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)

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)

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)

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)

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)

GIST: A Gibbs sampler to identify intracellular signal transduction pathways. - Jinghua Gu; Chen Wang 001; Ie-Ming Shih; Tian-Li Wang; Yue Wang 021; Robert Clarke; Jianhua Xuan (EMBC, 2011)

Detecting aberrant signal transduction pathways from high-throughput data using GIST algorithm. - Jinghua Gu; Jianhua Xuan; Chen Wang 001; Li Chen 018; Tian-Li Wang; Ie-Ming Shih (CIBCB, 2012)

Reconstruction of Transcription Regulatory Networks by Stability-Based Network Component Analysis. - Xi Chen 056; Chen Wang 001; Ayesha N. Shajahan; Rebecca B. Riggins; Robert Clarke; Jianhua Xuan (ISBRA, 2012)

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)

Regulatory component analysis: A semi-blind extraction approach to infer gene regulatory networks with imperfect biological knowledge. - Chen Wang 001; Jianhua Xuan; Ie-Ming Shih; Robert Clarke; Yue Joseph Wang (Signal Process., 2012)

Reconstruction of Transcriptional Regulatory Networks by Stability-Based Network Component Analysis. - Xi Chen 056; Jianhua Xuan; Chen Wang 001; Ayesha N. Shajahan; Rebecca B. Riggins; Robert Clarke (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

RVboost: RNA-seq variants prioritization using a boosting method. - Chen Wang 001; Jaime I. Dávila; Saurabh Baheti; Aditya Bhagwate; Xue Wang; Jean-Pierre A. Kocher; Susan L. Slager; Andrew L. Feldman; Anne J. Novak; James R. Cerhan; E. Aubrey Thompson; Yan W. Asmann (Bioinform., 2014)

PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data. - Chen Wang 001; Jared Evans; Aditya Bhagwate; Naresh Prodduturi; Vivekananda Sarangi; Mridu Middha; Hugues Sicotte; Peter T. Vedell; Steven N. Hart; Gavin R. Oliver; Jean-Pierre A. Kocher; Matthew J. Maurer; et al. (Bioinform., 2014)

Building an i2b2-Based Integrated Data Repository for Cancer Research: A Case Study of Ovarian Cancer Registry. - Na Hong; Zheng Li; Richard C. Kiefer; Melissa S. Robertson; Ellen L. Goode; Chen Wang 001; Guoqian Jiang (DMAH@VLDB, 2016)

Unraveling complex local genomic rearrangements from long-read data. - Zachary D. Stephens; Ravishankar K. Iyer; Chen Wang 001; Jean-Pierre A. Kocher (BIBM, 2017)

Building a Research-Quality Copy Number Variation Data Repository for Translational Research. - Chen Wang 001; Raymond M. Moore; Jared Evans; Xiao-Nan Hou; S. John Weroha; Guoqian Jiang (Poly/DMAH@VLDB, 2018)

Detection and visualization of complex structural variants from long reads. - Zachary Stephens; Chen Wang 001; Ravishankar K. Iyer; Jean-Pierre A. Kocher (BMC Bioinform., 2018)

Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models. - Nicholas B. Larson; Chen Wang 001; Jie Na; Ross A. Rowsey; William Edward Highsmith; Nicole L. Hoppman; Jean-Pierre A. Kocher; Eric W. Klee (J. Comput. Biol., 2018)

Extracting Patient Genetic Information from Unstructured Clinical Notes. - Yiqing Zhao; Hanzhong Yu; Luke A. Carlson; Feichen Shen; Sunyang Fu; Hongfang Liu; Chen Wang 001 (AMIA, 2020)

Coverage Profile Correction of Shallow-Depth Circulating Cell-Free DNA Sequencing via Multi-Distance Learning. - Nicholas B. Larson; Melissa C. Larson; Jie Na; Carlos P. Sosa; Chen Wang 001; Jean-Pierre A. Kocher; Ross A. Rowsey (PSB, 2020)

Excerno: Filtering Mutations Caused by the Clinical Archival Process in Sequencing Data. - Audrey Mitchell; Marco Ruiz; Soua Yang; Chen Wang 001; Jaime I. Dávila (ICCABS, 2021)

POKR: Building a Computable Heterogeneous Knowledge Resource for Precision Oncology. - Yanbo Guo; Chen Wang 001; Raymond M. Moore; Hongfang Liu; Feichen Shen (MedInfo, 2021)

Comparisons of Graph Neural Networks on Cancer Classification Leveraging a Joint of Phenotypic and Genetic Features. - David Oniani; Chen Wang 001; Yiqing Zhao; Andrew Wen; Hongfang Liu; Feichen Shen (CoRR, 2021)

Leveraging a Joint of Phenotypic and Genetic Features on Cancer Patient Subgrouping. - David Oniani; Chen Wang 001; Yiqing Zhao; Andrew Wen; Hongfang Liu; Feichen Shen (CoRR, 2021)

Modeling cancer clinical trials using HL7 FHIR to support downstream applications: A case study with colorectal cancer data. - Nansu Zong; Daniel J. Stone; Deepak K. Sharma; Andrew Wen; Chen Wang 001; Yue Yu; Ming Huang 006; Sijia Liu 002; Hongfang Liu; Qian Shi; Guoqian Jiang (Int. J. Medical Informatics, 2021)

Generating real-world evidence from unstructured clinical notes to examine clinical utility of genetic tests: use case in BRCAness. - Yiqing Zhao; Saravut J. Weroha; Ellen L. Goode; Hongfang Liu; Chen Wang 001 (BMC Medical Informatics Decis. Mak., 2021)

Semi-Supervised Topological Analysis for Elucidating Hidden Structures in High-Dimensional Transcriptome Datasets. - Tianshu Feng; Jaime I. Dávila; Yuanhang Liu; Sangdi Lin; Shuai Huang 001; Chen Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Leveraging a pharmacogenomics knowledgebase to formulate a drug response phenotype terminology for genomic medicine. - Yiqing Zhao; Matthew Brush; Chen Wang 001; Alex H. Wagner; Hongfang Liu; Robert R. Freimuth (Bioinform., 2022)

Batch-effect correction with sample remeasurement in highly confounded case-control studies. - Hanxuan Ye; Xianyang Zhang; Chen Wang 001; Ellen L. Goode; Jun Chen (Nat. Comput. Sci., 2023)

Excerno: Using Mutational Signatures in Sequencing Data to Filter False Variants Caused by Clinical Archival. - Audrey Mitchell; Marco Ruiz; Soua Yang; Chen Wang 001; Jaime I. Dávila (J. Comput. Biol., 2023)

Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup. - Nephi A. Walton; Radhakrishnan Nagarajan; Chen Wang 001; Murat Sincan; Robert R. Freimuth; David B. Everman; Derek C. Walton; Scott P. McGrath; Dominick J. Lemas; Panayiotis V. Benos; Alexander V. Alekseyenko; Qianqian Song; et al. (J. Am. Medical Informatics Assoc., 2024)