Year 2014

  • X. Chen, Xu Shi, A. N. Shajahan, L. Hilakivi-Clarke, and R. Clarke and J. Xuan, “BSSV: Bayesian based Somatic Structural Variation Identification with Whole Genome DNA-Seq Data,” in Proc. The 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Chicago, IL, USA, August 2014.
  • X. Wang, J. Gu, R. Clarke, L. Hilakivi-Clarke, and J. Xuan, “A Markov random field-based Bayesian model to identify genes with differential methylation,” in Proc. IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, Hawaii, USA, May 2014.
  • X. Chen, J. Xuan, A. N. Shajahan, L. Hilakivi-Clarke, and R. Clarke, “Statistical Identification of Co-regulatory Gene Modules Using Multiple ChIP-Seq Experiments,” in Proc. The 5th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2014), pp. 109 -116, Angers, France, March 2014.

 Year 2013

  • J. Gu, J. Xuan, X. Wang, A. N. Shajahan, L. Hilakivi-Clarke, and R. Clarke, “Reconstructing transcriptional regulatory networks by probabilistic network component analysis,” in Proc. The fourth ACM International Conference on Bioinformatics, Computational Biology, and Biomedical Informatics (ACM BCB 2013), pp. 96-105, Washington, DC, Sept. 2013.
  • X. Chen, J. Xuan, A. N. Shajahan, L. Hilakivi-Clarke, and R. Clarke, “A Novel Statistical Approach to Identify Co-regulatory Gene Modules,” in Proc. The IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013), pp. 16-18, Shanghai, China, Dec. 2013.

 Year 2012

  • X. Wang, J. Gu, L. Chen, A. N. Shajahan, R. Clarke, and J. Xuan, “Sampling-based Subnetwork Identification from Microarray Data and Protein-protein Interaction Network,” in Proc. ICMLA 2012: Machine Learning in Health Informatics Workshop, Vol. 2, pp. 158 – 163, Boca Raton, Florida, Dec. 2012.
  • X. Chen, C. Wang, A. N. Shajahan, R. B. Riggins, R. Clarke, and J. Xuan, “Reconstruction of Transcription Regulatory Networks by Stability-based Network Component Analysis,” in Proc. International Symposium on Bioinformatics Research and Applications, Lecture Notes in Computer Science, Vol. 7292, pp 36-47, Dallas, Texas, May 2012.
  • J. Gu, J. Xuan, C. Wang, L. Chen, T.-L. Wang, and I.-M. Shih, “Detecting Aberrant Signal Transduction Pathways From High-throughput Data Using GIST Algorithm,” in Proc. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp. 267-274, San Diego, CA, May 2012.
  • X. Chen, X. Wang, and J. Xuan, “Tracking Multiple Moving Objects Using Unscented Kalman Filtering Techniques,” in Proc. Int’l Conf. on Engineering and Applied Science, Beijing, China, July 2012.
  • F. Bao and J. Xuan, “Recovery of Nanowire Morphology and Distribution by a Computer Vision-assisted Approach,” in Proc. Int’l Conf. on Wavelet Analysis and Pattern Recognition, pp. 38-44, Xian, China, July 2012.
  • L. Chen, J. Xuan, J. Gu, Y. Wang, Z. Zhang, T.-L. Wang, and I.-M. Shih, “Integrative Network Analysis to Identify Aberrant Pathway Networks in Ovarian Cancer,” in Proc. Pacific Symposium on Biocomputing, 17:31-42, Hawaii, Jan. 2012.

 Year 2011

  • J. Gu, C. Wang, I.-M. Shih, T.-L. Wang, Y. Wang, R. Clarke, and J. Xuan, “GIST: A Gibbs Sampler to Identify Intracellular Signal Transduction Pathways,” in Proc. IEEE International Conference of the Engineering in Medicine and Biology Society, pp. 2434-2437, Boston, MA, Aug. 2011.

 Year 2010

  • J. Gu, J. Xuan, Y. Wang, R. B. Riggins, and R. Clarke, “Identification of Transcriptional Regulatory Networks by Learning the Marginal Function of Outlier Sum Statistic,” in Proc. IEEE the Ninth International Conference on Machine Learning and Applications (ICMLA 2010), pp. 281-286, Washington DC, Dec. 2010.
  • C. Wang, S. Ha, Y. Wang, E. Hoffman, and J. Xuan, “Computational Analysis of Muscular Dystrophy Sub-types Using A Novel Integrative Scheme,” in Proc. IEEE the Ninth International Conference on Machine Learning and Applications (ICMLA 2010), pp. 287-292, Washington DC, Dec. 2010.
  • Y. Zhang, J. Xuan, R. Clarke, and H. Ressom, “Module-Based Biomarker Discovery in Breast Cancer,” in Proc. IEEE International Conference on Bioinformatics & Biomedicine, Hong Kong, Dec. 2010.
  • J. Xuan, L. Chen, C. Wang, Y. Wang, R. B. Riggins, and R. Clarke, “Integrative Network Analysis to Predict Endocrine Resistance in Breast Cancer,” in Proc. 8th Annual Rocky Mountain Bioinformatics Conference, Aspen/Snowmass, Colorado, Dec. 2010. (Abstract)
  • L. Chen, L. Jin, J. Dai, and J. Xuan, “View Reconstruction from Images by Removing Vehicles,” in Proc. ACM SIGSPATIAL DMG Workshop, San Jose, CA, Nov. 2010.
  • Y. Tao, S.-C. B. Lo, M. T. Freedman, and J. Xuan, “Joint segmentation and spiculation detection for ill-defined and spiculated masses in mammograms,” in Proc. SPIE Medical Imaging, vol. 7624, doi:10.1117/12.844045, San Diego, CA, Feb. 2010.

 Year 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. 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. 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.
  • 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.
  • 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. 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.
  • 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.
  • 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.
  • 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.
  • J. Xuan, R. Lee, Y. Zhu, A. L. Zwart, R. Clarke and Y. Wang, “Tissue heterogeneity correction in gene expression mapping,” In: Proceedings of the 95th Annual Meeting of the American Association for Cancer Research; AACR Meeting Abstracts 2004, pp. 378 – 379. 2004. (Abstract)

 Year 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.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.
  • 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.
  • 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.

 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.