Intelligent DNA-Based Molecular Diagnostics Using Linked Genetic Markers. - Dhiraj K. Pathak; Eric P. Hoffman; Mark W. Perlin (ISMB, 1994)

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

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

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

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

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

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

Gene Selection by Weighted Fisher criterion for Multiclass Prediction. - Jianhua Xuan; Yibin Dong; Javed I. Khan; Robert Clarke; Eric P. Hoffman; Yue Wang 021 (Advances in Bioinformatics and Its Applications, 2005)

Normalization of Microarray Data by Iterative Nonlinear Regression. - Jianhua Xuan; Eric P. Hoffman; Robert Clarke; Yue Joseph Wang (BIBE, 2005)

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

Latent Variable and nICA Modeling of Pathway Gene Module Composite. - Ting Gong; Yitan Zhu; Jianhua Xuan; Huai Li; Robert Clarke; Eric P. Hoffman; Yue Wang 021 (EMBC, 2006)

Phenotypic-Specific Gene Module Discovery using a Diagnostic Tree and caBIGTM VISDA. - Yitan Zhu; Zuyi Wang; Yuanjian Feng; Jianhua Xuan; David J. Miller 001; Eric P. Hoffman; Yue Wang 021 (EMBC, 2006)

An interactive power analysis tool for microarray hypothesis testing and generation. - Jinwook Seo; Heather Gordish-Dressman; Eric P. Hoffman (Bioinform., 2006)

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

Probe set algorithms: is there a rational best bet? - Jinwook Seo; Eric P. Hoffman (BMC Bioinform., 2006)

Stability-Based Dimension Estimation of ICA with Application to Microarray Data Analysis. - Chen Wang 001; Jianhua Xuan; Ting Gong; Robert Clarke; Eric P. Hoffman; Yue Joseph Wang (BIOCOMP, 2007)

Biomarker Identification by Knowledge-Driven Multi-Level ICA and Motif Analysis. - Li Chen 018; Chen Wang 001; Ie-Ming Shih; Tian-Li Wang; Zhen Zhang; Yue Joseph Wang; Robert Clarke; Eric P. Hoffman; Jianhua Xuan (ICMLA, 2007)

Gene Selection for Multiclass Prediction by Weighted Fisher Criterion. - Jianhua Xuan; Yue Joseph Wang; Yibin Dong; Yuanjian Feng; Bin Wang 064; Javed I. Khan; Marina Bakay; Zuyi Wang; Lauren Pachman; Sara Winokur; Yi-Wen Chen; Robert Clarke; et al. (EURASIP J. Bioinform. Syst. Biol., 2007)

Reliability Analysis of Transcriptional Regulatory Networks. - Chen Wang 001; Jianhua Xuan; Li Chen 018; Eric P. Hoffman; Robert Clarke (BCBGC, 2008)

Inferring Condition-Specific miRNA-Gene Modules from miRNA and mRNA Profiling Data. - Jianghui Xiong; Chen Wang 001; Bai Zhang; Yue Joseph Wang; Eric P. Hoffman; Robert Clarke; Jianhua Xuan (BCBGC, 2008)

Identification of Condition-specific Regulatory Modules by Multi-level Motif and mRNA Expression Analysis. - Li Chen 018; Jianhua Xuan; Rebecca B. Riggins; Yue Joseph Wang; Eric P. Hoffman; Robert Clarke (BIOCOMP, 2008)

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

Sparse Decomposition of Gene Expression Data to Infer Transcriptional Modules Guided by Motif Information. - Ting Gong; Jianhua Xuan; Li Chen 018; Rebecca B. Riggins; Yue Joseph Wang; Eric P. Hoffman; Robert Clarke (ISBRA, 2008)

Integrative Network Component Analysis for Regulatory Network Reconstruction. - Chen Wang 001; Jianhua Xuan; Li Chen 018; Po Zhao; Yue Joseph Wang; Robert Clarke; Eric P. Hoffman (ISBRA, 2008)

Knowledge-guided multi-scale independent component analysis for biomarker identification. - Li Chen 018; Jianhua Xuan; Chen Wang 001; Ie-Ming Shih; Yue Joseph Wang; Zhen Zhang; Eric P. Hoffman; Robert Clarke (BMC Bioinform., 2008)

Motif-directed network component analysis for regulatory network inference. - Chen Wang 001; Jianhua Xuan; Li Chen 018; Po Zhao; Yue Joseph Wang; Robert Clarke; Eric P. Hoffman (BMC Bioinform., 2008)

caBIGTM VISDA: Modeling, visualization, and discovery for cluster analysis of genomic data. - Yitan Zhu; Huai Li; David J. Miller 001; Zuyi Wang; Jianhua Xuan; Robert Clarke; Eric P. Hoffman; Yue Joseph Wang (BMC Bioinform., 2008)

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

Identification of condition-specific regulatory modules through multi-level motif and mRNA expression analysis. - Li Chen 018; Jianhua Xuan; Yue Joseph Wang; Eric P. Hoffman; Rebecca B. Riggins; Robert Clarke (Int. J. Comput. Biol. Drug Des., 2009)

Biomarker identification by knowledge-driven multilevel ICA and motif analysis. - Li Chen 018; Jianhua Xuan; Chen Wang 001; Yue Joseph Wang; Ie-Ming Shih; Tian-Li Wang; Zhen Zhang; Robert Clarke; Eric P. Hoffman (Int. J. Data Min. Bioinform., 2009)

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

Multilevel support vector regression analysis to identify condition-specific regulatory networks. - Li Chen 018; Jianhua Xuan; Rebecca B. Riggins; Yue Joseph Wang; Eric P. Hoffman; Robert Clarke (Bioinform., 2010)

Knowledge-guided gene ranking by coordinative component analysis. - Chen Wang 001; Jianhua Xuan; Huai Li; Yue Joseph Wang; Ming Zhan; Eric P. Hoffman; Robert Clarke (BMC Bioinform., 2010)

Matched Gene Selection and Committee Classifier for Molecular Classification of Heterogeneous Diseases. - Guoqiang Yu; Yuanjian Feng; David J. Miller 001; Jianhua Xuan; Eric P. Hoffman; Robert Clarke; Ben Davidson; Ie-Ming Shih; Yue Joseph Wang (J. Mach. Learn. Res., 2010)

PUGSVM: a caBIGTM analytical tool for multiclass gene selection and predictive classification. - Guoqiang Yu; Huai Li; Sook Shin Ha; Ie-Ming Shih; Robert Clarke; Eric P. Hoffman; Subha Madhavan; Jianhua Xuan; Yue Joseph Wang (Bioinform., 2011)

DDN: a caBIG® analytical tool for differential network analysis. - 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 (Bioinform., 2011)

Motif-guided sparse decomposition of gene expression data for regulatory module identification. - Ting Gong; Jianhua Xuan; Li Chen 018; Rebecca B. Riggins; Huai Li; Eric P. Hoffman; Robert Clarke; Yue Joseph Wang (BMC Bioinform., 2011)

Computational analysis of muscular dystrophy sub-types using a novel integrative scheme. - Chen Wang 001; Sook Shin Ha; Jianhua Xuan; Yue Joseph Wang; Eric P. Hoffman (Neurocomputing, 2012)

The CAM software for nonnegative blind source separation in R-Java. - Niya Wang; Fan Meng; Li Chen 018; Subha Madhavan; Robert Clarke; Eric P. Hoffman; Jianhua Xuan; Yue Joseph Wang (J. Mach. Learn. Res., 2013)

Predicting age at loss of ambulation in Duchenne muscular dystrophy with deep phenotypic measures. - Yinxue Wang; Luca Bello; Yue Wang 021; Craig M. McDonald; Eric P. Hoffman; Guoqiang Yu (GlobalSIP, 2014)

Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks. - Ye Tian; Bai Zhang; Eric P. Hoffman; Robert Clarke; Zhen Zhang; Ie-Ming Shih; Jianhua Xuan; David M. Herrington; Yue Joseph Wang (BMC Syst. Biol., 2014)

KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring. - Ye Tian; Bai Zhang; Eric P. Hoffman; Robert Clarke; Zhen Zhang; Ie-Ming Shih; Jianhua Xuan; David M. Herrington; Yue Joseph Wang (Bioinform., 2015)