Computational Bioinformatics and Bioimaging Laboratory (CBIL)


 
 

Internal Use

 

Journal Papers

Conference Papers


 

 

 

Journal Papers (*Correspondence)

Submitted manuscripts

  • Mohammad R. Nezami Ranjbar, Mahlet G. Tadesse, Yue Wang, and Habtom W. Ressom, "Bayesian Normalization Model for Label-free Quantitative Analysis by LC-MS," IEEE/ACM Trans Computational Biology and Bioinformatics, 2014.

  • ArulMurugan Ambikapathi, Tsung-Han Chan, Chia-Hsiang Lin, Fei-Shih Yang, Chong-Yung Chi, and Yue Wang, "Reliable compartment modeling of DCE-MRI in heterogeneous prostate tumors," IEEE Trans. Biomedical Engineering, 2014.

 

Year 2014

  • J. Gu, X. Wang, L. Halakivi-Clarke, R. Clarke, and J. Xuan*, "BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data," BMC Bioinformatics (Suppl - Proceedings of RECOMB-seq 2014), 2014. (accepted)

  • B Zhang, X Hou, X Yuan, I-M Shih, Z Zhang, R Clarke, R R. Wang, Y Fu, S Madhavan, Y Wang, G Yu, "AISAIC: a software suite for accurate identification of significant aberrations in cancers," Bioinformatics,vol. 30, no. 3, 431-433, 2014. (IF=5.323; 2012 ISI)

  • B. Zhang, Y. Tian, Z. Zhang, "Network Biology in Medicine and Beyond," Circulation: Cardiovascular Genetics, 2014. (IF=6.105; 2012 ISI) accepted

  • Y. Tian, S. Wang, Z. Zhang, O.C. Rodriguez, E. Petricoin III, I-M Shih, D. Chan, M. Avantaggiati, G. Yu, S. Ye, R. Clarke, C. Wang, B. Zhang, Y. Wang and C. Albanese, "Integration of network biology and imaging to study cancer phenotypes and responses," IEEE/ACM Trans Computational Biology and Bioinformatics, 2014. accepted.

  • Li Chen, Peter L. Choyke, Niya Wang, Robert Clarke, Zaver M. Bhujwalla, Elizabeth M. C. Hillman, Ge Wang, and Yue Wang, "Unsupervised deconvolution of dynamic imaging reveals intratumor vascular heterogeneity and repopulation dynamics," PLoS One, 2014. minor revision

  • Sherry Dadgar, Zuyi Wang, Helen Johnston, Akanchha Kesari, Kanneboyina Nagaraju, Yi-Wen Chen, D. Ashley Hill, Terence A. Partridge, Mamta Giri, Javad Nazarian, Jianhua Xuan, Yue Wang, and Eric P. Hoffman, "Asynchronous remodelling as a driver for failed regeneration in Duchenne Muscular Dystrophy," The Journal of Cell Biology, 2014. (IF=10.822; 2012 ISI) minor revision

  • Ye Tian, Bai Zhang, Eric P. Hoffman, Robert Clarke, Zhen Zhang, Ie-Ming Shih, Jianhua Xuan, David M. Herrington, and Yue Wang, "Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks," BMC Systems Biology, 2014, 8:87, doi:10.1186/s12918-014-0087-12014.

  • Niya Wang, Ting Gong, Robert Clarke, Lulu Chen, Ie-Ming Shih, Zhen Zhang, Douglas A. Levine, Jianhua Xuan and Yue Wang, "UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples," Bioinformatics, 2014. major revision

  • Ye Tian, Bai Zhang, Eric P. Hoffman, Robert Clarke, Zhen Zhang, Ie-Ming Shih, Jianhua Xuan, David M. Herrington, and Yue Wang, "KDDN: An open-source Cytoscape app for constructing differential dependency networks with significant rewiring," Bioinformatics, 2014. major revision

 

Year 2013

  • M R N Ranjbar, Y. Zhao, M G Tadesse, Y. Wang, and H W Ressom, "Gaussian process regression model for normalization of LC-MS data," Proteome Science, vol. 11, no. Suppl 1, p. S13, 2013. (IF=2.42; 2012 ISI)

  • T-H Tsai, M G. Tadesse, C Di Poto, L K. Pannell, Y Mechref, Y. Wang, and H W. Ressom, "Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards," Bioinformatics, vol. 29, no. 21, 2774-2780, 2013. (IF=5.323, 2012 ISI)

  • N. Wang, F. Meng, Li. Chen, Subha Madhavan, Robert Clarke, E.P. Hoffman, J. Xuan, and Y. Wang, "The CAM Software for Nonnegative Blind Source Separation in R-Java," Journal of Machine Learning Research, 14 (2013) 2899-2903, 2013. (5-year IF=4.284, 2011 ISI)

  • Y. Song, W. Cai, H. Huang, Y. Wang, D. Feng, and M. Chen, "Region-based progressive localization of cell nuclei in microscopic images with data adaptive modeling," BMC Bioinformatics, 14:173, 2013. (IF=3.024, 2012 ISI)

  • Y. Tian, L. Chen, B. Zhang, Z. Zhang, G. Yu, R. Clarke, J. Xuan, I-M Shih, and Y. Wang, "Genomic and network analysis to study origin of ovarian cancer," Systems Biomedicine, 1:1, 62-71, 2013.

  • T-H Tsai, M. G. Tadesse, Y. Wang, H. W. Ressom, "Profile-based LC-MS data alignment: a Bayesian approach," IEEE/ACM Trans Computational Biology and Bioinformatics, vol. 10, no. 2, 494-503, 2013. (5-year IF=1.806, 2011 ISI)

  • C. Albanese, J. VanMeter, S. T. Frickey, B. Rood, O. C. Rodriguez, S. S. Wang, S. Madhavan, Y. Gusev, E. F. Petricoin III, and Y. Wang, "Preclinical magnetic resonance imaging and systems biology in cancer research: Current applications and challenges," The American Journal of Pathology, vol. 182, no. 2, pp. 312-318, Feb. 2013. (IF=5.224)

  • X. Shi, J. Gu, X. Chen, A. N. Shajahan, L. Hilakivi-Clarke, R. Clarke, and J. Xuan*, "mAPC-GibbsOS: An integrated approach for robust identification of gene regulatory networks," BMC Systems Biology, 7(Suppl 5):S4, 2013. (IF=2.98; 2012 ISI)

  • X. Chen, J. Xuan*, C. Wang, A. N. Shajahan, R. B. Riggins, and R. Clarke, "Reconstruction of Transcriptional Regulatory Networks by Stability-based Network Component Analysis," IEEE/ACM Trans. Computational Biology and Bioinformatics, 10(6):1347-1358, 2013. (IF=1.54, 2012 ISI)

  • Y. Zhang, J. Xuan, R. Clarke, and R. Habtom, "Module-Based Breast Cancer Classification," Intl J of Data Mining and Bioinformatics, 7(3):284-302, 2013.

  • L. Chen, J. Xuan*, R. Riggins, Y. Wang, and R. Clarke, "Identifying protein interaction subnetworks by a bagging Markov random field-based method," Nucleic Acids Research, 41(2):e42, 2013. (IF=8.278, ISI 2012)

 

Year 2012

  • X. Yuan, J. Zhang; S. Zhang; G. Yu, Y. Wang, "Comparative analysis of methods for identifying recurrent copy number alterations in cancer," PLoS ONE, vol. 7, no. 12, e52516, 2012. (IF=4.092; 2011 ISI)

  • K. B. Bouker, Y. Wang, J. Xuan, R. Clarke, "Antiestrogen resistance and the application of systems biology," Drug Discovery Today: Disease Mechanisms, 9(1-2):e11-e17, 2012.

  • P. Sirajuddin, S. Das, L. Ringer, A. Sivakumar, S. T. Fricke, B. Rood, A. Ozcan, S. S. Wang, V. Yenugonda, P. Salinas, E. Petricoin III, O. Rodriguez, M. Pishvaian, M. P. Lisanti, Y. Wang, R. Schlegel, B. Moasser, and C. Albanese, "Quantifying the CDK inhibitor VMY-1-103's activity at tissue levels in an in vivo tumor model by LC-MS/MS and MRI," Cell Cycle, vol. 11, no. 20, pp. 3801-3809, 2012. (IF=5.359)

  • S. de Assis, A. Warri, M. I. Cruz, O. Laja, Y. Tian, B. Zhang, Y. Wang, T. H-M Huang, and L. Hilakivi-Clarke, "High-fat or ethinyl-oestradiol intake during pregnancy increases mammary cancer risk in several generations of offspring," Nature Communications, 3:1053, 2012. DOI: 10.1038/ncomms2058 (IF=10.015)

  • E. Kuhn, R-C Wu, G. Wu, B. Guan, J. Zhang, Y. Wang, L. Song, X. Yuan, L. Wei, R. Roden, K-T Kuo, K. Nakayama, B. Clarke, P. Shaw, N. Olvera, D. Levine, R. Kurman, T-L Wang, and I-M Shih, "Identification of molecular pathway aberrations in uterine serous carcinoma by genome-wide analyses," Journal of The National Cancer Institute, vol. 104, no. 19, pp. 1503-1513, 2012. (IF=13.757; 2011 ISI)

  • X. Yuan, G. Yu, X. Hou, I-M Shih, R. Clarke, J. Zhang, E. P. Hoffman, R. R. Wang, Z. Zhang, Y. Wang*, "Genome-wide identification of significant aberrations in cancer genome," BMC Genomics, 13:342, 2012. (IF=4.07; 2011 ISI)

  • X. Yuan, J. Zhang; L. Yang; S. Zhang; B. Chen; Y. Geng; Y. Wang, "TAGCNA: a method to identify significant consensus events of copy number alterations in cancer," PLoS ONE, vol. 7, no. 7, e41082, 2012. (IF=4.092; 2011 ISI)

  • G. Wang, J. Zhang, H. Gao, V. Weir, H. Yu, W. Cong, X. Xu, H. Shen, J. Bennett, M. Furth, Y. Wang, M. Vannie, "Towards Omni-tomography - Grand Fusion of Multiple Modalities for Simultaneous Interior Tomography," PLoS ONE, vol. 7, no. 6, e39700, 2012. (IF=4.092; 2011 ISI)

  • J. Gu, J. Xuan*, R. B. Riggins, L. Chen, Y. Wang, and R. Clarke, "Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic," Bioinformatics, 28(15):1990-1997, 2012. (IF=5.323)

  • X. Chen, M. M. Thiaville, L. Chen, A. Stoeck, J. Xuan, M. Gao, I-M Shih, and T-L Wang, "Definition of NOTCH3 target genes in ovarian cancer," Cancer Research, 72(9):2294-2303 2012. (IF=8.65)

  • L. Chen, Y. Tian, G. Yu, D. J. Miller, I-M Shih, and Y. Wang, "Discriminant and network analysis to study origin of cancer," Invited Chapter, Statistical Diagnostics of Cancer: Analyzing High Dimensional Genetics and Genomics Data, Wiley-Blackwell, (Frank Emmert-Streib and Matthias Dehmer, co-eds.), 2012.

  • C. Wang, J. Xuan*, I.-M. Shih, R. Clarke, and Y. Wang, "Regulatory component analysis: a semi-blind extraction approach to infer gene regulatory networks with imperfect biological knowledge," Signal Processing, vol. 92, no. 8, pp. 1902-1915, 2012. (IF=1.503; 2011 ISI)

  • C. Wang, S. Ha, J. Xuan*, Y. Wang, and E. Hoffman, "Computational analysis of muscular dystrophy subtypes using a novel integrative scheme," Neuocomputing, vol. 92, pp. 9-17, 2012. (IF=1.580; 2011 ISI)

  • R Clarke, K L. Cook, R Hu, C O. B. Facey, I Tavasoly, J L. Schwartz, W T. Bauman, J J. Tyson, J Xuan, Y Wang, A Warri, A N. Shajahan, "Endoplasmic Reticulum Stress, the Unfolded Protein Response, Autophagy, and the Integrated Regulation of Breast Cancer Cell Fate," Cancer Research, 72:1321, 2012. (IF=8.65)

  • B Zhang, DJ Miller, and Y Wang*, "Nonlinear system modeling with random matrices: Echo state networks revisited," IEEE Transactions on Neural Networks and Learning Systems, vol. 23, no. 1, 2012. (5-year IF=3.370; 2011 ISI)

  • X. Yuan, DJ Miller, J. Zhang, D. Herrington, and Y. Wang*, "An overview of population genetic data simulation," Journal of Computational Biology,, vol. 9, no. 1, pp. 1-13, 2012. (IF=1.694; 2010 ISI)

 

Year 2011

  • L Chen, T-H Chan, PL Choyke, EMC Hillman, ZM Bhujwalla, C-Y Chi, G Wang, Z Szabo, Y Wang*, "CAM-CM: A signal deconvolution tool for in vivo dynamic contrast-enhanced imaging of complex tissues," Bioinformatics, vol. 27, no. 18, pp. 2607-2609, 2011. (IF=4.877; 2010 ISI)

  • L. Chen, J. Xuan*, R. B. Riggins, R. Clarke, and Y. Wang, "Identifying cancer biomarkers by network-constrained support vector machines," BMC Systems Biology, 5:161, 2011. (IF = 3.15)

  • S Madhavan, Y Gusev, M Harris, DM Tanenbaum, R Gauba, K Bhuvaneshwar, A Shinohara, K Rosso, LA Carabet, L Song, RB Riggins, S Dakshanamurthy, Y Wang, SW Byers, R Clarke, LM Weiner, "G-DOC: A systems medicine platform for personalized oncology," Neoplasia, vol. 13, no. 9, pp. 771-783, 2011. (IF=5.476; 2010 ISI)

  • L Chen, G Yu, CD Langefeld, DJ Miller, RT Guy, J Raghuram, X Yuan, D Herrington, Y Wang*, "Comparative analysis of methods for detecting interacting loci," BMC Genomics, 12:344, 2011. (IF=4.21; 2010 ISI)

  • L Chen, PL Choyke, T-H Chan, C-Y Chi, G Wang, and Y Wang*, "Tissue-specific compartmental analysis for dynamic contrast-enhanced MR imaging of complex tumors," IEEE Transactions on Medical Imaging, vol. 30, no. 12, pp. 2044-2058, December 2011. (IF=3.639; 2010 ISI)

  • JJ Tyson, WT Baumann, C Chen, A Verdugo, I Tavassoly, Y Wang, LM Weiner, and R Clarke, "Dynamic modeling of estrogen signaling and cell fate in breast cancer cells," Nature Reviews Cancer, vol. 11, pp. 523-532, July 2011. (IF=37.178; 2010 ISI)

  • G Yu, B Zhang, G S Bova, J Xu, I-M Shih, and Y Wang*, "BACOM: In silico detection of genomic deletion types and correction of normal cell contamination in copy number data," Bioinformatics, vol. 27, nol. 11, pp. 1473-1480, 2011. (IF=5.468)

  • B. Zhang, Y. Tian, L. Jin, H. Li, I.-M. Shih, S. Madhavan, R. Clarke, E.P. Hoffman, J. Xuan, L. Hilakivi-Clarke, and Y. Wang*, "DDN: A caBIG analytical tool for differential network analysis," Bioinformatics, vol. 27, no. 7, pp. 1036-1038, 2011. (IF=5.468)

  • G. Yu, H. Li, S. Ha, I.-M. Shih, R. Clarke, E.P. Hoffman, S. Madhavan, J. Xuan, and Y. Wang*, "PUGSVM: A caBIG analytical tool for multiclass gene selection and predictive classification," Bioinformatics, vol. 27, no. 5, pp.736-738, 2011. (IF=5.468)

  • T. Gong, J. Xuan*, L. Chen, R. B. Riggins, H. Li, E. P. Hoffman, R. Clarke, and Y. Wang, "Motif-guided sparse decomposition of gene expression data for regulatory module identification," BMC Bioinformatics, 12:82, 2011. (IF=2.75)

  • S. Ha, I. Kim, Y. Wang and J. Xuan*, "Applications of different weighting schemes to improve pathway-based analysis," Comparative and Functional Genomics, vol. 2011, Article ID 463645, 15 pages, 2011. doi:10.1155/2011/463645.

  • Y. Wang, H. Li, D J Miller, and J. Xuan, "Bioinformatics and public access resources," The Encyclopaedia of Sports Medicine - Genetic and Molecular Aspects of Sport Performance, The International Olympic Committee and Wiley-Blackwell (Claude Bouchard and Eric P. Hoffman, co-eds.), Oxford, England, Chapter 5, pp. 58-69, 2011.

  • X. Yuan, J. Zhang, and Y. Wang, "Simulating linkage disequilibrium structures in a human population for SNP association studies," Biochemical Genetics, vol. 49, no. 5-6, pp. 395-409, 2011. (IF=0.825; 2010 ISI)

  • X. Yuan, J. Zhang, and Y. Wang, "Mutual information and linkage disequilibrium based SNP association study by grouping case-control," Genes & Genomics, vol. 33, no. 1, pp. 65-73, 2011. (IF=0.453; 2010 ISI)

  • R Clarke, AN Shajahan, Y Wang, JJ Tyson, RB Riggins, LM Weiner, WT Bauman, J Xuan, B Zhang, C Facey, H Aiyer, K Cook, FE Hickman, I Tavassoly, A Verdugo, C Chen, A Zwart, A Warri, and LA Hilakivi-Clarke, "Endoplasmic reticulum stress, the unfolded protein response, and gene network modeling in antiestrogen resistant breast cancer," Horm Mol Biol Clin Invest, 5:35-44, 2011.

 

Year 2010

  • X. Yuan, J. Zhang, and Y. Wang, "Probability theory-based SNP association study method for identifying susceptibility loci and genetic disease models in human case-control data," IEEE Trans on NanoBioscience, vol. 9, no. 4, pp. 232 - 241, Dec. 2010. (IF=1.732)

  • G. Yu, Y. Feng, DJ Miller, J. Xuan, EP Hoffman, R Clarke, B Davidson, I-M Shih, and Y. Wang*, "Matched gene selection and committee classifier for molecular classification of heterogeneous diseases," Journal of Machine Learning Research, 11:2141-2167, 2010. (5-year IF=4.04)

  • L. Chen, J. Xuan*, R. B. Riggins, Y. Wang, E. P. Hoffman, and R. Clarke, "Multi-level support vector regression analysis to identify condition-specific regulatory networks," Bioinformatics, 26(11):1416-1422, 2010. (IF=4.877)

  • C. Wang, J. Xuan*, H. Li, Y. Wang, M. Zhan, E. P. Hoffman and R. Clarke, "Knowledge-guided gene ranking by coordinative component analysis," BMC Bioinformatics, 11:162, 2010. (IF=3.029)

  • I.-M. Shih, L. Chen, C. Wang, J. Gu, B. Davidson, L. Cope, R. J. Kurman, J. Xuan, and T.-L. Wang, "Distinct DNA methylation profiles in ovarian serous neoplasms and their implications in ovarian carcinogenesis," Am J Obstet Gynecol., 203(6):584, 2010. (IF=3.313)

  • Y. Zhang, J. Xuan, B. G. de los Reyes, R. Clarke, and H. W. Ressom, "Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration," PLoS ONE, 5(4): e10268, 2010. (IF=4.411)

  • 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. (IF=3.736; 2009 ISI)

  • 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. (IF=3.736; 2009 ISI)

  • 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, vol. 32, no. 5, pp. 875-887, 2010. (IF=5.308)

  • Bai Zhang, Huai Li, Robert Clarke, Leena Hilakivi-Clarke, and Yue Wang, "Differential dependency network analysis to identify topological changes in biological networks," Chapter 10, pp. 185-204, Medical Biostatistics for Complex Diseases, Wiley-VCH Verlag GmbH & Co. KGaA, (Frank Emmert-Streib and Matthias Dehmer, co-eds.), Weinheim, 2010.

  • Kuan-Ting Kuo, Tsui-Lien Mao, Xu Chen, Yuanjian Feng, Kentaro Nakayama, Yue Wang, Ruth Glas, M. Joe Ma, Robert J. Kurman, Ie-Ming Shih, and Tian-Li Wang, "DNA Copy Number Profiles in Affinity-Purified Ovarian Clear Cell Carcinoma," Clinical Cancer Research, vol. 14, pp. 1997-2008, April 2010. (IF=7.338)

  • Yuanjian Feng, Guoqiang Yu, Tian-Li Wang, Ie-Ming Shih, and Yue Wang*, "Analyzing DNA copy number changes using fused margin regression," Intl J of Functional Informatics and Personalized Medicine, vol.3, no. 1, pp.3-15, 2010.

  • Y. Tao, S.-H. B. Lo, M. T. Freedman, E. Makariou, and J. Xuan, "Multilevel Learning-based Segmentation of Ill-defined and Spiculated Masses in Mammograms," Med. Phys., 37:5993, 2010. (IF=3.07)

 

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. (IF=4.926)

  • 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.

  • 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.

  • 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. (IF=3.759)

  • 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.

  • 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. (IF=27.136)

  • 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. (IF=7.543)

  • 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. (IF=4.926)

 

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. (IF=3.781)

  • 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. (IF=7.514)

  • 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. (IF=3.781)

  • 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. (IF=2.335)

  • 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. (IF=3.781)

  • 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. (IF=1.703)

  • 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. (IF=3.749)

  • 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. (IF=4.846)

  • 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. (IF=3.308)

  • 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. (IF=30.762)

  • H. Li, J. Xuan, Y. Wang, and M. Zhan, "Inferring regulatory networks," Frontiers in Bioscience, vol. 13, pp. 263-275, Jan. 2008. (IF=3.308)

  • 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. (IF=3.781)

  • 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. (IF=3.308)

  • 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. (IF=3.308)

  • 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. (IF=3.308)

 

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. (IF=5.039)

  • 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. (IF=7.617)

  • 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. (IF=4.894)

  • 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. (IF=0.611)

 

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. (IF=6.495)

 

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. (IF=2.911)

  • 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. (IF=5.991)

  • 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. (IF=8.318)

  • 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. (IF=2.553)

 

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. (IF=3.142)

  • 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. (IF=3.142)

  • 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. (IF=1.096)

  • 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

 

 

 


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