A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction. - W. Jim Zheng; Velin Z. Spassov; Lisa Yan; Paul K. Flook; Sándor Szalma (Comput. Biol. Chem., 2004)

Capturing biological information with class?Cresponsibility?Ccollaboration cards. - Daniel Shegogue; W. Jim Zheng (Bioinform., 2005)

Object-oriented biological system integration: a SARS coronavirus example. - Daniel Shegogue; W. Jim Zheng (Bioinform., 2005)

Integration of the Gene Ontology into an object-oriented architecture. - Daniel Shegogue; W. Jim Zheng (BMC Bioinform., 2005)

Combining Comparative Genomics with de novo Motif Discovery to Identify Human Transcription Factor DNA-Binding Motifs. - Linyong Mao; W. Jim Zheng (IMSCCS (1), 2006)

Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs. - Linyong Mao; W. Jim Zheng (BMC Bioinform., 2006)

A method of microarray data storage using array data type. - Lam C. Tsoi; W. Jim Zheng (Comput. Biol. Chem., 2007)

Evaluation of genome-wide association study results through development of ontology fingerprints. - Lam C. Tsoi; Michael Boehnke; Richard L. Klein; W. Jim Zheng (Bioinform., 2009)

Text-mining approach to evaluate terms for ontology development. - Lam C. Tsoi; Ravi Patel; Wenle Zhao; W. Jim Zheng (J. Biomed. Informatics, 2009)

Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome. - Thomas M. Asbury; Matt Mitman; Jijun Tang; W. Jim Zheng (BMC Bioinform., 2010)

Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome. - William Arndt; Thomas M. Asbury; W. Jim Zheng; Matt Mitman; Jijun Tang (BIBM Workshops, 2011)

Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior. - Lam C. Tsoi; Tingting Qin; Elizabeth H. Slate; W. Jim Zheng (BMC Bioinform., 2011)

Ranking Gene-Drug Relationships in Biomedical Literature Using Latent Dirichlet Allocation. - Yonghui Wu; Mei Liu; W. Jim Zheng; Zhongming Zhao; Hua Xu 001 (Pacific Symposium on Biocomputing, 2012)

Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network. - Tingting Qin; Lam C. Tsoi; Kellie J. Sims; Xinghua Lu; W. Jim Zheng (BMC Syst. Biol., 2012)

Exploring genomes with a game engine. - Jeremiah J. Shepherd; Lingxi Zhou; Yan Zhang; W. Jim Zheng; Jijun Tang (BIBM, 2013)

Exploring genomes with a game engine. - Jeremiah J. Shepherd; Bill Arndt; W. Jim Zheng; Yun Zhu; Jijun Tang (FDG, 2013)

An Integrative Framework for Drug Target Prediction and Repurposing. - Jingchun Sun; Cui Tao; Kevin W. Zhu; W. Jim Zheng; Junjie Chen; Hua Xu 001 (AMIA, 2014)

Using Ontology Fingerprints to Disambiguate Gene Name Entities in the Biomedical Literature. - Guocai Chen; Jieyi Zhao; Trevor Cohen; Cui Tao; Jingchun Sun; Hua Xu 001; Elmer V. Bernstam; Jia Zeng; Amber M. Johnson; Vijaykumar Holla; Ann Balley; Funda Meric-Bernstam; et al. (ICBO, 2014)

Drug Target Prediction for Colorectal Cancer by Combining Ontology and Network Approaches. - Cui Tao; Jingchun Sun; W. Jim Zheng; Junjie Chen; Hua Xu 001 (ICBO, 2014)

GSO: A Semantic Web Ontology to Capture 3D Genome Structure. - W. Jim Zheng; Jingcheng Du; Jijun Tang; Cui Tao (SWAT4LS, 2014)

Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature. - Guocai Chen; Jieyi Zhao; Trevor Cohen; Cui Tao; Jingchun Sun; Hua Xu 001; Elmer V. Bernstam; Andrew Lawson; Jia Zeng; Amber M. Johnson; Vijaykumar Holla; Ann M. Bailey; et al. (Database J. Biol. Databases Curation, 2015)

Colorectal cancer drug target prediction using ontology-based inference and network analysis. - Cui Tao; Jingchun Sun; W. Jim Zheng; Junjie Chen; Hua Xu 001 (Database J. Biol. Databases Curation, 2015)

A comparative study of disease genes and drug targets in the human protein interactome. - Jingchun Sun; Kevin W. Zhu; W. Jim Zheng; Hua Xu 001 (BMC Bioinform., 2015)

A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. - Liang-Chin Huang; Ergin Soysal; W. Jim Zheng; Zhongming Zhao; Hua Xu 001; Jingchun Sun (BMC Syst. Biol., 2015)

Developing Combination Cancer Therapy from Ontology Fingerprint Derived Gene Network. - W. Jim Zheng; Guocai Chen; Lam C. Tsoi; Tingting Qin; Chia-Hua Chang; Geoffrey Bartholomeusz; Hua Xu 001 (CRI, 2016)

HiCComp: Multiple-level comparative analysis of Hi-C data by triplet network. - Yan Zhang; Bo Zhang; W. Jim Zheng; Jijun Tang; Feng Yue (BIBM, 2017)

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools. - Zhandong Liu; W. Jim Zheng; Genevera I. Allen; Yin Liu; Jianhua Ruan; Zhongming Zhao (BMC Bioinform., 2017)

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work. - W. Jim Zheng; Jianhua Ruan; Hua Xu 001; Zhongming Zhao; Zhangdong Liu (BMC Syst. Biol., 2017)

Predict effective drug combination by deep belief network and ontology fingerprints. - Guocai Chen; Alex Tsoi; Hua Xu 001; W. Jim Zheng (J. Biomed. Informatics, 2018)

A study of generalizability of recurrent neural network-based predictive models for heart failure onset risk using a large and heterogeneous EHR data set. - Laila Rasmy; Yonghui Wu; Ningtao Wang; Xin Geng; W. Jim Zheng; Fei Wang 001; Hulin Wu; Hua Xu 001; Degui Zhi (J. Biomed. Informatics, 2018)

Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis. - Guocai Chen; Juan Camilo Ramírez; Nan Deng; Xing Qiu; Canglin Wu; W. Jim Zheng; Hulin Wu (Database J. Biol. Databases Curation, 2019)

Gene fingerprint model for literature based detection of the associations among complex diseases: a case study of COPD. - Guocai Chen; Yuxi Jia; Lisha Zhu; Ping Li; Lin Zhang; Cui Tao; W. Jim Zheng (BMC Medical Informatics Decis. Mak., 2019)

Time-sensitive clinical concept embeddings learned from large electronic health records. - Yang Xiang 003; Jun Xu 007; Yuqi Si; Zhiheng Li 004; Laila Rasmy; Yujia Zhou 003; Firat Tiryaki; Fang Li 011; Yaoyun Zhang; Yonghui Wu; Xiaoqian Jiang; W. Jim Zheng; et al. (BMC Medical Informatics Decis. Mak., 2019)

Deep Representation Learning of Patient Data from Electronic Health Records: A Systematic Review. - Yuqi Si; Jingcheng Du; Zhao Li; Xiaoqian Jiang; Timothy A. Miller; Fei Wang 001; W. Jim Zheng; Kirk Roberts (AMIA, 2020)

An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries. - Braja Gopal Patra; Babak Soltanalizadeh; Nan Deng; Leqing Wu; Vahed Maroufy; Canglin Wu; W. Jim Zheng; Kirk Roberts; Hulin Wu; Ashraf Yaseen (Database J. Biol. Databases Curation, 2020)

Modelling of hypoxia gene expression for three different cancer cell lines. - Babak Soltanalizadeh; Erika Gonzalez Rodriguez; Vahed Maroufy; W. Jim Zheng; Hulin Wu (Int. J. Comput. Biol. Drug Des., 2020)

A transformation-based method for auditing the IS-A hierarchy of biomedical terminologies in the Unified Medical Language System. - Fengbo Zheng; Jay Shi; Yuntao Yang; W. Jim Zheng; Licong Cui (J. Am. Medical Informatics Assoc., 2020)

A content-based literature recommendation system for datasets to improve data reusability - A case study on Gene Expression Omnibus (GEO) datasets. - Braja Gopal Patra; Vahed Maroufy; Babak Soltanalizadeh; Nan Deng; W. Jim Zheng; Kirk Roberts; Hulin Wu (J. Biomed. Informatics, 2020)

Segmenting thoracic cavities with neoplastic lesions: a head-to-head benchmark with fully convolutional neural networks. - Zhao Li; Rongbin Li; Kendall J. Kiser; Luca Giancardo; W. Jim Zheng (BCB, 2021)

Anticancer drug synergy prediction in understudied tissues using transfer learning. - Yejin Kim 001; Shuyu Zheng; Jing Tang 002; W. Jim Zheng; Zhao Li; Xiaoqian Jiang (J. Am. Medical Informatics Assoc., 2021)

Deep representation learning of patient data from Electronic Health Records (EHR): A systematic review. - Yuqi Si; Jingcheng Du; Zhao Li; Xiaoqian Jiang; Timothy Miller 002; Fei Wang 001; W. Jim Zheng; Kirk Roberts (J. Biomed. Informatics, 2021)

Conversational Bots for Psychotherapy: A Study of Generative Transformer Models Using Domain-specific Dialogues. - Avisha Das; Salih Selek; Alia R. Warner; Xu Zuo; Yan Hu; Vipina Kuttichi Keloth; Jianfu Li; W. Jim Zheng; Hua Xu 001 (BioNLP@ACL, 2022)

An evidence-based lexical pattern approach for quality assurance of Gene Ontology relations. - Rashmie Abeysinghe; Yuntao Yang; Mason Bartels; W. Jim Zheng; Licong Cui (Briefings Bioinform., 2022)

CNGPLD: case-control copy-number analysis using Gaussian process latent difference. - David J. H. Shih; Ruoxing Li; Peter Müller; W. Jim Zheng; Kim-Anh Do; Shiaw-Yih Lin; Scott L. Carter (Bioinform., 2022)

GPU accelerated estimation of a shared random effect joint model for dynamic prediction. - Shikun Wang; Zhao Li; Lan Lan; Jieyi Zhao; W. Jim Zheng; Liang Li (Comput. Stat. Data Anal., 2022)

Extracting Drug-Protein Relation from Literature Using Ensembles of Biomedical Transformers. - Avisha Das; Zhao Li; Qiang Wei 002; Jianfu Li; Liang-Chin Huang; Yan Hu; Rongbin Li; Wenjin Jim Zheng; Hua Xu 001 (MedInfo, 2023)

Geneverse: A Collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research. - Tianyu Liu 001; Yijia Xiao; Xiao Luo 001; Hua Xu 001; Wenjin Jim Zheng; Hongyu Zhao 003 (EMNLP (Findings), 2024)

GPTON: Generative Pre-trained Transformers enhanced with Ontology Narration for accurate annotation of biological data. - Rongbin Li; Wenbo Chen; Jinbo Li; Hanwen Xing; Hua Xu 001; Zhao Li; W. Jim Zheng (CoRR, 2024)

Ensemble pretrained language models to extract biomedical knowledge from literature. - Zhao Li; Qiang Wei 002; Liang-Chin Huang; Jianfu Li; Yan Hu; Yao-Shun Chuang; Jianping He 002; Avisha Das; Vipina Kuttichi Keloth; Yuntao Yang; Chiamaka S. Diala; Kirk E. Roberts; et al. (J. Am. Medical Informatics Assoc., 2024)

Developing deep learning-based strategies to predict the risk of hepatocellular carcinoma among patients with nonalcoholic fatty liver disease from electronic health records. - Zhao Li; Lan Lan; Yujia Zhou 003; Ruoxing Li; Kenneth D. Chavin; Hua Xu 001; Liang Li; David J. H. Shih; W. Jim Zheng (J. Biomed. Informatics, 2024)

SAFER: sub-hypergraph attention-based neural network for predicting effective responses to dose combinations. - Yi-Ching Tang; Rongbin Li; Jing Tang 002; W. Jim Zheng; Xiaoqian Jiang (BMC Bioinform., 2024)