Publications Before 2010
You, ZH, Ke, LY, Huang, DS, Zhou, X, Using Manifold Embedding for Assessing and Predicting Protein Interactions from High-throughput Experimental Data, Bioinformatics, 26(21):2744-51,2010
Li, LM, Zhou, X, Wang, P, Chang, WK, Predicting Enzyme Targets for Cancer Drugs by Profiling Human Metabolic Reactions in NCI-60 Cell lines, BMC Bioinformatics, 11:501, 2010
Zhu, XW, Zhou, X, Lewis, M, and Xia, L, Wang, S, Cancer stem cell, niche and EGFR decide tumor development and treatment response: A bio-computational Simulation Study, J of Theoretical Biology, 269(1):138-49, 2010
You, ZH, Huang, DS, Yin, Z, Han, K, and Zhou, X., A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network, BMC Bioinformatics, 11:343, 2010
Huang D., Zhou, XB., Christopher, LJ., and Willa, HA., and Wong, STC, MicroRNA-integrated and Network-embedded Gene Selection with Diffusion Distance, Plos One, 5(10): e13748, 2010
Ren, XW, Zhou, XB, Wu, LY, and Zhang, XS, An information-flow-based model with dissipation, saturation and direction for active pathway inference, BMC Systems Biology, 4:72, 2010
Xia, XF, Yang, J., Li, F, Li, Y, Zhou, XB, Dai, Y, Wong, STC, Image-Based Chemical Screening Identifies Inhibitors of High Drug-efflux Lung Cancer Cells, Cancer Research, 70; 7723, 2010
Wang, P., Mao, Y., Moses, S., Razo, J., Zhou, X., Wong, STC, Patel, S., Elliott , J., and Gaber AO, Using Genetic and Clinical Factors to Predict Tacrolimus Dose in Renal Transplant Recipients, Pharmacogenomics, 11(10):1389-402, 2010.
Srinivasan, R., Li, Q., Zhou, X., Lu, J., Lichtman, Wong, STC, Reconstruction of the Neuromuscular Junction Connectome, Bioinformatics 26(12):i64-i70, 2010
Xia, Z, Wu , LY, Zhou, XB, Wong, STC, Semi-supervised Drug-Protein Interaction Prediction from Heterogeneous Biological Spaces, BMC System Biology,4:S6, 2010
Zhang, JQ, Zhou, XB, Wang HW, Suffredini, A, Huang, YF, Zhang, L, and Wong, STC, Bayesian Peptide Peak Detection for High Resolution TOF Mass Spectrometry, IEEE Trans on Signal Processing, 58: 5883-5894, 2010
Y.B. Chang, Xia JJ, Gateno J., Xiong, Z.X., Zhou, XB, and Wong STC, "An Automatic and Robust Algorithm of Reestablishment of Digital Dental Occlusion," IEEE Trans on Medical Imaging, 29(9):1652-63, 2010
Li, F, Zhou, X., Huang, WT, Wong STC, Chang CC, Conditional Random Pattern Model for Copy Number Aberration Detection, BMC Bioinformatics, 11:200, 2010
Cheng, J., Zhou, XB, Miller, EL, Alvarez, VA, Sabatini, BL, and Wong, STC. "Oriented Markov Random Field Based Dendritic Spine Segmentation for Fluorescence Microscopy Images," Neuroinformatics, 8(3):157-70, 2010
Huang, Y, Zhou, XB, Miao, BC, Lipinski, M, Zhang, Y., Li, F, Degterev, A., Yuan, JY, and Wong, STC, A computational framework for studying neuron morphology from in vitro high content neuron-based screening, Journal of Neuroscience Methods, 190(2): 299-309, 2010
C Chang, Zhou XB, JJ
Taylor, W Huang, X Ren, F Monzon, Y Feng, PH Rao, X Lu, F Fabio, S Hilsenbeck,
CJ Creighton, ES Jaffe, and C Lau, Genomic profiling of plasmablastic lymphoma
using array comparative genomic hybridization (aCGH): revealing significant
overlapping genomic lesions with diffuse large B-cell lymphoma, J Hematol
Oncol, 12:2-47, 2009.
D., Pham, T., and Zhou, X., Analysis and recognition of touching cell images
based on morphological structures, Computers in Biology and Medicine, 39 27-39
P, Liu KY, Misra V, Wacleche VS, Gosselin A, Zhou XB, and Gabuzda D,
Transcriptional profiling reveals developmental relationship and distinct
biological functions of CD16+ and CD16- monocyte subsets BMC Genomics, 10:403,
P, Li HQ, Wong STC, and Zhou X, Peak Tree: a New Tool for Multiscale
hierarchical Representation and Peak Detection of Mass Spectrometry Data.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 99:1-14,
GX, Zhou, XB, Cui, KM, Wong, STC, The network biomarker discovery in prostate
cancer from both genomics and proteomics levels, IET System Biology, 3(6),
GX, Cui, KM, Zhou, XB, Wong, STC, Unraveling the Signal-Transduction Networks
in Cancer Metastasis, IEEE Signal Processing Magazine, 26: 129-132, 2009
Zhou, X, and Wong STC, "Optimal Multiple Nuclei Tracking Using Integer
Programming for Quantitative Cancer Cell Cycle Analysis," IEEE Trans. on
Medical Imaging, 29(1):96-105, 2009.
W, Li, H.Q, Zhou, X, 3D neuron dendritic spine detection and dendrite
reconstruction, International J. Comp. Aided Eng. Tech. v.1(4), pp. 516 - 531,
S, DeGraba, T, Wong, HH, Hoehn, G, Gonzales, DA, Suffredini, AF, Ching, WK, Ng,
MK, Zhou, X, and Wong STC, A Novel Peak Detection Approach with Chemical Noise
Removal Using Short-Time FFT for prOTOF MS Data, Proteomics, 2009
T, Peng, H, and Zhou, X, Imaging Informatics for Personalized Medicine:
Applications and Challenges, International Journal of Functional Informatics
and Personalized Medicine, 2(2):125-135, 2009
Zhou X, Dy J, Zhang Y, Spires TL, Hyman BT, and Wong STC, An Automatic Approach
for Dendrite Spine Detection and Tracking in vivo 3D Confocal Microscopy
Images, Neuroinformatics, 7(2):113-130, 2009.
X. Zhou, X., Huang, W, Wu, L,Mozon, F., Chang, CC, and Wong, STC,
Pattern-selection Based Power Analysis and Discrimination of Low- and
High-Grade Myelodysplastic Syndromes Study Using SNP Arrays, Plos One,
X, Wang, HH, Wang, J, Hoehn, G, Azok, J, Brennan, ML, Hazen, SL, Li, K, Chang,
SF, and Wong, STC, "Biomarker Panel Discovery for Risk Stratification of
Cardiovascular Events Using Genetic Algorithm with Recursive Local Floating
Search Embedding," Proteomics, 9:2286-2294, 2009
XB, Li, F, Yan, J, and Wong, STC. A Novel Cell Segmentation Method and Cell
Phase Identification sing Markov Model. IEEE Trans on Information Technology in
Biomedicine, 13(2):152-157, 2009.
Zhou X, Li FH, Yang XR, Chang CC and Wong STC. Conditional Random Pattern
Algorithm for LOH Inference and Segmentation. Bioinformatics, 25(1):61-67, 2009
T, Zhou X: Special issue on pattern recognition in computational life sciences.
Pattern Recognition 42(4): 497, 2009
B, Zhou, XB, and Hung, YS, Growing Enzyme Gene Networks by Integration of Gene
Expression, Motif Sequence and Metabolic Information, Pattern recognition,
Zhou XB, Sun Y, and Wong STC. Online Phenotype Discovery based on Minimum
Classification Error Model, Pattern Recognition, 42(4):509-522, 2009
Pham T, Zhou X, Wong STC, Recognition and analysis of cell nuclear phases for
high-content screening based on morphological features. Pattern Recognition
42(4): 498-508 (2009)
WT, Yang X, Zhou X, ..., and Chang CC. Multiple distinct clones may co-exist in
different lineages in myelodysplastic syndromes. Leukemia Research,
P, Li, HQ, Zhou, XB, and Wong, STC, Peak Detection Using Peak Tree Approach for
Mass Spectrometry Data, International Journal of Hybrid Intelligent Systems,
M, Day LJ, Brooks DH, Zhou XB, and O'Malley DM, Automated Identification of
Neurons in 3D Confocal Datasets from Zebrafish Brainstem, Microscopy, 233, pp.
J, Zhou X, Li F, Bradley PL, Chang SF, Perrimon N, and Wong STC, An Image Score
Inference System for RNAi Genome-wide Screening Based on Fuzzy Mixture
Regression Modeling, Biomed Informatics, 42 (1): 32-40, 2009
Chahrour M, Jung SY, Shaw C, Zhou XB, Wong STC, Qin J, and Zoghbi HY. MeCP2, a Key Contributor to Neurological Disease, Activates and Represses Transcription. Science, 2008 May 30, Vol. 320. no. 5880, pp. 1224 - 1229
Jin, GX, Zhou, XB, Wang, HH; Zhao, H, Zhang, XS, Chen, L, Hazen, S, Li, K; Wong, STC, The knowledge-integrated network biomarkers discovery for Major Adverse Cardiac Events, Journal of Proteome Research, 7 (9): 4013-4021, 2008
Wang Y, Zhou X, Wang H, Li K, Yao L, and Wong STC, Reversible Jump MCMC Approach for Peak identification for Stroke SELDI Mass Spectrometry Using Mixture Model. Bioinformatics, 2008 24(13):i407-i413, 2008
Yin Z, Zhou XB, Bakal C, Li F, Sun Y, Perrimon Y, and Wong STC, Using Iterative Cluster Merging with Improved Gap Statistics to Perform Online Phenotype Discovery in the Context of High-throughput RNAi Screens. BMC Bioinformatics, 9:264, 2008.
Zhou X and Wong STC, Computational Systems Bioinformatics and Bioimaging for Pathway Analysis and Drug Screening, Proceedings of IEEE, 96(8): 1310-1331, 2008
Li FH, Zhou, X, Zhu, JM, Ma JW, Wong STC. High Content Cellular Image Based Calcium Signaling Analysis System for Cells with Mutant Presenilin-1 of Familial Alzheimer Disease. Neuroinformatics, 6(2): 97-108, 2008
Zhang K, Xiong HK, Zhou X, Yang L, Wang YL, and Wong STC, "An Object-Aware Representation Framework for Cell Migration Detection and Tracking," J of Microscopy, 231(3):395-407, 2008.
Zhang, Y, Zhou, X, Lu, J, Lichtman, J, Adjeroh, D, Wong, STC, "Axon Tracking Using 3D Curvilinear Structure Extraction and Dynamic Programming," Neural Computation, 20(8):1899-1927, 2008
Wang, M, Zhou, X, Li, FH, Huckins, J, King, RW, and Wong, STC, "Novel Cell Segmentation and Online SVM For Cell Phase Identification in Automated Time-Lapse Microscopy," Bioinformatics 24(1): 94-101 (2008)
Chen, C, Li, HQ, Zhou, X, Wong, STC, "Constraint Factor graph cut based active contour method for automated cellular image segmentation in RNAi screening, Journal of Microscopy, 230 (Partt 2):177-91, 2008
Wang, J, Zhou, X, Bradley, PL, Perrimon N, and Wong, STC. Phenotype recognition for high-content RNAi genome-wide screening. Journal of Molecular Screening, Vol. 13, No. 1, 29-39 (2008)
Geng B, Zhou X, Hung Y.S., and Wong STC, "Comparison of Bayesian and Regression Models in Missing Enzyme Identification," International Journal of Bioinformatics Research and Applications, 4(12):363-374, 2008
Geng, B, Zhou, X, Zhu, J, Hung, YS, and Wong, STC, "Missing enzyme identification using reversible-jump Markov-Chain-Monte-Carlo learning," Journal of Biomedical Informatics, 41(2): 272-281. 2008
Xia, Z., Huang, X., Zhou, X, Sun, Y, Ntziachristos, V., Wong, STC, "Registration of 3D CT and 2D Flat Images of Mouse via Affine Transformation, " IEEE Trans on Information Technology in Biomedicine, 12(5):569-78, 2008
Pham, T, Wang, HH, Zhou, X , Hoehn, G, Azok, J, Brennan, ML, Hazen, SL, Li, K, Chang, SF, and Wong, STC, "Linear Predictive Coding and its Decision Logic for Early Prediction of Major Adverse Cardiac Events using Mass Spectrometry Data, "IEEE Trans on Information Technology in Biomedicine, 12(5):636-43, 2008
Yan P, Zhou X, Shah M, and Wong STC, "Automatic Segmentation of RNAi Fluorescent Cellular Images with Interaction Model," IEEE Trans on Information Technology in Biomedicine, 12(1): 109-117, 2008
Jiang S, Zhou X, Kirchhausen, T, and Wong STC, "Tracking Molecular Particles in Live Cells Using Fuzzy Rule-Based System: Part II," Cytometry A, 71A(8): 576 - 584, 2008
Chen J, Zhu J, Cho HH, Cui K, Li F, Zhou X, Rogers JT, Wong STC, and Huang X. Differential cytotoxicity of metal oxide nanoparticles. J. of Experimental Nanoscience, 3(4): 321 - 328, 2008
Liu T, Li G, Nie J, Tarokh A, Zhou X, Guo L, Malicki J, Xia W, Wong STC. An Automated Cell Detection Method for Cell Detection in Zebrafish. Neuroinformatics, 6(1):5-21., 2008
Li, FH, Zhou, X, Zhu, J, Ma, J, Huang, XD, and Wong, STC, "High Content Image Analysis for H4 Human Neuroglioma Cells Exposed to CuO Nanoparticles," BMC Biotechnology, 2007; 7: 66.
Bai W, Zhou, X, Ji L., and Wong STC., "A Fully Automatic Dendritic Spine Analysis in Two-Photon, Laser Scanning Microscopy Images," Cytometry A, 71(10):818-26, 2007
Srinivasan R, Zhou X, Miller E, Lu J, Lichtman J, Wong STC. Automated Axon Tracking of 3D Confocal Laser Scanning Microscopy Images Using Guided Probabilistic Region Merging. Neuroinformatics, 5: 189-203(15), 2007
Cheng J, Zhou X, Miller E, Witt RM., Zhu J, Sabatini BL, and Wong STC, "A Novel Computational Approach for Automatic Dendrite Spines Detection in Two-Photon Laser Scan Microscopy," Neuroscience Methods, 165:122-134, 2007
Jiang S, Zhou X, Kirchhausen, T, and Wong STC, "Detection of Molecular Particles in Live Cells via Machine Learning: Part I," Cytometry A, 71A(8): 563 - 575, 2007
Zhang Y, Zhou, X., A. Degterev, M. Lipinski, D. Adjeroh, J. Yuan, S.T.C. Wong, "Dendritic Spine Detection Using Curvilinear Structure Detector and LDA Classifier," Neuroimage, 36:346-360, 2007.
Wang M, Zhou X, King, R, and Wong STC, "Context based mixture model for cell phase identification in automated fluorescence microscopy," BMC Bioinformatics, 8(32): 1-12, 2007
Pham, T, Tran, DT, Zhou, X, and Wong STC, "A Microscopic Image Classification System for High-Throughput Cell-Cycle Screening," International Journal of Intelligent Computing in Medical Sciences and Image Processing, 1(1): 67-77, 2007.
Xia, Z., Zhou, X., Sun, Y., and Wong, STC, "Automated Recognition of Cellular Phenotypes by Support Vector Machines with feature reduction," Journal of Knowledge-Based & Intelligent Engineering Systems, 11(4): 247-253, 2007
Mao Y, Xia Z., Yin Z, Zhou X, and Sun Y., "A Survey for Study of Feature Selection Algorithms," Journal Pattern Recognition and Artificial Intelligence; 20(2): 211-218, 2007.
Pham, T, Tran, DT, Zhou, X, and Wong STC, "Fuzzy Information Fusion of Classification Models for High-Throughput Image Screening of Cancer Cells in Time-Lapse Microscopy," Journal of Knowledge-Based & Intelligent Engineering Systems, 11(4): 237-246, 2007.
Li FH, Zhou, X, and Wong, STC. An automated feedback system with the hybrid model of scoring and classification for solving over-segmentation problems in RNAi high content screening. J of Microscopy, 2007. 226(2): 121-132.
Zhang Y, Zhou, X., A. Degterev, M. Lipinski, D. Adjeroh, J. Yuan, S.T.C. Wong, "Automated neurite extraction using dynamic programming for neuron assays based high-throughput screening," Neuroimage, Vol 35(4): 1502-1515, 2007
Zhang Y, Zhou, X., A. Degterev, M. Lipinski, D. Adjeroh, J. Yuan, S.T.C. Wong, "A novel tracing algorithm for high throughput imaging screening of neuron based assays," Journal of Neuroscience Methods, Vol. 160, pp149-162, 2007
Yang X, H. Li, and Zhou, X., "Nuclei segmentation using marker-controlled watershed, tracking using mean-shift and Kalman filter in time-lapse microscopy," IEEE Trans on Circuits and Systems - 1, 2006; 53(11): 2405-2414
Xiong G., Zhou X., L. Ji, Bradley, P., and Perrimon, N., "Automated segmentation of Drosophila RNAi fluorescence cellular images using deformable models," IEEE Trans on Circuits and Systems - 1, 2006; 53(11): 2415-2424
Xiong G, Zhou, X., A. Degterev, L. Ji, and S.T.C. Wong, "Automated neurite labeling and analysis in fluorescence microscopy images," Cytometry A, 2006 May 5; 69A (6):494-505
Liu KY, Zhou, X., and Wong STC, "Detailed replies to the reviewers Bayesian variable selection for gene expression modeling with regulatory motif binding sites in Neuroinflammatory events," Neuroinformatics, 2006; 4(1):95-117
Zhou, X., J. Zhu, K. L. Liu, B. Sabatini and Stephen, T.C. Wong, ``Mutual information based feature selection in studying perturbation of dendritic structure caused by TSC2 inactivation," Neuroinformatics, 2006;4(1):81-94.
Zhou, X., X. Cao, and STC. Wong, "Cell phase recognition and analysis of high content screening for drug discovery based on spindle model of mitosis," Journal of Biomedical Informatics, 2006 Apr;39(2):115-25.
Chen X, Zhou, X., and STC. Wong, "An image analysis system for segmentation, classification, and tracking of cell cycle phases in time-lapse fluorescence microscopy," IEEE Trans on Biomedical Engineering, 2006 Apr; 53(4):762-6.
Mao Y, Zhou, X., D. Pi, Y. Sun, "Constructing support vector machine ensemble for classification of cancer based on biochips data," Journal of Genomics, Proteomics & Bioinformatics. 3(4), 238-241. 2006.
Zhou, X., Chou J., and Wong STC, "Protein structure similarity from principle component correlation analysis," BMC Bioinformatics, 2006 Jan 25; 7-40.
Zhou, X., Wang X., and Dougherty E.R., "Multi-class cancer classification using multinomial probit regression with Bayesian gene selection," IEE System Biology, 153(2), pp. 70-78, 2006.
Zhou, X. and Wang X., "Optimization of Gaussian mixture model for satellite image classification," IEE Vision, Image & Signal Processing, 153(3), pp. 349-356, 2006.
Pham T.D., Tran D.T., Zhou, X.B. and Wong STC., Integrated algorithms for image analysis and classification of nuclear division for high-content cell-cycle screening. International Journal of Computational Intelligence and Applications, Vol. 6, No. 1 (2006) 21-43.
Zhou, X., and S.T.C. Wong, "High content cellular imaging for drug Development," IEEE Signal Processing Magazine, 2006 March, 23(2):170-174
Zhou, X. and S.T.C. Wong, "Informatics challenges of high-throughput microscopy," IEEE Signal Processing Magazine, 2006 May, 23(3): 63-72.
Liu K-Y, Lin J, Zhou, X., and Wong STC. "Boosting alternating decision trees (ADTrees) modeling of disease trait information." BMC Genetics, 2005, Vol.6, S 132.
Mao Y, Zhou, X., D. Pi, S. T.C. Wong, and Y. Sun, "Multi-class cancer classification by using fuzzy support vector machine and binary decision tree with gene selection," Journal of Biomedicine and Biotechnology, 2: 160-171, 2005.
Zhou, X, Wang, X, Dougherty, ER., Gene selection using logistic regressions based on AIC, BIC and MDL criteria. New Math. Nat. Comput. 1, No. 1, 129-145 (2005).
Mao Y, Zhou, X., D. Pi, Y. Sun, and STC Wong, "Parameters selection in gene selection using Gaussian Kernel support vector machines by genetic algorithm," International Journal of Zhejiang University SCIENCE, 6B (10), 961-973, 2005.
Zhou, X., X. Wang, and E.R. Dougherty, "Sequence Monte Carlo estimation for nonlinear-probit gene classification based on bootstrap Bayesian gene selection," Journal of Franklin Institute, special issue on Genomics, Signal Processing and Statistics, Vol. 341, pp.137-156, 2004.
Zhou X., K.Y. Liu, and Stephen, T.C. Wong, "Cancer classification and prediction based on logistic regression using approximate Bayesian gene selection," Journal of Biomedical Informatics, Vol. 37, pp. 249-259, 2004.
Zhou, X., X. Wang, M. Bittner, and E.R. Dougherty, "A Bayesian connective-based approach to constructing probabilistic gene regulatory networks," Bioinformatics, Vol. 20, pp. 2918-2927, 2004.
Zhou, X., X. Wang, and E.R. Dougherty, "Gene prediction and network construction using multinomial probit regression with Bayesian variable selection," Journal of Applied Signal Processing, special issue on Genomic Signal Processing, Vol. 3, No.1, pp.115-124, 2004.
Zhou, X., X. Wang, and E.R. Dougherty, "Nonlinear probit gene classification using mutual-Information and wavelet," Journal of Biological Systems, Vol. 12, No. 3, 371-386, 2004.
Zhou X., X. Wang, and E.R. Dougherty, "Gene clustering based on cluster-wide mutual information," Journal of Computational Biology, Vol. 11, No. 1, pp.151-165, 2004.
Zhou X. and X. Wang, "FIR-Median hybrid filters with polynomial fitting," Journal of Digital Signal Processing, Vol. 14, No. 1, pp.112-124, 2004.
G. Yue, Zhou X. and X. Wang, "Performance comparisons of channel estimations in multipath fading CDMA," IEEE Trans on Wireless Communications, Vol. 3, No.3, pp.716-724, 2004.
Zhou, X., X. Wang, and E.R. Dougherty, "Missing value estimation based on linear and nonlinear regression with Bayesian gene selection," Bioinformatics, Vol. 19, pp. 2302-2307, 2003.
Zhou X., X. Wang, and E.R. Dougherty, "Binarization of microarray data based on a mixture model," Journal of Molecular Cancer Therapeutics, vol. 2, no. 2, pp. 679-684, 2003.
Zhou X., X. Wang, and E.R. Dougherty, "Construction of genomic networks using mutual-information clustering and reversible-jump Markov-Chain-Monte-Carlo predictor design," Signal Processing Journal, special issue on Genomic Signal Processing, Vol. 83, No. 4, pp. 745-761, 2003.
Zhou X. and X. Wang, "Receiver techniques for Ultra-wide-band (UWB) multiuser systems over fading multipath channels," Journal of Communications and Networks, Vol. 5, no.2, pp. 1-7, 2003.
Zhou X. and X. Wang, "Channel estimation for OFDM system using radial basis function networks," IEEE Trans. on Vehicle Technology, Vol.52, No.1, pp.48-59, Jan. 2003.