W. Jim Zheng

54 papers C 1Misc 3Journal 39Unranked 11
YearRankTypeTitle / Venue / Authors
2026 J jnl
CeLLTra: aligning cell names with gene expression via a pathway-informed transformer.
Bioinform.
Zhao Li, Zaiyi Zheng, Rongbin Li, Wen Chen, Yuntao Yang, Meer A Ali, Jundong Li, W. Jim Zheng
2025 J jnl
A Brain Cell Type Resource Created by Large Language Models and a Multi-Agent AI System for Collaborative Community Annotation.
CoRR
Rongbin Li, Wenbo Chen, Zhao Li, Rodrigo Munoz-Castaneda, Jinbo Li, Neha S. Maurya, Arnav Solanki, Huan He, Hanwen Xing, Meaghan Ramlakhan, Zachary Wise, Zhuhao Wu, Hua Xu, Michael Hawrylycz, W. Jim Zheng
2025 — conf
Efficient Training Corpus Retrieval for Large Language Model Fine Tuning: A Case Study in Cancer.
MedInfo
Avisha Das, Chiamaka S. Diala, Guocai Chen, Zhao Li, Rongbin Li, Omer Anjum, W. Jim Zheng
2024 J jnl
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
Zhao Li, Lan Lan, Yujia Zhou, Ruoxing Li, Kenneth D. Chavin, Hua Xu, Liang Li, David J. H. Shih, W. Jim Zheng
2024 J jnl
Ensemble pretrained language models to extract biomedical knowledge from literature.
J. Am. Medical Informatics Assoc.
Zhao Li, Qiang Wei, Liang-Chin Huang, Jianfu Li, Yan Hu, Yao-Shun Chuang, Jianping He, Avisha Das, Vipina Kuttichi Keloth, Yuntao Yang, Chiamaka S. Diala, Kirk E. Roberts, Cui Tao, Xiaoqian Jiang, W. Jim Zheng, Hua Xu
2024 J jnl
GPTON: Generative Pre-trained Transformers enhanced with Ontology Narration for accurate annotation of biological data.
CoRR
Rongbin Li, Wenbo Chen, Jinbo Li, Hanwen Xing, Hua Xu, Zhao Li, W. Jim Zheng
2024 J jnl
Geneverse: A collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research.
CoRR
Tianyu Liu, Yijia Xiao, Xiao Luo, Hua Xu, W. Jim Zheng, Hongyu Zhao
2024 J jnl
SAFER: sub-hypergraph attention-based neural network for predicting effective responses to dose combinations.
BMC Bioinform.
Yi-Ching Tang, Rongbin Li, Jing Tang, W. Jim Zheng, Xiaoqian Jiang
2022 J jnl
An evidence-based lexical pattern approach for quality assurance of Gene Ontology relations.
Briefings Bioinform.
Rashmie Abeysinghe, Yuntao Yang, Mason Bartels, W. Jim Zheng, Licong Cui
2022 J jnl
CNGPLD: case-control copy-number analysis using Gaussian process latent difference.
Bioinform.
David J. H. Shih, Ruoxing Li, Peter Müller, W. Jim Zheng, Kim-Anh Do, Shiaw-Yih Lin, Scott L. Carter
2022 — conf
Conversational Bots for Psychotherapy: A Study of Generative Transformer Models Using Domain-specific Dialogues.
BioNLP@ACL
Avisha Das, Salih Selek, Alia R. Warner, Xu Zuo, Yan Hu, Vipina Kuttichi Keloth, Jianfu Li, W. Jim Zheng, Hua Xu
2022 J jnl
GPU accelerated estimation of a shared random effect joint model for dynamic prediction.
Comput. Stat. Data Anal.
Shikun Wang, Zhao Li, Lan Lan, Jieyi Zhao, W. Jim Zheng, Liang Li
2021 J jnl
Anticancer drug synergy prediction in understudied tissues using transfer learning.
J. Am. Medical Informatics Assoc.
Yejin Kim, Shuyu Zheng, Jing Tang, W. Jim Zheng, Zhao Li, Xiaoqian Jiang
2021 J jnl
Deep representation learning of patient data from Electronic Health Records (EHR): A systematic review.
J. Biomed. Informatics
Yuqi Si, Jingcheng Du, Zhao Li, Xiaoqian Jiang, Timothy Miller, Fei Wang, W. Jim Zheng, Kirk Roberts
2021 — conf
Segmenting thoracic cavities with neoplastic lesions: a head-to-head benchmark with fully convolutional neural networks.
BCB
Zhao Li, Rongbin Li, Kendall J. Kiser, Luca Giancardo, W. Jim Zheng
2020 J jnl
A content-based literature recommendation system for datasets to improve data reusability - A case study on Gene Expression Omnibus (GEO) datasets.
J. Biomed. Informatics
Braja Gopal Patra, Vahed Maroufy, Babak Soltanalizadeh, Nan Deng, W. Jim Zheng, Kirk Roberts, Hulin Wu
2020 J jnl
A transformation-based method for auditing the IS-A hierarchy of biomedical terminologies in the Unified Medical Language System.
J. Am. Medical Informatics Assoc.
Fengbo Zheng, Jay Shi, Yuntao Yang, W. Jim Zheng, Licong Cui
2020 J jnl
An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries.
Database J. Biol. Databases Curation
Braja Gopal Patra, Babak Soltanalizadeh, Nan Deng, Leqing Wu, Vahed Maroufy, Canglin Wu, W. Jim Zheng, Kirk Roberts, Hulin Wu, Ashraf Yaseen
2020 J jnl
Deep Representation Learning of Patient Data from Electronic Health Records (EHR): A Systematic Review.
CoRR
Yuqi Si, Jingcheng Du, Zhao Li, Xiaoqian Jiang, Timothy Miller, Fei Wang, W. Jim Zheng, Kirk Roberts
2020 Misc conf
Deep Representation Learning of Patient Data from Electronic Health Records: A Systematic Review.
AMIA
Yuqi Si, Jingcheng Du, Zhao Li, Xiaoqian Jiang, Timothy A. Miller, Fei Wang, W. Jim Zheng, Kirk Roberts
2020 J jnl
Modelling of hypoxia gene expression for three different cancer cell lines.
Int. J. Comput. Biol. Drug Des.
Babak Soltanalizadeh, Erika Gonzalez Rodriguez, Vahed Maroufy, W. Jim Zheng, Hulin Wu
2019 J jnl
Gene fingerprint model for literature based detection of the associations among complex diseases: a case study of COPD.
BMC Medical Informatics Decis. Mak.
Guocai Chen, Yuxi Jia, Lisha Zhu, Ping Li, Lin Zhang, Cui Tao, W. Jim Zheng
2019 J jnl
Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis.
Database J. Biol. Databases Curation
Guocai Chen, Juan Camilo Ramírez, Nan Deng, Xing Qiu, Canglin Wu, W. Jim Zheng, Hulin Wu
2019 J jnl
Time-sensitive clinical concept embeddings learned from large electronic health records.
BMC Medical Informatics Decis. Mak.
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
2018 J jnl
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
Laila Rasmy, Yonghui Wu, Ningtao Wang, Xin Geng, W. Jim Zheng, Fei Wang, Hulin Wu, Hua Xu, Degui Zhi
2018 J jnl
Predict effective drug combination by deep belief network and ontology fingerprints.
J. Biomed. Informatics
Guocai Chen, Alex Tsoi, Hua Xu, W. Jim Zheng
2017 — conf
HiCComp: Multiple-level comparative analysis of Hi-C data by triplet network.
BIBM
Yan Zhang, Bo Zhang, W. Jim Zheng, Jijun Tang, Feng Yue
2017 J jnl
The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools.
BMC Bioinform.
Zhandong Liu, W. Jim Zheng, Genevera I. Allen, Yin Liu, Jianhua Ruan, Zhongming Zhao
2017 J jnl
The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work.
BMC Syst. Biol.
W. Jim Zheng, Jianhua Ruan, Hua Xu, Zhongming Zhao, Zhangdong Liu
2016 — conf
Developing Combination Cancer Therapy from Ontology Fingerprint Derived Gene Network.
CRI
W. Jim Zheng, Guocai Chen, Lam C. Tsoi, Tingting Qin, Chia-Hua Chang, Geoffrey Bartholomeusz, Hua Xu
2015 J jnl
A comparative study of disease genes and drug targets in the human protein interactome.
BMC Bioinform.
Jingchun Sun, Kevin W. Zhu, W. Jim Zheng, Hua Xu
2015 J jnl
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case.
BMC Syst. Biol.
Liang-Chin Huang, Ergin Soysal, W. Jim Zheng, Zhongming Zhao, Hua Xu, Jingchun Sun
2015 J jnl
Colorectal cancer drug target prediction using ontology-based inference and network analysis.
Database J. Biol. Databases Curation
Cui Tao, Jingchun Sun, W. Jim Zheng, Junjie Chen, Hua Xu
2015 J jnl
Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature.
Database J. Biol. Databases Curation
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
2014 Misc conf
An Integrative Framework for Drug Target Prediction and Repurposing.
AMIA
Jingchun Sun, Cui Tao, Kevin W. Zhu, W. Jim Zheng, Junjie Chen, Hua Xu
2014 — conf
Drug Target Prediction for Colorectal Cancer by Combining Ontology and Network Approaches.
ICBO
Cui Tao, Jingchun Sun, W. Jim Zheng, Junjie Chen, Hua Xu
2014 — conf
GSO: A Semantic Web Ontology to Capture 3D Genome Structure.
SWAT4LS
W. Jim Zheng, Jingcheng Du, Jijun Tang, Cui Tao
2014 — conf
Using Ontology Fingerprints to Disambiguate Gene Name Entities in the Biomedical Literature.
ICBO
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
2013 — conf
Exploring genomes with a game engine.
BIBM
Jeremiah J. Shepherd, Lingxi Zhou, Yan Zhang, W. Jim Zheng, Jijun Tang
2013 C conf
Exploring genomes with a game engine.
FDG
Jeremiah J. Shepherd, Bill Arndt, W. Jim Zheng, Yun Zhu, Jijun Tang
2012 Misc conf
Ranking Gene-Drug Relationships in Biomedical Literature Using Latent Dirichlet Allocation.
Pacific Symposium on Biocomputing
Yonghui Wu, Mei Liu, W. Jim Zheng, Zhongming Zhao, Hua Xu
2012 J jnl
Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network.
BMC Syst. Biol.
Tingting Qin, Lam C. Tsoi, Kellie J. Sims, Xinghua Lu, W. Jim Zheng
2011 J jnl
Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior.
BMC Bioinform.
Lam C. Tsoi, Tingting Qin, Elizabeth H. Slate, W. Jim Zheng
2011 — conf
Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome.
BIBM Workshops
William Arndt, Thomas M. Asbury, W. Jim Zheng, Matt Mitman, Jijun Tang
2010 J jnl
Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome.
BMC Bioinform.
Thomas M. Asbury, Matt Mitman, Jijun Tang, W. Jim Zheng
2009 J jnl
Evaluation of genome-wide association study results through development of ontology fingerprints.
Bioinform.
Lam C. Tsoi, Michael Boehnke, Richard L. Klein, W. Jim Zheng
2009 J jnl
Text-mining approach to evaluate terms for ontology development.
J. Biomed. Informatics
Lam C. Tsoi, Ravi Patel, Wenle Zhao, W. Jim Zheng
2007 J jnl
A method of microarray data storage using array data type.
Comput. Biol. Chem.
Lam C. Tsoi, W. Jim Zheng
2006 — conf
Combining Comparative Genomics with de novo Motif Discovery to Identify Human Transcription Factor DNA-Binding Motifs.
IMSCCS (1)
Linyong Mao, W. Jim Zheng
2006 J jnl
Combining comparative genomics with
BMC Bioinform.
Linyong Mao, W. Jim Zheng
2005 J jnl
Capturing biological information with class?Cresponsibility?Ccollaboration cards.
Bioinform.
Daniel Shegogue, W. Jim Zheng
2005 J jnl
Integration of the Gene Ontology into an object-oriented architecture.
BMC Bioinform.
Daniel Shegogue, W. Jim Zheng
2005 J jnl
Object-oriented biological system integration: a SARS coronavirus example.
Bioinform.
Daniel Shegogue, W. Jim Zheng
2004 J jnl
A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction.
Comput. Biol. Chem.
W. Jim Zheng, Velin Z. Spassov, Lisa Yan, Paul K. Flook, Sándor Szalma