Publications

Books

Zhou X. and Wong STC. Computational Systems Bioinformatics - Methods and Biomedical Applications. World Scientific Publishers, Dec 2007

Pham and Zhou X, Eds. Computational Models For Life Sciences - CMLS '07. Mathematical and Statistical Phsyics, Vol. 952, 2008.


Selected Peer Reviewed Articles Since 2003

2014

156. Peng, HM, Peng, T, Wen, JG, Engler, D,  Matsunami, RK, Su, J, Zhang, L, Chang, C, and Zhou, XB, Characterization of p38 MAPK Isoforms for Drug Resistance Study Using Systems Biology Approach, Bioinformatics, accepted for publications, 2014

155. Mandl, K, Murphy,S, Kohane, I, …, Zhou, X., and et., al., Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS): Architecture, Journal of the American Medical Informatics Association, accepted for publications, 2014

154. Tang, L, van de Ven, A, Guo, DM, Andasari, V, Li, KS, Zhou, XB, Computational Modeling of 3D Tumor Growth and Angiogenesis for Chemotherapy Evaluation, Plos One, DOI: 10.1371/journal.pone.0083962, 2014.

153. Su, J, Zhang, L, Zhang, W, Choi, DS, Wen, JG, Jiang, BN, Chang, CC, and Zhou, XB, Targeting the Biophysical Properties of the Myeloma Initiating Cell Niches: A Pharmaceutical Synergism Analysis Using Multi-scale Agent-based Modeling, Plos One, DOI: 10.1371/journal.pone.0085059, 2014.

152. Xing, J., Huang, L, Lu, JH, Zhou, XB, Li, HW, and Bian, JW, HMMotif: predicting sequence motifs, governing constitutive exon splicing, Research Journal of Biotechnology, accepted for publication, 2014

151. Zhang, RJ, Zhao, C, Xiong, ZX, and Zhou, XB, Pathway Bridge Based Multi-objective Optimization Approach for Lurking Pathway Prediction, BioMed Research International, accepted for publication, 2014

2013

150. Sun, XQ, Bao, JG, Nelson, KC, Li, KC, Kulik, G, and Zhou, XB, Systems Modeling of Anti-apoptotic Pathways in Prostate Cancer: Psychological Stress Triggers, a Synergism Pattern Switch in Drug Combination Therapy, Plos Computational Biology, 9(12): e1003358. doi:10.1371/journal.pcbi.1003358, 2013

149. Wang, HY, Wen, JG, Chang CC, and Zhou, XB, Discovering Transcription and Splicing Networks in Myelodysplastic Syndromes, Plos One, DOI: 10.1371/journal.pone.0079118, 2013

148. Su, J, Zhang, L, Zhang, W, Choi, DS, Wen, JG, Jiang, BN, Chang, CC, and Zhou, XB, Targeting the Biophysical Properties of the Myeloma Initiating Cell Niches: A Pharmaceutical Synergism Analysis Using Multi-scale Agent-based Modeling, Plos One, accepted for publication, 2013

147. Shao HW, Peng T, Ji ZW, Su, J, Zhou, XB, Systematically Studying Kinase Inhibitor Induced Signaling Network Signatures by Integrating both Therapeutic and Side Effects, PLoS ONE 8(12): e80832. doi:10.1371/journal.pone.0080832, 2013

146. Tan, H, Kun, W, Bao, GG, and Zhou, XB, In silico study on multidrug resistance conferred by I223R/H275Y double mutant neuraminidase, Molecular Biosystems, 9(11):2764-74. doi: 10.1039/c3mb70253g, 2013

145. Peng, T, Choi, D, Peng, H, Su, J, Chang, CC, and Zhou, XB, Modeling Cell-Cell Interactions in Regulating Multiple Myeloma Initiating Cell Fate, IEEE Journal of Biomedical and Health Informatics, Vol. PP, No. 99, doi:10.1109/JBHI.2013.2281774, 2013

144. Guo, DM, and Zhou, XB, Red Blood Cells Tracking Using Optical Flow Methods, IEEE Journal of Biomedical and Health Informatics, , Vol. PP, No.99, doi:10.1109/JBHI.2013.2281915, 2013

143. Liu, CL, Ma, JW, Chang, CC and Zhou, XB, FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq, BMC Bioinformatics, 2013, 14:193.

142. Bian J, Liu C, Wang H, Xing J, Kachroo P, and Zhou, XB, SNVHMM: predicting single nucleotide variants from next generation sequencing, BMC Bioinformatics, 2013, 14:225.

141. Wang J., Zhang, L., Jing, CY, Ye, G., Wu, HL, Miao, HY, Wu, YK, Zhou, XB, Multi-scale agent-based modeling on melanoma and its related angiogenesis analysis, Theoretical Biology and Medical Modelling, 2013, 10: 41.

140. Shao, HW and Zhou, XB, A System Mathematical Model of Cell-cell Communication Network in Amyotrophic Lateral Sclerosis", Molecular BioSystems, 2013 Mar 5;9(3):398-406.

139. Liu GH, Deng CH,Bodin A, Sun XZ, Bharadwaj S, Zhou, XB, Wang XS, Atala A and Zhang Y. Cell injection therapy of urine derived stem cells expressing VEGF for urinary incontinence. Tissue Engineering, 2013

138. Sun CL, Shi Z-Z, Zhou, XB, Chen LN, and Zhao XM, Prediction of S-Glutathionylation Sites Based on Protein Sequences, Plos One, 2013; 8(2):e55512

137. Lin, JZ, Sieglaff, DH, Yuan, CS, Su, J, Arumanayagam, As, Firouzbakht, S, Cantu Pompa, JJ, Reynolds, FD, Zhou, XB, Cvoro, A, Webb, P, Gene Specific Actions of Thyroid Hormone Receptor Subtypes, PLoS One, 8(1):e52407, (2013)

136. Sun X, Kang Y, Zhang Y, Yang Y, Zhou, XB, Three-Dimensional System Modeling for Vascularized Bone Regeneration Within a Porous Biodegradable CaP Scaffold Loaded with Growth Factors, Biomaterials, 34: 4971-4981, 2013

135. O'Neill, BE, Vo, HQ, Shao, HW, Karmonik, C., Zhou, XB, and King C. Li, Title: MRI-based prediction of pulsed high-intensity focused ultrasound effect on tissue transport in rabbit muscle, Journal of Magnetic Resonance Imaging , 2013 Nov;38(5):1094-102.

134. Chang, YB, Yuan P, J Xia, Zhou, XB, “shared 3D Segmentation of Maxilla in Cone-beam Computed Tomography Imaging Using Base Invariant Wavelet Active Shape Model on Customized Two-manifold Topology, Journal of X-Ray Science and Technology, 2013;21(2):251-82.

133. Wang, HY and Zhou, XB, Detection and characterization of regulatory elements using graphical probabilistic models, Chinese Journal of Cancer, 2013, 4:186-194.

132. Fan, J, JG, Dy, Chang, CC, and Zhou, XB, Identification of SNP‐containing regulatory motifs in the myelodysplastic syndromes model using SNP arrays and gene expression arrays, Chinese Journal of Cancer, 2013, 4: 170-185

131. Zhou, XB, Editorial Preface: Genomic Informatics: Detection of Chromatin states, SNP-containing Motifs, and Functional Enrichment Modules, Chinese Journal of Cancer, 2013, 4:153-54.

130. Zhang, L. Xue, Y, Jiang, B, Wu, Y., Su, J, and Zhou, XB, Multiscale agent-based modelling of ovarian cancer progression under the stimulation of the STAT 3 pathway, Int. J. Data Mining and Bioinformatics, 9(3):235-253, 2013.

129. Xia, Z, Chen, W., and Chang, CQ, Zhou, XB*, A Graph-based Elastic Net for Variable Selection and Module Identification for Genomic Data Analysis, Int. Jour. of Data Mining & Bioinformatics, 8(3): 311-325 (2013)

128. Liu GH, Rajesh Pareta, Bharadwaj S, Zhou, XB, Liu YM, Liu H, Sun XZ, Deng CH, Opera E, Atala A and Zhang Y. Sk myogenic differentiation of USC and angiogenesis in alginate beads with VEGF for SUI. Biomaterials, 2013 Jan;34(4):1311-26. 

2012

127. Sun XQ, Zhang L., Tan H., Bao JG, Strouthos, C., and Zhou, XB, Multi-scale Agent-Based Brain Cancer Modeling and Quantitative Prediction of TKIs Treatment Response: Incorporating EGFR Signaling Pathway and Angiogenesis, BMC Bioinformatics, 2012, 13:218.

126. Lang R, Liu GH, Bharadwaj S, Leng XY, Zhou, XB, Liu H, Atala A, Zhang, YY, Self-Renewal and Differentiation Capacity of Urine-Derived Stem Cells after Urine Preservation for 24 Hours, Plos One, 2012

125. Li, FF, Zhao CB, Xia Z, Wang YQ, Zhou, XB, Li, GZ, Computer-assisted lip diagnosis on traditional Chinese medicine using multi-class support vector machines, BMC Complementary and Alternative Medicine, 12:127, 2012

124. Sun X, Su J, Bao J, Peng T, Zhang L, Zhang YY, Yang YZ, Zhou, XB. Cytokine combination therapy prediction for bone remodeling in tissue engineering based on the intracellular signaling pathway. Biomaterials. 2012 Nov;33(33):8265-76.

123. Tan, H, Gan, J, Bao, JG, Dy, JG, Zhou, XB, A Computational model for compressed sensing RNAi cellular screening, BMC Bioinformatics 2012, 13:337.

122. Chang YB, Xia JJ, Gateno J, et al, Zhou, XB,: In vitro evaluation of new approach to digital dental model articulation. J Oral Maxillofac Surg 70:952, 2012

121. Pan B, Xia JJ, Yuan P, et al, Zhou, XB: Incremental kernal ridge regression for prediction of soft tissue deformations. Med Image Comput Comput Assist Interv (MICCAI 2012) 15, 2012

120. Peng, HM, Wen, JG, Li, HW, Chang, CC, and Zhou, XB*. Systematic Modeling Study on the Mechanism of p38 MAPK Activation in Myelodysplastic syndromes. Molecular BioSystems. 2012 Apr;8(4):1366-74.

119. Zhang, L, Xue, Y., Jiang, BN, Strouthos, C., Duan, ZF, Wu, YK, Su, J, Zhou, XB*, Multiscale agent-based modeling of ovarian cancer progression under the stimulation of the STAT 3 pathway," Int. Jour. of Data Mining & Bioinformatics, 2012.

118. Tan, H, Bao, JG, and Zhou, XB*, A Novel Missense-Mutation-Related Feature Extraction Scheme for ‘driver’ Mutation identification, Bioinformatics. 2012 Nov 15;28(22):2948-55.

117. Tang L, Su,J, Huang, DS, Lee, DY, Li, KCP, and Zhou, XB*. An Integrated Multi-scale Mechanistic Model for Cancer Drug Therapy. ISRN Biomathematics. 2012:1-12.

116. Hsu SS, Gateno J, Bell RB, Hirsch DL, Markiewicz MR, Teichgraeber JF, Zhou, XB*, Xia JJ. Accuracy of a Computer-Aided Surgical Simulation Protocol for Orthognathic Surgery: A Prospective Multicenter Study. J Oral Maxillofac Surg. 2012 Jun 11.

2011

115. Xia, Z, Wen, J, Chang CC, and Zhou, XB, NSMAP: A Method for Spliced Isoforms Identification and Quantification from RNA-Seq, BMC Bioinformatics, 2011, 12:162

114. Zhang, L, Jiang, BN, Wu, YK, Strouthos, C., Su, J., Sun, Z., and Zhou, XB*, Developing a multi-scale, multi-resolution agent-based brain tumor model by graphics processing units, Journal of Theoretical Biology and Medical Modeling, 2011, 8:46 doi:10.1186/1742-4682-8-46.

113. Sigoillot FD, Huckins JF, Li F, Zhou, XB, Wong STC, et al., A Time-Series Method for Automated Measurement of Changes in Mitotic and Interphase Duration from Time-Lapse Movies. PLoS ONE 6(9): e25511.

112. Ito, M., Zhao, NX, Zeng, ZH, Zhou, XB, Chang, CC, and Zu, YL, Interleukin-2 Functions in Anaplastic Large Cell Lymphoma Cells through Augmentation of Extracellular Signal-Regulated Kinases 1/2 Activation, Int. J. of Biomedical Science, 7(3), 181-190, Sep 15, 2011

111. Ren, X., Chang, CC, and Zhou, XB*, The network properties of Myledysplastic Syndromes pathogenesis revealed by an integrative systems biological method, Molecular BioSystems, 2011 Jun;7(6):2048-54

110. Peng, HM, Wen, JG, Li, HW, Chang J, Zhou XB*, Drug Inhibition Profile Prediction for NFκB Pathway in Multiple Myeloma, Plos One, 6(3): e14750, 2011

109. Zhang Z, Ge Y, Zhang D, Zhou, XB. High-content analysis in monastrol suppressor screens. A neural network based classification approach. Methods Inf Med. 2011 May 13;50(3):265-72.

108. Zhang, P., Li, HQ, Wang HW, Wong STC, and Zhou, XB*: Peak Tree: A New Tool for Multiscale Hierarchical Representation and Peak Detection of Mass Spectrometry Data. IEEE/ACM Trans. Comput. Biology Bioinform. 2011, 8(4): 1054-1066.

107. Jin GX, Zhao, H, and Zhou, XB, Wang, S, An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data, Bioinformatics, 2011: (2011) 27 (13): i310-i316.

106. Chang, YB, Xia, J, I Gateno, J, Xiong, ZX, Teichgraeber, J, Lasky, RE, Zhou, XB*, In-Vitro Evaluation of a New Approach to Digital Dental Model Articulation Journal of Oral and Maxillofacial Surgery, J. of Oral andMaxillofacial Surgery, 2011.

105. Beck, D, Ayers, S, Wen,J, Brandl, M, Pham, T, Webb, P., Chang, CC, and Zhou, XB, Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in Myelodysplastic Syndromes, BMC Medical Genomics, 4:19, 2011.

104. Jiang B, Struthers A, Zhang L, Zhou, XB, and Barrens, M, Employing graphics processing unit technology, alternating direction implicit method and domain decomposition to speed up the numerical diffusion solver for the biomedical engineering research. Int. J. for Numerical Methods in Biomedical Engineering, 2011;DOI: 10.1002/cnm.

103. Li, Q., Zhang, Y., Zhou, XB, Deng, ZG, A Global Spatial Similarity Optimization Scheme to Track Large Numbers of Dendritic Spines in Time-lapse Confocal Microscopy, IEEE Trans on Medical Imaging, 30(2): 632- 641, 2011

2010

102. 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

101. 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

100. 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

099. 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

098. 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

097. 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

096. 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

095. 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.

094. Srinivasan, R., Li, Q., Zhou, X., Lu, J., Lichtman, Wong, STC, Reconstruction of the Neuromuscular Junction Connectome, Bioinformatics 26(12):i64-i70, 2010

093. Xia, Z, Wu , LY, Zhou, XB, Wong, STC, Semi-supervised Drug-Protein Interaction Prediction from Heterogeneous Biological Spaces, BMC System Biology,4:S6, 2010

092. 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

091. 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

090. Li, F, Zhou, X., Huang, WT, Wong STC, Chang CC, Conditional Random Pattern Model for Copy Number Aberration Detection, BMC Bioinformatics, 11:200, 2010

089. 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

088. 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

2009

087. 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.

086. Yu, 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 (2009)

085. Ancuta 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, 2009.

084. Zhang 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, 2009.

083. Jin, 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), 475-486, 2009

082. Jin, GX, Cui, KM, Zhou, XB, Wong, STC, Unraveling the Signal-Transduction Networks in Cancer Metastasis, IEEE Signal Processing Magazine, 26: 129-132, 2009

081. Li, F, 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.

080. Zhou, 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, 2009.

079. Zhang, 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 Aug;9(15):3833-42.

078. Liu, 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

077. Fan J, 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.

076. Yang, 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, 4(4):e5054, 2009

075. Zhou, 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

074. Zhou, 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.

073. Wu LY, 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

072. Pham T, Zhou X: Special issue on pattern recognition in computational life sciences. Pattern Recognition 42(4): 497, 2009

071. Geng, B, Zhou, XB, and Hung, YS, Growing Enzyme Gene Networks by Integration of Gene Expression, Motif Sequence and Metabolic Information, Pattern recognition, 42(4):557-561, 2009

070. Yin Z, Zhou XB, Sun Y, and Wong STC. Online Phenotype Discovery based on Minimum Classification Error Model, Pattern Recognition, 42(4):509-522, 2009

069. Yu D, 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)

068. Huang WT, Yang X, Zhou X, ..., and Chang CC. Multiple distinct clones may co-exist in different lineages in myelodysplastic syndromes. Leukemia Research, 33(6):847-853,2009

067. Zhang, P, Li, HQ, Zhou, XB, and Wong, STC, Peak Detection Using Peak Tree Approach for Mass Spectrometry Data, International Journal of Hybrid Intelligent Systems, 5:197-208, 2009

066. Kamali 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. 114-131, 2009

065. Wang 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

2008

064. 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

063. 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

062. 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

061. 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.

060. Zhou X and Wong STC, Computational Systems Bioinformatics and Bioimaging for Pathway Analysis and Drug Screening, Proceedings of IEEE, 96(8): 1310-1331, 2008

059. 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

058. 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.

057. 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

056. 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)

055. 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

054. 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)

053. 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

052. 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

051. 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

050. 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

049. 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

048. 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

047. 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

046. 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

2007

045. 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.

044. 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

043. 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

042. 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

041. 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

040. 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.

039. 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

038. 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.

037. 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

036. 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.

035. 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.

034. 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.

033. 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

032. 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

2006

031. 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

030. 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

029. 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

028. 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

027. 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.

026. 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.

025. 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.

024. 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.

023. Zhou, X., Chou J., and Wong STC, "Protein structure similarity from principle component correlation analysis," BMC Bioinformatics, 2006 Jan 25; 7-40.

022. 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.

021. 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.

020. 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.

019. Zhou, X., and S.T.C. Wong, "High content cellular imaging for drug Development," IEEE Signal Processing Magazine, 2006 March, 23(2):170-174

018. Zhou, X. and S.T.C. Wong, "Informatics challenges of high-throughput microscopy," IEEE Signal Processing Magazine, 2006 May, 23(3): 63-72.

2005

017. 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.

016. 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.

015. 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).

014. 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.

2004

013. 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.

012. 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.

011. 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.

010. 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.

009. 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.

008. 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.

007. 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.

006. 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.

2003

005. 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.

004. 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.

003. 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.

002. 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.

001. 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.


Book Chapters

010. Jin GX, Zhou XB, Huang HH, Wong, STC, The Challenges in Blood Proteomic Biomarker Discovery, 273-299, Springer New York, 2009.

009. Wu LY, Zhou XB, Wong STC. Chapter 10-Computational Imaging and Modeling for Systems Biology, In the book of System Biology, in press, 2008.

008. Xia Z, Zhou X, Sun Y, and Wong STC. "Small animal imaging." In the book "Microscopy Imaging" Edited by Raghu, Wong, Nicholas, 2007

007. Zhou X. and Wong STC. "A Primer on Image Informatics of High Content Screening." In the book "High Content Screening", edited by Steven Haney, Wiley, 2007

006. Zhou X., X Chen, KL Liu, and STC Wong, "Data mining on time-lapse cell-IQ data analysis" in the Book "Life Science Data Mining", eds: S.T.C. Wong and C.S. Li, World Scientific Inc, 2007

005. Chen X, Zhou X., and STC Wong, "An automated method for cell phase identification in high throughput time-lapse screens," in the Book "Life Science Data Mining", eds: S.T.C. Wong and C.S. Li, World Scientific Inc, 2007.

004. Zhou X., and Stephen, T.C. Wong, "Inference of transcriptional regulatory networks based on cancer microassay data," in the Book "Life Science Data Mining", eds: S.T.C. Wong and C.S. Li, World Scientific Inc, 2007.

003. Zhou X., K.Y. Liu, and S.T.C. Wong, "Microarray cross-platform study: Normalization, comparison, and meta analysis," invited chapter for book "Advanced Computational Methods for Biocomputing and Bioimaging", eds, Pham Tuan, et. al., Nova Science Publishers, New York, 2007.

002. Pham T, D. Tran, Zhou X., and S.T.C. Wong, "Cell phase identification by vector quantization and Markov model," in the book "Progress in Cell Research," Nova Science, 2006

001. Zhou X., X. Wang, and E.R. Dougherty, "Statistical Inference of Genomic Networks Based on Microarray Data," Wiley Encyclopedia of Biomedical Engineering, edited by Metin Akay, 2006.


Selected Recent Abstracts/Scientific Exhibits

007. Li F, Zhou XB, Huang WT, Yang XR, Ma JW, Monzon FA, Chang CC, and Wong STC. Conditional Random Pattern Model based Copy Number Aberration Detection Using High Density Single Nucleotide Polymorphism Array. 16th Annual International Conference Intelligent Systems for Molecular Biology (ISMB 2008), Metro Toronto Convention Centre, Toronto, Canada, July 19-23, 2008.

006. Fan J, Zhou XB, Wu LY, Huang WT, Chang CC, Wong STC. The Association study of gene expression data and SNP array data on MDS model. 16th Annual International Conference Intelligent Systems for Molecular Biology (ISMB 2008), Metro Toronto Convention Centre, Toronto, Canada, July 19-23, 2008.

005. Zhu JM, Chen J, Zhou X, Ye W, Xia WM, Wong STC, Regulation of Calcium Signaling in Cells Expressing Familial Alzheimer Disease Mutant Presenilin 1 via High-Content Cell Imaging Analysis. Annual Meeting of Neuroscience, Atlanta, Oct., 2006.

004. Zhou X., Wang J, Lu J., Lichtman J., Wong STC, "Automated axon tracing and reconstruction of 3D confocal neuron circuitry imagery," Annual Meeting of Neuroscience, Atlanta, Oct., 2006.

003. Zhou X, Zhu JM, Sabatini B, Wong STC. Mutual Information Based Feature Selection in Studying Perturbation of Dendritic Structure, Caused by TSC2 Inactivation, Annual Meeting of Neuroscience, Washington DC, Nov., 2005.

002. Zhu J, Chen X., Zhou X., and STC Wong, "Application of NeuroIQ in Studying Perturbation of Dendritic Structure Caused by Genetic Mutations," A decade of neuroscience informatics: looking ahead -Workshop, Natcher conference center, NIH, April 26 - 27, 2004.

001. Wong STC, Cao XH, Chen XW, Liu KY, Zhu JM, Zhou X, Xu XY. An automated image informatics system for cell-based assay. Academic and Industrial Approaches to HTS & Drug Discovery, Regional Meeting of the Society for Biomolecular Screening, Boston, MA, May 2004.


Presentations & Conference Proceedings

106. Pan B, Xia JJ, Yuan P, et al, Zhou, B*: Incremental kernal ridge regression for prediction of soft tissue deformations. Med Image Comput Comput Assist Interv (MICCAI 2012) 15, 2012

105. Peng, T., Choi, DS, peng H., Zhou, X, Systematically Model Cell-Cell Interactions in Regulating Multiple Myeloma Initiating Cell Fate, in The Tenth International Conference on Intelligent Systems for Molecular Biology (ISMB 2012). July 2012. Long Beach, CA.

104. Liu CL, and Zhou, X, FusionQ: A Novel Approach for Detection and Quantification of Gene Fusion from Paired-end RNA-Seq, in The Tenth International Conference on Intelligent Systems for Molecular Biology (ISMB 2012). July 2012. Long Beach, CA.

103. Su, J., Wen, JG, Chang CC, and Zhou, XB, A Supply Chain Landscape Model for Mechanisms Investigation and Drug Efficacy Prediction of Multiple Myeloma Drug Resistant, in The Tenth International Conference on Intelligent Systems for Molecular Biology (ISMB 2012). July 2010. Long Beach, CA.

102. Robert Azencott, Bernhard Bodmann, Demetrio Labate, Anando Sen, King C. Li, Zhou, X, Searchlight CT: A new reconstruction method for collimated X-ray tomography. 1st International ICST Workshop on New Computational Methods for Inverse Problems, Cachan (South of Paris), France, May 16, 2011.

101. Zhou, XB, Wang, Y, Wang, HH, Pham, TD, and Li K, Biomarker Motif Discovery by Integrating Mass Spectrometry and PPI Network, AIP Conf. Proc. 1371, pp. 225-233; http://dx.doi.org/10.1063/1.3596646, 2011 INTERNATIONAL SYMPOSIUM ON COMPUTATIONAL MODELS FOR LIFE SCIENCES (CMLS‐11), 11–13 October 2011, Toyama City, Japan.

100. Jiang, BL, Zhang, L, Zhang, W, Struthers, A, Berens, ME, Zhou, XB, Employing Graphic Programming Unit Technology to Accelerate Numerical Diffusion Solver in 2D Multi-scale, Multi-resolution Agent-based Brain Cancer Model, BIOCOMP'11: July 18-21, 2011, USA.  

099. Xiao, Y, Pham, T., Chang, J., and Zhou, X, Symmetry-based Presentation for Stem-Cell Image Segmentation, IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS'11), Orlando, Florida, Feb. 2-5, 2011.

098. Zhou, X, Wang, Y, Wang, H, Pham, T, Li, K, Biomarker Motif Discovery by Integrating Mass Spectrometry and Protein-Protein Interaction Network, 2011 International Symposium on Computational Models for Life Sciences - CMLS-11, June 22-24, 2011, Tokyo, Japan.

097. Xia, Z., and Zhou, XB, A Graph-based Elastic Net for Variable Selection and Module Identification for Genomic Data Analysis. IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2010), 18-21 Dec 2010, Hong Kong.

096. Peng, H.M., Wen, J.G., Chang C.C., and Zhou, X.B. NFkB pathway modeling for optimal drug combination therapy on multiple myeloma. in International Conference on Mathematical Biology and Ecology. May 2010. Tokyo, Japan.

095. Xia, Z., Wen, JG, Chang, CC, and Zhou, X. Isofroms identification and quantification from RNA-Seq using MAP approach. in The Eighteenth International Conference on Intelligent Systems for Molecular Biology (ISMB 2010). July 2010. Boston, MA.

094. Peng, H.M., Wen, J.G., Chang C.C., and Zhou, X.B., Systematic modeling study on mechanism of p38 MAPK activation in MDS, in The Eighteenth International Conference on Intelligent Systems for Molecular Biology (ISMB 2010). July 2010. Boston, MA.

093. Shi, P, Zhou, XB, Lipinski, M, Degterev, A, An Integrated High Content Analysis Pipeline for Alzheimer's Disease Drug Discovery, in The Eighteenth International Conference on Intelligent Systems for Molecular Biology (ISMB 2010). July 2010. Boston, MA.

092. Srinivasan, R., Li, Q., Zhou, X., Lu, J., Lichtman, Wong, STC, Reconstruction of the Neuromuscular Junction Connectome, in The Eighteenth International Conference on Intelligent Systems for Molecular Biology (ISMB 2010). July 2010. Boston, MA.

091. Yang XR, and Zhou, XB, Transcriptional Regulatory Network Discovery via Information Mining Approach in Rett Syndromes Study, The 4th International Conference on Computational Systems Biology (ISB 2010), Suzhou, China, Sept. 9-11, 2010.

090. Xia, J., Chang, Y.B., Gateno, J, Xiong, Z.X., Zhou, X.B., Automated Digital Dental Articulation, MICCAI 2010 (The 13th International Conference on Medical Image Computing and Computer Assisted Intervention), Sept., Beijing, China, 201

089. Li, FH, Zhou, XB, Zhao, H, Wong, STC, Optimal Live Cell Tracking for Cell Cycle Study Using Time-lapse Fluorescent Microscopy Images, MICCAI workshop 2010, Sept., Beijing, China

088. Cai, M, Zhao, H, Zhou X, Wang, Y., Wong STC. Mathematic modeling of drug combination effects using protein-protein interaction sub-networks. The IASTED International Conference on Modeling, Simulation and Identification (MSI) 2009, Beijing China.

087. Xia, Z., Zhou, X., and Sun, Y., "Semi-supervised Drug-Protein Interaction Prediction from Heterogeneous Spaces", The Third International Symposium on Optimization and Systems Biology, Zhangjiajie, China, Sept. 20-22, 2009. Lecture Notes in Operations Research (LNOR).

086. Peng, H, Zhou, XB, Li, F, Xia, XF, Wong, STC, INTEGRATING MULTI-SCALE BLOB/CURVILINEAR DETECTOR TECHNIQUES AND MULTI-LEVEL SETS FOR AUTOMATED SEGMENTATION OF STEM CELL IMAGES, IEEE International Symposium on Biomedical Imaging (ISBI'09), June 28 - July 1, 2009 in Boston, Massachusetts, U.S.A.

085. Li, Q, Zhou, XB, Deng, ZG , and Wong, STC, AUTOMATED DENDRITIC SPINE DETECTION AND 3D RECONSTRUCTION FROM FLUORESCENCE MICROSCOPY IMAGES, IEEE International Symposium on Biomedical Imaging (ISBI'09), June 28 - July 1, 2009 in Boston, Massachusetts, U.S.A.

084. Shi, P., Zhou, XB, Li, Q., Baron, M., Teylan MA, Kim, Y., and Wong, STC, ONLINE THREE-DIMENSIONAL DENDRITIC SPINES MOPHOLOGICAL CLASSIFICATION BASED ON SEMI-SUPERVISED LEARNING, The Sixth IEEE International Symposium on Biomedical Imaging (ISBI'09), June 28 - July 1, 2009 in Boston, Massachusetts, U.S.A.

083. Li, FH, Zhou, XB, Zhao, H, and Wong, STC, Cell Segmentation Using Front Vector Flow Guided Active Contours, MICCAI 2009 (The 12th International Conference on Medical Image Computing and Computer Assisted Intervention), Sept 20-24, Imperial College London, England

082. Zhao, Y, Xiong, H.K., Zhang, K, and Zhou, XB, Equilibrium modeling for 3D curvilinear structure tracking of confocal microscopy images. ICIP 2009: 2533-2536, Cairo, Egypt, Nov.7 - 10, 2009.

081. Le BH, Deng ZG, Chang, YB, Xia, J., and Zhou, XB, An Interactive Geometrical Technique for Upper and Lower Teeth Segmentation, MICCAI 2009 (The 12th International Conference on Medical Image Computing and Computer Assisted Intervention), Sept 20-24, Imperial College London, England

080. Huang, D., Zhou, XB, and Wong STC, Inferring Cancer-associated Signaling Networks Based on Significance Analysis of microRNA-mRNA Targeting, in The Nineteenth International Conference on Intelligent Systems for Molecular Biology (ISMB 2009). July 2009. Stockholm, Sweden.

079. Yin, Z, Zhou, XB, and Wong STC, An integrative pipeline for automated data analysis and gene function annotation for genome wide high content RNAi screening, in The Nineteenth International Conference on Intelligent Systems for Molecular Biology (ISMB 2009). July 2009. Stockholm, Sweden.

078. Wu LY, Zhou XB, Chang CC, and Wong STC, Model Based Probe Fitting and Selection for SNP Array. The 2nd International Symposium on Optimization and Systems Biology (OSB 2008), Lijiang, China, Oct. 31-Nov3, 2008.

077. Jin GX, Zhou XB, Cui K, Wong STC, Network biomarker discovery for prostate cancer. The 2nd International Symposium on Optimization and Systems Biology (OSB 2008), Lijiang, China, Oct. 31-Nov3, 2008.

076. Zhou WG, Li HQ, Zhou XB, 3D Dendrite Reconstruction and Spine Identification, MICCAI 2008, the 11th International Conference on Medical Image Computing and Computer Assisted Intervention, Sept. 6-10, 2008, New York City, USA.

075. 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. 16th Annual International Conference 
Intelligent Systems for Molecular Biology (ISMB 2008), Toronto, Canada, 2008

074. Wang J, Chang SF, Zhou X, Wong STC. Active Microscopic Cellular Image Annotation by Superposable Graph Transduction with Imbalanced Labels. In IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), Anchorage, Alaska, USA, June 2008.

073. Zhang J, Wang HH, Suffredini AA, Gonzales D, Gonzalez E, Huang Y, Zhou X. Bayesian Peak Detection for pro-TOF MS MALDI Data, IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP 08), Las Vegas, Nevada, USA, 2008

072. Tran D, Pham T, Zhou X. Subspace Vector Quantization and Markov Modeling for Cell Phase Classification. International Conference on Image Analysis and Recognition (ICIAR) 2008: 844-853

071. Pham T, Beck D, Brandl M, Zhou X. Classification of Proteomic Signals by Block Kriging Error Matching. International Conference on Image and Signal Processing(ICISP) 2008: 281-288

070. Zhang Y, Zhou X, Lu J, Adjeroh D, Litchman J, and Wong STC. 3-D Axon Structure Extraction and Analysis in Confocal Fluorescence Microscopy Images. The third IEEE-NIH LIfe Science Systems and Applications (LISSA 2007) workshop, Bethesda, Maryland, Nov. 8-9, 2007

069. Fan J, Zhou, X, Dye J, Zhang Y, Spire T, Hayman B, and Wong STC. Spine Detection Using Curvilinear Structure Detector and Spine Tracking in in vivo image. The third IEEE-NIH LIfe Science Systems and Applications (LISSA 2007) workshop, Bethesda, Maryland, Nov. 8-9, 2007

068. Li FH, Zhou X, Zhu J, and Wong STC. High Content Image Sequence Analysis for Quantifying Calcium Signals inside Cells with Mutant Presenilin-1 of Familial Alzheimer Disease. The third IEEE-NIH LIfe Science Systems and Applications (LISSA 2007) workshop, Bethesda, Maryland, Nov. 8-9, 2007

067. Li C, Zhou X, Li FH, and Wong STC. Mitosis Cell identification with Conditional Random Fields. The third IEEE-NIH LIfe Science Systems and Applications (LISSA 2007) workshop, Bethesda, Maryland, Nov. 8-9, 2007

066. Cheng J, Zhou X, Wong STC. NeuronIQ: A Novel Computational Approach for Automatic Dendrite Spines Detection and Analysis. The third IEEE-NIH LIfe Science Systems and Applications (LISSA 2007) workshop, Bethesda, Maryland, Nov. 8-9, 2007

065. Liang C, Zhou X, and Wong STC. Analysis of the Hot Spots of Coated pits in Live Cells. The third IEEE-NIH LIfe Science Systems and Applications (LISSA 2007) workshop, Bethesda, Maryland, Nov. 8-9, 2007

064. Zhang L, Xiong H, Zhang K. and Zhou X. Graph Theory Application in Cell Nucleus Segmentation, Tracking and Identification. IEEE 7th International Symposium on Bioinformatics & BioEngineering (BIBE 07), Boston, MA, Oct 14-17 2007

063. Zhang K, Xiong HK, Zhou X and Wong STC. A Simulation-Based 3D Axon Axis Extraction in Confocal Fluorescence Microscopy Images. IEEE 7th International Symposium on Bioinformatics & BioEngineering (BIBE 07), Boston, MA, Oct 14-17 2007

062. Xia, Z, Zhou X, Sun Y, Wong STC, Registration of 3D FMT and CT Images of Mouse via Affine Transformation using Sequential Monte Carlo. 2007 International Symposium on Computational Models for Life Sciences (CMLS 2007), Gold Coast, Queensland, Australia, December 17-19, 2007

061. Zhang P, Li H, Zhou X, and Wong STC, Peak tree and peak detection for mass spectrometry data. 2007 International Symposium on Computational Models for Life Sciences (CMLS 2007), Gold Coast, Queensland, Australia, December 17-19, 2007.

060. Zhou W, Li H, Zhou X, and Wong STC, A new algorithm for 3D dendritic spine detection. 2007 International Symposium on Computational Models for Life Sciences (CMLS 2007), Gold Coast, Queensland, Australia, December 17-19, 2007.

059. Geng B, Zhou X, Hung Y.S., Wong STC, Growing Gene Network by Integration of Gene Expression, Motif Sequence and Metabolic Information. 2007 International Symposium on Computational Models for Life Sciences (CMLS 2007), Gold Coast, Queensland, Australia, December 17-19, 2007

058. Yu D, Pham T, Zhou X, and Wong STC, Segmentation, recognition and tracing analysis for high-content cell-cycle screening. 2007 International Symposium on Computational Models for Life Sciences (CMLS 2007), Gold Coast, Queensland, Australia, December 17-19, 2007

057. Zhang Y, Young G, Zhou X, Srinivasan R, Wong STC. Cerebral Artery Extraction Using Level Set Segmentation and Adaptive Tracking for CT Angiography. 2007 International Symposium on Computational Models for Life Sciences (CMLS 2007), Gold Coast, Queensland, Australia, December 17-19, 2007

056. Li F, Zhou X, Wong STC, "Novel Nuclei Segmentation and Cell Phase Identification Using Markov Model," 2007 International Symposium on Computational Models for Life Sciences (CMLS 2007), Gold Coast, Queensland, Australia, December 17-19, 2007

055. Yin Z, Zhou X, Bakal C, Li F, Sun Y, Perrimon N, and Wong STC, Online Phenotype Discovery in High-content RNAi Screens using Gap Statistics. 2007 International Symposium on Computational Models for Life Sciences (CMLS 2007), Gold Coast, Queensland, Australia, December 17-19, 2007

054. Zhang L, Xiong HK, Zhao Y, Zhang K, Zhou X. Computational Graph Model for 3D Cells Tracking in Zebra Fish Datasets. 2007 International Symposium on Computational Models for Life Sciences (CMLS 2007), Gold Coast, Queensland, Australia, December 17-19, 2007

053. Zhang SQ, Zhou X, Wang HH, Suffredini A, Gonzales D, Ching WK, Ng MK, Wong STC, A novel peak Detection with Chemical Noise Removal in MALDI MS Data, The International Symposium on Optimization and Systems Biology (OSB 2007), Aug. 8-10, Beijing, 2007 (Lecture Notes in Operations Research)

052. Geng B, Zhou X, Zhu J., Hung YS, and Wong STC. Missing Enzyme Identification Using Reversible-Jump Markov-Chain-Monte-Carlo Learning Approach. The International Symposium on Optimization and Systems Biology (OSB 2007), Aug. 8-10, Beijing, 2007 (Lecture Notes in Operations Research)

051. Yu DG, Phan TD, and Zhou X. Tracing and Recognition of Cell-Cycle Screening. Proc. of International Conference of Machine Learning and Cybernetics (ICMLC), Hongkong, Aug. 19-21 2007.

050. Chen, J, Zhu, J, Cho, H.-H., Cui, K., Li, F., Zhou, X., J.T. Rogers, Wong, STC and Huang, X., Differential Cytotoxicity of Metal Oxide Nanoparticles, Nanotech 2007, Santa Clara, May 20-24, 2007.

049. Zheng X, Zhou, X, Sun Y, and Wong STC. Registration of 3D FMT and CT Images of Mouse Via Affine Transformation. The Fourth International Symposium on Neural Networks (ISNN 2007), Nanjing China, June 3-7, 2007. (Lecture Notes in Computer Science)

048. X Zhou, Chen J, Zhu J, Huang XD, and Wong STC. Study of CuO Nanoparticle-Induced Cell Death by High Content Cellular Fluorescence Imaging and Analysis. 2007 IEEE International Symposium on Circuits and Systems, New Orleans, USA, May 27-30, 2007.

047. Srinivasan R, Zhou X, Miller E, Lu J, Lichtman J, Wong STC. 3D Centerline extraction of axons in microscopic stacks for the study of motor neuron behavior in development muscles. Accepted in the IEEE International Symposium on Biomedical Imaging (ISBI '07), April 12-15, 2007, Washington DC, USA.

046. Bai WJ, Zhou X, Zhu JM, Ji L, Wong STC. Tracking of migrating glioma cells in feature space. Accepted in the IEEE International Symposium on Biomedical Imaging (ISBI '07), April 12-15, 2007, Washington DC, USA.

045. Chen C, Li HQ, Zhou X, Wong STC. Graph cut based active contour for automated cellular image segmentation in high throughput RNA interference (RNAi) screening. Accepted in the IEEE International Symposium on Biomedical Imaging (ISBI '07), April 12-15, 2007, Washington DC, USA.

044. Zhang Y, Zhou X, Witt R, Sabatini B, Adjeroh D, Wong STC. Automated spine detection using curvilinear structure detector and LDA classifier. Accepted in the IEEE International Symposium on Biomedical Imaging (ISBI '07), April 12-15, 2007, Washington DC, USA

043. Wang J, Zhou X, Ju L, Lichtman J, Chang SF, Wong STC. Dyanmic local tracking for 3D Axon curvilinear structure detection from microscopic image stack. Accepted in the IEEE International Symposium on Biomedical Imaging (ISBI '07), April 12-15, 2007, Washington DC, USA.

042. Wang M, Zhou X, Li FH, king RW, Huckins J, Wong STC. Novel cell segmentation and online learning algorithms for cell phase identification in automated flourescience microscopy. Accepted in the IEEE International Symposium on Biomedical Imaging (ISBI '07), April 12-15, 2007, Washington DC, USA

041. Zheng Y, Zhou, X, Huang H, Sun Y, and Wong STC. A PLS-Linear SVM Solution to Biomarker Discovery for Major Adverse Cardiac Events. The Fourth International Symposium on Neural Networks (ISNN 2007), Nanjing China, June 3-7, 2007. (Lecture Notes in Computer Science)

040. Pham T, Wong H, Zhou X, ..., Wong STC, Linear Predictive Coding and Its Decision Logic for Early Prediction of Major Adverse Cardiac Events Using Mass Spectrometry Data. 19th Australian Joint Conference on Artificial Intelligence - Workshop on Intelligent Systems for Bioinformatics, Hobart, Tasmania, Australia, 4th to 8th December, 2006.

039. Zhang K, Xiong H., and Zhou X, A Coarse-to-Fine Adaptation Segmentation Approach for Cellular Image Analysis, International MultiMedia Modeling Conference (MMM), Singapore, Jan 9-12, 2006. (Lecture Notes in Computer Science)

038. Chen C, Li, H, and Zhou X, Automated Segmentation of Drosophila RNAi Fluorescence Cellular Images Using Graph Cuts, Asia-Pacific Workshop on Visual Information Processing, Beijing China, 7-9, Nov, 2006

037. Pham TD, Chandramohan V, Zhou X, and Wong STC. Robust Feature Extraction and Reduction of Mass Spectrometry Data for Cancer Classification. IEEE ICDM 2006 Workshop on Data Mining in Bioinformatics (DMB 2006). Dec. 18-22, Hong Kong, 2006.

036. Zhou X, Wang H, Wang J, Hoehn G, Azok J, Brennan ML, Hazen SL, Li K, and Wong STC, "Biomarker Discovery for Risk Stratification of Cardiovascular Events Using an Improved Genetic Algorithm," 2006 IEEE International Symposium on Life Science and Multimodality, Washington, D.C. July 13-14, 2006.

035. Wang J, Zhou X, Li F, and Wong STC, "Classify cellular phenotype in high-throughput fluorescence microcopy images for RNAi genome-wide screening," 2006 IEEE International Symposium on Life Science and Multimodality, Washington, D.C.

034. Mao Y, Zhou, X. Xia, D. Pi, Y. Sun, STC Wong, "Automated Recognition of Cellular Phenotypes by Support Vector Machines with feature reduction," KES 2006. Lecture Notes in Computer Science.

033. Mao Y, Zhou X, D. Pi, Y. Sun, S.T.C. Stephen. "Gene selection using recursive feature elimination based on Gaussian kernel support vector machine with adaptive kernel width strategy," International conference on rough sets and knowledge technology, 2006. Lecture notes in computer science/Lecture notes in artificial intelligence.

032. Yang X, H. Li, Zhou X., STC Wong, "Identification of cell-cycle phases using neural network and steerable filter features," ISNN2006, Chengdu, P.R. China. Lecture Notes in Computer Science, 2006.

031. Yan J, Zhou X., Q. Cheng, and S.T.C. Wong, "An effective system for optical microscopy cell image segmentation, tracking and cell phase identification," The International Conference on Image Processing, Atlanta, GA, USA, 2006.

030. Chen L, R. Wang, Zhou X., and S.T.C. Wong, "Designing synthetic biological networks," IEEE International Symposium on Circuits and Systems, Island of Kos, Greece, May 21-24, 2006.

029. Zhang Y, Zhou X., A. Degterev, M. Lipinski, D. Adjeroh, J. Yuan, S.T.C. Wong, "A novel tracing approach for high-throughout screening of neuron based assays," 2006 IEEE International Symposium on Life Science and Multimodality, Washington, D.C.

028. Tarokh, AB, Liu KY, Zhou X, and Wong STC, "An Iterative Approach to Nucleus Segmentation," 2006 IEEE International Symposium on Life Science and Multimodality, Washington, D.C.

027. Zhou X., J. Yan, M. Wang, and S.T.C. Wong, "A novel cell tracking algorithm and continuous hidden markov model for cell phase identification," IEEE/NLM International Workshop on Life Science Systems and Applications, Washington, D.C., July 13-14, 2006

026. Chen C, H. Li, and Zhou X., "Graph cuts based automated segmentation of multiple cancer cell nuclei in time-lapse microscopy," International Conference on Multimedia, Beijing, P.R. China, 2006

025. Xiong G, Zhou X., L. Ji, P. Bradley, N. Perrimon, and S.T.C. Wong, "Automated segmentation of RNAi cellular images using level sets," The International Conference on Image Processing, Atlanta, GA, USA, 2006.

024. Xiong G, Zhou X., A. Degterev, S.T.C. Wong, and L. Ji, "Automated Neurite Labeling and Analysis in Fluorescence Microscopy Images using curvilinear structure detection," 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Washington, D.C.

023. Pham TD, Tran D, Zhou X & Wong STC. An Automated Procedure for Cell-Phase Imaging Identification. In: Workshop on Learning Algorithms for Pattern Recognition 52 - 59 (eds G Ranadhir et al). University of Technology, Sydney, 2005.

022. Tran T, T. Pham and Zhou X.. Cell phase identification using fuzzy Gaussian mixture models, International Symposium on Intelligent Signal Processing and Communication Systems, Hong Kong, China, Dec 14-17, 2005.

021. Hu Z, Zhou X., and X. Yan, "A Continuous-Time Dynamical Model of Probabilistic Boolean Networks," . ISPACS 2005, International Symposium on Intelligent Signal Processing and Communication Systems, Hong Kong, China, Dec 14-17, 2005.

020. Yang XD, Li HQ, Zhou XB, and Wong STC. Automated segmentation and tracking of cells in time-lapse microscopy using watershed and mean shift. ISPACS 2005, International Symposium on Intelligent Signal Processing and Communication Systems, Hong Kong, China, Dec 14-17, 2005.

019. Zhou X., K.-Y. Liu, Pam Bradley, N. Perrimon, and STC Wong, "Towards Automated Cellular Image Segmentation for RNAi Genome-Wide Screening," MICCAI, 2005. Lecture Notes in Computer Science, Vol. 3749, pp. 885-892, 2005.

018. Zhou X., K.-Y. Liu, and STC Wong, "Model the relationship between gene expression and regulatory motif binding sites using a simplified neural network with Bayesian variable selection," ISNN2005, 30-June, 2005, Chongqing, P.R. China. Lecture Notes on Computer Science, Vol. 3498, pp.719-724, 2005.

017. Zhou X., and STC Wong, "Dynamic sub-cellular behavior study in high content imaging using a novel approach," Proc. of IEEE conference on circuit and systems, Japan, 2005.

016. Xu X, Zhou X., and STC Wong, "A computer-based system to analyze neuron images," Proc. of IEEE conference on circuit and systems, May, Kobe, Japan, 2005.

015. Zhang J, J. Fejzo, J. Luo, Zhou X., V. Chen, N. Reo, A. Neuforth, "An expert system for the pattern recognition of biological effects," Protein Biomarkers 2004, Sep. 8-10, Philadelphia, Pennsylvania.

014. Zhou X., X. Chen, K.L. Liu and STC Wong, "Some data mining issues on time-lapse cell-IQ data analysis " IEEE Life Science Data mining, England, 2004.

013. Chen X, Zhou X., and STC Wong, "An automated method for cell phase identification in high throughput time-lapse screens," IEEE Life Science Data mining, England, 2004.

012. Lu W and Zhou X., "High-resolution multi-path time-delay estimation using 2D blind deconvolution in third order cross-moment domain," Proceedings of the International Conference on Neural Networks and Signal Processing, Vol. 2, pp. 1425-1428, Dec. 14-17, 2003.

011. Zhou X., X. Wang, and E.R. Dougherty, "Construction of genomic networks using MI clustering and reversible-jump MCMC predictor design," in the IEEE Workshop of Genomic Signal Processing and Statistical, Raleigh, North Carolina, Oct. 2002.

010. Zhou X. and W. Lu, "Performance comparison of iterative multiuser detection techniques in synchronous coded CDMA systems," In Proc. of the 17th IEEE International Conference on Computers, Communications, Control and Power Engineering (IEEE TENCON' 02), Beijing, China, Oct. 2002.

009. Zhou X. and W. Lu, "Parallel interference cancellation in Time-Frequency channel model," In the Proc. of 17th IEEE International Conference On Computers, Communications, Control and Power Engineering (IEEE TENCON' 02). Beijing, China, Oct. 2002.

008. Zhou X. and W. Lu, "Performance analysis of LAS codes in LAS-CDMA systems," In Proc. of the International Conference on Signal Processing (ICSP), Beijing, China, Aug. 2002.

007. Zhao Y, Zhou X., K. Palaninappan, and X. Zhuang, "Statistical modeling for improved land cover classification," in Proc. of SPIE on Aerospace/Defense Sensing, Simulation, and Controls, Vol. 4741. Orlando FL, 2002.

006. Zhou X., S. Zhao, and X. Wang, "Adaptive and integrated video communications for wireless ATM in WCDMA systems," IEEE Vehicular Technology Conference VTC 2001 spring, Phodes, Greece, vol. 3, pp. 2147-2151, Apr. 2001.

005. Zhou X. and X. Wang, "Adapted nonlinear prediction and smoothing filters," IEEE Workshop on Nonlinear Signal and Image Processing 2001, Baltimore, Maryland, USA, March, 3-6, 2001.

004. Zhou X., Yunxin Zhao, and Xinhua Zhuang, "Kalman filter channel tracking algorithm based on AR model in WCDMA systems," Proc. of World Computer Congress, Beijing, China. pp. 1759 -1762, Aug. 2000.

003. Sun Y, Zhou X., L. Zhou, and Xianda Zhang, "Adaptive parallel interference cancellation performance in Rayleigh fading time-multiplexed pilot channel," Proc. of World Computer Congress--Communication Technology, Beijing, China. Vol. 1, pp. 196 -199, Aug. 2000.

002. Zhu Y, Y. Zhao, K. Palaniappan, Zhou X., and Xinhua Zhuang, "Optimal Bayesian classifier for landcover classification using Landsat TM data," Proc. of IEEE International Geoscience and Remote Sensing Symposium, Toronto, Canada, Vol. 1, pp.447-450, June 2000.

001. Zhou X and Cheng Q, "A class of new nonlinear digital filters," International Conference on Signal Processing (ICSP), Beijing, China, pp. 237-240.

Last Updated: 04-15-2014
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