W. Jim Zheng

Publication Activity (10 Years)

Years Active: 2004-2024
Publications (10 Years): 29

Top Topics

Colorectal Cancer

Gene Expression

Medical Literature

Gpu Accelerated

Top Venues

J. Biomed. Informatics

Database J. Biol. Databases Curation

Publications

Zhao Li, Lan Lan, Yujia Zhou, Ruoxing Li, Kenneth D. Chavin, Hua Xu, Liang Li, David J. H. Shih, W. Jim Zheng
Developing deep learning-based strategies to predict the risk of hepatocellular carcinoma among patients with nonalcoholic fatty liver disease from electronic health records. J. Biomed. Informatics 152 (2024)
Tianyu Liu, Yijia Xiao, Xiao Luo, Hua Xu, W. Jim Zheng, Hongyu Zhao
Geneverse: A collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research. CoRR (2024)
Yi-Ching Tang, Rongbin Li, Jing Tang, W. Jim Zheng, Xiaoqian Jiang
SAFER: sub-hypergraph attention-based neural network for predicting effective responses to dose combinations. BMC Bioinform. 25 (1) (2024)
Shikun Wang, Zhao Li, Lan Lan, Jieyi Zhao, W. Jim Zheng, Liang Li
GPU accelerated estimation of a shared random effect joint model for dynamic prediction. Comput. Stat. Data Anal. 174 (2022)
Avisha Das, Salih Selek, Alia R. Warner, Xu Zuo, Yan Hu, Vipina Kuttichi Keloth, Jianfu Li, W. Jim Zheng, Hua Xu
Conversational Bots for Psychotherapy: A Study of Generative Transformer Models Using Domain-specific Dialogues. BioNLP@ACL (2022)
David J. H. Shih, Ruoxing Li, Peter Müller, W. Jim Zheng, Kim-Anh Do, Shiaw-Yih Lin, Scott L. Carter
CNGPLD: case-control copy-number analysis using Gaussian process latent difference. Bioinform. 38 (8) (2022)
Rashmie Abeysinghe, Yuntao Yang, Mason Bartels, W. Jim Zheng, Licong Cui
An evidence-based lexical pattern approach for quality assurance of Gene Ontology relations. Briefings Bioinform. 23 (3) (2022)
Zhao Li, Rongbin Li, Kendall J. Kiser, Luca Giancardo, W. Jim Zheng
Segmenting thoracic cavities with neoplastic lesions: a head-to-head benchmark with fully convolutional neural networks. BCB (2021)
Yejin Kim, Shuyu Zheng, Jing Tang, W. Jim Zheng, Zhao Li, Xiaoqian Jiang
Anticancer drug synergy prediction in understudied tissues using transfer learning. J. Am. Medical Informatics Assoc. 28 (1) (2021)
Yuqi Si, Jingcheng Du, Zhao Li, Xiaoqian Jiang, Timothy A. Miller, Fei Wang, W. Jim Zheng, Kirk Roberts
Deep representation learning of patient data from Electronic Health Records (EHR): A systematic review. J. Biomed. Informatics 115 (2021)
Braja Gopal Patra, Vahed Maroufy, Babak Soltanalizadeh, Nan Deng, W. Jim Zheng, Kirk Roberts, Hulin Wu
A content-based literature recommendation system for datasets to improve data reusability - A case study on Gene Expression Omnibus (GEO) datasets. J. Biomed. Informatics 104 (2020)
Yuqi Si, Jingcheng Du, Zhao Li, Xiaoqian Jiang, Timothy A. Miller, Fei Wang, W. Jim Zheng, Kirk Roberts
Deep Representation Learning of Patient Data from Electronic Health Records: A Systematic Review. AMIA (2020)
Babak Soltanalizadeh, Erika Gonzalez Rodriguez, Vahed Maroufy, W. Jim Zheng, Hulin Wu
Modelling of hypoxia gene expression for three different cancer cell lines. Int. J. Comput. Biol. Drug Des. 13 (1) (2020)
Braja Gopal Patra, Babak Soltanalizadeh, Nan Deng, Leqing Wu, Vahed Maroufy, Canglin Wu, W. Jim Zheng, Kirk Roberts, Hulin Wu, Ashraf Yaseen
An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries. Database J. Biol. Databases Curation 2020 (2020)
Yuqi Si, Jingcheng Du, Zhao Li, Xiaoqian Jiang, Timothy A. Miller, Fei Wang, W. Jim Zheng, Kirk Roberts
Deep Representation Learning of Patient Data from Electronic Health Records (EHR): A Systematic Review. CoRR (2020)
Fengbo Zheng, Jay Shi, Yuntao Yang, W. Jim Zheng, Licong Cui
A transformation-based method for auditing the IS-A hierarchy of biomedical terminologies in the Unified Medical Language System. J. Am. Medical Informatics Assoc. 27 (10) (2020)
Yang Xiang, Jun Xu, Yuqi Si, Zhiheng Li, Laila Rasmy, Yujia Zhou, Firat Tiryaki, Fang Li, Yaoyun Zhang, Yonghui Wu, Xiaoqian Jiang, W. Jim Zheng, Degui Zhi, Cui Tao, Hua Xu
Time-sensitive clinical concept embeddings learned from large electronic health records. BMC Medical Informatics Decis. Mak. (2) (2019)
Guocai Chen, Yuxi Jia, Lisha Zhu, Ping Li, Lin Zhang, Cui Tao, W. Jim Zheng
Gene fingerprint model for literature based detection of the associations among complex diseases: a case study of COPD. BMC Medical Informatics Decis. Mak. (1) (2019)
Guocai Chen, Juan Camilo Ramírez, Nan Deng, Xing Qiu, Canglin Wu, W. Jim Zheng, Hulin Wu
Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis. Database J. Biol. Databases Curation 2019 (2019)
Guocai Chen, Alex Tsoi, Hua Xu, W. Jim Zheng
Predict effective drug combination by deep belief network and ontology fingerprints. J. Biomed. Informatics 85 (2018)
Laila Rasmy, Yonghui Wu, Ningtao Wang, Xin Geng, W. Jim Zheng, Fei Wang, Hulin Wu, Hua Xu, Degui Zhi
A study of generalizability of recurrent neural network-based predictive models for heart failure onset risk using a large and heterogeneous EHR data set. J. Biomed. Informatics 84 (2018)
W. Jim Zheng, Jianhua Ruan, Hua Xu, Zhongming Zhao, Zhangdong Liu
The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work. BMC Syst. Biol. 11 (S-5) (2017)
Zhandong Liu, W. Jim Zheng, Genevera I. Allen, Yin Liu, Jianhua Ruan, Zhongming Zhao
The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools. BMC Bioinform. 18 (S-11) (2017)
Yan Zhang, Bo Zhang, W. Jim Zheng, Jijun Tang, Feng Yue
HiCComp: Multiple-level comparative analysis of Hi-C data by triplet network. BIBM (2017)
W. Jim Zheng, Guocai Chen, Lam C. Tsoi, Tingting Qin, Chia-Hua Chang, Geoffrey Bartholomeusz, Hua Xu
Developing Combination Cancer Therapy from Ontology Fingerprint Derived Gene Network. CRI (2016)
Guocai Chen, Jieyi Zhao, Trevor Cohen, Cui Tao, Jingchun Sun, Hua Xu, Elmer V. Bernstam, Andrew Lawson, Jia Zeng, Amber M. Johnson, Vijaykumar Holla, Ann M. Bailey, Humberto Lara-Guerra, Beate Litzenburger, Funda Meric-Bernstam, W. Jim Zheng
Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature. Database J. Biol. Databases Curation 2015 (2015)
Cui Tao, Jingchun Sun, W. Jim Zheng, Junjie Chen, Hua Xu
Colorectal cancer drug target prediction using ontology-based inference and network analysis. Database J. Biol. Databases Curation 2015 (2015)
Jingchun Sun, Kevin W. Zhu, W. Jim Zheng, Hua Xu
A comparative study of disease genes and drug targets in the human protein interactome. BMC Bioinform. 16 (S-5) (2015)
Liang-Chin Huang, Ergin Soysal, W. Jim Zheng, Zhongming Zhao, Hua Xu, Jingchun Sun
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. BMC Syst. Biol. 9 (S-4) (2015)
Jingchun Sun, Cui Tao, Kevin W. Zhu, W. Jim Zheng, Junjie Chen, Hua Xu
An Integrative Framework for Drug Target Prediction and Repurposing. AMIA (2014)
Cui Tao, Jingchun Sun, W. Jim Zheng, Junjie Chen, Hua Xu
Drug Target Prediction for Colorectal Cancer by Combining Ontology and Network Approaches. ICBO (2014)
W. Jim Zheng, Jingcheng Du, Jijun Tang, Cui Tao
GSO: A Semantic Web Ontology to Capture 3D Genome Structure. SWAT4LS (2014)
Guocai Chen, Jieyi Zhao, Trevor Cohen, Cui Tao, Jingchun Sun, Hua Xu, Elmer V. Bernstam, Jia Zeng, Amber M. Johnson, Vijaykumar Holla, Ann Balley, Funda Meric-Bernstam, W. Jim Zheng
Using Ontology Fingerprints to Disambiguate Gene Name Entities in the Biomedical Literature. ICBO (2014)
Jeremiah J. Shepherd, Lingxi Zhou, Yan Zhang, W. Jim Zheng, Jijun Tang
Exploring genomes with a game engine. BIBM (2013)
Jeremiah J. Shepherd, Bill Arndt, W. Jim Zheng, Yun Zhu, Jijun Tang
Exploring genomes with a game engine. FDG (2013)
Yonghui Wu, Mei Liu, W. Jim Zheng, Zhongming Zhao, Hua Xu
Ranking Gene-Drug Relationships in Biomedical Literature Using Latent Dirichlet Allocation. Pacific Symposium on Biocomputing (2012)
Tingting Qin, Lam C. Tsoi, Kellie J. Sims, Xinghua Lu, W. Jim Zheng
Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network. BMC Syst. Biol. 6 (S-3) (2012)
Lam C. Tsoi, Tingting Qin, Elizabeth H. Slate, W. Jim Zheng
Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior. BMC Bioinform. 12 (2011)
William Arndt, Thomas M. Asbury, W. Jim Zheng, Matt Mitman, Jijun Tang
Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome. BIBM Workshops (2011)
Thomas M. Asbury, Matt Mitman, Jijun Tang, W. Jim Zheng
Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome. BMC Bioinform. 11 (2010)
Lam C. Tsoi, Michael Boehnke, Richard L. Klein, W. Jim Zheng
Evaluation of genome-wide association study results through development of ontology fingerprints. Bioinform. 25 (10) (2009)
Lam C. Tsoi, Ravi Patel, Wenle Zhao, W. Jim Zheng
Text-mining approach to evaluate terms for ontology development. J. Biomed. Informatics 42 (5) (2009)
Lam C. Tsoi, W. Jim Zheng
A method of microarray data storage using array data type. Comput. Biol. Chem. 31 (2) (2007)
Linyong Mao, W. Jim Zheng
motif discovery to identify human transcription factor DNA-binding motifs. BMC Bioinform. 7 (S-4) (2006)
Linyong Mao, W. Jim Zheng
Combining Comparative Genomics with de novo Motif Discovery to Identify Human Transcription Factor DNA-Binding Motifs. IMSCCS (1) (2006)
Daniel Shegogue, W. Jim Zheng
Object-oriented biological system integration: a SARS coronavirus example. Bioinform. 21 (10) (2005)
Daniel Shegogue, W. Jim Zheng
Capturing biological information with class?Cresponsibility?Ccollaboration cards. Bioinform. 21 (3) (2005)
Daniel Shegogue, W. Jim Zheng
Integration of the Gene Ontology into an object-oriented architecture. BMC Bioinform. 6 (2005)
W. Jim Zheng, Velin Z. Spassov, Lisa Yan, Paul K. Flook, Sándor Szalma
A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction. Comput. Biol. Chem. 28 (4) (2004)