
Journal Papers (PDF copy available upon request) 
Submitted manuscripts

Leena HilakiviClarke, A. Warri, X. Zhang, KL Cook, J. Lu, A. Zwart, N. Nguyen, R. Hu, KB Bouker, MI Cruz, S. de Assis, X. Wang, J. Xuan, Y. Wang, B. Wehrenberg, and R. Clarke, "Epigenetic preprogramming of tamoxifen resistance," Nature Communications, 2015.

Yitan Zhu, Niya Wang, David J. Miller, and Yue Wang, "Convex analysis of mixtures for separating nonnegative wellgrounded sources," IEEE Trans Neural Networks and Learning Systems, 2014. (IF=4.291) R1 submitted

Afaf Tareef, Yang Song, Weidong Cai, Heng Huang,
Hang Chang, Yue Wang, Dagan Feng, "Superpixel and contour based nuclei and
cytoplasm segmentation of overlapping cervical cells," IEEE Journal on Biomedical and Health Informatics, 2015.

Moxi Zhou, Vani Pariyadath, ChiungTing Wu, Colin A. Hodgkinson, Guoqiang Yu, Yue Wang, David Goldman, and Elliot A. Stein, "Early life stress interacts with monoaminergic genes to increase risk for nicotine addiction," Genes Brain Behavior, 2015. (IF=3.661) to be submitted

Hui Zhang, Tao Liu, Zhen Zhang, Samuel H Payne, Bai Zhang, Jason E McDermott, JianYing Zhou, Vladislav A Petyuk, Li Chen, Debjit Ray, Shisheng Sun, Feng Yang, Lijun Chen, Jing Wang, Punit Shah, Seong Won Cha, Paul Aiyetan, Sunghee Woo, Yuan Tian, Marina A Gritsenko, Caitlin Choi, Matthew E Monroe, Stefani Thomas, Ronald J Moore, KunHsing Yu, David L Tabb, David Fenyo, Vineet Bafna, Yue Wang, Henry Rodriguez, Emily S Boja, Tara Hiltke, Robert C Rivers, Lori Sokoll, Heng Zhu, IeMing Shih, Akhilesh Pandey, Bing Zhang, Michael P Snyder, Douglas A Levine, Richard D Smith, Daniel W Chan, Karin D Rodland, and the CPTAC investigators, "Deep proteogenomic characterization of human ovarian cancer," Nature, 2015. (IF=41.456) R2 submitted
Year 2015

Niya Wang, Ting Gong, Robert Clarke, Lulu Chen, IeMing 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, vol. 31, pp. 137139, 2015.

Ye Tian, Bai Zhang, Eric P. Hoffman, Robert Clarke, Zhen Zhang, IeMing Shih, Jianhua Xuan, David M. Herrington, and Yue Wang, "KDDN: An opensource Cytoscape app for constructing differential dependency networks with significant rewiring," Bioinformatics, vol. 31, pp. 287298, 2015.

X. Shi, R. O. Barnes, L. Chen, A. N. ShajahanHaq, L. HilakiviClarke, R. Clarke, Y. Wang, J. Xuan*, "BMRFNet: a software tool for identification of protein interaction subnetworks by a bagging Markov random fieldbased method," Bioinformatics, 31(14):24122414, 2015. (IF=4.621; 2014 ISI)

X. Shi, X. Wang, A. Shajahan, L. HilakiviClarke, R. Clarke and J. Xuan* , "BMRFMI: integrative identification of protein interaction network by modeling the gene dependency," BMC Genomics , 16(Suppl 7):S10, 2015. (IF=3.986; 2014 ISI)

Y. Kobayashi, H. Kashima, R.C. Wu, J.G. Jung, J.C. Kuan, J. Gu, J. Xuan, L. Sokoll, K. Visvanathan, I.M. Shih, T.L. Wang, "Mevalonate pathway antagonist inhibits proliferation of serous tubal intraepithelial carcinoma and ovarian carcinoma in mouse models," Clinical Cancer Research , Published OnlineFirst June 24, 2015; doi: 10.1158/10780432.CCR143368. (IF=8.722; 2014 ISI)

Y. Liu, L. HilakiviClarke, Y. Zhang, X. Wang, Y. Pan, J. Xuan, S. Fleck, D. Doerge, W. Helferich, "Isoflavones in soy flour diet have different effects on wholegenome expression patterns than purified isoflavone mix in human MCF7 breast tumors in ovariectomized athymic nude mice," Molecular Nutrition and Food Research, 2015. doi: 10.1002/mnfr.201500028. [Epub ahead of print] (IF=4.909; 2013 ISI)

Yang Song, Weidong Cai, Heng Huang, Yun Zhou, David Dagan
Feng, Yue Wang, Michael J. Fulham, and Mei Chen, "Large margin local estimate with applications to medical image classification," IEEE Trans Medical Imaging, 2015. (IF=3.799) accepted

Yang Song, Weidong Cai, Heng Huang, Yun Zhou, Yue Wang, David Dagan Feng, "Localityconstrained subcluster representation
ensemble for lung image classication," Medical Image Analysis, 2015. (IF=3.681) accepted

Mohammad R. Nezami Ranjbar, Cristina Di Poto, Yue Wang and Habtom W. Ressom, "SIMAT: GCSIMMS analysis tool," BMC Bioinformatics, 2015. accepted

Mohammad R. Nezami Ranjbar, Mahlet G. Tadesse, Yue Wang, and Habtom W. Ressom, "Bayesian Normalization Model for Labelfree
Quantitative Analysis by LCMS," IEEE/ACM Trans Computational Biology and Bioinformatics, 2015. in press

ArulMurugan Ambikapathi, TsungHan Chan, ChiaHsiang Lin, FeiShih Yang, ChongYung Chi, and Yue Wang, "Accurate compartmental pharmacokinetic analysis for prostate tumor characterization using DCEMRI," IEEE Trans. Biomedical Engineering, 2015. accepted

Yi Fu, Guoqiang Yu, Douglas A. Levine, Niya Wang, IeMing Shih, Zhen Zhang, Robert Clarke and Yue Wang, "BACOM2.0 facilitates absolute normalization and quantification of somatic copy number alterations in heterogeneous tumor," Scientific Reports, 5, 13955; doi: 10.1038/srep13955, 2015. (IF=5.578)

Niya Wang, Eric P Hoffman, Lulu Chen, Li Chen, Zhen Zhang, Chunyu Liu, Guoqiang Yu, David M Herrington, Robert Clarke and Yue Wang, "Mathematical modelling of transcriptional heterogeneity identifies novel markers and subpopulations in complex tissues," Scientific Reports, 2015. (IF=5.578) Accepted
Year 2014

J. Gu, X. Wang, L. HalakiviClarke, R. Clarke, and J. Xuan*, "BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNASeq data," BMC Bioinformatics, 15(Suppl 9):S6, 2014. (IF=2.67)

B Zhang, X Hou, X Yuan, IM 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, 431433, 2014. (IF=5.323; 2012 ISI)

B. Zhang, Y. Tian, Z. Zhang, "Network Biology in Medicine and Beyond," Circulation: Cardiovascular Genetics, 7: 536547, 2014. (IF=6.105; 2012 ISI)

Y. Tian, S. Wang, Z. Zhang, O.C. Rodriguez, E. Petricoin III, IM 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, vol. 11, no. 6, pp. 10091019, 2014.

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, vol. 9, no. 11, e112143, 2014.

Sherry Dadgar, Zuyi Wang, Helen Johnston, Akanchha Kesari, Kanneboyina Nagaraju, YiWen 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, vol. 207, pp. 139158, 2014. (IF=10.822; 2012 ISI)

Ye Tian, Bai Zhang, Eric P. Hoffman, Robert Clarke, Zhen Zhang, IeMing Shih, Jianhua Xuan, David M. Herrington, and Yue Wang, "Knowledgefused differential dependency network
models for detecting significant rewiring in biological
networks," BMC Systems Biology, 2014, 8:87, doi:10.1186/s12918014008712014.

Yiming Zuo, Guoqiang Yu, Mahlet G. Tadesse, Habtom W. Ressom, "Biological network inference using low order partial correlation," Methods, vol. 69, no. 3, pp. 266273, 2014.
Year 2013

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

TH Tsai, M G. Tadesse, C Di Poto, L K. Pannell, Y Mechref, Y. Wang, and H W. Ressom, "Multiprofile Bayesian alignment model for LCMS data analysis with integration of internal standards," Bioinformatics, vol. 29, no. 21, 27742780, 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 RJava," Journal of Machine Learning Research, 14 (2013) 28992903, 2013. (5year IF=4.284, 2011 ISI)

Y. Song, W. Cai, H. Huang, Y. Wang, D. Feng, and M. Chen, "Regionbased 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, IM Shih, and Y. Wang,
"Genomic and network analysis to study origin of ovarian cancer," Systems Biomedicine, 1:1, 6271, 2013.

TH Tsai, M. G. Tadesse, Y. Wang, H. W. Ressom,
"Profilebased LCMS data alignment: a Bayesian approach," IEEE/ACM Trans Computational Biology and Bioinformatics, vol. 10, no. 2, 494503, 2013. (5year 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. 312318, Feb. 2013. (IF=5.224)

X. Shi, J. Gu, X. Chen, A. N. Shajahan, L. HilakiviClarke, R. Clarke, and J. Xuan*, "mAPCGibbsOS: An integrated approach for robust identification of gene regulatory networks," BMC Systems Biology, 7(Suppl 5):S4, 2013. (IF=2.853)

X. Chen, J. Xuan*, C. Wang, A. N. Shajahan, R. B. Riggins, and R. Clarke,
"Reconstruction of Transcriptional Regulatory Networks by Stabilitybased Network Component Analysis," IEEE/ACM Trans. Computational Biology and Bioinformatics, 10(6):13471358, 2013. (IF=1.536)

Y. Zhang, J. Xuan, R. Clarke, and R. Habtom, "ModuleBased Breast Cancer Classification,"
Intl J of Data Mining and Bioinformatics, 7(3):284302, 2013.

L. Chen, J. Xuan*, R. Riggins, Y. Wang, and R. Clarke,
"Identifying protein interaction subnetworks by a bagging Markov random fieldbased method," Nucleic Acids Research, 41(2):e42, 2013. (IF=8.808)
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(12):e11e17, 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 VMY1103's activity at tissue levels in an in vivo tumor model by LCMS/MS and MRI," Cell Cycle, vol. 11, no. 20, pp. 38013809, 2012. (IF=5.359)

S. de Assis, A. Warri, M. I. Cruz, O. Laja, Y. Tian, B. Zhang, Y. Wang, T. HM Huang, and L. HilakiviClarke,
"Highfat or ethinyloestradiol 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, RC Wu, G. Wu, B. Guan, J. Zhang, Y. Wang, L. Song, X. Yuan, L. Wei, R. Roden, KT Kuo, K. Nakayama, B. Clarke, P. Shaw, N. Olvera, D. Levine, R. Kurman, TL Wang, and IM Shih, "Identification of molecular pathway aberrations in uterine serous carcinoma by genomewide analyses," Journal of The National Cancer Institute, vol. 104, no. 19, pp. 15031513, 2012. (IF=13.757; 2011 ISI)

X. Yuan, G. Yu, X. Hou, IM Shih, R. Clarke, J. Zhang, E. P. Hoffman, R. R. Wang, Z. Zhang, Y. Wang*,
"Genomewide 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 Omnitomography  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):19901997, 2012. (IF=5.323)

X. Chen, M. M. Thiaville, L. Chen, A. Stoeck, J. Xuan, M. Gao, IM Shih, and TL Wang, "Definition of NOTCH3 target genes in ovarian cancer," Cancer Research, 72(9):22942303 2012. (IF=8.65)

L. Chen, Y. Tian, G. Yu, D. J. Miller, IM 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, WileyBlackwell, (Frank EmmertStreib and Matthias Dehmer, coeds.), 2012.

C. Wang, J. Xuan*, I.M. Shih, R. Clarke, and Y.
Wang, "Regulatory component analysis: a semiblind extraction approach
to infer gene regulatory networks with imperfect biological knowledge,"
Signal Processing, vol. 92, no. 8, pp. 19021915, 2012. (IF=1.851)

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. 917, 2012. (IF=1.635)

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. (5year 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. 113, 2012. (IF=1.694; 2010 ISI)
Year 2011

L Chen, TH Chan, PL Choyke, EMC Hillman, ZM
Bhujwalla, CY Chi, G Wang, Z Szabo, Y Wang*, "CAMCM: A signal
deconvolution tool for in vivo dynamic contrastenhanced imaging of
complex tissues," Bioinformatics, vol. 27, no. 18, pp. 26072609, 2011. (IF=4.877; 2010 ISI)

L. Chen, J. Xuan*, R. B. Riggins, R. Clarke, and Y. Wang,
"Identifying cancer biomarkers by networkconstrained 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,
"GDOC: A systems medicine platform for personalized oncology," Neoplasia, vol. 13, no. 9, pp. 771783, 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, TH Chan, CY Chi, G Wang, and Y
Wang*, "Tissuespecific compartmental analysis for dynamic
contrastenhanced MR imaging of complex tumors," IEEE Transactions on Medical Imaging, vol. 30, no. 12, pp. 20442058, 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. 523532, July 2011. (IF=37.178; 2010 ISI)

G Yu, B Zhang, G S Bova, J Xu, IM 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. 14731480, 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. HilakiviClarke, and Y.
Wang*, "DDN: A caBIG analytical tool for differential network analysis,"
Bioinformatics, vol. 27, no. 7, pp. 10361038, 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.736738, 2011. (IF=5.468)

T. Gong, J. Xuan*, L. Chen, R. B. Riggins, H. Li, E.
P. Hoffman, R. Clarke, and Y. Wang, "Motifguided 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 pathwaybased 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 WileyBlackwell (Claude Bouchard
and Eric P. Hoffman, coeds.), Oxford, England, Chapter 5, pp. 5869,
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. 56, pp. 395409, 2011. (IF=0.825; 2010 ISI)

X. Yuan, J. Zhang, and Y. Wang, "Mutual information
and linkage disequilibrium based SNP association study by grouping
casecontrol," Genes & Genomics, vol. 33, no. 1, pp. 6573, 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 HilakiviClarke, "Endoplasmic reticulum stress, the unfolded protein response,
and gene network modeling in antiestrogen resistant
breast cancer,"
Horm Mol Biol Clin Invest, 5:3544, 2011.
Year 2010

X. Yuan, J. Zhang, and Y. Wang, "Probability theorybased SNP association study method for identifying susceptibility loci and genetic disease models in human casecontrol 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, IM Shih, and Y. Wang*, "Matched gene selection and committee classifier for molecular classification of heterogeneous diseases,"
Journal of Machine Learning Research, 11:21412167, 2010. (5year IF=4.04)

L. Chen, J. Xuan*, R. B. Riggins, Y. Wang, E. P. Hoffman,
and R. Clarke, "Multilevel support vector regression
analysis to identify
conditionspecific regulatory networks,"
Bioinformatics, 26(11):14161422, 2010. (IF=4.877)

C. Wang, J. Xuan*, H. Li, Y. Wang, M. Zhan, E. P. Hoffman and R. Clarke, "Knowledgeguided 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 multisource 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. 171186, Jan. 2010. (IF=3.736; 2009 ISI)

ChuChuan Liu, ShihChung Ben Lo, Matthew T Freedman, Marvin E Lasser, John Kula, Anita Sarcone, and Yue Wang*, "Cscan Ultrasound Imaging with a CMOSbased Piezoelectric Sensing Array: A Comparative Study of Foreign Object Detection in Soft Tissue," Frontiers in Bioscience, vol. E2, pp. 241249, Jan. 2010. (IF=3.736; 2009 ISI)

FaYu Wang, ChongYung Chi, TsungHan Chan, and Yue Wang, "Nonnegative leastcorrelated component analysis for separation of dependent sources by volume maximization," IEEE Trans Pattern Analysis and Machine Intelligence, vol. 32, no. 5, pp. 875887, 2010. (IF=5.308)

Bai Zhang, Huai Li, Robert Clarke, Leena HilakiviClarke, and Yue Wang, "Differential dependency network analysis to identify
topological changes in biological networks," Chapter 10, pp. 185204, Medical Biostatistics for Complex Diseases, WileyVCH Verlag GmbH & Co. KGaA, (Frank EmmertStreib and Matthias Dehmer, coeds.), Weinheim, 2010.

KuanTing Kuo, TsuiLien Mao, Xu Chen, Yuanjian Feng, Kentaro Nakayama, Yue Wang,
Ruth Glas, M. Joe Ma, Robert J. Kurman, IeMing Shih, and TianLi Wang, "DNA Copy Number Profiles in AffinityPurified Ovarian Clear Cell Carcinoma," Clinical Cancer Research, vol. 14, pp. 19972008, April 2010. (IF=7.338)

Yuanjian Feng, Guoqiang Yu, TianLi Wang, IeMing 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.315, 2010.

Y. Tao, S.H. B. Lo, M. T. Freedman, E. Makariou, and J. Xuan, "Multilevel Learningbased Segmentation of Illdefined 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 conditionspecific topological changes in biological networks," Bioinformatics, 25(4):526532, 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(12):820, 2009.

L. Chen, J. Xuan*, R. B. Riggins, Y. Wang, E. P. Hoffman, and R. Clarke, "Identification of Conditionspecific Regulatory Modules by Multilevel Motif and mRNA Expression Analysis," Intl J. of Computational Biology and Drug Design, 2(1):120, 2009.

Y. Zhang, J. Xuan, B. G. de los Reyes, R. Clarke, and H. W. Ressom, "Reverse engineering module networks by PSORNN 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 knowledgedriven multilevel ICA and motif analysis," Intl J. Data Mining and Bioinformatics, vol. 3, no. 4, pp. 365381, 2009.

WingKin Ma, TsungHan Chan, ChongYung Chi, and Yue Wang, "Convex analysis for nonnegative 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. 559565, 2009. (IF=27.136)

KuanTing Kuo, Bin Guan, Yuanjian Feng, TsuiLien Mao, Xu Chen, Natini Jinawath, Yue Wang, Robert J. Kurman, IeMing Shih, and TianLi Wang, "Analysis of DNA copy number alterations in ovarian serous tumors identifies new molecular genetic changes in lowgrade and highgrade carcinomas," Cancer Research, vol. 69, no. 9, pp. 40364042, 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):24782485, 2009. (IF=4.926)
Year
2008

S. OlivoMarston, Y. Zhu, R. Lee, A. Cabanes, G. Khan, A. Zwart, Y. Wang, R. Clarke, L. HilakiviClarke, "Gene signaling pathways mediating the opposite effects of prepubertal low and high fat n3 polyunsaturated fatty acid diets on mammary cancer risk," Cancer Prevention Res., vol. 1, no. 7, pp. 532545, Dec. 2008.

L. Chen, J. Xuan*, C. Wang, I.M. Shih, Y. Wang, Z. Zhang, E. Hoffman, and R. Clarke, "Knowledgeguided multiscale independent component analysis for biomarker identification," BMC Bioinformatics, 9:416, 2008. (IF=3.781)

R. B. Riggins, J. PJ. 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):89088917, 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 nonnegative sources," IEEE Trans. Signal Processing, vol. 56, no. 10, pp. 51205134, Oct. 2008. (IF=2.335)

J. Zhang, L. Wei, X. Feng, Z. Ma, and Y. Wang, "Pattern expression nonnegative 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 motifbased transcription factortarget gene relationships by integrating multisource 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. 119125, 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. 17191732, 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. 10231028, 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. 38393849, 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 highdimensional data spaces:
implications for exploring gene and protein expression data," Nature Reviews Cancer, vol. 8, pp. 3749, Jan. 2008. (IF=30.762)

H. Li, J. Xuan, Y. Wang, and M. Zhan, "Inferring regulatory networks," Frontiers in Bioscience, vol. 13, pp. 263275, Jan. 2008. (IF=3.308)

C. Wang, J. Xuan*, L. Chen, P. Zhao, Y. Wang, R. Clarke, and E. P. Hoffman, "Motifdirected 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. 677690, 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. 691708, 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. 12811293, 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. 349363, 2007.

W. Cong, H. Shen, A. Cong, Y. Wang, and G. Wang, "Modeling photon propagation in biological tissues using a generalized DeltaEddington 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 opensource caBIG analytical tool for data clustering and beyond," Bioinformatics, vol. 23, no. 15, pp. 20242027, 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. 1119, 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, "Nonrigid medical image registration by finite element deformable sheetcurve 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, YW 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 RbMyoD pathways in muscle regeneration," Brain, vol. 129, pp. 9961013, 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. 755761, 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. 15811589, 2006.
Year
2005

J. Xuan*, Y. Wang, Q. Zheng, and T. Adali, "Discontinuityembedded deformable models for surface reconstruction from range images," IEEE Signal Processing Letters, vol. 12, no. 12, pp. 805808, 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 JP8 jet fuel," Toxicology and Applied Pharmacology, vol. 200, pp. 93102, June 2004.

R.
Srikanchana, J. Xuan, K. Huang, M. T. Freedman, C. Nguyen,
and Y. Wang*, "Nonrigid image registration by neural
computation," Journal of VLSI Signal Processing, vol. 37, pp. 237246, JuneJuly 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. 197216, 2004.
Year
2003

Z.
Wang, Y. Wang*, J. Lu, SY 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. 255272, 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. 10491065, 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. HilakiviClarke, "Antiestrogen
resistance in breast cancer and the role of estrogen receptor
signaling," Oncogene, vol. 22, pp. 73167339, Oct. 2003. (IF=6.495)
Year
2002

SC
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. 150158, 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.
2937, 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. 11551166, 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 factor1, nucleophosmin, nuclear factor6B, and
cAMP response element binding with acquired resistance to
Faslodex (ICI 182,780)," Cancer Research, vol. 62, pp.
34283437, June 2002. (IF=8.318)

Y.
Wang*, K. Woods, and M. McClain, "InformationTheoretic
Matching of Two Point Sets," IEEE Transactions on Image
Processing, vol. 11, no. 8, pp. 868872, August 2002. (IF=2.553)
Year
2001

H.
Li, Y. Wang, KJ R. Liu, SH B. Lo, and M. T. Freedman,
"Computerized Radiographic Mass DetectionPart I: Lesion
Site Selection by Morphological Enhancement and Contextual
Segmentation," IEEE Transactions on Medical Imaging,
vol. 20, no. 4, pp. 289301, April 2001. (IF=3.142)

H.
Li, Y. Wang, KJ R. Liu, SH B. Lo, and M. T. Freedman,
"Computerized Radiographic Mass DetectionPart II:
Decision Support by Featured Database Visualization and
Modular Neural Networks," IEEE Transactions on Medical
Imaging, vol. 20, no. 4, pp. 302313, 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. 150158, 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. 391403, 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. 635646, 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. 425431,
2000.
Year
1998

Y.
Wang*, T. Adali, CM Lau, and SY Kung, "Quantitative
Analysis of MR Brain Image Sequences by Adaptive SelfOrganizing
Mixtures," Journal of VLSI Signal Processing, vol.
8, pp. 219239, 1998.

T. Adali, Y. Wang, N. Gupta, "A Blockwise Relaxation
Labeling Scheme for Edge Detection in Cardiac MR Image Sequences,"
International Journal of Imaging Science and Technology,
vol. 9, pp. 340350, 1998.

Y. Wang*, T. Adali, SY 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. 11651181, August 1998.

Y.
Wang*, SH Lin, H. Li, and SY Kung, "Data Mapping by
Probabilistic Modular Networks and Information Theoretic
Criteria," IEEE Transactions on Signal Processing,
vol. 46, no.12, pp. 33783397, December 1998.
Year
1997

Y.
Wang*, T. Adali, and SC B. Lo, "Automatic Threshold Selection
Using Histogram Quantization," Journal of Biomedical
Optics, vol. 2, no. 2, pp. 211217, 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.
34553461, December 1997.
Year
1996

Y.
Wang* and J. M. Morris, "On Numerical Verification of
TimeDomain Moment Method in Ultrasound Tomography,"
Journal of Biomedical Optics, vol. 1, no. 3, pp. 324329,
July 1996.
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