Publications

2023

C. Zhou, S. Dai, S. Lai, Y. Lin, X. Zhang, N. Li, W. Yu.
"ECL 3.0: a sensitive peptide identification tool for cross-linking mass spectrometry data analysis."
BMC Bioinformatics, 24: 351, 2023.

S. Dai, S. Liu, C. Zhou, F. Yu, G. Zhu, W. Zhang, H. Deng, A. Burlingame, W. Yu, T. Wang, N. Li.
"Capturing the hierarchically assorted modules of protein-protein interactions in the organized nucleome."
Molecular Plant, 16(5): 930-961, 2023.

X. Zhang, I. Cheng, S. Liu, C. Li, J. Xue, L. Tam, and W. Yu.
"Automatic 3D joint erosion detection for the diagnosis and monitoring of rheumatoid arthritis using hand HR-pQCT images."
Computerized Medical Imaging and Graphics, 106, 2023.

C. Zhou, S. Dai, Y. Lin, S. Lian, X. Fan, N. Li, W. Yu.
"Exhaustive cross-linking search with protein feedback."
Journal of Proteome Research, 22: 101-113, 2023.

2022

C. Zhou, W. Yu.
"Cross-linking mass spectrometry data analysis."
Handbook of Statistical Bioinformatics, 339-370, 2022.

W. He, H. Tang, J. Li, C. Hou, X. Shen, C. Li, H. Liu, W. Yu.
"Feature-based quality assessment of middle cerebral artery occlusion using 18F-fluorodeoxyglucose positron emission tomography."
Neuroscience Bulletin, 38: 1057-1068, 2022.

2021

J. Dai, F. Yu, C. Zhou, and W. Yu.
"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, 18(6), 2884-2890, 2021.

2020

Y. Gao, G. Chuai, W. Yu, S. Qu, and Q. Liu.
"Data imbalance in CRISPR off-target prediction."
Briefings in Bioinformatics, 21(4): 1448-1454, 2020.

2019

S. Zhang, W. Jiang, R. Ma, and W. Yu
"Region-based interaction detection in genome-wide case-control studies."
BMC Medical Genomics, 12(133), 2019.

J. Dai, W. Jiang, F. Yu, and W. Yu
"Xolik: finding cross-linked peptides with maximum paired scores in linear time."
Bioinformatics, 35(2): 251-257, 2019.

2018

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, 27(9), 2795-2808, 2018.

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.

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

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, 34: 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, 87(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, 24: 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, 1: 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, 31: 215-221, 2007.