Publications of Weichuan Yu

Book

Weichuan Yu
"Local Orientation Analysis in Images and Image Sequences Using Steerable Filters"
Shaker Verlag, February 2001, ISBN 3-8265-8442-2

Refereed Journal Papers

45.  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.
44.  X. Zhou, C. Yang, and W. Yu
       "Moving Object Detection by Detecting Contiguous Outliers in the Low-Rank Representation"
      
IEEE Trans. on Pattern Analysis and Machine Intelligence, 35:597-610, 2013.
43.  X. Zhou, 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.
42.  X. Wan, C. Yang, Q. Yang, H. Zhao, and W. Yu
       "The Complete Compositional Epistasis Detection in Genome-wide Association Studies"
     
BMC Genetics, 14:7, 2013.
41.  X. Zhou, C. Yang, X. Wan, H. Zhao, and W. Yu
       "Multi-sample aCGH Data Analysis via Total Variation and Spectral Regularization"
      
IEEE/ACM Trans. on Computational Biology and Bioinformatics, 10:230-235, 2013.
40.  X. Wan, C. Yang, Q. Yang, H. Zhao, and W. Yu
       "HapBoost: A fast approach to boosting haplotype association analyses in genome-wide association studies"
      
IEEE/ACM Trans. on Computational Biology and Bioinformatics, 10:207-212, 2013.
39.  T. Liang, L. Yung, and W. Yu
       "On Feature Motion Decorrelation in Ultrasound Speckle Tracking"
      
IEEE Trans. on Medical Imaging, 32:435-448, 2013.
38.  Z. He, 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.
37.   T. Huang, J. Wang, W. Yu and Z. He.
       "Protein Inference: A Review"
      
Briefings in Bioinformatics, 13:586-614, 2012.
36.  Ch. Yang, C. Yang, Z. He and W. Yu
       "Peptide Re-ranking with Protein-peptide Correspondence and Precursor Peak Intensity Information"
      
IEEE/ACM Trans. on Computational Biology and Bioinformatics, 9:1212-1219, 2012.
35.  X. Wan, C. Yang, and W. Yu
       "Comments on "An empirical comparison of several recent epistatic interaction detection methods""
       Bioinformatics, 28:145-146, 2012.
34.  C. Yang, X. Zhou, X. Wan, Q. Yang, H. Xue, and W. Yu
       "Identifying Disease-associated SNP Clusters via Contiguous Outlier Detection"
       Bioinformatics, 27:2578-2587, 2011. 
33.  L. Yung, C. Yang, X. Wan, and W. Yu
       "GBOOST: A GPU-Based Tool for Detecting Gene-Gene Interactions in Genome-Wide Case Control Studies"
       Bioinformatics, 27:1309-1310, 2011.
32.  C. Yang, X. Wan, 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.
31.  C. Yang, X. Wan, Z. He, 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.
30.  Z. He, C. Yang, G. Guo, N. Li, and W. Yu
       "Motif-All: Discovering All Phosphorylation Motifs"
       BMC Bioinformatics, 12(Suppl 1): S22, 2011.
29.  Z. He, H. Zhao, and W. Yu
       "Score Regularization for Peptide Identification"
       BMC Bioinformatics, 12(Suppl 2): S2, 2011.
28.    Z. He, C. Yang, and W. Yu
  "A Partial Set Covering Model for Protein Mixture Identification from MS Data"
  IEEE/ACM Trans. on Computational Biology and Bioinformatics, 8:368-380, 2011.
27.  Z. He and W. Yu
       "Stable Feature Selection for Biomarker Discovery"
       Computational Biology and Chemistry, 34:215-225, 2010.
26.  X. Wan, C. Yang, 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. 
25.  X. Wan, C. Yang, 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.  
24.  Ch. Yang, C. Yang, and W. Yu
       "A Regularized Regression Method for Peptide Quantification"
       Journal of Proteome Research, 9:2705-2712, 2010.
23.   C. Yang, X. Wan, Q. Yang, H. Xue, N. Tang, 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.
22.  Z. He, Ch. Yang, C. Yang, 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.
21.  X. Wan, C. Yang, 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.
20.  Z. He and W. Yu
"
Improving Peptide Identification with Single-Stage Mass Spectrum Peaks"
Bioinformatics, 25:2969-2974, 2009.
19.  C. Yang, Z. He, X. Wan, 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.
18.  X. Wan, C. Yang, 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.
17.  Ch. Yang, Z. He, and W. Yu
"
Comparison of Public Peak Detection Algorithms for MALDI Mass Spectrometry Data Analysis"
BMC Bioinformatics, 10:4, 2009.
16. M Dakna,  Z. He, 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.
15. Q. Xu, D. Hu, H. Xue, W. Yu and Q. Yang  
"
Semi-supervised protein subcellular localization"
BMC Bioinformatics, 10 (Suppl 1): S47, 2008.
14.  Z. He, C. Yang, and W. Yu
"
Peak Bagging for Peptide Mass Fingerprinting"
Bioinformatics, Vol. 24, pp.1293-1299, 2008.
13.  W. Yu, Z. He, J. Liu, and H. Zhao
"Improving Mass Spectrometry Peak Detection Using Multiple Peak Alignment Results"
Journal of Proteome Research,
Vol. 7, pp.123-129, 2008.
12.  J. Liu, H. Zhao, J. Tan, D. Luo, W. Yu and E.J. Harner
"
Is Sub-Cellular Localization Informative for Modeling Protein-Protein Interaction Signal?"
Research Letters in Signal Processing, Vol. 1, pp.1-5, 2008.
11.  W. Yu, J. Liu, C. Colangelo, E. Gulcicek, and H. Zhao
"A New Protocol to Analyze ICAT Data from High Resolution HP-LC MS/MS Spectrometry"
Computational Biology and Chemistry, Vol. 31, pp.215-221, 2007.
10.  J. Liu, W. Yu, B. Wu, and H. Zhao
"Bayesian Mass Spectra Peak Alignment from Mass Charge Ratios"
Cancer Informatics, Vol. 2, pp.395-419, 2006.
9.      W. Yu, J. Liu, B. Wu, K. Williams, and H. Zhao
"Multiple Peak Alignment in Sequential Data Analysis: A Scale-Space Based Approach"
IEEE/ACM Trans. on Computational Biology and Bioinformatics, Vol. 3, No. 3, pp.208-219, 2006.
8.      W. Yu, B. Wu, N. Lin, K. Stone, K. Williams, and H. Zhao
"Detecting and Aligning Peaks in Analyzing MALDI Mass Spectrometry Data"
Computational Biology and Chemistry, Vol. 30, pp.27-38, 2006.
7.      W. Yu, P. Yan, A. Sinusas, K. Thiele, J.S. Duncan
"Toward Pointwise Motion Tracking in Echocardiographic Images --- Comparison of Different Features for Speckle Tracking"
Medical Image Analysis, Vol. 10, pp. 495-508, 2006.     
6.      W. Yu, G. Sommer, K. Daniilidis, J. S. Duncan
"Using Skew Gabor Filter in Source Signal Separation and Local Spectral Orientation Analysis"
Image and Vision Computing, Vol. 23, No. 4, pp.377-392, 2005.
5.      W. Yu, G. Sommer, K. Daniilidis
"3D-Orientation Signatures with Conic Kernel Filtering for Multiple Motion Analysis"  
Image and Vision Computing, Vol. 21, No. 5, pp. 447-458, 2003.
4.      W. Yu, G. Sommer, K. Daniilidis
"Multiple Motion Analysis: in Spatial Domain or in Spectral Domain?"
Computer Vision and Image Understanding, Vol. 90, No. 2, pp. 129-152, 2003.
3.      N. Lin, W. Yu, J.S. Duncan
"Combinative Multi-Scale Level Set Framework for Echocardiographic Image Segmentation"
Medical Image Analysis, Vol. 7, No. 4, pp. 529-537, 2003.
2.      W. Yu, G. Sommer, S. Beauchemin, K. Daniilidis
"Oriented Structure of the Occlusion Distortion: Is It Reliable?"
IEEE Trans. on Pattern Analysis and Machine Intelligence, Vol. 24, No. 9, pp. 1286-1290, 2002.
1.      W. Yu, K. Daniilidis, G. Sommer
"Approximate Orientation Steerability Based on Angular Gaussians"
IEEE Trans. on Image Processing, Vol. 10, No. 2, pp. 193-205, 2001.
 

Refereed Conference Papers

T.

1.       Active Contours with Group Similarity
X. Zhou, X. Huang, J.S. Duncan, and W. Yu
CVPR 2013
2.       Automatic Mitral Leaflet Tracking in Echocardiography by Outlier Detection in the Low-rank Representation
X. Zhou, C. Yang, and W. Yu
CVPR 2012
3.       Score Regularization for Peptide Identification
Z. He, H. Zhao, and W. Yu
APBC 2011, (Oral Presentation)
4.      Motif-All: Discovering All Phosphorylation Motifs
Z. He, C. Yang, G. Guo, N. Li, and W. Yu
APBC 2011, (Oral Presentation)
5.      The Choice of Null Distributions for Detecting Gene-Gene Interactions in Genome-Wide Association Studies
C. Yang, X. Wan, Q. Yang, H. Xue, N. Tang, and W. Yu
APBC 2011, (Oral Presentation)
6.      Solving the Feature-Motion Decorrelation Problem in Ultrasound Speckle Tracking
T. Liang and W. Yu
ISBI 2010
7.      Accurate Segmentation of Ultrasound Images Using the Motion Cue
X. Zhou, T. Liang, and W. Yu
ISBI 2010
8.      A Regularized Regression Method for Peptide Quantification
Ch. Yang, C. Yang, and W. Yu
RECOMB Satellite Conference on Computational Proteomics, 2010 (Oral Presentation)
9.      Identifying Main Effects and Epistatic Interactions from Large-scale SNP Data via Adaptive Group Lasso
C. Yang, X. Wan, Q. Yang, H. Xue, N. Tang, and W. Yu
APBC 2010, (Oral Presentation)
10.  Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification
Z. He, C. Yang, C. Yang, R.Z. Qi,  J.P. Tam and W. Yu
RECOMB 2009, (Oral Presentation)
11.  Pointwise Motion Tracking in Echocardiographic Images
W. Yu, P. Yan, A. Sinusas, K. Thiele, J.S. Duncan
  
CVPR 2004
12.  Using Skew Gabor Filter in Source Signal Separation and Local Spectral Multi-Orientation Analysis
W. Yu, G. Sommer, K. Daniilidis
CVPR 2004, (Oral Presentation)
13.  The Choice of Tracking Feature in Ultrasound-Based Strain Imaging Analysis
W. Yu, J.S. Duncan
ISBI 2004, (Oral Presentation)
14.  Motion Analysis of 3D Ultrasound Texture Patterns.
W. Yu, N. Lin, P. Yan, K. Purushothaman, A. Sinusas, K. Thiele, J.S. Duncan
FIMH 2003, pp. 252-261, June 2003
15.  Combinative Multi-Scale Level Set Framework for Echocardiographic Image Segmentation
N. Lin, W. Yu, J.S. Duncan
MICCAI 2002, Vol. 1, pp. 682-689, September 2002
16.  3D-Orientation Signatures with Conic Kernel Filtering for Multiple Motion Analysis
W. Yu, G. Sommer, K. Daniilidis
CVPR 2001, (Oral Presentation)
17.  Skewness of Gabor Wavelets and Source Signal Separation 
W. Yu, G. Sommer, K. Daniilidis
ICWAA 2001, pp. 269-283, December 2001
18.  A New 3D Orientation Steerable Filter 
W. Yu, K. Daniilidis, G. Sommer
DAGM 2000, pp. 203-212, September 2000
19.  Eliminating Outliers in Motion Occlusion Analysis 
W. Yu, K. Daniilidis, G. Sommer
DAGM 2000, pp. 373-380, September 2000
20.  Detection and Characterization of Multiple Motion Points 
W. Yu, K. Daniilidis, S. Beauchemin, G. Sommer
CVPR99, Vol. 1, pp. 171-177, June 1999
21.  Low-cost Junction Characterization Using Polar Averaging Filters 
W. Yu, K. Daniilidis, G. Sommer
ICIP98, Vol. 3, pp. 41-44, October 1998
22.  Junction Characterization Using Polar Pyramid 
W. Yu, K. Daniilidis, G. Sommer
DAGM98, pp. 69-76, September-October 1998
23.  Rotated Wedge Averaging Method for Junction Characterization
W. Yu, K. Daniilidis, G. Sommer
CVPR98, pp. 390-395, June 1998

Book Chapters

1.      W. Yu, B. Wu, T. Huang, X. Li, K. Williams, and H.Zhao
"Statistical Methods In Proteomics"
in Springer Handbook of Engineering Statistics (editor: H. Pham),
Springer-Verlag, London, UK, pp. 623-638, 2006.
2.      W. Yu, B. Wu, J. Liu, X. Li, K. Williams, and H. Zhao
"MALDI-MS Data Analysis for Diseas 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.
3.      N. Lin, W. Yu, and J.S. Duncan
"Echocardiographic Image Analysis"
in Medical Imaging Systems (editor: C.T. Leondes),
World Scientific Publishing Company, New Jersey, USA, pp.89-108, 2005.

Conference Abstracts

1.      W. Yu and H.Zhao
Aligning Spectral Peaks in Mass Spectrometry Data with a Robust Point Matching Approach
in 52nd ASMS Conference on Mass Spectrometry and Allied Topics,
May 23-27, Nashville, TN, 2004.
2.      W. Yu, X. Li, J. Liu, B. Wu, K. Williams, and H Zhao
Multiple Peak Alignment in Sequential Data Analysis: A Scale-Space Based Approach
in 2005 IEEE Computational Systems Bioinformatics Conference,
August 8-11, Stanford, CA, 2005. 
3.      W. Yu, J. Liu, C. Colangelo, E. Gulcicek, and H Zhao
A New Protocol of Analyzing Isotope-Coded Affinity Tag Data from High-Resolution LC-MS Spectrometry
in Pacific Symposium on Biocomputing,
January 3-7, Maui, Hawaii, 2007.
4.      W. Yu, Z. He, J. Liu, and H Zhao
Improving Mass Spectrometry Peak Detection Using Multiple Peak Alignment Results
in
5th International Conference on Pathways, Networks, and Systems
J
une 24-29, Porto Heli, Greece, 2007.
5.      Z. He and W. Yu
Cancer Biomarker Identification from Mass Spectrometry Data Using Protein Database Search
in
HUPO 6th Annual World Congress
October 6-10, Seoul, Korea, 2007.
6.      C. Yang, X. Wan, Q. Yang, H. Xue, and W. Yu
Rule Ensembles for Identification of SNP Interactions in Large-Scale Case-Control Studies
in
XX International Congress of Genetics
J
uly 12-17, Berlin, Germany, 2008.