Publications

2018

J. Dai, F. Yu, and W. Yu
"Understanding the limit of open search in the identification of peptides with post-translational modifications — A simulation-based study."
Bioinformatics Under review.
Part of the preliminary result has appeared as a poster in The 21st Annual International Conference on Research in Computational Molecular Biology (RECOMB 2017).

S. Liu, F. Yu, Q. Hu, T. Wang, L. Yu, S. Du, W. Yu, and N. Li
"Development of in planta chemical cross-linking-based quantitative interactomics in Arabidopsis."
Journal of Proteome Research, 17(9), 3195-3213, 2018.

J. Dai, W. Jiang, F. Yu, and W. Yu
"Xolik: finding cross-linked peptides with maximum paired scores in linear time."
Bioinformatics, in press, 2018.

D. Yip, L. Chan, I. Pang, W. Jiang, N. Tang, W. Yu, and K. Yip
"A network approach to exploring the functional basis of gene–gene epistatic interactions in disease susceptibility."
Bioinformatics, 34(10):1741-1749, 2018.

S. Liu, F. Yu, Z. Yang, T. Wang, H. Xiong, C. Chang, W. Yu, and N. Li
"Establishment of Dimethyl Labeling-based Quantitative Acetylproteomics in Arabidopsis."
Molecular & Cellular Proteomics, 17(5): 1010-1027, 2018.

2017

Y. An, G. Xue, S. Yang, M. Deng, X. Zhou, W. Yu, T. Ishibashi, L. Zhang, and Y. Yan
"Apical constriction is driven by a pulsatile apical myosin network in delaminating Drosophila neuroblasts."
Development, 144(12):2153-2164, 2017.

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, 18(6): 928-939, 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, 16(5): 314-325, 2017

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, 962280216687168, 2017

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

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.