Inference of Gene Regulatory Networks from Time Course Gene Expression Data Using Neural Networks and Swarm Intelligence. - Habtom W. Ressom; Yuji Zhang 001; Jianhua Xuan; Yue Joseph Wang; Robert Clarke (CIBCB, 2006)

Inferring Network Interactions Using Recurrent Neural Networks and Swarm Intelligence. - Habtom W. Ressom; Yuji Zhang 001; Jianhua Xuan; Yue Wang 021; Robert Clarke (EMBC, 2006)

Reverse Engineering Module Networks by PSO-RNN Hybrid Modeling. - Yuji Zhang 001; Jianhua Xuan; Benildo de los Reyes; Robert Clarke; Habtom W. Ressom (BIOCOMP, 2008)

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data. - Yuji Zhang 001; Jianhua Xuan; Benildo de los Reyes; Robert Clarke; Habtom W. Ressom (BMC Bioinform., 2008)

Module-based biomarker discovery in breast cancer. - Yuji Zhang 001; Jianhua Jason Xuan; Robert Clarke; Habtom W. Ressom (BIBM, 2010)

Optimizing semantic MEDLINE for translational science studies using semantic web technologies. - Cui Tao; Yuji Zhang 001; Guoqian Jiang; Matt-Mouley Bouamrane; Christopher G. Chute (MIX-HS, 2012)

Identification of aberrant pathways and network activities from high-throughput data. - Jinlian Wang; Yuji Zhang 001; Catalin Marian; Habtom W. Ressom (Briefings Bioinform., 2012)

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. - Yan W. Asmann; Sumit Middha; Asif Hossain; Saurabh Baheti; Ying Li; High-Seng Chai; Zhifu Sun; Patrick H. Duffy; Ahmed A. Hadad; Asha A. Nair; Xiaoyu Liu; Yuji Zhang 001; et al. (Bioinform., 2012)

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. - Zhifu Sun; Saurabh Baheti; Sumit Middha; Rahul Kanwar; Yuji Zhang 001; Xing Li; Andreas S. Beutler; Eric W. Klee; Yan W. Asmann; E. Aubrey Thompson; Jean-Pierre A. Kocher (Bioinform., 2012)

An integrative computational approach to identify disease-specific networks from PubMed literature information. - Yuji Zhang 001; Dingcheng Li; Cui Tao; Feichen Shen; Hongfang Liu (BIBM, 2013)

Analysis of Vaccine-related Networks using Semantic MEDLINE and the Vaccine Ontology. - Yuji Zhang 001; Cui Tao; Yongqun He; Pradip Kanjamala; Hongfang Liu (VDOS+DO@ICBO, 2013)

Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. - Yuji Zhang 001; Cui Tao; Yongqun He; Pradip Kanjamala; Hongfang Liu (J. Biomed. Semant., 2013)

Module-based breast cancer classification. - Yuji Zhang 001; Jianhua Xuan; Robert Clarke; Habtom W. Ressom (Int. J. Data Min. Bioinform., 2013)

Calculating Sample Size Estimates for RNA Sequencing Data. - Steven N. Hart; Terry M. Therneau; Yuji Zhang 001; Gregory A. Poland; Jean-Pierre A. Kocher (J. Comput. Biol., 2013)

Linked Vaccine Adverse Event Data Representation from VAERS for Biomedical Informatics Research. - Cui Tao; Puqiang Wu; Yuji Zhang 001 (PAKDD Workshops, 2014)

Linked vaccine adverse event data from VAERS for biomedical data analysis and longitudinal studies. - Cui Tao; Puqiang Wu; Yi Luo; Yuji Zhang 001 (BioData Min., 2014)

Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network. - Yuji Zhang 001; Cui Tao; Guoqian Jiang; Asha A. Nair; Jian Su; Christopher G. Chute; Hongfang Liu (J. Biomed. Semant., 2014)

Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge. - Yuji Zhang 001 (BioData Min., 2015)

Next generation informatics for big data in precision medicine era. - Yuji Zhang 001; Qian Zhu 003; Hongfang Liu (BioData Min., 2015)

Identification of sex-associated network patterns in Vaccine-Adverse Event Association Network in VAERS. - Yuji Zhang 001; Puqiang Wu; Yi Luo; Cui Tao (J. Biomed. Semant., 2015)

Adverse event detection by integrating twitter data and VAERS. - Junxiang Wang; Liang Zhao 002; Yanfang Ye 001; Yuji Zhang 001 (J. Biomed. Semant., 2018)

A statistical analysis of vaccine-adverse event data. - Jian-Jian Ren; Tingni Sun; Yongqun He; Yuji Zhang 001 (BMC Medical Informatics Decis. Mak., 2019)

Knowledge Graph-based Neurodegenerative Diseases and Diet Relationship Discovery. - Yi Nian; Jingcheng Du; Larry Bu; Fang Li 011; Xinyue Hu 002; Yuji Zhang 001; Cui Tao (CoRR, 2021)

Mining on Alzheimer's diseases related knowledge graph to identity potential AD-related semantic triples for drug repurposing. - Yi Nian; Xinyue Hu 002; Rui Zhang 028; Jingna Feng; Jingcheng Du; Fang Li 011; Larry Bu; Yuji Zhang 001; Yong Chen 016; Cui Tao (BMC Bioinform., 2022)