Computational Bioinformatics and Bioimaging Laboratory (CBIL)


 
 

Internal Use

 

Journal Papers

Conference Papers
 

 

 

Journal Papers

 

Year 2010

  • J. Xuan, Y. Wang, E. Hoffman, and R. Clarke, "Cross phenotype normalization of microarray data," Frontiers in Bioscience, vol. E2, pp. 171-186, Jan. 2010.

  • Chu-Chuan Liu, Shih-Chung Ben Lo, Matthew T Freedman, Marvin E Lasser, John Kula, Anita Sarcone, and Yue Wang, "C-scan Ultrasound Imaging with a CMOS-based Piezoelectric Sensing Array: A Comparative Study of Foreign Object Detection in Soft Tissue," Frontiers in Bioscience, vol. E2, pp. 241-249, Jan. 2010.

 

Year 2009

  • B. Zhang, H. Li, R. B. Riggins, M. Zhan, J. Xuan, Z. Zhang, E. P. Hoffman, R. Clarke, and Y. Wang, "Differential dependency network analysis to identify condition-specific topological changes in biological networks," Bioinformatics, 25(4):526-532, 2009.

  • R. Clarke, A. N. Shajahan, R. B. Riggins, Y. Cho, A. Crawford, J. Xuan, Y. Wang, A. Zwart, R. Nehra, and M. C. Liu, "Gene network signaling in hormone responsiveness modifies apoptosis and autophagy in breast cancer cells," Journal of Steroid Biochemistry and Molecular Biology, 114(1-2):8-20, 2009.

  • Y. Zhang, J. Xuan, B. G. de los Reyes, R. Clarke, and H. W. Ressom, "Reverse engineering module networks by PSO-RNN hybrid modeling," BMC Genomics,10(S1):S15, 2009.

  • L. Chen, J. Xuan, R. B. Riggins, Y. Wang, E. P. Hoffman, and R. Clarke, "Identification of Condition-specific Regulatory Modules by Multi-level Motif and mRNA Expression Analysis," Intl J. of Computational Biology and Drug Design, 2(1):1-20, 2009.

  • Fa-Yu Wang, Chong-Yung Chi, Tsung-Han Chan, and Yue Wang, "Non-negative least-correlated component analysis for separation of dependent sources by volume maximization," IEEE Trans Pattern Analysis and Machine Intelligence, 2009. (in press)

  • L. Chen, J. Xuan, C. Wang, I.-M. Shih, T.-L. Wang, Z. Zhang, R. Clarke, E. Hoffman and Y. Wang, "Biomarker identification by knowledge-driven multi-level ICA and motif analysis," Intl J. Data Mining and Bioinformatics, vol. 3, no. 4, pp. 365-381, 2009.

  • Wing-Kin Ma, Tsung-Han Chan, Chong-Yung Chi, and Yue Wang, "Convex analysis for non-negative blind source separation with application in imaging," Chapter 1, Convex Optimization in Signal Processing and Communications, Cambridge University Press, 2009. (in press)

  • Wennuan Liu, Sari Laitinen, Sofia Khan, Mauno Vihinen, Jeanne Kowalski, Guoqiang Yu, Li Chen, Srinivasan Yegnasubramanian, Jun Luo, Yue Wang, Jianfeng Xu, William B. Isaacs, Tapio Visakorpi, and G. Steven Bova, "Copy Number Analysis Indicates Monoclonal Origin of Lethal Metastatic Prostate Cancer," Nature Medicine, vol. 15, no. 5, pp. 559-565, 2009.

  • Kuan-Ting Kuo, Bin Guan, Yuanjian Feng, Tsui-Lien Mao, Xu Chen, Natini Jinawath, Yue Wang, Robert J. Kurman, Ie-Ming Shih, and Tian-Li Wang, "Analysis of DNA copy number alterations in ovarian serous tumors identifies new molecular genetic changes in low-grade and high-grade carcinomas," Cancer Research, vol. 69, no. 9, pp. 4036-4042, 2009.

  • D. J. Miller, Y. Zhang, G. Yu, Y. Liu, L. Chen, C. D. Langefeld, D. Herrington, and Y. Wang, "An Algorithm for Learning Maximum Entropy Probability Models of Disease Risk That Efficiently Searches and Sparingly Encodes Multilocus Genomic Interactions," Bioinformatics, 25(19):2478-2485, 2009.

 

Year 2008

  • S. Olivo-Marston, Y. Zhu, R. Lee, A. Cabanes, G. Khan, A. Zwart, Y. Wang, R. Clarke, L. Hilakivi-Clarke, "Gene signaling pathways mediating the opposite effects of prepubertal low and high fat n-3 polyunsaturated fatty acid diets on mammary cancer risk," Cancer Prevention Res., vol. 1, no. 7, pp. 532-545, Dec. 2008.

  • L. Chen, J. Xuan, C. Wang, I.-M. Shih, Y. Wang, Z. Zhang, E. Hoffman, and R. Clarke, "Knowledge-guided multi-scale independent component analysis for biomarker identification," BMC Bioinformatics, 9:416, 2008.

  • R. B. Riggins, J. P-J. Lan, U. Klimach, A. Zwart, L. R. Cavalli, B. R. Haddad, L. Chen, T. Gong, J. Xuan, S. P. Ethier, and R. Clarke, "ERRγ mediates Tamoxifen resistance in novel models of invasive lobular breast cancer," Cancer Research, 68(21):8908-8917, 2008.

  • Y. Zhu, H. Li, D. J. Miller, Z. Wang, J. Xuan, R. Clarke, E. P. Hoffman, and Y. Wang, "caBIG VISDA: modeling, visualization, and discovery for cluster analysis of genomic data," BMC Bioinformatics, 9:383, 2008.

  • T.-H. Chan, W.-K. Ma, C.-Y. Chi, and Y. Wang, "A convex analysis framework for blind separation of non-negative sources," IEEE Trans. Signal Processing, vol. 56, no. 10, pp. 5120-5134, Oct. 2008.

  • J. Zhang, L. Wei, X. Feng, Z. Ma, and Y. Wang, "Pattern expression non-negative matrix factorization: Algorithm and applications to blind source separation," Computational Intelligence and Neuroscience, ID168769, 2008.

  • Y. Zhang, J. Xuan, B. G. de los Reyes, R. Clarke and H. W Ressom, "Identification of network motif-based transcription factor-target gene relationships by integrating multi-source biological data," BMC Bioinformatics, 9:203, 2008.

  • D. J. Miller, S. Pal, and Y. Wang, "Extensions for transductive learning for distributed ensemble classification and application to biometric authentification," Neurocomputing, , vol. 72, pp. 119-125, 2008.

  • G. Wang, H Shen, Y Liu, A Cong, W Cong, Y Wang, and P Dubey, "Digital spectral separation methods and systems for bioluminescence imaging," Optics Express, vol. 16, no.3, pp. 1719-1732, Jan. 2008.

  • Y. Wang, D.J. Miller, and R. Clarke, "Approaches to working in high dimensional data spaces: gene expression microarrays," British Journal of Cancer, vol. 98, pp. 1023-1028, 2008.

  • Y. Zhu, Z. Wang, D. J. Miller, R. Clarke, J. Xuan, E. P. Hoffman, and Y. Wang, "A ground truth based comparative study on clustering of gene expression data," Frontiers in Bioscience, vol. 13, pp. 3839-3849, May 2008.

  • R. Clarke, H. W. Ressom, A. Wang, J. Xuan, M. C. Liu, E. A. Gehan, and Y. Wang, "The properties of high-dimensional data spaces: implications for exploring gene and protein expression data," Nature Reviews | Cancer, vol. 8, pp. 37-49, Jan. 2008.

  • H. Li, J. Xuan, Y. Wang, and M. Zhan, "Inferring regulatory networks," Frontiers in Bioscience, vol. 13, pp. 263-275, Jan. 2008.

  • C. Wang, J. Xuan, L. Chen, P. Zhao, Y. Wang, R. Clarke, and E. P. Hoffman, "Motif-directed network component analysis for regulatory network inference," BMC Bioinformatics, vol. 9, (S1):S21, 2008.

  • D. J. Miller, Y. Wang, and G. Kesidis, "Emergent unsupervised clustering paradigms with potential application to bioinformatics," Frontiers in Bioscience, vol. 13, pp. 677-690, Jan. 2008.

  • H. W. Ressom, R. S. Varghese, Z. Zhang , J. Xuan, and R. Clarke, "Classification algorithms for phenotype prediction in genomics and proteomics," Frontiers in Bioscience, vol. 13, pp. 691-708, Jan. 2008.

  • G. Wang, W. Cong, H. Shen, X. Qian, M. Henry, and Y. Wang, "Overview of bioluminescence tomography - a new molecular imaging modality," Frontiers in Bioscience, vol. 13, pp. 1281-1293, Jan. 2008.

 

Year 2007

  • T. Gong, J. Xuan, C. Wang, H. Li, E. Hoffman, R. Clarke, and Y. Wang, "Gene module identification from microarray data using nonnegative independent component analysis," Gene Regulation and Systems Biology, vol. 1, pp. 349-363, 2007.

  • W. Cong, H. Shen, A. Cong, Y. Wang, and G. Wang, "Modeling photon propagation in biological tissues using a generalized Delta-Eddington phase function," Physical Review E, vol. 76, no. 5, 051913, Nov. 2007.

  • J. Wang, H. Li, Y. Zhu, M. Yousef, M. Nebozhyn, M. Showe, L. Showe, J. Xuan, R. Clarke, and Y. Wang, "VISDA: An open-source caBIG analytical tool for data clustering and beyond," Bioinformatics, vol. 23, no. 15, pp. 2024-2027, 2007.

  • J. Xuan, U. Klimach, H. Zhao, Q. Chen, Y. Zou, and Y. Wang, "Improved diagnostics using polarization imaging and artificial neural networks," International Journal of Biomedical Imaging, vol. 2007, Article ID 74143, 11 pages, 2007.

  • J. Xuan, Y. Wang, R. Clarke, and E. Hoffman, "An iterative nonlinear regression method for microarray data normalization," The Open Applied Informatics Journal, vol. 1, pp. 11-19, 2007.

  • J. Xuan, Y. Wang, Y. Dong, Y. Feng, B. Wang, J. Khan, M. Bakay, Z. Wang, L. Pachman, S. Winokur, Y.-W. Chen, R. Clarke, and E. Hoffman, "Gene selection for multiclass prediction by weighted Fisher criterion," EURASIP Journal of Bioinformatics and Systems Biology, Article ID 64628, 15 pages, 2007. [Supplemental material: http://www.cbil.ece.vt.edu/publications/EURASIP_BSB_64628_Suppl_Web.pdf]

 

Year 2006

  • J. Xuan, Y. Wang, M. T. Freedman, T. Adali, and P. G. Shields, "Non-rigid medical image registration by finite element deformable sheet-curve models," International Journal of Biomedical Imaging, Article ID 73430, 9 pages, 2006.

  • M. Bakay, Z. Wang, G. Melcon, L. Schilta, J. Xuan, P. Zhao, V. Sartorelli, J. Seo, E. Pegoraro, C. Angelini, B. Shneiderman, D. Escolar, Y-W Chen, S. T. Winokur, L. M. Pachman, C. Fan, R. Mandler, Y. Nevo, E. Gordon, Y. Zhu, Y. Dong, Y. Wang, and E. P. Hoffman, "Nuclear envelope dystrophies show a transcriptional fingerprint suggesting disruption of Rb-MyoD pathways in muscle regeneration," Brain, vol. 129, pp. 996-1013, 2006. http://www.cbil.ece.vt.edu/publications/EDMD_Brain06.pdf

  • Z. Wang, Y. Wang, J. Xuan, Y. Dong, M. Bakay, Y. Feng, R. Clarke, and E. P. Hoffman, "Optimized multilayer perceptrons for molecular classification and diagnosis using genomic data," Bioinformatics, vol. 22, no. 6, pp. 755-761, 2006.

  • Y. Wang, J. Xuan, R. Srikanchana, and P. L. Choyke, "Modeling and reconstruction of mixed functional and molecular patterns," International Journal of Biomedical Imaging, Article ID 29707, 9 pages, 2006.

  • J. Zhu, A. Wang, M. C. Liu, A. Zwart, R. Y. Lee, A. Gallapher, Y. Wang, W. R. Miller, J. M. Dixon, and R. Clarke, "Estrogen receptor alpha positive breast tumors and breast cancer cell lines share similarities in their transcriptome data structures," Intl. J. Oncology, vol. 29, no. 6, pp. 1581-1589, 2006.

 

Year 2005

  • J. Xuan, Y. Wang, Q. Zheng, and T. Adali, "Discontinuity-embedded deformable models for surface reconstruction from range images," IEEE Signal Processing Letters, vol. 12, no. 12, pp. 805-808, Dec. 2005.

 

Year 2004

  • L. A. Espinoza, P. Li, R. Lee, Y. Wang, A. H. Boulares, R. Clarke, and M. E. Smulson, "Evaluation of gene expression profiles of keratinocytes in response to JP-8 jet fuel," Toxicology and Applied Pharmacology, vol. 200, pp. 93-102, June 2004.

  • R. Srikanchana, J. Xuan, K. Huang, M. T. Freedman, C. Nguyen, and Y. Wang, "Non-rigid image registration by neural computation," Journal of VLSI Signal Processing, vol. 37, pp. 237-246, June-July 2004.

  • E. P. Hoffman, Y. Wang, D. Massaro, G. Massaro, and L. Clerch, "Expression profiling as a tool for diagnosis and pathway discovery: experimental design and technical considerations," Lung Development and Regeneration, D.J. Massaro, G D Massaro, and P. Chambon, eds., Marcel Dekker, Inc, New York, NY. 197-216, 2004.

 
Year 2003

  • Z. Wang, Y. Wang, J. Lu, S-Y Kung, J. Zhang, R. Lee, J. Xuan, J. Khan, and R. Clarke, "Discriminatory Mining of Gene Expression Microarray Data," Journal of VLSI Signal Processing, vol. 35, pp. 255-272, 2003.

  • P. Zhao, J. Seo, Z. Wang, Y. Wang, B. Shneiderman, and E. P. Hoffman, "In vivo filtering of in vitro expression data reveals MyoD targets," Comptes Rendus Biologies, vol. 326, no. 10, pp. 1049-1065, Oct. 2003.

  • R. Clarke, M. Liu, K. Bouker, Z. Gu, R. Lee, Y. Zhu, T. Skaar, B. Gomez, K. O'Brien, Y. Wang, and L. Hilakivi-Clarke, "Antiestrogen resistance in breast cancer and the role of estrogen receptor signaling," Oncogene, vol. 22, pp. 7316-7339, Oct. 2003.

 

Year 2002

  • S-C B. Lo, H. Li, Y. Wang, and M. T. Freedman, "A Multiple Circular Path Neural Network Architecture for Detection of Mammographic Masses," IEEE Transactions on Medical Imaging, vol. 21, no. 2, pp. 150-158, February 2002.

  • Y. Wang, J. Lu, R. Lee, Z. Gu, and R. Clarke, "Iterative Normalization of cDNA Microarray Data," IEEE Transactions on Information Technology in Biomedicine, vol. 6, no. 1, pp. 29-37, March 2002.

  • E. Matthew, Davis, N., Coop, A., Liu, M., Schumaker, L., Lee, R. Y., Srikanchana, R., Russell, C., Singh, B., Miller, W. R., Stearns, V., Pennanen, M., Tsangaris, T., Gallagher, A., Liu, A., Zwart, A., Hayes, D. F., Lippman, M. E., Y. Wang, and R. Clarke, " Development and Validation of a Method for Using Breast Core Needle Biopsies for Gene Expression Microarray Analysis," Clinical Cancer Research, vol. 8, pp. 1155-1166, May 2002.

  • Gu, Z., Lee, R. Y., Skaar, T., Bouker, K. B., Welch, J. N., Lu, J., Liu, A., Zhu, Y., Davis, N., Leonessa, F., Brünner, N., Y. Wang, and Clarke, R., "Association of interferon regulatory factor-1, nucleophosmin, nuclear factor-6B, and cAMP response element binding with acquired resistance to Faslodex (ICI 182,780)," Cancer Research, vol. 62, pp. 3428-3437, June 2002.

  • Y. Wang, K. Woods, and M. McClain, "Information-Theoretic Matching of Two Point Sets," IEEE Transactions on Image Processing, vol. 11, no. 8, pp. 868-872, August 2002.

 

Year 2001

  • H. Li, Y. Wang, K-J R. Liu, S-H B. Lo, and M. T. Freedman, "Computerized Radiographic Mass Detection-Part I: Lesion Site Selection by Morphological Enhancement and Contextual Segmentation," IEEE Transactions on Medical Imaging, vol. 20, no. 4, pp. 289-301, April 2001.

  • H. Li, Y. Wang, K-J R. Liu, S-H B. Lo, and M. T. Freedman, "Computerized Radiographic Mass Detection-Part II: Decision Support by Featured Database Visualization and Modular Neural Networks," IEEE Transactions on Medical Imaging, vol. 20, no. 4, pp. 302-313, April 2001.

  • Y. Wang, T. Adali, J. Xuan, and Z. Szabo, "Magnetic Resonance Image Analysis by Information Theoretic Criteria and Stochastic Site Models," IEEE Transactions on Information Technology in Biomedicine, vol. 5, no. 2, pp. 150-158, June 2001.

  • J. Xuan, T. Adali, Y. Wang, W. Hayes, J. Lynch, M. T. Freedman, and S. K. Mun, "A Computerized Simulation System for Prostate Needle Biopsy," Simulation and Gaming, vol. 32, no. 3, pp. 391-403, September 2001.

 

Year 2000

  • Y. Wang, L. Luo, M. T. Freedman, and S. Y. Kung, "Probabilistic Principal Component Subspaces: A Hierarchical Finite Mixture Model for Data Visualization," IEEE Transactions on Neural Networks, vol. 11, no. 3, pp. 635-646, May 2000.

  • J. Xuan, T. Adali, Y. Wang, and E. Siegel, "Automatic Detection of Foreign Objects in Computed Radiography," Journal of Biomedical Optics, vol.5, no. 4, pp. 425-431, 2000.

 

Year 1998

  • Y. Wang, T. Adali, C-M Lau, and S-Y Kung, "Quantitative Analysis of MR Brain Image Sequences by Adaptive Self-Organizing Mixtures," Journal of VLSI Signal Processing, vol. 8, pp. 219-239, 1998.

  • T. Adali, Y. Wang, N. Gupta, "A Block-wise Relaxation Labeling Scheme for Edge Detection in Cardiac MR Image Sequences," International Journal of Imaging Science and Technology, vol. 9, pp. 340-350, 1998.

  • Y. Wang, T. Adali, S-Y Kung, and Z. Szabo, "Quantification and Segmentation of Brain Tissues from MR Images: A Probabilistic Neural Network Approach," IEEE Transactions on Image Processing, vol. 7, no. 8, pp. 1165-1181, August 1998.

  • Y. Wang, S-H Lin, H. Li, and S-Y Kung, "Data Mapping by Probabilistic Modular Networks and Information Theoretic Criteria," IEEE Transactions on Signal Processing, vol. 46, no.12, pp. 3378-3397, December 1998.

 

Year 1997

  • Y. Wang, T. Adali, and S-C B. Lo, "Automatic Threshold Selection Using Histogram Quantization," Journal of Biomedical Optics, vol. 2, no. 2, pp. 211-217, April 1997.

  • J. Zeng, Y. Wang, M. T. Freedman, and S. K. Mun, "Finger Tracking for Breast Palpation Quantification using Color Image Features," Optical Engineering, vol. 36, no. 12, pp. 3455-3461, December 1997.

 

Year 1996

  • Y. Wang and J. M. Morris, "On Numerical Verification of Time-Domain Moment Method in Ultrasound Tomography," Journal of Biomedical Optics, vol. 1, no. 3, pp. 324-329, July 1996.

 
 
 

 

Conference Papers

 

 

Year 2009

  • G. Yu, B. Zhang, J. Xu, I.-M. Shih, and Y. Wang, "Accurate Estimation of Genomic Deletions and Normal Cell Contamination by Bayesian Analysis of Mixtures", Proc. IEEE Intl Conf. on Bioinformatics & Biomedicine, Washington D.C., USA, Nov. 2009. (best student's paper)

  • Y. Feng, G. Yu, T.-L. Wang, I.-M. Shih, and Y. Wang, "Analyzing DNA Copy Number Changes Using Fused Margin Regression", Proc. IEEE Intl Conf. on Bioinformatics & Biomedicine, Washington D.C., USA, Nov. 2009.

  • S. Ha, I. Kim and J. Xuan, "Enhancing Pathway Based Analysis Using Different Weighting Schemes," Proc. IEEE Intl Conf. on Bioinformatics & Biomedicine, Washington D.C., USA, Nov. 2009.

  • Y. Tao, L. Lu, D. Maneesh, A. Y. Chen, J. Corso, J. Xuan, M. Salganicoff, and A. Krishnan, "Robust Multi-level Ground Glass Nodule Detection and Segmentation in CT Lung Images," to appear in Proc. The 12th Intl Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI), London, UK, Sept. 2009.

  • Y. Tao, Z. Peng, B. Jian, J. Xuan, A. Krishnan, and X. S. Zhou, "Robust Learning-based Annotation of Medical Radiographs," Intl Workshop on Medical Content-based Retrieval for Clinical Decision Support, in conjunction with MICCAI, London, UK, Sept. 2009.

  • T. Gong, J. Xuan, R. B. Riggins, and R. Clarke, "A Systems Biology Approach to Identify Affected Regulatory and Signaling Circuits in Protein Interaction Networks," in Proc. Intl Joint Conf. on Bioinformatics, Systems Biology and Intelligent Computing, pp. 297-300, Shanghai, China, Aug. 2009.

 

Year 2008

  • G. Yu, D. Herrington, C. Langefeld, and Y. Wang, "Detection of complex interactions of multi-locus SNPs," in Proc. IEEE Machine Learning for Signal Processing, Cancun, Mexico, pp. 85-90, 2008.

  • Y. Tao, J. Xuan, M. T. Freedman, P. G. Shields, and Y. Wang, "Imaging Biomarker Analysis of Rat Mammary Fat Pads and Glandular Tissues in MRI Images," in Proc. Intl Conf. on Pattern Recognition (ICPR), Tampa, FL, Dec. 2008.

  • L. L. Chen, J. Xuan, Y. Wang, R. B. Riggins, and R. Clarke, "Network-constrained SVM for Classification," in Proc. Intl Conf. on Machine Learning and Applications, San Diego, CA, Dec. 2008.

  • Y. Zhang, J. Xuan, B. G. de los Reyes, R. Clarke, and H. W. Ressom, "Network Motif-Based Identification of Breast Cancer Susceptibility Genes," in Proc. IEEE Intl Conference of the Engineering in Medicine and Biology Society, Vancouver, British Columbia, Canada, August 2008.

  • T. Gong, J. Xuan, R. B. Riggins, Y. Wang, E. P. Hoffman, and R. Clarke, "Exploring Transcriptional Modules by Integrative Gene Clustering Guided by Transcription Factor Binding Information," in Proc. The 2008 Intl Conference on Bioinformatics & Computational Biology, Las Vegas, Nevada, July 2008.

  • L. L. Chen, J. Xuan, R. B. Riggins, Y. Wang, E. P. Hoffman, and R. Clarke, "Identification of Condition-specific Regulatory Modules by Multi-level Motif and mRNA Expression Analysis," in Proc. The 2008 Intl Conference on Bioinformatics & Computational Biology, Las Vegas, Nevada, July 2008.

  • Y. Zhang, J. Xuan, B. G. de los Reyes, R. Clarke, and H. W. Ressom, "Reverse Engineering Module Networks by PSO-RNN Hybrid Modeling," in Proc. The 2008 Intl Conference on Bioinformatics & Computational Biology, Las Vegas, Nevada, July 2008.

  • C. Wang, J. Xuan, L. L. Chen, R. B. Riggins, E. P. Hoffman, and R. Clarke, "Reliability Analysis of Transcriptional Regulatory Networks," in Proc. Intl Conf. on Bioinformatics, Computational Biology, Genomics and Chemoinformatics, Orlando, FL, July 2008.

  • J. Xiong, C. Wang, B. Zhang, Y. Wang, E. P. Hoffman, R. Clarke, and J. Xuan, "Inferring Condition-Specific miRNA-Gene Modules from miRNA and mRNA Profiling Data," in Proc. Intl Conf. on Bioinformatics, Computational Biology, Genomics and Chemoinformatics, Orlando, FL, July 2008.

  • B. Zhou, J. Xuan, J. Q. Wu, and Y. Wang, "3-D Deformation Guided On-line Modification of Multi-leaf Collimators for Adaptive Radiation Therapy," in Proc. Intl Conf. on Image Analysis and Recognition, pp. 798-806, Povoa de Varzim, Portugal, June 2008.

  • L. Chen, T.-H. Chan, P. L. Choyke, C.-Y. Chi, G. Wang, and Y. Wang, "Convex Analysis and Separation of Composite Signals in DCE-MRI," in Proc. 5th IEEE Intl Symposium on Biomedical Imaging: From Nano to Macro, Paris, France, May 2008.

  • T. Gong, J. Xuan, L. L. Chen, R. B. Riggins, Y. Wang, E. P. Hoffman, and R. Clarke, "Sparse Decomposition of Gene Expression Data to Infer Transcriptional Modules Guided by Motif Information," in Proc. Fourth Intl Symposium on Bioinformatics Research and Applications, pp. 244-255, Atlanta, Georgia, May 2008.

  • C. Wang, J. Xuan, L. L. Chen, P. Zhao, Y. Wang, R. Clarke, and E. P. Hoffman, "Integrative Network Component Analysis for Regulatory Network Reconstruction," in Proc. Fourth Intl Symposium on Bioinformatics Research and Applications, pp. 196-207, Atlanta, Georgia, May 2008.

  • T.-H. Chan, W.-K. Ma, C.-Y. Chi, and Y. Wang, "Blind Separation of Non-negative Sources by Convex Analysis: Effective Method Using Linear Programming," in Proc. IEEE International Conference on Acoustics, Speech and Signal Processing, Las Vegas, Nevada, April 2008.

  • B. Wang, J. Xuan, J. Q. Wu, S. Zhang and Y. Wang, "Deformation Estimation and Analysis for Adaptive Radiation Therapy," in Proc. SPIE Medical Imaging, vol. 6914, DOI: 10.1117/12.773548, San Diego, CA, Feb. 2008.

  • Y. Tao, S.-C. B. Lo, M. T. Freedman, E. Makariouc and J. Xuan, "Automatic Categorization of Mammographic Masses Using BI-RADS as a Guidance," in Proc. SPIE Medical Imaging, vol. 6915, DOI: 10.1117/12.772808, San Diego, CA, Feb. 2008.

 

Year 2007

  • L. L. Chen, C. Wang, I.-M. Shih, T.-L. Wang, Z. Zhang, Y. Wang, R. Clarke, E. Hoffman and J. Xuan, "Biomarker Identification by Knowledge-Driven Multi-Level ICA and Motif Analysis," Proc. Sixth Intl Conf. on Machine Learning and Applications, pp. 560-566, Cincinnati, Ohio, Dec. 2007.

  • B. Wang, J. Xuan, M. Freedman, P. Shields and Y. Wang, "Extraction of Breast Cancer Related Biomarkers in T1 Weighted MR Images of a Rodent Model," Proc. Third IEEE/NIH Life Science Systems and Applications Workshop, pp. 269-272, Bethesda, MD, Nov. 2007. (best student's paper)

  • B. Zhou, J. Xuan, H. Zhao, G. J. Chepko, M. T. Freedman, K. Y. Zou, "Polarization Imaging for Breast Cancer Diagnosis Using Texture Analysis and SVM," Proc. Third IEEE/NIH Life Science Systems and Applications Workshop, pp. 217-220, Bethesda, MD, Nov. 2007.

  • L. L. Chen, J. Xuan, R. Clarke and Y. Wang, "Biomarker Identification by Knowledge-Driven Multi-Scale Independent Component Analysis," Proc. Third IEEE/NIH Life Science Systems and Applications Workshop, pp. 261-264, Bethesda, MD, Nov. 2007. (best student's paper)

  • H. W. Ressom, Y. Zhang, J. Xuan, Y. Wang and R. Clarke, "Integrating Multi-Source Biological Data for Transcriptional Regulatory Module Discovery," Proc. Third IEEE/NIH Life Science Systems and Applications Workshop, pp. 184-187, Bethesda, MD, Nov. 2007.

  • L. Chen, Y. Wang, C.-Y. Chi, Z. Szabo, and P. L. Choyke, "Separating composite signals in multi-probe dynamic biomedical imaging," Proc. 41st Annual Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, Nov. 2007.

  • B. Wang, J. Xuan, M. Freedman, P. Shields and Y. Wang, "Rat Mammary Fat Pad Segmentation and Growth Rate Evaluation in T1 Weighted MR Images," Proc. IEEE 7th Symposium on Bioinformatics and Bioengineering, vol. 1, pp. 240-245, Boston, Massachusetts, Oct. 2007.

  • C. Wang, J. Xuan, T. Gong, R. Clarke, E. Hoffman, Y. Wang, "Stability Based Dimension Estimation of ICA with Application to Microarray Data Analysis," Proc. The 2007 Intl Conference on Bioinformatics & Computational Biology, vol. 1, pp. 132-138, Las Vegas, Nevada, June 2007.

  • B. Wang, J. Xuan, M. Freedman, P. Shields and Y. Wang, "Rat Mammary Gland Analysis in T1 Weighted MR Images," Proc. The 10th IAPR Conference on Machine Vision Applications, pp. 520-523, Tokyo, Japan, May 2007.

  • T-H Chan, W-K Ma, C-Y Chi, and Y. Wang, "A convex based analysis criterion for blind separation of non-negative sources," Proc. IEEE Intl Conf. Acoust., Speech, and Signal Processing, vol. 3, pp. 961-964, Honolulu, Hawaii, April 2007.

  • Y. Tao, S.-C. B. Lo, M. T. Freedman and J. Xuan, "A Preliminary Study of Content-Based Mammographic Masses Retrieval," Proc. SPIE Medical Imaging, vol. 6514, DOI: 10.1117/12.711528, San Diego, CA, Feb. 2007.

 

Year 2006

  • J. Molineaux, J. Xuan, T. Gong, Y. Zhu, E. Hoffman, R. Clarke and Y. Wang, "ModVis: an Information Visualization Tool for Gene Module Discovery," Proc. 19th Intl Conf. Computer Applications in Industry and Engineering, pp. 24-31, Las Vegas, Nevada, Nov. 2006.

  • H. Zhao, Q. Chen, U. Klimach, Y. K. Zou and J. Xuan, "Polarization imaging sensor for cell and tissue imaging and diagnostics," Proc. SPIE Smart Medical and Biomedical Sensor Technology IV, vol. 6380, DOI: 10.1117/12.685007, Boston, MA, Oct. 2006.

  • Y. Feng, Z. Wang, Y. Zhu, J. Xuan, D. Miller, R. Clarke, E. Hoffman and Y. Wang, "Learning the Tree of Phenotype Based on Gemonic Data," Proc. IEEE 6th Symposium on Bioinformatics and Bioengineering, paper-ID 0-7695-2727-2/06, Washington, DC, Oct. 2006.

  • H. Ressom, Y. Zhang, J. Xuan, Y. Wang and R. Clarke, "Inference of Gene Regulatory Networks from Time Course Gene Expression Data Using Neural Networks and Swarm Intelligence," Proc. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, Toronto, Canada, Sept. 2006.

  • T. Gong, Y. Zhu, J. Xuan, H. Li, R. Clarke, E. Hoffman and Y. Wang, "Latent Variable and nICA Modeling of Pathway Gene Module Composite," Proc. IEEE Intl Conference of the Engineering in Medicine and Biology Society, pp. 5872-5875, New York City, New York, August 2006.

  • Y. Zhu, Z. Wang, J. Xuan, E. Hoffman and Y. Wang, "Phenotypic-Specific Gene Module Discovery using Diagnostic Tree and VISDA," Proc. IEEE Intl Conference of the Engineering in Medicine and Biology Society, pp. 5767-5770, New York City, New York, August 2006.

  • H. Ressom, Y. Zhang, J. Xuan, Y. Wang and R. Clarke, "Inferring Network Interactions Using Recurrent Neural Networks and Swarm Intelligence," Proc. IEEE Intl Conference of the Engineering in Medicine and Biology Society, pp. 4241-4244, New York City, New York, August 2006.

  • F. Wang, Y. Wang, TH. Chan, and CY. Chi, "Blind separation of multichannel biomedical image patterns by non-negative least-correlated component analysis," Proc. Intl Workshop on Pattern Recognition in Bioinformatics, Hong Kong, China, August 2006; Lecture Notes in Bioinformatics, vol. 4146, pp. 151-162, Springer-Verlag, Berlin, 2006.

  • H. Ressom, Y. Zhang, J. Xuan, Y. Wang and R. Clarke, "Inferring Network Interactions Using Recurrent Neural Networks and Particle Swarm Optimization," Proc. of the First International Conference on Computational Systems Biology, Shanghai, China, August 2006.

  • T. Gong, J. Xuan, Y. Zhu, H. Li, R. Clarke, E. Hoffman and Y. Wang, "Composite Gene Module Discovery using Non-negative Independent Component Analysis," Proc. IEEE/NLM Life Science Systems & Applications Workshop, Bethesda, MD, July 2006.

  • U. Klimach, H. Zhao, Q. Chen, Y. Zhou, Y. Wang and J. Xuan, "Improved Diagnostics using Polarization Imaging and Artificial Neural Networks," Proc. SPIE Medical Imaging 2006, vol. 6142, pp. 1345-1354, San Diego, CA, Feb. 2006.

 

Year 2005

  • J. Xuan, E. Hoffman, R. Clarke, and Y. Wang, "Normalization of Microarray Data by Iterative Nonlinear Regression," Proc. Fifth IEEE Symposium on Bioinformatics and Bioengineering, pp. 267-270, Minneapolis, Minnesota, Oct. 2005.

 

Year 2004

  • J. Xuan, Y. Dong, J. Khan, R. Clarke, E. Hoffman and Y. Wang, "Gene Selection by Weighted Fisher Criterion for Multiclass Prediction," Proc. Intl Conf. Bioinformatics and Applications, pp. 252-263, Fort Lauderdale, Florida, Dec. 2004.

  • J. Xuan, Y. Wang, Q. Zheng and T. Adali, "A Discontinuity-Embedded Deformable Model for Surface Modeling," Proc. IASTED Intl Conf. Circuits, Signals, and Systems, pp. 273-277, Clearwater Beach, Florida, Nov. 2004.

  • Y. Wang, Z. Wang, J. Xuan, E. Hoffman, R. Clarke, and J. Khan, "Optimizing Multilayer Perceptrons By Discriminatory Component Analysis," Proc. IEEE Intl Workshop Machine Learning for Signal Processing, pp. 273-282, Sao Luis, Brazil, Sept. 2004.

  • J. Xuan, Y. Dong, J. Khan, E. Hoffman, R. Clarke, and Y. Wang, "Robust Feature Selection by Weighted Fisher Criterion for Multiclass Prediction in Gene Expression Profiling," Proc. Intl Conf. Pattern Recognition, vol. 2, pp. 291-294, Cambridge, UK, Aug. 2004.

  • Y. Wang, R. Srikanchana, P. Choyke, J. Xuan, and Z. Szabo, "Computed simultaneous imaging of multiple functional biomarkers," Proc. IEEE Intl Symposium on Biomedical Imaging, vol. 1, pp. 225-228, Arlington, VA, April 2004.

 

Year 2003

  • Y. Wang, J. Zhang, J. Khan, R. Clarke, and Z. Gu, "Partially-independent component analysis for tissue heterogeneity correction in microarray gene expression analysis," Proc. IEEE Workshop on Neural Networks for Signal Processing, Toulouse, France, Sept. 2003.

  • Z. Wang, S.-Y. Kung, J. Zhang, J. Khan, J. Xuan and Y. Wang, "Computational intelligence approach for gene expression data mining and classification," Proc. Intl Conf. Multimedia and Expo, vol. 3, pp. 449-452, Baltimore, MD, July 2003.

  • J. Xuan, M. Freedman, and Y. Wang, "Deformable Sheet-Curve Models for Registration of MR Breast Images," Proc. SPIE Medical Imaging, vol. 5032, p. 165-176, San Diego, CA, Feb. 2003.

  • J. Zhang, R. Srikanchana, J. Xuan, P. Choyke, K. Li, and Y. Wang, "Partially-Independent Component Analysis of Tumor Heterogeneity by DCE-MRI," Proc. SPIE Medical Imaging, vol. 5032, pp. 222-233, San Diego, CA, Feb. 2003.

 

Year 2002

  • R. Srikanchana, J. Xuan, K. Huang, M. Freedman, and Y. Wang, "Mixture of Principal Axes Registration: A Neural Computation Approach," Proc. SPIE Medical Imaging, vol. 4684, pp. 923-932, San Diego, CA, Feb. 2002.

  • Y. Wang, J. Zhang, K. Huang, J. Khan, and Z. Szabo, "Independent component imaging of disease signatures," Proc. IEEE Intl Symp. Biomed. Imaging, pp. 178-181, Washington, DC, July 2002.

  • J. Zhang, K. Huang, J. Khan, K. Li, Z. Bhujwalla, R. Clarke, Z. Gu, Z. Szabo, J. Xuan, and Y. Wang, "Computational decomposition of molecular signatures," Proc. Intl Conf. Diagnositic Imaging and Analysis, pp. 312-317, Shanghai, August 2002.

  • Varga J., Pham D.L., Wang Y., Huang K., Szabo Z., "Comparison of MRI brain segmentation methods for the partial volume correction of coregistered PET," Eur. J. Nucl. Med. 29: S157, 2002.

 

Year 2001

  • L. Lu, Y. Wang, Z. Wang, J. Xuan, S-Y. Kung, Z. Gu, and R. Clarke, "Discriminative mining of gene microarray data," Proc. IEEE Workshop on Neural Networks for Signal Processing, pp. 23-32, Falmouth, MA, Sept. 2001.

 

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