Publications

2017

F. Yu, N. Li, and W. Yu
"Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity."
Journal of Proteome Research, 16(10): 3942-3952, 2017.

C. Zhang, T. Liang, P. Mok and W. Yu
"FPGA Implementation of the Coupled Filtering Method and the Affine Warping Method."
IEEE Transactions on NanoBioscience, doi:10.1109/TNB.2017.2705104, in press

W. Jiang and W. Yu
"Controlling the joint local false discovery rate is more powerful than meta-analysis methods in joint analysis of summary statistics from multiple genome-wide association studies."
Bioinformatics, 33(4): 500-507, 2017.

2016

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

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

W. Jiang, J-H. Xue, and W. Yu
"What is the probability of replicating a statistically significant association in genome-wide association studies?"
Briefings in Bioinformatics, doi:10.1093/bib/bbw091, in press.

X. Zhu, F. Yu, Z. Yang, C. Dai, X. Lu, W. Yu, and N. Li
"In planta chemical cross-linking and mass spectrometry analysis of protein structure and interaction in Arabidopsis."
Proteomics, 16(13):1915-1927, 2016.

F. Yu, N. Li, and W. Yu
"ECL: An Exhaustive Search Tool for the Identification of Cross-Linked Peptides Using Whole Database."
BMC Bioinformatics, 17(1):1-8, 2016.

W. Jiang and W. Yu
"Power estimation and sample size determination for replication studies of genome-wide association studies."
BMC Genomics, 17(Suppl 1):3, 2016.

2015

G. Yang, W. Jiang, Q. Yang, and W. Yu
"PBOOST: A GPU based tool for parallel permutation tests in genome-wide association studies."
Bioinformatics, 31(9):1460-2, 2015.

2014

X. Zhou, C. Yang, H. Zhao, and W. Yu
"Low-Rank Modeling and Its Applications in Image Analysis."
ACM Computing Surveys, 47(2), 36, 2014.

X. Zhou, J. Liu, X. Wan and W. Yu
"Piecewise-constant and low-rank approximation for identification of recurrent copy number variations."
Bioinformatics, 30(14):1943-9, 2014.

2013

C. Yang, Z. He and W. Yu
"A Combinatorial Perspective of the Protein Inference Problem."
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10:1542-1547,2013.

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.

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. Computational Biology and Bioinformatics,, 10:207-12, 2013.

X. Zhou, C. Yang, X. Wan, H. Zhao and W. Yu
"Multi-sample aCGH Data Analysis via Total Variation and Spectral Regularization."
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10:230-5, 2013.

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.

H. Liu, X. Shen, H. Tang, Jia 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.

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

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

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.

2012

T. Huang, J. Wang, W. Yu, Z. He
"Protein inference: a review."
Briefings in Bioinformatics, 13(5):586-614, 2012.

X. Wan, C. Yang, and W. Yu.
"Comments on “An empirical comparison of several recent epistatic interaction detection methods”."
Bioinformatics, 28:145-146, 2012.

Ch. Yang, Z. He, C. Yang and W. Yu.
"Peptide re-ranking with protein-peptide correspondence and precursor peak intensity information."
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9:1212-1219, 2012.

2011

C. Yang, X. Zhou, X. Wan, Q. Yang, H. Xue, and W. Yu.
"Identifying Disease-associated SNP Clusters via Contiguous Outlier Detection."
Bioinformatics, 27:2578-2585, 2011.

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.

L. S. 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.

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.

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

Z. He, H. Zhao, and W. Yu
"Score Regularization for Peptide Identification"
BMC Bioinformatics, 12 (Suppl 1):S2, 2011.

Z. He, C. Yang, and W. Yu
A Partial Set Covering Model for Protein Mixture Identification from MS Data
IEEE/ACM Trans. Computational Biology and Bioinformatics, 8:368-380, 2011.

2010

Z. He and W. Yu
"Stable Feature Selection for Biomarker Discovery"
Computational Biology and Chemistry, Vol. 34, pp.215-255, 2010.

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, Volume 87, Issue 3, 325-340, 2010.

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, 26:2517-25, 2010.

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

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.

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.

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.

2009

Z. He and W. Yu
Improving Peptide Identification with Single-Stage Mass Spectrum Peaks
Bioinformatics, 25:2969-2974, 2009.

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.

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.

C. Yang, Z. He, and W. Yu
Comparison of Different Single Spectrum Based Peak Detection Algorithms for Mass Spectrometry Data Analysis
BMC Bioinformatics, 10:4, 2009.

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.

2008

Q. Xu, D. Hu, H. Xue, W. Yu and Q. Yang
Semi-supervised Protein Subcellular Localization
BMC Bioinformatics, 10 (Suppl 1): S47, 2008.

Z. He, C. Yang, and W. Yu
Peak Bagging for Peptide Mass Fingerprinting
Bioinformatics, Vol. 24, pp.1293-1299, 2008.

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.

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.

2007

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.

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