, 27:1309-1310, 2011.

          The GBOOST software has been downloaded over 2300 times since its publication in March 2011 according to the download counter on our software webpage.

J31.   C. Yang1, X. Wan2, Z. He2, Q. Yang, H. Xue, and W. Yu. The Choice of Null Distributions for Detecting Gene-Gene Interactions in Genome-Wide Association Studies. BMC Bioinformatics, 12(Suppl 1): S26, 2011.

J30.   Z. He2, C. Yang1, G. Guo, N. Li, and W. Yu. Motif-All: Discovering All Phosphorylation Motifs. BMC Bioinformatics, 12(Suppl 1): S22, 2011.  

J29.  Z. He2, H. Zhao3 and W. Yu. Score Regularization for Peptide Identification. BMC Bioinformatics, 12(Suppl 1): S2, 2011.  

J28.  Z. He2, C. Yang1, and W. Yu. A partial set covering model for protein mixture identification using MS data. IEEE/ACM Trans. Computational Biology and Bioinformatics, 8:368-380, 2011.

J27.  X. Wan2, C. Yang1, Q. Yang, H. Xue, X. Fan, N. Tang, and W. Yu. BOOST: A Boolean Representation-based Method for Detecting SNP-SNP Interactions in Genome-wide Association Studies. The American Journal of Human Genetics, 87:325-340, 2010.

         The BOOST software has been downloaded over 1700 times since its publication in September 2010 according to the download  counter on our software webpage.

J26.  X. Wan2, C. Yang1, Q. Yang, H. Xue, N. Tang, and W. Yu. Detecting Two-Locus Associations Allowing for Interactions in Genome-wide Association Studies. Bioinformatics, 26:2517-2525, 2010.

J25.  Ch. Yang1, C. Yang1, and W. Yu. A Regularized Regression Method for Peptide Quantification. Journal of Proteome Research, 9:2705-2712, 2010.

J24.  Z. He2 and W. Yu. Stable Feature Selection for Biomarker Discovery. Computational Biology and Chemistry , 34:215-225, 2010.  

J23.  Z. He2, Ch. Yang1, C. Yang1, R.Z. Qi,  J.P. Tam and W. Yu. Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification. Journal of Computational Biology, 17:221-235, 2010.   

J22.  C. Yang1, X. Wan2, Q. Yang, H. Xue, and W. Yu. Identifying Main Effects and Epistatic Interactions from Large-scale SNP Data via Adaptive Group Lasso. BMC Bioinformatics, 11 (Suppl. 1): S18, 2010.

J21.  X. Wan2, C. Yang1, Q. Yang, H. Xue, N. Tang, and W. Yu. SNPRuler: Predictive rule inference for epistatic interaction detection in genome-wide association studies. Bioinformatics, 26:30-37, 2010.

J20.   Z. He2 and W. Yu. Improving Peptide Identification with Single-Stage Mass Spectrum Peaks.

         Bioinformatics, 25:2969-2974, 2009.

J19.  C. Yang1, Z. He2, X. Wan2, Q. Yang, H. Xue, and W. Yu. SNPHarvester: A filtering-based approach for detecting epistatic interactions in genome-wide association studies. Bioinformatics, 25:504-511, 2009.

J18.  X. Wan2, C. Yang1, Q. Yang, H. Xue, N. Tang, and W. Yu. MegaSNPHunter: A Learning Approach to Detect Disease predisposition SNPs and High Level Interactions from Whole Genome Data.

         BMC Bioinformatics, 10:13, 2009.

J17.  Ch. Yang1, Z. He2, and W. Yu. Comparison of Public Peak Detection Algorithms for MALDI Mass Spectrometry Data Analysis. BMC Bioinformatics, 10:4, 2009.

J16.  M Dakna, Z. He2, W. Yu, H. Mischak, and W. Kolch. Technical, bioinformatical and statistical aspects of liquid chromatography-mass spectrometry (LC-MS) and capillary electrophoresis-mass spectrometry (CE-MS) based clinical proteomics: A critical assessment. Journal of Chromatography B, 877:1250-1258, 2009.

J15.  Q. Xu, D. Hu, H. Xue, W. Yu and Q. Yang.  Semi-supervised protein subcellular localization.
BMC Bioinformatics, 10 (Suppl. 1): S47, 2009.

J14.  Z. He2, C. Yang1, and W. Yu. Peak Bagging for Peptide Mass Fingerprinting. Bioinformatics, 24:1293-1299, 2008.

J13.  W. Yu, Z. He2, J. Liu, and H. Zhao3. Improving Mass Spectrometry Peak Detection Using Multiple Peak Alignment Results. Journal of Proteome Research, 7:123-129, 2008.

J12.   J.  Liu, H.  Zhao3, J. Tan, D. Luo, W. Yu and E. James Harner. Is SubcellularLocalization Informative for Modeling Protein-protein Interaction Signal? Research Letters in Signal Processing, 1:1-5, 2008.

J11.   W. Yu, J. Liu, C. Colangelo, E. Gulcicek, and H. Zhao3. A New Protocol of Analyzing Isotope Coded Affinity Tag Data from High Resolution LC-MS Spectrometry. Computational Biology and Chemistry, 31:215-221, 2007. 

J10.   J. Liu, W. Yu, B. Wu, and H. Zhao3. Bayesian Mass Spectra Peak Alignment from Mass Charge Ratios. Cancer Informatics, 2:395-419, 2006.

J9.    W. Yu,  X. Li, J. Liu, B. Wu,  K. Williams,  and  H. Zhao3.  Multiple Peak Alignment in Sequential Data Analysis:  A Scale-Space Based Approach.  IEEE/ACM Trans. Computational Biology and Bioinformatics, 3:208-219, 2006.

J8.    W. Yu, B.Wu, N.Lin, K.Stone, K.Williams, and H. Zhao3. Detecting and Aligning Peaks in Analyzing MALDI Mass Spectrometry Data. Computational Biology and Chemistry, 30:27-38, 2006.

J7.    W. Yu,  P. Yan,  A. Sinusas, K. Thiele, and J. S. Duncan3. Towards Pointwise Motion Tracking in Echocardiographic Images --- Comparison of Different Features for Speckle Tracking. 

         Medical Image Analysis, 10:495-508, 2006.

J6.    W. Yu, G. Sommer3,  K. Daniilidis3, and J. S. Duncan3. Using Skew Gabor Filter in Source Signal Separation and Local Spectral Orientation Analysis. Image and Vision Computing, 23:377-392, 2005.

       J5.    W. Yu, G. Sommer3,  and K. Daniilidis3. Multiple Motion Analysis: in Spatial Domain or in Spectral Domain?  Computer Vision and Image Understanding, 90:129-152, 2003.

       J4.    W. Yu, G. Sommer3, and K. Daniilidis3. 3D-Orientation Signatures with Conic Kernel Filtering for      Multiple Motion Analysis. Image and Vision Computing, 21:447-458, 2003.

J3.    N. Lin, W. Yu, and J. S. Duncan3. Combinative Multi-Scale Level Set Framework for Echocardiographic Image Segmentation. Medical Image Analysis, 7:529-537, 2003.

J2.    W. Yu, G. Sommer3, S. Beauchemin, and K. Daniilids3. Oriented Structure of the Occlusion Distortion: Is it Reliable?  IEEE Trans. Pattern Analysis and Machine Intelligence, 24: 1286-1290, 2002.

J1.    W. Yu, K. Daniilidis3, and G. Sommer3. Approximate Orientation Steerability Based on Angular  Gaussians.  IEEE Trans. Image Processing, 10:193-205, 2001.

 

Articles in Refereed Conference Proceedings

C1.    F. Yu, N. Li, and W. Yu. ECL 2.0: Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity. Submitted to The 21st Annual International Conference on Research in Computational Molecular Biology (RECOMB 2017), Hong Kong, May 3-7, 2017.

C2.    J. Dai, F. Yu, N. Li, and W. Yu. Is it feasible to only use tags in database search for peptide identification? --- A simulation-based study. Submitted to The 21st Annual International Conference on Research in Computational Molecular Biology (RECOMB 2017), Hong Kong, May 3-7, 2017

C3.   C. Zhang1, T. Liang, P. K.T. Mok, and W. Yu.  FPGA Implementation of the Coupled Filtering Method.

         In the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016), Shenzhen, China, December 15-18, 2016. (Oral presentation, acceptance rate: 19% out of 361 submissions).

C4.   M. Wang1, W. Jiang1, R. C.W. Ma, and W. Yu. GBOOST 2.0: A GPU-based Tool for Detecting Gene-Gene Interactions With Covariates Adjustment in Genome-Wide Association Studies. In the 2016 Workshop on Accelerator-Enabled Algorithms and Applications in Bioinformatics (WACEBI 2016) in conjunction with IEEE BIBM 2016, Shenzhen, China, December 15-18, 2016. (Oral presentation)

C5.   W. Jiang1 and W. Yu. Power Estimation and Sample Size Determination for Replication Studies of Genome-Wide Association Studies. In the Fourteenth Asia Pacific Bioinformatics Conference (APBC2016), San Francisco, CA, USA,  January 11-13, 2016. (Best Paper Award)

C6.   X. Zhou1, X. Huang, J.S. Duncan3, and W. Yu. Active Contours with Group Similarity. In IEEE International Conference on Computer Vision and Pattern Recognition (CVPR 2013), pp.2969 - 2976 Portland, Oregon, USA, June 23-28, 2013.

C7.   X. Zhou1, and W. Yu. Low-rank Modeling and Its Applications in Medical Image Analysis. In SPIE Conference on Independent Component Analyses, Compressive Sampling, Wavelets, Neural Net, Biosystems, and Nanoengineering, Baltimore, MD, USA, 2013.

C8.   X. Zhou1, C. Yang1, and W. Yu. Automatic Mitral Leaflet Tracking in Echocardiography by Outlier Detection in the Low-rank Representation. In IEEE International Conference on Computer Vision and Pattern Recognition (CVPR 2012), Providence, RI, USA, 2012.

C9.   Ch. Yang1, and W. Yu. A Brief Review of Signal Processing Issues in Mass Spectrometry-based Proteomics Studies. In The Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, USA, 2011.

C10.  C. Yang1, X. Wan2, Z. He2, Q. Yang, H. Xue, and W. Yu. The Choice of Null Distributions for Detecting Gene-Gene Interactions in Genome-Wide Association Stuides. In the Ninth Asia Pacific Bioinformatics Conference (APBC2011), Incheon, Korea,  January 11-14, 2011. (Oral presentation)

C11.  Z. He2, C. Yang1, G. Guo, N. Li, and W. Yu. Motif-All: Discovering All Phosphorylation Motifs. In the Ninth Asia Pacific Bioinformatics Conference (APBC2011), Incheon, Korea, 2011. (Oral presentation)

C12.  Z. He2, H. Zhao3 and W. Yu. Score Regularization for Peptide Identification. In the Ninth Asia Pacific Bioinformatics Conference (APBC¡¦11), Incheon, Korea, 2011. (Oral presentation)

C13.  T. Liang1 and W. Yu.  Solving the Feature-Motion Decorrelation Problem in Ultrasound Speckle Tracking. In the 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2010), Rotterdam, The Netherlands, April 14-17, 2010. 

C14. X. Zhou1, T. Liang1 and W. Yu. Accurate Segmentation of Ultrasound Images Using the Motion Cue. 

         In  2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2010), Rotterdam, The Netherlands, April 14-17, 2010. 

C15.  Ch. Yang1, C. Yang1, and W. Yu. A Regularized Regression Method for Peptide Quantification. In  RECOMB Satellite Conference on Computational Proteomics, San Diego, USA, March 27-28, 2010.

C16.  C. Yang1, X. Wan2, Q. Yang, H. Xue, and W. Yu. Identifying Main Effects and Epistatic Interactions from Large-scale SNP Data via Adaptive Group Lasso. In the Eighth Asia Pacific Bioinformatics Conference (APBC2010), Bangalore, India, January 18-21, 2010. (Oral presentation, acceptance rate: 67/231=29%)

C17.  Z. He2, Ch. Yang1, C. Yang1, R.Z. Qi,  J.P. Tam and W. Yu. Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification. In 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB2009), Arizona, USA, pp.16-30, 2009.

         (Oral presentation, acceptance rate: 37/166= 22%)

C18.  W. Yu,  P. Yan, A.  Sinusas,  K. Thiele, and J.S. Duncan3. Pointwise Motion Tracking in Echocardiographic Images.  In IEEE International Conference on Computer Vision and Pattern Recognition (CVPR 2004), Vol. 1, pp.676-683, 2004. (acceptance rate: 22.9%)

C19.  W. Yu,  G. Sommer3, and K. Daniilidis3. Using Skew Gabor Filter in Source Signal Separation and Local Spectral Multi-Orientation Analysis. In IEEE International Conference on Computer Vision and Pattern Recognition (CVPR 2004), Vol. 1, 262-269, 2004. (Oral presentation, top 6.4%)

C20.  W. Yu and J.S. Duncan3. The Choice of Tracking Feature in Ultrasound-Based Strain Imaging Analysis. In the 2004 IEEE International Symposium on Biomedical Imaging: From Nano to Macro  (ISBI 2004), pp. 304-307, 2004. (Oral presentation) 

C21.  W. Yu,  N. Lin, P. Yan, K. Purushothaman, A. Sinusas, K. Thiele, and J.S. Duncan3. Motion Analysis of 3D Ultrasound Texture Patterns. In the Second International Workshop on Functional Imaging and Modeling of  the Heart (FIMH2003),  pp.252-261, 2003.

C22.  N. Lin, W. Yu, and J.S. Duncan3.  Combinative Multi-Scale Level Set Framework for Echocardiographic Image Segmentation. In International Conference on Medical Image Computing and Computer-Assisted Intervention, vol.1,  pp. 682-689, 2002.

C23.  W. Yu, G. Sommer3, and K. Daniilidis3. 3D-Orientation Signatures with Conic Kernel Filtering for Multiple Motion Analysis. In IEEE International Conference on Computer Vision and Pattern Recognition,  vol. 1,  pp. 299-306, 2001. (Oral presentation, top 8.5%)

C24.   W. Yu, G. Sommer3, and K. Daniilidis3.  Skewness of Gabor Wavelets and Source Signal Separation. In the second International Conference on Wavelet Analysis and Its Applications, pp. 269-283, 2001.

C25.   W. Yu,  K. Daniilidis3, and G. Sommer3.  A New 3D Orientation Steerable Filter. In the 22nd DAGM-Symposium on Pattern Recognition (DAGM 2000),  pp.203-212, 2000.

C26.   W. Yu,  K. Daniilidis3, and G. Sommer3. Eliminating Outliers in Motion Occlusion Analysis. In the 22nd DAGM-Symposium on Pattern Recognition (DAGM 2000),   pp. 373-380, 2000.

C27.  W. Yu, K. Daniilidis3, S. Beauchemin, and G. Sommer3. Detection and Characterization of Multiple Motion Points. In IEEE International Conference on Computer Vision and Pattern Recognition, vol. 1,  pp. 171-177, 1999.

C28.   W. Yu, K. Daniilidis3,  and G. Sommer3. Low-cost Junction Characterization Using Polar Averaging Filters. In   IEEE International Conference on Image Processing, vol. 3, pp. 41-44,  1998.

C29.   W. Yu,   K. Daniilidis3,  and G. Sommer3. Junction Characterization Using Polar Pyramid.  In the 20th DAGM-Symposium on Pattern Recognition (DAGM 1998),  pp.69-76,  1998.

C30.   W. Yu, K. Daniilidis3, and G. Sommer3. Rotated Wedge Averaging Method for Junction Characterization. In IEEE International Conference on Computer Vision and Pattern Recognition,  pp.390-395, 1998.