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ORCIDEric P. Hoffman
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2010 – 2019
- 2015
[j25]Ye Tian, Bai Zhang, Eric P. Hoffman
, Robert Clarke, Zhen Zhang, Ie-Ming Shih, Jianhua Xuan, David M. Herrington, Yue Joseph Wang:
KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring. Bioinform. 31(2): 287-289 (2015)- 2014
- [j24]Ye Tian, Bai Zhang, Eric P. Hoffman, Robert Clarke, Zhen Zhang, Ie-Ming Shih, Jianhua Xuan, David M. Herrington, Yue Joseph Wang:
Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks. BMC Syst. Biol. 8: 87 (2014) - [c17]Yinxue Wang, Luca Bello, Yue Wang, Craig M. McDonald, Eric P. Hoffman, Guoqiang Yu:
Predicting age at loss of ambulation in Duchenne muscular dystrophy with deep phenotypic measures. GlobalSIP 2014: 1344-1347 - 2013
- [j23]Niya Wang, Fan Meng, Li Chen, Subha Madhavan, Robert Clarke, Eric P. Hoffman, Jianhua Xuan, Yue Joseph Wang:
The CAM software for nonnegative blind source separation in R-Java. J. Mach. Learn. Res. 14(1): 2899-2903 (2013) - 2012
- [j22]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) - 2011
- [j21]Guoqiang Yu, Huai Li, Sook S. Ha, Ie-Ming Shih, Robert Clarke, Eric P. Hoffman, Subha Madhavan, Jianhua Xuan, Yue Joseph Wang:
PUGSVM: a caBIGTM analytical tool for multiclass gene selection and predictive classification. Bioinform. 27(5): 736-738 (2011) - [j20]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. Bioinform. 27(7): 1036-1038 (2011) - [j19]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 Bioinform. 12: 82 (2011) - 2010
- [j18]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. Bioinform. 26(11): 1416-1422 (2010) - [j17]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 Bioinform. 11: 162 (2010) - [j16]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. J. Mach. Learn. Res. 11: 2141-2167 (2010) - [c16]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
2000 – 2009
- 2009
- [j15]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. Bioinform. 25(4): 526-532 (2009) - [j14]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. Int. J. Comput. Biol. Drug Des. 2(1): 1-20 (2009) - [j13]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. Int. J. Data Min. Bioinform. 3(4): 365-381 (2009) - [j12]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) - 2008
- [j11]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 Bioinform. 9 (2008) - [j10]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 Bioinform. 9(S-1) (2008) - [j9]Yitan Zhu, Huai Li, David J. Miller, Zuyi Wang, Jianhua Xuan, Robert Clarke, Eric P. Hoffman, Yue Joseph Wang:
caBIGTM VISDA: Modeling, visualization, and discovery for cluster analysis of genomic data. BMC Bioinform. 9 (2008) - [c15]Chen Wang, Jianhua Xuan, Li Chen, Eric P. Hoffman, Robert Clarke:
Reliability Analysis of Transcriptional Regulatory Networks. BCBGC 2008: 42-48 - [c14]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 - [c13]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 - [c12]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 - [c11]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 - [c10]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 - 2007
- [j8]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. Bioinform. Syst. Biol. 2007 (2007) - [c9]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 - [c8]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 - 2006
- [j7]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. Bioinform. 22(6): 755-761 (2006) - [j6]Jinwook Seo, Heather Gordish-Dressman, Eric P. Hoffman:
An interactive power analysis tool for microarray hypothesis testing and generation. Bioinform. 22(7): 808-814 (2006) - [j5]Jinwook Seo, Eric P. Hoffman:
Probe set algorithms: is there a rational best bet? BMC Bioinform. 7: 395 (2006) - [c7]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 - [c6]Yitan Zhu, Zuyi Wang, Yuanjian Feng, Jianhua Xuan, David J. Miller, Eric P. Hoffman, Yue Wang:
Phenotypic-Specific Gene Module Discovery using a Diagnostic Tree and caBIGTM VISDA. EMBC 2006: 5767-5770 - [c5]Ting Gong, Yitan Zhu, Jianhua Xuan, Huai Li, Robert Clarke, Eric P. Hoffman, Yue Wang:
Latent Variable and nICA Modeling of Pathway Gene Module Composite. EMBC 2006: 5872-5875 - 2005
- [c4]Jianhua Xuan, Eric P. Hoffman, Robert Clarke, Yue Joseph Wang:
Normalization of Microarray Data by Iterative Nonlinear Regression. BIBE 2005: 267-270 - [p1]Jianhua Xuan, Yibin Dong, Javed I. Khan, Robert Clarke, Eric P. Hoffman, Yue Wang:
Gene Selection by Weighted Fisher criterion for Multiclass Prediction. Advances in Bioinformatics and Its Applications 2005 - 2004
- [j4]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. Bioinform. 20(16): 2534-2544 (2004) - [j3]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 Res. 32(Database-Issue): 578-581 (2004) - [c3]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 - 2003
- [c2]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 - 2002
- [j2]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 Bioinform. 3: 4 (2002) - [j1]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 Bioinform. 3: 33 (2002)
1990 – 1999
- 1994
- [c1]Dhiraj K. Pathak, Eric P. Hoffman, Mark W. Perlin:
Intelligent DNA-Based Molecular Diagnostics Using Linked Genetic Markers. ISMB 1994: 331-339
Coauthor Index
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