Eric P. Hoffman

Chen Wang, Sook S. Ha, Jianhua Xuan, Yue Joseph Wang, Eric P. Hoffman: Computational analysis of muscular dystrophy sub-types using a novel integrative scheme. Neurocomputing 92: 9-17 (2012)

Guoqiang Yu, Huai Li, Sook S. Ha, Ie-Ming Shih, Robert Clarke, Eric P. Hoffman, Subha Madhavan, Jianhua Xuan, Yue Joseph Wang: PUGSVM: a caBIG^TM analytical tool for multiclass gene selection and predictive classification. Bioinformatics 27(5): 736-738 (2011)

Bai Zhang, Ye Tian, Lu Jin, Huai Li, Ie-Ming Shih, Subha Madhavan, Robert Clarke, Eric P. Hoffman, Jianhua Xuan, Leena Hilakivi-Clarke, Yue Joseph Wang: DDN: a caBIG^® analytical tool for differential network analysis. Bioinformatics 27(7): 1036-1038 (2011)

Ting Gong, Jianhua Xuan, Li Chen, Rebecca B. Riggins, Huai Li, Eric P. Hoffman, Robert Clarke, Yue Joseph Wang: Motif-guided sparse decomposition of gene expression data for regulatory module identification. BMC Bioinformatics 12: 82 (2011)

Li Chen, Jianhua Xuan, Rebecca B. Riggins, Yue Joseph Wang, Eric P. Hoffman, Robert Clarke: Multilevel support vector regression analysis to identify condition-specific regulatory networks. Bioinformatics 26(11): 1416-1422 (2010)

Chen Wang, Jianhua Xuan, Huai Li, Yue Joseph Wang, Ming Zhan, Eric P. Hoffman, Robert Clarke: Knowledge-guided gene ranking by coordinative component analysis. BMC Bioinformatics 11: 162 (2010)

Guoqiang Yu, Yuanjian Feng, David J. Miller, Jianhua Xuan, Eric P. Hoffman, Robert Clarke, Ben Davidson, Ie-Ming Shih, Yue Joseph Wang: Matched Gene Selection and Committee Classifier for Molecular Classification of Heterogeneous Diseases. Journal of Machine Learning Research 11: 2141-2167 (2010)

Chen Wang, Sook S. Ha, Yue Joseph Wang, Jianhua Xuan, Eric P. Hoffman: Computational Analysis of Muscular Dystrophy Sub-types Using a Novel Integrative Scheme. ICMLA 2010: 287-292

Bai Zhang, Huai Li, Rebecca B. Riggins, Ming Zhan, Jianhua Xuan, Zhen Zhang, Eric P. Hoffman, Robert Clarke, Yue Joseph Wang: Differential dependency network analysis to identify condition-specific topological changes in biological networks. Bioinformatics 25(4): 526-532 (2009)

Li Chen, Jianhua Xuan, Yue Joseph Wang, Eric P. Hoffman, Rebecca B. Riggins, Robert Clarke: Identification of condition-specific regulatory modules through multi-level motif and mRNA expression analysis. I. J. Computational Biology and Drug Design 2(1): 1-20 (2009)

Li Chen, Jianhua Xuan, Chen Wang, Yue Joseph Wang, Ie-Ming Shih, Tian-Li Wang, Zhen Zhang, Robert Clarke, Eric P. Hoffman: Biomarker identification by knowledge-driven multilevel ICA and motif analysis. IJDMB 3(4): 365-381 (2009)

Bo Hyoung Kim, Bongshin Lee, Susan Knoblach, Eric P. Hoffman, Jinwook Seo: GeneShelf: A Web-based Visual Interface for Large Gene Expression Time-Series Data Repositories. IEEE Trans. Vis. Comput. Graph. 15(6): 905-912 (2009)

Li Chen, Jianhua Xuan, Chen Wang, Ie-Ming Shih, Yue Joseph Wang, Zhen Zhang, Eric P. Hoffman, Robert Clarke: Knowledge-guided multi-scale independent component analysis for biomarker identification. BMC Bioinformatics 9 (2008)

Chen Wang, Jianhua Xuan, Li Chen, Po Zhao, Yue Joseph Wang, Robert Clarke, Eric P. Hoffman: Motif-directed network component analysis for regulatory network inference. BMC Bioinformatics 9(S-1) (2008)

Yitan Zhu, Huai Li, David J. Miller, Zuyi Wang, Jianhua Xuan, Robert Clarke, Eric P. Hoffman, Yue Joseph Wang: caBIG^TM VISDA: Modeling, visualization, and discovery for cluster analysis of genomic data. BMC Bioinformatics 9 (2008)

Chen Wang, Jianhua Xuan, Li Chen, Eric P. Hoffman, Robert Clarke: Reliability Analysis of Transcriptional Regulatory Networks. BCBGC 2008: 42-48

Jianghui Xiong, Chen Wang, Bai Zhang, Yue Joseph Wang, Eric P. Hoffman, Robert Clarke, Jianhua Xuan: Inferring Condition-Specific miRNA-Gene Modules from miRNA and mRNA Profiling Data. BCBGC 2008: 49-55

Li Chen, Jianhua Xuan, Rebecca B. Riggins, Yue Joseph Wang, Eric P. Hoffman, Robert Clarke: Identification of Condition-specific Regulatory Modules by Multi-level Motif and mRNA Expression Analysis. BIOCOMP 2008: 23-28

Ting Gong, Jianhua Xuan, Rebecca B. Riggins, Yue Joseph Wang, Eric P. Hoffman, Robert Clarke: Exploring Transcriptional Modules Through Integrative Gene Clustering Guided by Transcription Factor Binding Information. BIOCOMP 2008: 191-197

Chen Wang, Jianhua Xuan, Li Chen, Po Zhao, Yue Joseph Wang, Robert Clarke, Eric P. Hoffman: Integrative Network Component Analysis for Regulatory Network Reconstruction. ISBRA 2008: 196-207

Ting Gong, Jianhua Xuan, Li Chen, Rebecca B. Riggins, Yue Joseph Wang, Eric P. Hoffman, Robert Clarke: Sparse Decomposition of Gene Expression Data to Infer Transcriptional Modules Guided by Motif Information. ISBRA 2008: 244-255

Jianhua Xuan, Yue Joseph Wang, Yibin Dong, Yuanjian Feng, Bin Wang, Javed I. Khan, Marina Bakay, Zuyi Wang, Lauren Pachman, Sara Winokur, Yi-Wen Chen, Robert Clarke, Eric P. Hoffman: Gene Selection for Multiclass Prediction by Weighted Fisher Criterion. EURASIP J. Bioinformatics and Systems Biology 2007 (2007)

Chen Wang, Jianhua Xuan, Ting Gong, Robert Clarke, Eric P. Hoffman, Yue Joseph Wang: Stability-Based Dimension Estimation of ICA with Application to Microarray Data Analysis. BIOCOMP 2007: 132-138

Li Chen, Chen Wang, Ie-Ming Shih, Tian-Li Wang, Zhen Zhang, Yue Joseph Wang, Robert Clarke, Eric P. Hoffman, Jianhua Xuan: Biomarker Identification by Knowledge-Driven Multi-Level ICA and Motif Analysis. ICMLA 2007: 560-566

Zuyi Wang, Yue Joseph Wang, Jianhua Xuan, Yibin Dong, Marina Bakay, Yuanjian Feng, Robert Clarke, Eric P. Hoffman: Optimized multilayer perceptrons for molecular classification and diagnosis using genomic data. Bioinformatics 22(6): 755-761 (2006)

Jinwook Seo, Heather Gordish-Dressman, Eric P. Hoffman: An interactive power analysis tool for microarray hypothesis testing and generation. Bioinformatics 22(7): 808-814 (2006)

Jinwook Seo, Eric P. Hoffman: Probe set algorithms: is there a rational best bet? BMC Bioinformatics 7: 395 (2006)

Justin Molineaux, Jianhua Xuan, Ting Gong, Yitan Zhu, Eric P. Hoffman, Robert Clarke, Yue Joseph Wang: ModVis: An information visualization tool for gene module discovery. CAINE 2006: 24-31

Jianhua Xuan, Eric P. Hoffman, Robert Clarke, Yue Joseph Wang: Normalization of Microarray Data by Iterative Nonlinear Regression. BIBE 2005: 267-270

Jinwook Seo, Marina Bakay, Yi-Wen Chen, Sara Hilmer, Ben Shneiderman, Eric P. Hoffman: Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays. Bioinformatics 20(16): 2534-2544 (2004)

Josephine Chen, Po Zhao, Donald Massaro, Linda B. Clerch, Richard R. Almon, Debra C. DuBois, William J. Jusko, Eric P. Hoffman: The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface. Nucleic Acids Research 32(Database-Issue): 578-581 (2004)

Jianhua Xuan, Yibin Dong, Javed I. Khan, Eric P. Hoffman, Robert Clarke, Yue Joseph Wang: Robust Feature Selection by Weighted Fisher Criterion for Multiclass Prediction in Gene Expression Profiling. ICPR (2) 2004: 291-294

Jinwook Seo, Marina Bakay, Po Zhao, Yi-Wen Chen, Priscilla Clarkson, Ben Shneiderman, Eric P. Hoffman: Interactive color mosaic and dendrogram displays for signal/noise optimization in microarray data analysis. ICME 2003: 461-464

Marina Bakay, Yi-Wen Chen, Rehannah H. A. Borup, Po Zhao, Kanneboyina Nagaraju, Eric P. Hoffman: Sources of variability and effect of experimental approach on expression profiling data interpretation. BMC Bioinformatics 3: 4 (2002)

Rehannah H. A. Borup, Stefano Toppo, Yi-Wen Chen, Tanya M. Teslovich, Gerolamo Lanfranchi, Giorgio Valle, Eric P. Hoffman: Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs. BMC Bioinformatics 3: 33 (2002)

Dhiraj K. Pathak, Eric P. Hoffman, Mark W. Perlin: Intelligent DNA-Based Molecular Diagnostics Using Linked Genetic Markers. ISMB 1994: 331-339