Weichuan YU
余維川
PhD in Computer Science
University of Kiel, 2001

Professor
Department of Electronic and Computer Engineering



(852) 2358 7054
eeyu@ust.hk
Room 2428
Personal Web

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Google Scholar
G9t_DSUAAAAJ

ORCID
0000-0002-5510-6916

Scopus ID
7403913214




Research Interest Publications Projects Teaching Assignment RPG Supervision Space used




Research Interest

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Bioinformatics
Computational biology
Biomedical engineering (BME)
Statistical pattern recognition
Computer vision



Publications

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All Years 114 2022 0 2021 2 2020 2 2019 3 2018 5 2017 13 2016 89

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2021 2

Development of genome-wide polygenic risk scores for lipid traits and clinical applications for dyslipidaemia, subclinical atherosclerosis and diabetes cardiovascular complications among East Asians
Genome Medicine, v. 13, (1), February 2021, article number 29
Tam, Claudia H. T.; Lim, Cadmon K. P.; Yu, Weichuan; Ma, Ronald; The Hong Kong Diabetes Register TRS Study Group; The Hong Kong Diabetes Biobank Study Group Article
Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis Of Phosphoproteomes Of Soybean Cultivars
Biomolecules, v. 11, (8), August 2021, article number 1218
Moradi, Atieh; Dai, Shuaijian; Wong,Oi Ying; Zhu, Guang; Yu, Fengchao; Lam, Hon-Ming; Wang, Zhiyong; Burlingame, Alma L.; Lin, Chengtao; Afsharifar, Alireza; Yu, Weichuan; Wang, Tingliang; Li, Ning Article

2020 2

Data imbalance in CRISPR off-target prediction
Briefings in Bioinformatics, v. 21, (4), July 2020, p. 1448-1454
Gao, Yuli; Chuai, Guohui; Yu, Weichuan; Shen, Qu; Liu, Qi Article
Understanding the limit of open search in the identification of peptides with post-translational modifications — A simulation-based study
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 29 April 2020
Dai, Jiaan; Yu, Fengchao; Zhou, Chen; Yu, Weichuan Article

2019 3

Xolik: Finding Cross-linked Peptides With Maximum Paired Scores in Linear Time
Bioinformatics, v. 35, (2), January 2019, p. 251-257
Dai, Jiaan; Jiang, Wei; Yu, Fengchao; Yu, Weichuan Article
Assessment of Middle Cerebral Artery Occlusion in Rat Stroke Model Using Pearson Correlation Coefficients
IEEE International Symposium on Biomedical Imaging (ISBI 2019), Venice, Italy, 8-11 April 2019
He, Wuxian; Tang, Hongtu; Li, Jia; Hou, Chenze; Shen, Xiaoyan; Liu, Huafeng; Yu, Weichuan Conference paper
Region-Based Interaction Detection in Genome-Wide Case-Control Studies
BMC Medical Genomics, v. 12, (Supp. 7), December 2019, article number 13
Zhang, Sen; Jiang, Wei; Ma, Ronald CW; Yu, Weichuan Conference paper

2018 5

A Network Approach to Exploring the Functional Basis of Gene-gene Epistatic Interactions in Disease Susceptibility
Bioinformatics, v. 34, (10), May 2018, p. 1741-1749
Yip, Danny Kit-Sang; Chan, Landon L.; Pang, Iris K.; Jiang, Wei; Tang, Nelson L. S.; Yu, Weichuan; Yip, Kevin Y. Article
Development of in planta chemical cross-linking-based quantitative interactomics in Arabidopsis
Journal of Proteome Research, v. 17, (9), September 2018, p. 3195-3213
Liu, Shichang; Yu, Fengchao; Hu, Qiu; Wang, Tingliang; Yu, Lujia; Du, Shengwang; Yu, Weichuan; Li, Ning Article
Establishment of Dimethyl Labelling-based Quantitative Acetylproteomics in Arabidopsis
Molecular & Cellular Proteomics, v. 17, (5), 13 February 2018, p. 1010-1027
Liu, Shichang; Yu, Fengchao; Yang, Zhu; Wang, Tingliang; Xiong, Hairong; Chang, Caren; Yu, Weichuan; Li, Ning Article
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, v. 27, (9), 1 September 2018, p. 2795-2808
Jiang, Wei; Yu, Weichuan Article
Low-Rank Adaptive Clutter Filtering for Robust Ultrasound Vector Flow Imaging
IEEE International Ultrasonics Symposium, IUS, v. 2018-October, December 2018, article number 8580077
Du, Yigang; Zhang, Mengyi; Yu, Alfred C.H.; Yu, Weichuan Conference paper

2017 13

Apical constriction is driven by a pulsatile apical myosin network in delaminating Drosophila neuroblasts
Development, v. 144, (12), June 2017, p. 2153-2164
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan Article
Apical Constriction is Driven by a Pulsatile Apical Myosin Network in Delaminating Drosophila Neuroblasts
Journal of Cell Science, v. 130, (13), 2017, p. 2153-2164
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan Article
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, v. 33, (4), 15 February 2017, p. 500-507
Jiang, Wei; Yu, Weichuan Article
Exhaustively Identifying Cross-linked Peptides with a Linear Computational Complexity
Journal of Proteome Research, v.16, (10), October 2017, p. 3942-3952
Yu, Fengchao; Li, Ning; Yu, Weichuan Article
FPGA Implementation of the Coupled Filtering Method and the Affine Warping Method
IEEE TRANSACTIONS ON NANOBIOSCIENCE, v. 16, (5), July 2017, article number 7930498, p. 314-325
Zhang, Chen; Liang, Tianzhu; Mok, Philip K. T.; Yu, Weichuan Article
Apical constriction is driven by a pulsatile apical myosin network in delaminating Drosophila neuroblasts
The 18th International Congress of Developmental Biology, Singapore, 18-22 June 2017
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan Conference paper
Apical Constriction is Driven by a Pulsatile Apical Myosin Network in Delaminating Drosophila Neuroblasts
2017 Hong Kong Inter-University Postgraduate Symposium in Biochemical Sciences, The University of Hong Kong, Hong Kong, 16 June 2017
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan Conference paper
ECL 2.0: Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity
The 21st Annual International Conference on Research in Computational Molecular Biology, Hong Kong, 3-7 May 2017
Yu, Fengchao; Li, Ning; Yu, Weichuan Conference paper
FPGA Implementation of the Coupled Filtering Method
Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, January 2017, article number 7822556, p. 435-442
Zhang, Chen; Liang, Tianzhu; Mok, Philip K T; Yu, Weichuan Conference paper
GBOOST 2.0: A GPU-Based Tool for Detecting Gene-Gene Interactions with Covariates Adjustment in Genome-Wide Association Studies
Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, January 2017, article number 7822734, p. 1437-1437
Wang, Meng; Jiang, Wei; Ma, Ronald Ching Wan; Yu, Weichuan Conference paper
Is it feasible to only use tags in database search for peptide identification? --- A simulation-based study
21st Annual International Conference on Research in Computational Molecular Biology (RECOMB 2017), Hong Kong, 3-7 May 2017
Dai, Jiaan; Yu, Fengchao; Li, Ning; Yu, Weichuan Conference paper
Is it feasible to only use tags in database search for PTM-invariant peptide identification? - A simulation-based study
The 21st Annual International Conference on Research in Computational Molecular Biology (RECOMB 2017), Hong Kong, China, 3 - 7 May 2017
Dai, Jiaan; Yu, Fengchao; Li, Ning; Yu, Weichuan Conference paper
PIPI: PTM-Invariant Peptide Identification Using Coding Method
11th International Conference on Computational Systems Biology (ISB 2017), Shenzhen, China, 18-21 August 2017
Yu, fengchao; Li, Ning; Yu, Weichuan Conference paper

2016 5

ECL: An Exhaustive Search Tool for the Identification of Cross-linked Peptides Using Whole Database
BMC Bioinformatics, v. 17, (1), 2016, article number 217
Yu, Fengchao; Li, Ning; Yu, Weichuan Article
In Planta Chemical Cross-linking and Mass Spectrometry Analysis of Protein Structure and Interaction in Arabidopsis
Proteomics, v. 16, (13), July 2016, p. 1915-1927
Zhu, Xinliang; Yu, Fengchao; Yang, Zhu; Liu, Shichang; Dai, Chen; Lu, Xiaoyun; Liu, Chenyu; Yu, Weichuan; Li, Ning Article
PIPI: PTM-Invariant Peptide Identification Using Coding Method
Journal of Proteome Research, v. 15, (12), December 2016, p. 4423-4435
Yu, Fengchao; Li, Ning; Yu, Weichuan Article
What is the Probability of Replicating a Statistically Significant Association in Genome-Wide Association Studies?
Briefings in Bioinformatics, v. 18, (6), 1 November 2017, p. 928-939
Jiang, Wei; Xue, Jing-Hao; Yu, Weichuan Article
Power estimation and sample size determination for replication studies of genome-wide association studies
BMC Genomics, v. 17, (1), January 2016, p. 19-32
Jiang, Wei; Yu, Weichuan Conference paper

2015 2

Low-Rank Modeling and Its Applications in Image Analysis
ACM Computing Surveys, v. 47, (2), January 2015, article number 36
Zhou, Xiaowei; Yang, Can; Zhao, Hongyu; Yu, Weichuan Article
PBOOST: a GPU-based tool for parallel permutation tests in genome-wide association studies
Bioinformatics, v. 31, (9), 2015, p. 1460-1462
Yang, Guangyuan; Jiang, Wei; Yang, Qiang; Yu, Weichuan Article

2014 1

Piecewise-constant and low-rank approximation for identification of recurrent copy number variations
Bioinformatics, v. 30, (14), July 2014, p. 1943-1949
Zhou, Xiaowei; Liu, Jiming; Wan, Xiang; Yu, Weichuan Article

2013 11

A Combinatorial Perspective of the Protein Inference Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 10, (6), November 2013, article number 6600680, p. 1542-1547
Yang, Chao; He, Zengyou; Yu, Weichuan Article
Bioinformatic Analysis of Data Generated from MALDI Mass Spectrometry for Biomarker Discovery
Topics in Current Chemistry, v. 331, 2013, p. 193-210
He, Zengyou; Qi, Robert Z.; Yu, Weichuan Article
HapBoost: A Fast Approach to Boosting Haplotype Association Analyses in Genome-Wide Association Studies
IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 10, (1), 2013, article number 6419694, p. 207-212
Wan, Xiang; Yang, Can; Yang, Qiang; Zhao, Hongyu; Yu, Weichuan Article
Moving Object Detection by Detecting Contiguous Outliers in the Low-Rank Representation
IEEE Transactions on Pattern Analysis and Machine Intelligence, v. 35, (3), March 2013, article number 6216381, p. 597-610
Zhou, Xiaowei; Yang, Can; Yu, Weichuan Article
Multisample aCGH Data Analysis via Total Variation and Spectral Regularization
IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 10, (1), January-February 2013, article number 6517420, p. 230-235
Zhou, Xiaowei; Yang, Can; Wan, Xiang; Zhao, Hongyu; Yu, Weichuan Article
On Feature Motion Decorrelation in Ultrasound Speckle Tracking
IEEE Transactions on Medical Imaging, v. 32, (2), February 2013, article number 6362227, p. 435-448
Liang, Tianzhu; Yung, Ling Sing; Yu, Weichuan Article
The Complete Compositional Epistasis Detection in Genome-wide Association Studies
BMC Genetics, v. 14, February 2013, article number 7
Wan, Xiang; Yang, Can; Yang, Qiang; Zhao, Hongyu; Yu, Weichuan Article
Ultrasound Bio-Microscopic Image Segmentation for Evaluation of Zebrafish Cardiac Function
IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, v. 60, (4), 2013, article number 6489806, p. 718-726
Zhou, Xiaowei; Sun, Lei; Yu, Yanyan; Qiu, Weibao; Lien, Ching-Ling; Shung, K. Kirk; Yu, Weichuan Article
Using microPET imaging in quantitative verification of the acupuncture effect in ischemia stroke treatment
Scientific Reports, v. 3, 2013, article number 1070
Liu, Huafeng; Shen, Xiaoyan; Tang, Hongtu; Li, Jia; Xiang, Ting; Yu, Weichuan Article
Active Contours with Group Similarity
2013 IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2013), Institute of Electrical and Electronics Engineers (IEEE), 2013, p. 2969-2976
Zhou, Xiaowei; Huang, Xiaojie; Duncan, James S.; Yu, Weichuan Conference paper
Low-rank Modeling and its Applications in Medical Image Analysis
SPIE Proceedings, v. 8750, May 2013
Zhou, Xiaowei; Yu, Weichuan Conference paper

2012 4

Guest Editors' Introduction to the Special Issue on "New Trends in Signal Processing and Biomedical Engineering"
Computers & electrical engineering, v. 38, (1), January 2012, p. 1-2
Yu, Weichuan; Tan, Zheng-Hua; Wan, Yi Article
Peptide Reranking with Protein-Peptide Correspondence and Precursor Peak Intensity Information
IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 9, (4), July-August 2012, article number 6202798, p. 1212-1219
Yang, Chao; He, Zengyou; Yang, Can; Yu, Weichuan Article
Protein inference: a review
Briefings in bioinformatics, v. 13, (5), September 2012, p. 586-614
Huang, Ting; Wang, Jingjing; Yu, Weichuan; He, Zengyou Article
Automatic Mitral Leaflet Tracking in Echocardiography by Outlier Detection in the Low-rank Representation
IEEE Conference on Computer Vision and Pattern Recognition, August 2012, article number 6247773, p. 972-979
Zhou, Xiaowei; Yang, Can; Yu, Weichuan Conference paper

2011 8

A Hidden Two-locus Disease Association Pattern in Genome-wide Association Studies
BMC bioinformatics, v. 12, (156), May 2011, article number 156, p. 1-14
Yang, Can; Wan, Xiang; Yang, Qiang; Xue, Hong; Tang, Nelson L.S.; Yu, Weichuan Article
A Partial Set Covering Model for Protein Mixture Identification Using Mass Spectrometry Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 8, (2), March-April 2011, article number 5066962, p. 368-380
He, Zengyou; Yang, Can; Yu, Weichuan Article
GBOOST: a GPU-based Tool for Detecting Gene-gene Interactions in Genome-wide Case Control Studies
Bioinformatics, v. 27, (9), May 2011, article number btr114, p. 1309-1310
Yung, Ling Sing; Yang, Can; Wan, Xiang; Yu, Weichuan Article
Identifying Disease-associated SNP Clusters via Contiguous Outlier Detection
Bioinformatics, v. 27, (18), September 2011, article number btr424, p. 2578-2585
Yang, Can; Zhou, Xiaowei; Wan, Xiang; Yang, Qiang; Xue, Hong; Yu, Weichuan Article
Motif-All: Discovering All Phosphorylation Motifs
BMC Bioinformatics, v. 12, (supplement 1), February 2011, article number S22
He, Zengyou; Yang, Can; Guo, Guangyu; Li, Ning; Yu, Weichuan Article
Score regularization for peptide identification
BMC bioinformatics, v. 12, (SUPPL. 1), art. no. S2, February 2011
He, Zengyou; Zhao, Hongyu; Yu, Weichuan Article
A brief review of signal processing issues in mass spectrometry-based proteomics studies
Conference record - Asilomar Conference on Signals, Systems, & Computers, 2011, p. 1036-1040
Yang, Chao; Yu, Weichuan Conference paper
The Choice of Null Distributions for Detecting Gene-Gene Interactions in Genome-Wide Association Studies
BMC Bioinformatics, v. 12, (Supplement 1), February 2011, article number S26
Yang, Can; Wan, Xiang; He, Zengyou; Yang, Qiang; Xue, Hong; Yu, Weichuan Conference paper

2010 16

A Recombination Hotspot in a Schizophrenia-Associated Region of GABRB2
PLoS ONE, v. 5, (3), 8 March 2010, Article number e9547
Ng, Siu Kin; Lo, Wing Sze; Pun, Frank Wing; Zhao, Cunyou; Yu, Zhiliang; Chen, Jianhuan; Tong, Ka Lok; Xu, Zhiwen; Tsang, Shui Ying; Yang, Qiang; Yu, Weichuan; Nimgaonkar, Vishwajit Laxmikant; Stober, Gerald; Harano, Mutsuo; Xue, Hong Article
A Regularized Method for Peptide Quantification
Journal of Proteome Research, v. 9, (5), May 2010, p. 2705-2712
Yang, Chao; Yang, Can; Yu, Weichuan Article
BOOST: A Fast Approach to Detecting Gene-Gene Interactions in Genome-wide Case-Control Studies
American Journal of Human Genetics, v. 87, (3), September 2010, p. 325-340
Wan, Xiang; Yang, Can; Yang, Qiang; Xue, Hong; Fan, Xiaodan; Tang, Nelson L.S.; Yu, Weichuan Article
Detecting Two-locus Associations Allowing for Interactions in Genome-wide Association Studies
Bioinformatics, v. 26, (20), August 2010, article number btq486, p. 2517-2525
Wan, Xiang; Yang, Can; Yang, Qiang; Xue, Hong; Tang, Nelson L.S.; Yu, Weichuan Article
Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification
Journal of Computational Biology, v. 17, (3), March 2010, p. 221-235
He, Zengyou; Yang, Chao; Yang, Can; Qi, Robert Zhong; Tam, P.M.; Yu, Weichuan Article
Predictive Rule Inference for Epistatic Interaction Detection in Genome-wide Association Studies
Bioinformatics, v. 26, (1), January 2010, article number btp622, p. 30-37
Wan, Xiang; Yang, Can; Yang, Qiang; Xue, Hong; Tang, Nelson L.S.; Yu, Weichuan Article
Stable feature selection for biomarker discovery
Computational Biology and Chemistry, v. 34, (4), 2010, p. 215-225
He, Z.; Yu, W. Article
Proceedings 2010 3rd International Conference on Biomedical Engineering and Informatics: BMEI 2010: 16-18 October 2010, Yantai, China
Proceedings 2010 3rd International Conference on Biomedical Engineering and Informatics: BMEI 2010: 16-18 October 2010, Yantai, China / Edited by Weichuan Yu etc. Piscataway, NJ: IEEE, c2010
Yu, Weichuan Book
A coupled filtering method to solve feature-motion decorrelation in speckle tracking
2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings, 2010, p. 312-315
Liang, Tianzhu; Yu, Weichuan Conference paper
A Regularized Regression Method for Peptide Quantification
RECOMB Satellite Conference on Computational Protemics, San Diego, USA, March 27-28, 2010
Yang, Chao; Yang, Can; Yu, Weichuan Conference paper
Accurate segmentation of ultrasound images using the motion cue
2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings, 2010, p. 332-335, Article number 5490343
Zhou, Xiaowei; Liang, Tianzhu; Yu, Weichuan Conference paper
Identifying Main Effects and Epistatic Interactions from Large-scale SNP Data via Adaptive Group Lasso
BMC Bioinformatics, v. 11, (Supplement 1), January 2010, article number S18
Yang, Can; Wan, Xiang; Yang, Qiang; Xue, Hong; Yu, Weichuan Conference paper
Motif-All: Discovering All Phosphorylation Motifs
Ninth Asia Pacific Bioinformatics Conference (APBC'11), Incheon, Korea, January 11-14, 2011(accepted in 2010)
He, Zengyou; Yang, Can; Guo, Guangyu; Li, Ning; Yu, Weichuan Conference paper
Score Regularization for Peptide Identification
Ninth Asia Pacific Bioinformatics Conference (APBC'11), Incheon, Korea, January 11-14, 2011 (accepted in 2010)
He, Zengyou; Zhao, Hongyu; Yu, Weichuan Conference paper
Solving the Feature-Motion Decorrelation Problem in Ultrasound Speckle Tracking
2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Rotterdam, The Netherlands, April 14-17, 2010
Liang, T.; Yu, Weichuan Conference paper
SyncPro: A synchronized visualization tool for differential analysis of proteomics data sets
2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010, 2010, p. 95-100
Yung, L.S.; Yang, C.; Dakna, M.; Mischak, H.; Yu, W. Conference paper

2009 7

Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis
BMC Bioinformatics, v. 10, 2009, JAN 6
Yang, Chao; He, Zengyou; Yu, Weichuan Article
Improving peptide identification with single-stage mass spectrum peaks
Bioinformatics, v. 25, (22), 2009, NOV 15, p. 2969-2974
He, Zengyou; Yu, Weichuan Article
MegaSNPhunter: a Learning Approach to Detect Disease Predisposition SNPs and High Level Interactions in Genome Wide Association Study
BMC Bioinformatics, v. 10, January 2009, article number 13
Wan, Xiang; Yang, Can; Yang, Qiang; Xue, Hong; Tang, Nelson L.S.; Yu, Weichuan Article
Semi-supervised protein subcellular localization
BMC bioinformatics, v. 10, (Suppl. 1), 30 January 2009, Article number S47
Xu, Qian; Hu, Derekhao; Xue, Hong; Yu, Weichuan; Yang, Qiang Article
SNPharvester: a Filtering-based Approach for Detecting Epistatic Interactions in Genome-wide Association Studies
Bioinformatics, v. 25, (4), February 2009, p. 504-511
Yang, Can; He, Zengyou; Wan, Xiang; Yang, Qiang; Xue, Hong; Yu, Weichuan Article
On ACO-based fuzzy clustering for image segmentation
Lecture Notes in Computer Science, v. 5552, (PART 2), 2009, p. 717-726
Yu, Z.; Yu, W.; Zou, R.; Yu, S. Conference paper
Optimization-based Peptide Mass Fingerprinting for Protein Mixture Identification
Research in Computational Molecular Biology, 5541, 2009, p. 16-30
He, Zengyou; Yang, Chao; Qi, Robert Zhong; Tam, Jason Po-Ming; Yu, Weichuan Conference paper

2008 4

Bayesian mass spectra peak alignment from mass charge ratios
Cancer Informatics, v. 6, 2008, p. 217-241
Liu, J.; Yu, W.; Wu, B.; Zhao, H. Article
Improving mass spectrometry peak detection using multiple peak alignment results
Journal of proteome research, v. 7, (1), 2008, JAN, p. 123-129
Yu, Weichaun; He, Zengyou; Liu, Junfeng; Zhao, Hongyu Article
Is SubcellularLocalization Informative for Modeling Protein-protein Interaction Signal?
Research Letters in Signal Processing, v. 1, 2008, p. 1-5
Liu, J.; Zhao, H.; Tan, J.; Luo, D.; Yu, W.; James Harner, E. Article
Peak bagging for peptide mass fingerprinting
Bioinformatics, v. 24, (10), May 2008, p. 1293-1299
He, Zengyou; Yang, Can; Yu, Weichuan Article

2007 3

A new protocol of analyzing isotope-coded affinity tag data from high-resolution LC-MS spectrometry
Computational biology and chemistry, v. 31, (3), 2007, JUN, p. 215-221
Yu, Weichuan; Liu, Junfeng; Colangelo, Chris; Gulcicek, Erol; Zhao, Hongyu Article
A New Protocol of Analyzing Isotope Coded Affinity Tag Data from High Resolution LC-MS Spectrometry
Pacific Symposium on Biocomputing 2007, Maui, Hawaii, USA, January 3-7, 2007
Yu, Weichuan; Liu, Junfeng; Colangelo, Chris; Gulcicek, Erol; Zhao, Hongyu Conference paper
Improving Mass Spectrometry Peak Detection Using Multiple Peak Alignment Results
5th International Conference on Pathways, Networks, and Systems, Porto Heli, Greece, June 24-29, 2007
Yu, Weichuan; He, Zengyou; Liu, Junfeng; Zhao, Hongyu Conference paper

2006 6

Bayesian Mass Spectra Peak Alignment from Mass Charge Ratios
Cancer Informatics, Vol. 2, pp.395-419
Liu, Junfeng; Yu, Weichuan; Wu, Baolin; Zhao, Hongyu Article
Detecting and aligning peaks in mass spectrometry data with applications to MALDI
Computational biology and chemistry, v. 30, (1), 2006, p. 27-38
Yu, Weichuan; Wu, Baolin; Lin, Ning; Stone, Kathy; Williams, Kenneth; Zhao, Hongyu Article
MALDI-MS data analysis for disease biomarker discovery.
Methods in molecular biology, v. 328, 2006, p. 199-216
Yu, W.; Wu, B.; Liu, J.; Li, X.; Stone, K.; Williams, K.R.; Zhao, H. Article
Multiple peak alignment in sequential data analysis: A scale-space-based approach
Ieee-acm TRANSACTIONS on COMPUTATIONAL BIOLOGY and Bioinformatics, v. 3, (3), 2006, JUL-SEP, p. 208-219
Yu, Weichuan; Li, Xiaoye; Liu, Junfeng; Wu, Baolin; Williams, Kenneth R.; Zhao, Hongyu Article
Towards pointwise motion tracking in echocardiographic image sequences - Comparing the reliability of different features for speckle tracking
Medical image analysis, v. 10, (4), August 2006, p. 495-508
Yu, Weichuan; Yan, Ping; Sinusas, Albert J.; Thiele, Karl; Duncan, James S. Article
Statistical Methods In Proteomics
Springer Handbook of Engineering Statistics / Edited by Hoang Pham. London: Springer, c2006, p. 623-638
Yu, W.; Wu, Baolin; Huang, Too; Li, Xiaoye; Williams, Kenneth; Zhao, Hongyu Book chapter

2005 3

Using skew Gabor filter in source signal separation and local spectral orientation analysis
Image and vision computing, v. 23, (4), 2005, p. 377-392
Yu, W.; Sommer, G.; Daniilidis, K.; Duncan, J.S. Article
Echocardiographic Image Analysis
Medical Imaging Systems / Edited by Leondes, New Jersey USA: C.T. World Scientific Publishing Company, 2005, p. 89-108
Lin, N.; Yu, W.; Duncan, J.S. Book chapter
Aligning peaks across multiple mass spectrometry data sets using a scale-space based approach
2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts, 2005, p. 126-127
Yu, W.; Li, X.; Zhao, H. Conference paper

2004 3

Pointwise Motion Tracking in Echocardiographic Images
IEEE International Conference on Computer Vision and Pattern Recognition (CVPR 2004), v. 1, 2004, p. 676-683
Yu, W.; Yan, P.; Sinusas, A.; Thiele, K.; Duncan, J.S. Conference paper
The choice of tracking features in ultrasound-based strain imaging analysis
2004 2nd IEEE International Symposium on Biomedical Imaging: Macro to Nano, v. 1, 2004, p. 304-307
Yu, W.; Duncan, J.S. Conference paper
Using Skew Gabor Filter in Source Signal Separation and Local Spectral Multi-Orientation Analysis
IEEE International Conference on Computer Vision and Pattern Recognition (CVPR 2004), v. 1, 2004, p.262-269
Yu, W.; Sommer, G.; Daniilidis, K. Conference paper

2003 5

Combinative multi-scale level set framework for echocardiographic image segmentation
Medical image analysis, v. 7, (4), 2003, p. 529-537
Lin, N.; Yu, W.; Duncan, J.S. Article
Motion analysis of 3D ultrasound texture patterns
Lecture Notes in Computer Science, v. 2674, 2003, p. 252-261
Yu, W.; Lin, N.; Yan, P.; Purushothaman, K.; Sinusas, A.; Thiele, K.; Duncan, J.S. Article
Multiple motion analysis: In spatial or in spectral domain?
Computer vision and image understanding, v. 90, (2), 2003, p. 129-152
Yu, W.; Sommer, G.; Daniilidis, K. Article
Three dimensional orientation signatures with conic kernel filtering for multiple motion analysis
Image and vision computing, v. 21, (5), 2003, p. 447-458
Yu, W.; Sommer, G.; Daniilidis, K. Article
Motion Analysis of 3D Ultrasound Texture Patterns.
the Second International Workshop on Functional Imaging and Modeling of the Heart (FIMH'03), 2003, p. 252-261
Yu, W.; Lin, N.; Yan, P.; Purushothaman, K.; Sinusas, A.; Thiele, K.; Duncan, J.S. Conference paper

2002 2

Oriented structure of the occlusion distortion: Is it reliable?
IEEE transactions on pattern analysis and machine intelligence, v. 24, (9), 2002, p. 1286-1290
Yu, W.; Sommer, G.; Beauchemin, S.; Daniilidis, K. Article
Combinative Multi-Scale Level Set Framework for Echocardiographic Image Segmentation
International Conference on Medical Image Computing and Computer-Assisted Intervention, v.1, 2002, p. 682-689
Lin, N.; Yu, W.; Duncan, J.S. Conference paper

2001 4

Approximate Orientation Steerability Based on Angular Gaussians
IEEE Trans. Image Processing (Impact Factor: 2.8), v. 10, 2001, p. 193-205
Yu, W.; Daniilidis, K.; Sommer, G. Article
3D-orientation signatures with conic kernel filtering for multiple motion analysis
IEEE Conference on Computer Vision & Pattern Recognition (CVPR), v. 1, 2001, p. I299-I306
Yu, W.; Sommer, G.; Daniilidis, K. Conference paper
A New 3D Orientation Steerable Filter
22nd DAGM-Symposium on Pattern Recognition (DAGM 2000), 2001, p. 203-212
Yu, W.; Daniilidis, K.; Sommer, G. Conference paper
Skewness of Gabor Wavelets and Source Signal Separation
the second International Conference on Wavelet Analysis and Its Applications, 2001, p. 269-283
Yu, W.; Sommer, G.; Daniilidis, K. Conference paper

2000 1

Eliminating Outliers in Motion Occlusion Analysis
22nd DAGM-Symposium on Pattern Recognition (DAGM 2000), 2000, p. 373-380
Yu, W.; Daniilidis, K.; Sommer, G. Conference paper

1999 1

Detection and characterization of multiple motion points
IEEE Conference on Computer Vision & Pattern Recognition (CVPR), v. 1, 1999, p. 171-177
Yu, Weichuan; Daniilidis, Kostas; Beauchemin, Steven; Sommer, Gerald Article

1998 3

Junction Characterization Using Polar Pyramid
20th DAGM-Symposium on Pattern Recognition (DAGM 1998), 1998, p. 69-76
Yu, W.; Daniilidis, K.; Sommer, G. Conference paper
Low-cost junction characterization using polar averaging filters
IEEE International Conference on Image Processing, v. 3, 1998, p. 41-44
Yu, Weichuan; Daniilidis, Kostas; Sommer, Gerald Conference paper
Rotated wedge averaging method for junction characterization
IEEE Conference on Computer Vision & Pattern Recognition (CVPR), 1998, p. 390-395
Yu, Weichuan; Daniilidis, Kostas; Sommer, Gerald Conference paper


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Article 2

Development of genome-wide polygenic risk scores for lipid traits and clinical applications for dyslipidaemia, subclinical atherosclerosis and diabetes cardiovascular complications among East Asians
Genome Medicine, v. 13, (1), February 2021, article number 29
Tam, Claudia H. T.; Lim, Cadmon K. P.; Yu, Weichuan; Ma, Ronald; The Hong Kong Diabetes Register TRS Study Group; The Hong Kong Diabetes Biobank Study Group
Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis Of Phosphoproteomes Of Soybean Cultivars
Biomolecules, v. 11, (8), August 2021, article number 1218
Moradi, Atieh; Dai, Shuaijian; Wong,Oi Ying; Zhu, Guang; Yu, Fengchao; Lam, Hon-Ming; Wang, Zhiyong; Burlingame, Alma L.; Lin, Chengtao; Afsharifar, Alireza; Yu, Weichuan; Wang, Tingliang; Li, Ning


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Article 2

Data imbalance in CRISPR off-target prediction
Briefings in Bioinformatics, v. 21, (4), July 2020, p. 1448-1454
Gao, Yuli; Chuai, Guohui; Yu, Weichuan; Shen, Qu; Liu, Qi
Understanding the limit of open search in the identification of peptides with post-translational modifications — A simulation-based study
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 29 April 2020
Dai, Jiaan; Yu, Fengchao; Zhou, Chen; Yu, Weichuan


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Article 1

Xolik: Finding Cross-linked Peptides With Maximum Paired Scores in Linear Time
Bioinformatics, v. 35, (2), January 2019, p. 251-257
Dai, Jiaan; Jiang, Wei; Yu, Fengchao; Yu, Weichuan

Conference paper 2

Assessment of Middle Cerebral Artery Occlusion in Rat Stroke Model Using Pearson Correlation Coefficients
IEEE International Symposium on Biomedical Imaging (ISBI 2019), Venice, Italy, 8-11 April 2019
He, Wuxian; Tang, Hongtu; Li, Jia; Hou, Chenze; Shen, Xiaoyan; Liu, Huafeng; Yu, Weichuan
Region-Based Interaction Detection in Genome-Wide Case-Control Studies
BMC Medical Genomics, v. 12, (Supp. 7), December 2019, article number 13
Zhang, Sen; Jiang, Wei; Ma, Ronald CW; Yu, Weichuan


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Article 4

A Network Approach to Exploring the Functional Basis of Gene-gene Epistatic Interactions in Disease Susceptibility
Bioinformatics, v. 34, (10), May 2018, p. 1741-1749
Yip, Danny Kit-Sang; Chan, Landon L.; Pang, Iris K.; Jiang, Wei; Tang, Nelson L. S.; Yu, Weichuan; Yip, Kevin Y.
Development of in planta chemical cross-linking-based quantitative interactomics in Arabidopsis
Journal of Proteome Research, v. 17, (9), September 2018, p. 3195-3213
Liu, Shichang; Yu, Fengchao; Hu, Qiu; Wang, Tingliang; Yu, Lujia; Du, Shengwang; Yu, Weichuan; Li, Ning
Establishment of Dimethyl Labelling-based Quantitative Acetylproteomics in Arabidopsis
Molecular & Cellular Proteomics, v. 17, (5), 13 February 2018, p. 1010-1027
Liu, Shichang; Yu, Fengchao; Yang, Zhu; Wang, Tingliang; Xiong, Hairong; Chang, Caren; Yu, Weichuan; Li, Ning
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, v. 27, (9), 1 September 2018, p. 2795-2808
Jiang, Wei; Yu, Weichuan

Conference paper 1

Low-Rank Adaptive Clutter Filtering for Robust Ultrasound Vector Flow Imaging
IEEE International Ultrasonics Symposium, IUS, v. 2018-October, December 2018, article number 8580077
Du, Yigang; Zhang, Mengyi; Yu, Alfred C.H.; Yu, Weichuan


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Article 5

Apical constriction is driven by a pulsatile apical myosin network in delaminating Drosophila neuroblasts
Development, v. 144, (12), June 2017, p. 2153-2164
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan
Apical Constriction is Driven by a Pulsatile Apical Myosin Network in Delaminating Drosophila Neuroblasts
Journal of Cell Science, v. 130, (13), 2017, p. 2153-2164
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan
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, v. 33, (4), 15 February 2017, p. 500-507
Jiang, Wei; Yu, Weichuan
Exhaustively Identifying Cross-linked Peptides with a Linear Computational Complexity
Journal of Proteome Research, v.16, (10), October 2017, p. 3942-3952
Yu, Fengchao; Li, Ning; Yu, Weichuan
FPGA Implementation of the Coupled Filtering Method and the Affine Warping Method
IEEE TRANSACTIONS ON NANOBIOSCIENCE, v. 16, (5), July 2017, article number 7930498, p. 314-325
Zhang, Chen; Liang, Tianzhu; Mok, Philip K. T.; Yu, Weichuan

Conference paper 8

Apical constriction is driven by a pulsatile apical myosin network in delaminating Drosophila neuroblasts
The 18th International Congress of Developmental Biology, Singapore, 18-22 June 2017
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan
Apical Constriction is Driven by a Pulsatile Apical Myosin Network in Delaminating Drosophila Neuroblasts
2017 Hong Kong Inter-University Postgraduate Symposium in Biochemical Sciences, The University of Hong Kong, Hong Kong, 16 June 2017
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan
ECL 2.0: Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity
The 21st Annual International Conference on Research in Computational Molecular Biology, Hong Kong, 3-7 May 2017
Yu, Fengchao; Li, Ning; Yu, Weichuan
FPGA Implementation of the Coupled Filtering Method
Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, January 2017, article number 7822556, p. 435-442
Zhang, Chen; Liang, Tianzhu; Mok, Philip K T; Yu, Weichuan
GBOOST 2.0: A GPU-Based Tool for Detecting Gene-Gene Interactions with Covariates Adjustment in Genome-Wide Association Studies
Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, January 2017, article number 7822734, p. 1437-1437
Wang, Meng; Jiang, Wei; Ma, Ronald Ching Wan; Yu, Weichuan
Is it feasible to only use tags in database search for peptide identification? --- A simulation-based study
21st Annual International Conference on Research in Computational Molecular Biology (RECOMB 2017), Hong Kong, 3-7 May 2017
Dai, Jiaan; Yu, Fengchao; Li, Ning; Yu, Weichuan
Is it feasible to only use tags in database search for PTM-invariant peptide identification? - A simulation-based study
The 21st Annual International Conference on Research in Computational Molecular Biology (RECOMB 2017), Hong Kong, China, 3 - 7 May 2017
Dai, Jiaan; Yu, Fengchao; Li, Ning; Yu, Weichuan
PIPI: PTM-Invariant Peptide Identification Using Coding Method
11th International Conference on Computational Systems Biology (ISB 2017), Shenzhen, China, 18-21 August 2017
Yu, fengchao; Li, Ning; Yu, Weichuan


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Article 4

ECL: An Exhaustive Search Tool for the Identification of Cross-linked Peptides Using Whole Database
BMC Bioinformatics, v. 17, (1), 2016, article number 217
Yu, Fengchao; Li, Ning; Yu, Weichuan
In Planta Chemical Cross-linking and Mass Spectrometry Analysis of Protein Structure and Interaction in Arabidopsis
Proteomics, v. 16, (13), July 2016, p. 1915-1927
Zhu, Xinliang; Yu, Fengchao; Yang, Zhu; Liu, Shichang; Dai, Chen; Lu, Xiaoyun; Liu, Chenyu; Yu, Weichuan; Li, Ning
PIPI: PTM-Invariant Peptide Identification Using Coding Method
Journal of Proteome Research, v. 15, (12), December 2016, p. 4423-4435
Yu, Fengchao; Li, Ning; Yu, Weichuan
What is the Probability of Replicating a Statistically Significant Association in Genome-Wide Association Studies?
Briefings in Bioinformatics, v. 18, (6), 1 November 2017, p. 928-939
Jiang, Wei; Xue, Jing-Hao; Yu, Weichuan

Conference paper 1

Power estimation and sample size determination for replication studies of genome-wide association studies
BMC Genomics, v. 17, (1), January 2016, p. 19-32
Jiang, Wei; Yu, Weichuan


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Article 2

Low-Rank Modeling and Its Applications in Image Analysis
ACM Computing Surveys, v. 47, (2), January 2015, article number 36
Zhou, Xiaowei; Yang, Can; Zhao, Hongyu; Yu, Weichuan
PBOOST: a GPU-based tool for parallel permutation tests in genome-wide association studies
Bioinformatics, v. 31, (9), 2015, p. 1460-1462
Yang, Guangyuan; Jiang, Wei; Yang, Qiang; Yu, Weichuan


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Article 1

Piecewise-constant and low-rank approximation for identification of recurrent copy number variations
Bioinformatics, v. 30, (14), July 2014, p. 1943-1949
Zhou, Xiaowei; Liu, Jiming; Wan, Xiang; Yu, Weichuan


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Article 9

A Combinatorial Perspective of the Protein Inference Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 10, (6), November 2013, article number 6600680, p. 1542-1547
Yang, Chao; He, Zengyou; Yu, Weichuan
Bioinformatic Analysis of Data Generated from MALDI Mass Spectrometry for Biomarker Discovery
Topics in Current Chemistry, v. 331, 2013, p. 193-210
He, Zengyou; Qi, Robert Z.; Yu, Weichuan
HapBoost: A Fast Approach to Boosting Haplotype Association Analyses in Genome-Wide Association Studies
IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 10, (1), 2013, article number 6419694, p. 207-212
Wan, Xiang; Yang, Can; Yang, Qiang; Zhao, Hongyu; Yu, Weichuan
Moving Object Detection by Detecting Contiguous Outliers in the Low-Rank Representation
IEEE Transactions on Pattern Analysis and Machine Intelligence, v. 35, (3), March 2013, article number 6216381, p. 597-610
Zhou, Xiaowei; Yang, Can; Yu, Weichuan
Multisample aCGH Data Analysis via Total Variation and Spectral Regularization
IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 10, (1), January-February 2013, article number 6517420, p. 230-235
Zhou, Xiaowei; Yang, Can; Wan, Xiang; Zhao, Hongyu; Yu, Weichuan
On Feature Motion Decorrelation in Ultrasound Speckle Tracking
IEEE Transactions on Medical Imaging, v. 32, (2), February 2013, article number 6362227, p. 435-448
Liang, Tianzhu; Yung, Ling Sing; Yu, Weichuan
The Complete Compositional Epistasis Detection in Genome-wide Association Studies
BMC Genetics, v. 14, February 2013, article number 7
Wan, Xiang; Yang, Can; Yang, Qiang; Zhao, Hongyu; Yu, Weichuan
Ultrasound Bio-Microscopic Image Segmentation for Evaluation of Zebrafish Cardiac Function
IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, v. 60, (4), 2013, article number 6489806, p. 718-726
Zhou, Xiaowei; Sun, Lei; Yu, Yanyan; Qiu, Weibao; Lien, Ching-Ling; Shung, K. Kirk; Yu, Weichuan
Using microPET imaging in quantitative verification of the acupuncture effect in ischemia stroke treatment
Scientific Reports, v. 3, 2013, article number 1070
Liu, Huafeng; Shen, Xiaoyan; Tang, Hongtu; Li, Jia; Xiang, Ting; Yu, Weichuan

Conference paper 2

Active Contours with Group Similarity
2013 IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2013), Institute of Electrical and Electronics Engineers (IEEE), 2013, p. 2969-2976
Zhou, Xiaowei; Huang, Xiaojie; Duncan, James S.; Yu, Weichuan
Low-rank Modeling and its Applications in Medical Image Analysis
SPIE Proceedings, v. 8750, May 2013
Zhou, Xiaowei; Yu, Weichuan


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Article 3

Guest Editors' Introduction to the Special Issue on "New Trends in Signal Processing and Biomedical Engineering"
Computers & electrical engineering, v. 38, (1), January 2012, p. 1-2
Yu, Weichuan; Tan, Zheng-Hua; Wan, Yi
Peptide Reranking with Protein-Peptide Correspondence and Precursor Peak Intensity Information
IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 9, (4), July-August 2012, article number 6202798, p. 1212-1219
Yang, Chao; He, Zengyou; Yang, Can; Yu, Weichuan
Protein inference: a review
Briefings in bioinformatics, v. 13, (5), September 2012, p. 586-614
Huang, Ting; Wang, Jingjing; Yu, Weichuan; He, Zengyou

Conference paper 1

Automatic Mitral Leaflet Tracking in Echocardiography by Outlier Detection in the Low-rank Representation
IEEE Conference on Computer Vision and Pattern Recognition, August 2012, article number 6247773, p. 972-979
Zhou, Xiaowei; Yang, Can; Yu, Weichuan


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Article 6

A Hidden Two-locus Disease Association Pattern in Genome-wide Association Studies
BMC bioinformatics, v. 12, (156), May 2011, article number 156, p. 1-14
Yang, Can; Wan, Xiang; Yang, Qiang; Xue, Hong; Tang, Nelson L.S.; Yu, Weichuan
A Partial Set Covering Model for Protein Mixture Identification Using Mass Spectrometry Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 8, (2), March-April 2011, article number 5066962, p. 368-380
He, Zengyou; Yang, Can; Yu, Weichuan
GBOOST: a GPU-based Tool for Detecting Gene-gene Interactions in Genome-wide Case Control Studies
Bioinformatics, v. 27, (9), May 2011, article number btr114, p. 1309-1310
Yung, Ling Sing; Yang, Can; Wan, Xiang; Yu, Weichuan
Identifying Disease-associated SNP Clusters via Contiguous Outlier Detection
Bioinformatics, v. 27, (18), September 2011, article number btr424, p. 2578-2585
Yang, Can; Zhou, Xiaowei; Wan, Xiang; Yang, Qiang; Xue, Hong; Yu, Weichuan
Motif-All: Discovering All Phosphorylation Motifs
BMC Bioinformatics, v. 12, (supplement 1), February 2011, article number S22
He, Zengyou; Yang, Can; Guo, Guangyu; Li, Ning; Yu, Weichuan
Score regularization for peptide identification
BMC bioinformatics, v. 12, (SUPPL. 1), art. no. S2, February 2011
He, Zengyou; Zhao, Hongyu; Yu, Weichuan

Conference paper 2

A brief review of signal processing issues in mass spectrometry-based proteomics studies
Conference record - Asilomar Conference on Signals, Systems, & Computers, 2011, p. 1036-1040
Yang, Chao; Yu, Weichuan
The Choice of Null Distributions for Detecting Gene-Gene Interactions in Genome-Wide Association Studies
BMC Bioinformatics, v. 12, (Supplement 1), February 2011, article number S26
Yang, Can; Wan, Xiang; He, Zengyou; Yang, Qiang; Xue, Hong; Yu, Weichuan


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Article 7

A Recombination Hotspot in a Schizophrenia-Associated Region of GABRB2
PLoS ONE, v. 5, (3), 8 March 2010, Article number e9547
Ng, Siu Kin; Lo, Wing Sze; Pun, Frank Wing; Zhao, Cunyou; Yu, Zhiliang; Chen, Jianhuan; Tong, Ka Lok; Xu, Zhiwen; Tsang, Shui Ying; Yang, Qiang; Yu, Weichuan; Nimgaonkar, Vishwajit Laxmikant; Stober, Gerald; Harano, Mutsuo; Xue, Hong
A Regularized Method for Peptide Quantification
Journal of Proteome Research, v. 9, (5), May 2010, p. 2705-2712
Yang, Chao; Yang, Can; Yu, Weichuan
BOOST: A Fast Approach to Detecting Gene-Gene Interactions in Genome-wide Case-Control Studies
American Journal of Human Genetics, v. 87, (3), September 2010, p. 325-340
Wan, Xiang; Yang, Can; Yang, Qiang; Xue, Hong; Fan, Xiaodan; Tang, Nelson L.S.; Yu, Weichuan
Detecting Two-locus Associations Allowing for Interactions in Genome-wide Association Studies
Bioinformatics, v. 26, (20), August 2010, article number btq486, p. 2517-2525
Wan, Xiang; Yang, Can; Yang, Qiang; Xue, Hong; Tang, Nelson L.S.; Yu, Weichuan
Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification
Journal of Computational Biology, v. 17, (3), March 2010, p. 221-235
He, Zengyou; Yang, Chao; Yang, Can; Qi, Robert Zhong; Tam, P.M.; Yu, Weichuan
Predictive Rule Inference for Epistatic Interaction Detection in Genome-wide Association Studies
Bioinformatics, v. 26, (1), January 2010, article number btp622, p. 30-37
Wan, Xiang; Yang, Can; Yang, Qiang; Xue, Hong; Tang, Nelson L.S.; Yu, Weichuan
Stable feature selection for biomarker discovery
Computational Biology and Chemistry, v. 34, (4), 2010, p. 215-225
He, Z.; Yu, W.

Book 1

Proceedings 2010 3rd International Conference on Biomedical Engineering and Informatics: BMEI 2010: 16-18 October 2010, Yantai, China
Proceedings 2010 3rd International Conference on Biomedical Engineering and Informatics: BMEI 2010: 16-18 October 2010, Yantai, China / Edited by Weichuan Yu etc. Piscataway, NJ: IEEE, c2010
Yu, Weichuan

Conference paper 8

A coupled filtering method to solve feature-motion decorrelation in speckle tracking
2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings, 2010, p. 312-315
Liang, Tianzhu; Yu, Weichuan
A Regularized Regression Method for Peptide Quantification
RECOMB Satellite Conference on Computational Protemics, San Diego, USA, March 27-28, 2010
Yang, Chao; Yang, Can; Yu, Weichuan
Accurate segmentation of ultrasound images using the motion cue
2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings, 2010, p. 332-335, Article number 5490343
Zhou, Xiaowei; Liang, Tianzhu; Yu, Weichuan
Identifying Main Effects and Epistatic Interactions from Large-scale SNP Data via Adaptive Group Lasso
BMC Bioinformatics, v. 11, (Supplement 1), January 2010, article number S18
Yang, Can; Wan, Xiang; Yang, Qiang; Xue, Hong; Yu, Weichuan
Motif-All: Discovering All Phosphorylation Motifs
Ninth Asia Pacific Bioinformatics Conference (APBC'11), Incheon, Korea, January 11-14, 2011(accepted in 2010)
He, Zengyou; Yang, Can; Guo, Guangyu; Li, Ning; Yu, Weichuan
Score Regularization for Peptide Identification
Ninth Asia Pacific Bioinformatics Conference (APBC'11), Incheon, Korea, January 11-14, 2011 (accepted in 2010)
He, Zengyou; Zhao, Hongyu; Yu, Weichuan
Solving the Feature-Motion Decorrelation Problem in Ultrasound Speckle Tracking
2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Rotterdam, The Netherlands, April 14-17, 2010
Liang, T.; Yu, Weichuan
SyncPro: A synchronized visualization tool for differential analysis of proteomics data sets
2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010, 2010, p. 95-100
Yung, L.S.; Yang, C.; Dakna, M.; Mischak, H.; Yu, W.


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Article 5

Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis
BMC Bioinformatics, v. 10, 2009, JAN 6
Yang, Chao; He, Zengyou; Yu, Weichuan
Improving peptide identification with single-stage mass spectrum peaks
Bioinformatics, v. 25, (22), 2009, NOV 15, p. 2969-2974
He, Zengyou; Yu, Weichuan
MegaSNPhunter: a Learning Approach to Detect Disease Predisposition SNPs and High Level Interactions in Genome Wide Association Study
BMC Bioinformatics, v. 10, January 2009, article number 13
Wan, Xiang; Yang, Can; Yang, Qiang; Xue, Hong; Tang, Nelson L.S.; Yu, Weichuan
Semi-supervised protein subcellular localization
BMC bioinformatics, v. 10, (Suppl. 1), 30 January 2009, Article number S47
Xu, Qian; Hu, Derekhao; Xue, Hong; Yu, Weichuan; Yang, Qiang
SNPharvester: a Filtering-based Approach for Detecting Epistatic Interactions in Genome-wide Association Studies
Bioinformatics, v. 25, (4), February 2009, p. 504-511
Yang, Can; He, Zengyou; Wan, Xiang; Yang, Qiang; Xue, Hong; Yu, Weichuan

Conference paper 2

On ACO-based fuzzy clustering for image segmentation
Lecture Notes in Computer Science, v. 5552, (PART 2), 2009, p. 717-726
Yu, Z.; Yu, W.; Zou, R.; Yu, S.
Optimization-based Peptide Mass Fingerprinting for Protein Mixture Identification
Research in Computational Molecular Biology, 5541, 2009, p. 16-30
He, Zengyou; Yang, Chao; Qi, Robert Zhong; Tam, Jason Po-Ming; Yu, Weichuan


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Article 4

Bayesian mass spectra peak alignment from mass charge ratios
Cancer Informatics, v. 6, 2008, p. 217-241
Liu, J.; Yu, W.; Wu, B.; Zhao, H.
Improving mass spectrometry peak detection using multiple peak alignment results
Journal of proteome research, v. 7, (1), 2008, JAN, p. 123-129
Yu, Weichaun; He, Zengyou; Liu, Junfeng; Zhao, Hongyu
Is SubcellularLocalization Informative for Modeling Protein-protein Interaction Signal?
Research Letters in Signal Processing, v. 1, 2008, p. 1-5
Liu, J.; Zhao, H.; Tan, J.; Luo, D.; Yu, W.; James Harner, E.
Peak bagging for peptide mass fingerprinting
Bioinformatics, v. 24, (10), May 2008, p. 1293-1299
He, Zengyou; Yang, Can; Yu, Weichuan


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Article 1

A new protocol of analyzing isotope-coded affinity tag data from high-resolution LC-MS spectrometry
Computational biology and chemistry, v. 31, (3), 2007, JUN, p. 215-221
Yu, Weichuan; Liu, Junfeng; Colangelo, Chris; Gulcicek, Erol; Zhao, Hongyu

Conference paper 2

A New Protocol of Analyzing Isotope Coded Affinity Tag Data from High Resolution LC-MS Spectrometry
Pacific Symposium on Biocomputing 2007, Maui, Hawaii, USA, January 3-7, 2007
Yu, Weichuan; Liu, Junfeng; Colangelo, Chris; Gulcicek, Erol; Zhao, Hongyu
Improving Mass Spectrometry Peak Detection Using Multiple Peak Alignment Results
5th International Conference on Pathways, Networks, and Systems, Porto Heli, Greece, June 24-29, 2007
Yu, Weichuan; He, Zengyou; Liu, Junfeng; Zhao, Hongyu


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Article 5

Bayesian Mass Spectra Peak Alignment from Mass Charge Ratios
Cancer Informatics, Vol. 2, pp.395-419
Liu, Junfeng; Yu, Weichuan; Wu, Baolin; Zhao, Hongyu
Detecting and aligning peaks in mass spectrometry data with applications to MALDI
Computational biology and chemistry, v. 30, (1), 2006, p. 27-38
Yu, Weichuan; Wu, Baolin; Lin, Ning; Stone, Kathy; Williams, Kenneth; Zhao, Hongyu
MALDI-MS data analysis for disease biomarker discovery.
Methods in molecular biology, v. 328, 2006, p. 199-216
Yu, W.; Wu, B.; Liu, J.; Li, X.; Stone, K.; Williams, K.R.; Zhao, H.
Multiple peak alignment in sequential data analysis: A scale-space-based approach
Ieee-acm TRANSACTIONS on COMPUTATIONAL BIOLOGY and Bioinformatics, v. 3, (3), 2006, JUL-SEP, p. 208-219
Yu, Weichuan; Li, Xiaoye; Liu, Junfeng; Wu, Baolin; Williams, Kenneth R.; Zhao, Hongyu
Towards pointwise motion tracking in echocardiographic image sequences - Comparing the reliability of different features for speckle tracking
Medical image analysis, v. 10, (4), August 2006, p. 495-508
Yu, Weichuan; Yan, Ping; Sinusas, Albert J.; Thiele, Karl; Duncan, James S.

Book chapter 1

Statistical Methods In Proteomics
Springer Handbook of Engineering Statistics / Edited by Hoang Pham. London: Springer, c2006, p. 623-638
Yu, W.; Wu, Baolin; Huang, Too; Li, Xiaoye; Williams, Kenneth; Zhao, Hongyu


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Article 1

Using skew Gabor filter in source signal separation and local spectral orientation analysis
Image and vision computing, v. 23, (4), 2005, p. 377-392
Yu, W.; Sommer, G.; Daniilidis, K.; Duncan, J.S.

Book chapter 1

Echocardiographic Image Analysis
Medical Imaging Systems / Edited by Leondes, New Jersey USA: C.T. World Scientific Publishing Company, 2005, p. 89-108
Lin, N.; Yu, W.; Duncan, J.S.

Conference paper 1

Aligning peaks across multiple mass spectrometry data sets using a scale-space based approach
2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts, 2005, p. 126-127
Yu, W.; Li, X.; Zhao, H.


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Conference paper 3

Pointwise Motion Tracking in Echocardiographic Images
IEEE International Conference on Computer Vision and Pattern Recognition (CVPR 2004), v. 1, 2004, p. 676-683
Yu, W.; Yan, P.; Sinusas, A.; Thiele, K.; Duncan, J.S.
The choice of tracking features in ultrasound-based strain imaging analysis
2004 2nd IEEE International Symposium on Biomedical Imaging: Macro to Nano, v. 1, 2004, p. 304-307
Yu, W.; Duncan, J.S.
Using Skew Gabor Filter in Source Signal Separation and Local Spectral Multi-Orientation Analysis
IEEE International Conference on Computer Vision and Pattern Recognition (CVPR 2004), v. 1, 2004, p.262-269
Yu, W.; Sommer, G.; Daniilidis, K.


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Article 4

Combinative multi-scale level set framework for echocardiographic image segmentation
Medical image analysis, v. 7, (4), 2003, p. 529-537
Lin, N.; Yu, W.; Duncan, J.S.
Motion analysis of 3D ultrasound texture patterns
Lecture Notes in Computer Science, v. 2674, 2003, p. 252-261
Yu, W.; Lin, N.; Yan, P.; Purushothaman, K.; Sinusas, A.; Thiele, K.; Duncan, J.S.
Multiple motion analysis: In spatial or in spectral domain?
Computer vision and image understanding, v. 90, (2), 2003, p. 129-152
Yu, W.; Sommer, G.; Daniilidis, K.
Three dimensional orientation signatures with conic kernel filtering for multiple motion analysis
Image and vision computing, v. 21, (5), 2003, p. 447-458
Yu, W.; Sommer, G.; Daniilidis, K.

Conference paper 1

Motion Analysis of 3D Ultrasound Texture Patterns.
the Second International Workshop on Functional Imaging and Modeling of the Heart (FIMH'03), 2003, p. 252-261
Yu, W.; Lin, N.; Yan, P.; Purushothaman, K.; Sinusas, A.; Thiele, K.; Duncan, J.S.


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Article 1

Oriented structure of the occlusion distortion: Is it reliable?
IEEE transactions on pattern analysis and machine intelligence, v. 24, (9), 2002, p. 1286-1290
Yu, W.; Sommer, G.; Beauchemin, S.; Daniilidis, K.

Conference paper 1

Combinative Multi-Scale Level Set Framework for Echocardiographic Image Segmentation
International Conference on Medical Image Computing and Computer-Assisted Intervention, v.1, 2002, p. 682-689
Lin, N.; Yu, W.; Duncan, J.S.


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Article 1

Approximate Orientation Steerability Based on Angular Gaussians
IEEE Trans. Image Processing (Impact Factor: 2.8), v. 10, 2001, p. 193-205
Yu, W.; Daniilidis, K.; Sommer, G.

Conference paper 3

3D-orientation signatures with conic kernel filtering for multiple motion analysis
IEEE Conference on Computer Vision & Pattern Recognition (CVPR), v. 1, 2001, p. I299-I306
Yu, W.; Sommer, G.; Daniilidis, K.
A New 3D Orientation Steerable Filter
22nd DAGM-Symposium on Pattern Recognition (DAGM 2000), 2001, p. 203-212
Yu, W.; Daniilidis, K.; Sommer, G.
Skewness of Gabor Wavelets and Source Signal Separation
the second International Conference on Wavelet Analysis and Its Applications, 2001, p. 269-283
Yu, W.; Sommer, G.; Daniilidis, K.


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Conference paper 1

Eliminating Outliers in Motion Occlusion Analysis
22nd DAGM-Symposium on Pattern Recognition (DAGM 2000), 2000, p. 373-380
Yu, W.; Daniilidis, K.; Sommer, G.


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Article 1

Detection and characterization of multiple motion points
IEEE Conference on Computer Vision & Pattern Recognition (CVPR), v. 1, 1999, p. 171-177
Yu, Weichuan; Daniilidis, Kostas; Beauchemin, Steven; Sommer, Gerald


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Conference paper 3

Junction Characterization Using Polar Pyramid
20th DAGM-Symposium on Pattern Recognition (DAGM 1998), 1998, p. 69-76
Yu, W.; Daniilidis, K.; Sommer, G.
Low-cost junction characterization using polar averaging filters
IEEE International Conference on Image Processing, v. 3, 1998, p. 41-44
Yu, Weichuan; Daniilidis, Kostas; Sommer, Gerald
Rotated wedge averaging method for junction characterization
IEEE Conference on Computer Vision & Pattern Recognition (CVPR), 1998, p. 390-395
Yu, Weichuan; Daniilidis, Kostas; Sommer, Gerald


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2016 5

ECL: An Exhaustive Search Tool for the Identification of Cross-linked Peptides Using Whole Database
BMC Bioinformatics, v. 17, (1), 2016, article number 217
Yu, Fengchao; Li, Ning; Yu, Weichuan Article
In Planta Chemical Cross-linking and Mass Spectrometry Analysis of Protein Structure and Interaction in Arabidopsis
Proteomics, v. 16, (13), July 2016, p. 1915-1927
Zhu, Xinliang; Yu, Fengchao; Yang, Zhu; Liu, Shichang; Dai, Chen; Lu, Xiaoyun; Liu, Chenyu; Yu, Weichuan; Li, Ning Article
PIPI: PTM-Invariant Peptide Identification Using Coding Method
Journal of Proteome Research, v. 15, (12), December 2016, p. 4423-4435
Yu, Fengchao; Li, Ning; Yu, Weichuan Article
What is the Probability of Replicating a Statistically Significant Association in Genome-Wide Association Studies?
Briefings in Bioinformatics, v. 18, (6), 1 November 2017, p. 928-939
Jiang, Wei; Xue, Jing-Hao; Yu, Weichuan Article
Power estimation and sample size determination for replication studies of genome-wide association studies
BMC Genomics, v. 17, (1), January 2016, p. 19-32
Jiang, Wei; Yu, Weichuan Conference paper

2015 2

Low-Rank Modeling and Its Applications in Image Analysis
ACM Computing Surveys, v. 47, (2), January 2015, article number 36
Zhou, Xiaowei; Yang, Can; Zhao, Hongyu; Yu, Weichuan Article
PBOOST: a GPU-based tool for parallel permutation tests in genome-wide association studies
Bioinformatics, v. 31, (9), 2015, p. 1460-1462
Yang, Guangyuan; Jiang, Wei; Yang, Qiang; Yu, Weichuan Article

2014 1

Piecewise-constant and low-rank approximation for identification of recurrent copy number variations
Bioinformatics, v. 30, (14), July 2014, p. 1943-1949
Zhou, Xiaowei; Liu, Jiming; Wan, Xiang; Yu, Weichuan Article

2013 11

A Combinatorial Perspective of the Protein Inference Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 10, (6), November 2013, article number 6600680, p. 1542-1547
Yang, Chao; He, Zengyou; Yu, Weichuan Article
Bioinformatic Analysis of Data Generated from MALDI Mass Spectrometry for Biomarker Discovery
Topics in Current Chemistry, v. 331, 2013, p. 193-210
He, Zengyou; Qi, Robert Z.; Yu, Weichuan Article
HapBoost: A Fast Approach to Boosting Haplotype Association Analyses in Genome-Wide Association Studies
IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 10, (1), 2013, article number 6419694, p. 207-212
Wan, Xiang; Yang, Can; Yang, Qiang; Zhao, Hongyu; Yu, Weichuan Article
Moving Object Detection by Detecting Contiguous Outliers in the Low-Rank Representation
IEEE Transactions on Pattern Analysis and Machine Intelligence, v. 35, (3), March 2013, article number 6216381, p. 597-610
Zhou, Xiaowei; Yang, Can; Yu, Weichuan Article
Multisample aCGH Data Analysis via Total Variation and Spectral Regularization
IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 10, (1), January-February 2013, article number 6517420, p. 230-235
Zhou, Xiaowei; Yang, Can; Wan, Xiang; Zhao, Hongyu; Yu, Weichuan Article
On Feature Motion Decorrelation in Ultrasound Speckle Tracking
IEEE Transactions on Medical Imaging, v. 32, (2), February 2013, article number 6362227, p. 435-448
Liang, Tianzhu; Yung, Ling Sing; Yu, Weichuan Article
The Complete Compositional Epistasis Detection in Genome-wide Association Studies
BMC Genetics, v. 14, February 2013, article number 7
Wan, Xiang; Yang, Can; Yang, Qiang; Zhao, Hongyu; Yu, Weichuan Article
Ultrasound Bio-Microscopic Image Segmentation for Evaluation of Zebrafish Cardiac Function
IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, v. 60, (4), 2013, article number 6489806, p. 718-726
Zhou, Xiaowei; Sun, Lei; Yu, Yanyan; Qiu, Weibao; Lien, Ching-Ling; Shung, K. Kirk; Yu, Weichuan Article
Using microPET imaging in quantitative verification of the acupuncture effect in ischemia stroke treatment
Scientific Reports, v. 3, 2013, article number 1070
Liu, Huafeng; Shen, Xiaoyan; Tang, Hongtu; Li, Jia; Xiang, Ting; Yu, Weichuan Article
Active Contours with Group Similarity
2013 IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2013), Institute of Electrical and Electronics Engineers (IEEE), 2013, p. 2969-2976
Zhou, Xiaowei; Huang, Xiaojie; Duncan, James S.; Yu, Weichuan Conference paper
Low-rank Modeling and its Applications in Medical Image Analysis
SPIE Proceedings, v. 8750, May 2013
Zhou, Xiaowei; Yu, Weichuan Conference paper

2012 4

Guest Editors' Introduction to the Special Issue on "New Trends in Signal Processing and Biomedical Engineering"
Computers & electrical engineering, v. 38, (1), January 2012, p. 1-2
Yu, Weichuan; Tan, Zheng-Hua; Wan, Yi Article
Peptide Reranking with Protein-Peptide Correspondence and Precursor Peak Intensity Information
IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 9, (4), July-August 2012, article number 6202798, p. 1212-1219
Yang, Chao; He, Zengyou; Yang, Can; Yu, Weichuan Article
Protein inference: a review
Briefings in bioinformatics, v. 13, (5), September 2012, p. 586-614
Huang, Ting; Wang, Jingjing; Yu, Weichuan; He, Zengyou Article
Automatic Mitral Leaflet Tracking in Echocardiography by Outlier Detection in the Low-rank Representation
IEEE Conference on Computer Vision and Pattern Recognition, August 2012, article number 6247773, p. 972-979
Zhou, Xiaowei; Yang, Can; Yu, Weichuan Conference paper

2011 8

A Hidden Two-locus Disease Association Pattern in Genome-wide Association Studies
BMC bioinformatics, v. 12, (156), May 2011, article number 156, p. 1-14
Yang, Can; Wan, Xiang; Yang, Qiang; Xue, Hong; Tang, Nelson L.S.; Yu, Weichuan Article
A Partial Set Covering Model for Protein Mixture Identification Using Mass Spectrometry Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 8, (2), March-April 2011, article number 5066962, p. 368-380
He, Zengyou; Yang, Can; Yu, Weichuan Article
GBOOST: a GPU-based Tool for Detecting Gene-gene Interactions in Genome-wide Case Control Studies
Bioinformatics, v. 27, (9), May 2011, article number btr114, p. 1309-1310
Yung, Ling Sing; Yang, Can; Wan, Xiang; Yu, Weichuan Article
Identifying Disease-associated SNP Clusters via Contiguous Outlier Detection
Bioinformatics, v. 27, (18), September 2011, article number btr424, p. 2578-2585
Yang, Can; Zhou, Xiaowei; Wan, Xiang; Yang, Qiang; Xue, Hong; Yu, Weichuan Article
Motif-All: Discovering All Phosphorylation Motifs
BMC Bioinformatics, v. 12, (supplement 1), February 2011, article number S22
He, Zengyou; Yang, Can; Guo, Guangyu; Li, Ning; Yu, Weichuan Article
Score regularization for peptide identification
BMC bioinformatics, v. 12, (SUPPL. 1), art. no. S2, February 2011
He, Zengyou; Zhao, Hongyu; Yu, Weichuan Article
A brief review of signal processing issues in mass spectrometry-based proteomics studies
Conference record - Asilomar Conference on Signals, Systems, & Computers, 2011, p. 1036-1040
Yang, Chao; Yu, Weichuan Conference paper
The Choice of Null Distributions for Detecting Gene-Gene Interactions in Genome-Wide Association Studies
BMC Bioinformatics, v. 12, (Supplement 1), February 2011, article number S26
Yang, Can; Wan, Xiang; He, Zengyou; Yang, Qiang; Xue, Hong; Yu, Weichuan Conference paper

2010 16

A Recombination Hotspot in a Schizophrenia-Associated Region of GABRB2
PLoS ONE, v. 5, (3), 8 March 2010, Article number e9547
Ng, Siu Kin; Lo, Wing Sze; Pun, Frank Wing; Zhao, Cunyou; Yu, Zhiliang; Chen, Jianhuan; Tong, Ka Lok; Xu, Zhiwen; Tsang, Shui Ying; Yang, Qiang; Yu, Weichuan; Nimgaonkar, Vishwajit Laxmikant; Stober, Gerald; Harano, Mutsuo; Xue, Hong Article
A Regularized Method for Peptide Quantification
Journal of Proteome Research, v. 9, (5), May 2010, p. 2705-2712
Yang, Chao; Yang, Can; Yu, Weichuan Article
BOOST: A Fast Approach to Detecting Gene-Gene Interactions in Genome-wide Case-Control Studies
American Journal of Human Genetics, v. 87, (3), September 2010, p. 325-340
Wan, Xiang; Yang, Can; Yang, Qiang; Xue, Hong; Fan, Xiaodan; Tang, Nelson L.S.; Yu, Weichuan Article
Detecting Two-locus Associations Allowing for Interactions in Genome-wide Association Studies
Bioinformatics, v. 26, (20), August 2010, article number btq486, p. 2517-2525
Wan, Xiang; Yang, Can; Yang, Qiang; Xue, Hong; Tang, Nelson L.S.; Yu, Weichuan Article
Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification
Journal of Computational Biology, v. 17, (3), March 2010, p. 221-235
He, Zengyou; Yang, Chao; Yang, Can; Qi, Robert Zhong; Tam, P.M.; Yu, Weichuan Article
Predictive Rule Inference for Epistatic Interaction Detection in Genome-wide Association Studies
Bioinformatics, v. 26, (1), January 2010, article number btp622, p. 30-37
Wan, Xiang; Yang, Can; Yang, Qiang; Xue, Hong; Tang, Nelson L.S.; Yu, Weichuan Article
Stable feature selection for biomarker discovery
Computational Biology and Chemistry, v. 34, (4), 2010, p. 215-225
He, Z.; Yu, W. Article
Proceedings 2010 3rd International Conference on Biomedical Engineering and Informatics: BMEI 2010: 16-18 October 2010, Yantai, China
Proceedings 2010 3rd International Conference on Biomedical Engineering and Informatics: BMEI 2010: 16-18 October 2010, Yantai, China / Edited by Weichuan Yu etc. Piscataway, NJ: IEEE, c2010
Yu, Weichuan Book
A coupled filtering method to solve feature-motion decorrelation in speckle tracking
2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings, 2010, p. 312-315
Liang, Tianzhu; Yu, Weichuan Conference paper
A Regularized Regression Method for Peptide Quantification
RECOMB Satellite Conference on Computational Protemics, San Diego, USA, March 27-28, 2010
Yang, Chao; Yang, Can; Yu, Weichuan Conference paper
Accurate segmentation of ultrasound images using the motion cue
2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings, 2010, p. 332-335, Article number 5490343
Zhou, Xiaowei; Liang, Tianzhu; Yu, Weichuan Conference paper
Identifying Main Effects and Epistatic Interactions from Large-scale SNP Data via Adaptive Group Lasso
BMC Bioinformatics, v. 11, (Supplement 1), January 2010, article number S18
Yang, Can; Wan, Xiang; Yang, Qiang; Xue, Hong; Yu, Weichuan Conference paper
Motif-All: Discovering All Phosphorylation Motifs
Ninth Asia Pacific Bioinformatics Conference (APBC'11), Incheon, Korea, January 11-14, 2011(accepted in 2010)
He, Zengyou; Yang, Can; Guo, Guangyu; Li, Ning; Yu, Weichuan Conference paper
Score Regularization for Peptide Identification
Ninth Asia Pacific Bioinformatics Conference (APBC'11), Incheon, Korea, January 11-14, 2011 (accepted in 2010)
He, Zengyou; Zhao, Hongyu; Yu, Weichuan Conference paper
Solving the Feature-Motion Decorrelation Problem in Ultrasound Speckle Tracking
2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Rotterdam, The Netherlands, April 14-17, 2010
Liang, T.; Yu, Weichuan Conference paper
SyncPro: A synchronized visualization tool for differential analysis of proteomics data sets
2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010, 2010, p. 95-100
Yung, L.S.; Yang, C.; Dakna, M.; Mischak, H.; Yu, W. Conference paper

2009 7

Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis
BMC Bioinformatics, v. 10, 2009, JAN 6
Yang, Chao; He, Zengyou; Yu, Weichuan Article
Improving peptide identification with single-stage mass spectrum peaks
Bioinformatics, v. 25, (22), 2009, NOV 15, p. 2969-2974
He, Zengyou; Yu, Weichuan Article
MegaSNPhunter: a Learning Approach to Detect Disease Predisposition SNPs and High Level Interactions in Genome Wide Association Study
BMC Bioinformatics, v. 10, January 2009, article number 13
Wan, Xiang; Yang, Can; Yang, Qiang; Xue, Hong; Tang, Nelson L.S.; Yu, Weichuan Article
Semi-supervised protein subcellular localization
BMC bioinformatics, v. 10, (Suppl. 1), 30 January 2009, Article number S47
Xu, Qian; Hu, Derekhao; Xue, Hong; Yu, Weichuan; Yang, Qiang Article
SNPharvester: a Filtering-based Approach for Detecting Epistatic Interactions in Genome-wide Association Studies
Bioinformatics, v. 25, (4), February 2009, p. 504-511
Yang, Can; He, Zengyou; Wan, Xiang; Yang, Qiang; Xue, Hong; Yu, Weichuan Article
On ACO-based fuzzy clustering for image segmentation
Lecture Notes in Computer Science, v. 5552, (PART 2), 2009, p. 717-726
Yu, Z.; Yu, W.; Zou, R.; Yu, S. Conference paper
Optimization-based Peptide Mass Fingerprinting for Protein Mixture Identification
Research in Computational Molecular Biology, 5541, 2009, p. 16-30
He, Zengyou; Yang, Chao; Qi, Robert Zhong; Tam, Jason Po-Ming; Yu, Weichuan Conference paper

2008 4

Bayesian mass spectra peak alignment from mass charge ratios
Cancer Informatics, v. 6, 2008, p. 217-241
Liu, J.; Yu, W.; Wu, B.; Zhao, H. Article
Improving mass spectrometry peak detection using multiple peak alignment results
Journal of proteome research, v. 7, (1), 2008, JAN, p. 123-129
Yu, Weichaun; He, Zengyou; Liu, Junfeng; Zhao, Hongyu Article
Is SubcellularLocalization Informative for Modeling Protein-protein Interaction Signal?
Research Letters in Signal Processing, v. 1, 2008, p. 1-5
Liu, J.; Zhao, H.; Tan, J.; Luo, D.; Yu, W.; James Harner, E. Article
Peak bagging for peptide mass fingerprinting
Bioinformatics, v. 24, (10), May 2008, p. 1293-1299
He, Zengyou; Yang, Can; Yu, Weichuan Article

2007 3

A new protocol of analyzing isotope-coded affinity tag data from high-resolution LC-MS spectrometry
Computational biology and chemistry, v. 31, (3), 2007, JUN, p. 215-221
Yu, Weichuan; Liu, Junfeng; Colangelo, Chris; Gulcicek, Erol; Zhao, Hongyu Article
A New Protocol of Analyzing Isotope Coded Affinity Tag Data from High Resolution LC-MS Spectrometry
Pacific Symposium on Biocomputing 2007, Maui, Hawaii, USA, January 3-7, 2007
Yu, Weichuan; Liu, Junfeng; Colangelo, Chris; Gulcicek, Erol; Zhao, Hongyu Conference paper
Improving Mass Spectrometry Peak Detection Using Multiple Peak Alignment Results
5th International Conference on Pathways, Networks, and Systems, Porto Heli, Greece, June 24-29, 2007
Yu, Weichuan; He, Zengyou; Liu, Junfeng; Zhao, Hongyu Conference paper

2006 6

Bayesian Mass Spectra Peak Alignment from Mass Charge Ratios
Cancer Informatics, Vol. 2, pp.395-419
Liu, Junfeng; Yu, Weichuan; Wu, Baolin; Zhao, Hongyu Article
Detecting and aligning peaks in mass spectrometry data with applications to MALDI
Computational biology and chemistry, v. 30, (1), 2006, p. 27-38
Yu, Weichuan; Wu, Baolin; Lin, Ning; Stone, Kathy; Williams, Kenneth; Zhao, Hongyu Article
MALDI-MS data analysis for disease biomarker discovery.
Methods in molecular biology, v. 328, 2006, p. 199-216
Yu, W.; Wu, B.; Liu, J.; Li, X.; Stone, K.; Williams, K.R.; Zhao, H. Article
Multiple peak alignment in sequential data analysis: A scale-space-based approach
Ieee-acm TRANSACTIONS on COMPUTATIONAL BIOLOGY and Bioinformatics, v. 3, (3), 2006, JUL-SEP, p. 208-219
Yu, Weichuan; Li, Xiaoye; Liu, Junfeng; Wu, Baolin; Williams, Kenneth R.; Zhao, Hongyu Article
Towards pointwise motion tracking in echocardiographic image sequences - Comparing the reliability of different features for speckle tracking
Medical image analysis, v. 10, (4), August 2006, p. 495-508
Yu, Weichuan; Yan, Ping; Sinusas, Albert J.; Thiele, Karl; Duncan, James S. Article
Statistical Methods In Proteomics
Springer Handbook of Engineering Statistics / Edited by Hoang Pham. London: Springer, c2006, p. 623-638
Yu, W.; Wu, Baolin; Huang, Too; Li, Xiaoye; Williams, Kenneth; Zhao, Hongyu Book chapter

2005 3

Using skew Gabor filter in source signal separation and local spectral orientation analysis
Image and vision computing, v. 23, (4), 2005, p. 377-392
Yu, W.; Sommer, G.; Daniilidis, K.; Duncan, J.S. Article
Echocardiographic Image Analysis
Medical Imaging Systems / Edited by Leondes, New Jersey USA: C.T. World Scientific Publishing Company, 2005, p. 89-108
Lin, N.; Yu, W.; Duncan, J.S. Book chapter
Aligning peaks across multiple mass spectrometry data sets using a scale-space based approach
2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts, 2005, p. 126-127
Yu, W.; Li, X.; Zhao, H. Conference paper

2004 3

Pointwise Motion Tracking in Echocardiographic Images
IEEE International Conference on Computer Vision and Pattern Recognition (CVPR 2004), v. 1, 2004, p. 676-683
Yu, W.; Yan, P.; Sinusas, A.; Thiele, K.; Duncan, J.S. Conference paper
The choice of tracking features in ultrasound-based strain imaging analysis
2004 2nd IEEE International Symposium on Biomedical Imaging: Macro to Nano, v. 1, 2004, p. 304-307
Yu, W.; Duncan, J.S. Conference paper
Using Skew Gabor Filter in Source Signal Separation and Local Spectral Multi-Orientation Analysis
IEEE International Conference on Computer Vision and Pattern Recognition (CVPR 2004), v. 1, 2004, p.262-269
Yu, W.; Sommer, G.; Daniilidis, K. Conference paper

2003 5

Combinative multi-scale level set framework for echocardiographic image segmentation
Medical image analysis, v. 7, (4), 2003, p. 529-537
Lin, N.; Yu, W.; Duncan, J.S. Article
Motion analysis of 3D ultrasound texture patterns
Lecture Notes in Computer Science, v. 2674, 2003, p. 252-261
Yu, W.; Lin, N.; Yan, P.; Purushothaman, K.; Sinusas, A.; Thiele, K.; Duncan, J.S. Article
Multiple motion analysis: In spatial or in spectral domain?
Computer vision and image understanding, v. 90, (2), 2003, p. 129-152
Yu, W.; Sommer, G.; Daniilidis, K. Article
Three dimensional orientation signatures with conic kernel filtering for multiple motion analysis
Image and vision computing, v. 21, (5), 2003, p. 447-458
Yu, W.; Sommer, G.; Daniilidis, K. Article
Motion Analysis of 3D Ultrasound Texture Patterns.
the Second International Workshop on Functional Imaging and Modeling of the Heart (FIMH'03), 2003, p. 252-261
Yu, W.; Lin, N.; Yan, P.; Purushothaman, K.; Sinusas, A.; Thiele, K.; Duncan, J.S. Conference paper

2002 2

Oriented structure of the occlusion distortion: Is it reliable?
IEEE transactions on pattern analysis and machine intelligence, v. 24, (9), 2002, p. 1286-1290
Yu, W.; Sommer, G.; Beauchemin, S.; Daniilidis, K. Article
Combinative Multi-Scale Level Set Framework for Echocardiographic Image Segmentation
International Conference on Medical Image Computing and Computer-Assisted Intervention, v.1, 2002, p. 682-689
Lin, N.; Yu, W.; Duncan, J.S. Conference paper

2001 4

Approximate Orientation Steerability Based on Angular Gaussians
IEEE Trans. Image Processing (Impact Factor: 2.8), v. 10, 2001, p. 193-205
Yu, W.; Daniilidis, K.; Sommer, G. Article
3D-orientation signatures with conic kernel filtering for multiple motion analysis
IEEE Conference on Computer Vision & Pattern Recognition (CVPR), v. 1, 2001, p. I299-I306
Yu, W.; Sommer, G.; Daniilidis, K. Conference paper
A New 3D Orientation Steerable Filter
22nd DAGM-Symposium on Pattern Recognition (DAGM 2000), 2001, p. 203-212
Yu, W.; Daniilidis, K.; Sommer, G. Conference paper
Skewness of Gabor Wavelets and Source Signal Separation
the second International Conference on Wavelet Analysis and Its Applications, 2001, p. 269-283
Yu, W.; Sommer, G.; Daniilidis, K. Conference paper

2000 1

Eliminating Outliers in Motion Occlusion Analysis
22nd DAGM-Symposium on Pattern Recognition (DAGM 2000), 2000, p. 373-380
Yu, W.; Daniilidis, K.; Sommer, G. Conference paper

1999 1

Detection and characterization of multiple motion points
IEEE Conference on Computer Vision & Pattern Recognition (CVPR), v. 1, 1999, p. 171-177
Yu, Weichuan; Daniilidis, Kostas; Beauchemin, Steven; Sommer, Gerald Article

1998 3

Junction Characterization Using Polar Pyramid
20th DAGM-Symposium on Pattern Recognition (DAGM 1998), 1998, p. 69-76
Yu, W.; Daniilidis, K.; Sommer, G. Conference paper
Low-cost junction characterization using polar averaging filters
IEEE International Conference on Image Processing, v. 3, 1998, p. 41-44
Yu, Weichuan; Daniilidis, Kostas; Sommer, Gerald Conference paper
Rotated wedge averaging method for junction characterization
IEEE Conference on Computer Vision & Pattern Recognition (CVPR), 1998, p. 390-395
Yu, Weichuan; Daniilidis, Kostas; Sommer, Gerald Conference paper


No Publications






Teaching Assignment

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2021-22 Winter 0 2021-22 Fall 4 2020-21 Summer 1 2020-21 Spring 4 2020-21 Winter 0 2020-21 Fall 4

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EESM5900J Diagnostic Medical Imaging
ELEC2910 Academic and Professional Development I
ELEC3910 Academic and Professional Development II
ELEC4820 Medical Imaging


ELEC4900 Final Year Design Project


CPEG4911 Computer Engineering Final Year Project in ELEC
EESM5547 Multimedia Signal Processing
ELEC4900 Final Year Design Project
ELEC5810 Introduction to Bioinformatics Algorithms


CPEG4911 Computer Engineering Final Year Project in ELEC
ELEC5300 Stochastic Processes
ELEC6950A Departmental Seminar
ELEC6950B Departmental Seminar


No Teaching Assignments


No Teaching Assignments






Research Postgraduate (RPG) Supervision From January 2019 to December 2022 (As of 30 January 2022)

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All Supervisions Current RPGs Graduated RPGs

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Current RPGs

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Doctor of Philosophy DAI, Shuaijian (co-supervision)
Bioengineering( 2021 - )

REN, Jia (co-supervision)
Bioscience and Biomedical Engineering( 2021 - )

SHENG, Rui
Electronic and Computer Engineering( 2021 - )

WU, Junjie (co-supervision)
Artificial Intelligence( 2021 - )

WU, Kebin (co-supervision)
Life Science( 2021 - )

LAI, Shengzhi
Electronic and Computer Engineering( 2020 - )

LI, Chenrui
Electronic and Computer Engineering( 2020 - )

ZHANG, Xuechen
Electronic and Computer Engineering( 2020 - )

ZHAO, Juntao
Electronic and Computer Engineering( 2020 - )

ZHAO, Peize
Bioscience and Biomedical Engineering( 2020 - )

ZHENG, Jingwen
Electronic and Computer Engineering( 2019 - )

ZHOU, Chen
Electronic and Computer Engineering( 2019 - )

HE, Wuxian
Electronic and Computer Engineering( 2018 - )

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Graduated RPGs

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Master of Philosophy PU, Yu
Electronic and Computer Engineering( Completed in 2019 )









ProjectsFrom January 2020 to December 2022

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All Projects 5 Leading Projects 3 Participating Projects 2

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Detection and Functional Study of Genetic Structure Variations in Familial Breast Cancer Using the Third Generation Sequencing Technology


應用第三代測序技術對家族性乳腺癌基因結構變異的檢測及功能研究 Leading


Innovation and Technology Fund


Project Team (HKUST)
YU Weichuan (Lead)
ISHIBASHI Toyotaka


2022 -




X-GPU: An Extreme GPU Cluster for Interdisciplinary Research on Molecular Dynamics Simulations and Genomics Studies


X-GPU:一個極高性能的GPU計算集群用於分子動力學模擬和基因組學的跨學科研究 Participating


RGC - Collaborative Research Fund


Project Team (HKUST)
YANG Can (Lead)
HAN Yilong
LUO Qiong
PAN Ding
SANDER Pedro
SU Haibin
WANG Jiguang
YAO Yuan
YU Weichuan


2020 -




Translating multi-omic discoveries to transform diabetes care and reduce diabetic complications


轉化多種創新生物標記物以改善糖尿病治療及減少糖尿病併發癥 Participating


Research Impact Fund


Project Team (HKUST)
YU Weichuan


2019 -




Identifying peptides with unlimited post-translational modifications using high-resolution mass spectrometry data


使用高分辨率質譜數據鑒定具有任意翻譯后修飾的多肽 Leading


RGC - General Research Fund


Project Team (HKUST)
YU Weichuan (Lead)


2019 -




Using Imaging Data and Genomic Data to Predict Metastasis of Breast Cancer after Treatment


利用圖像數據和基因組數據預測乳腺癌治療後的轉移 Leading


Innovation and Technology Fund


Project Team (HKUST)
YU Weichuan (Lead)
CHENG Tim Kwang-Ting
WANG Jiguang
WU Angela Ruohao


2019 -