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2020 – today
- 2024
[j34]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): 250 (2024)- [j33]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:
Ensemble pretrained language models to extract biomedical knowledge from literature. J. Am. Medical Informatics Assoc. 31(9): 1904-1911 (2024) - [j32]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: 104626 (2024) - [c16]Tianyu Liu, Yijia Xiao, Xiao Luo, Hua Xu, Wenjin Jim Zheng, Hongyu Zhao:
Geneverse: A Collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research. EMNLP (Findings) 2024: 4819-4836 - [i3]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 abs/2406.15534 (2024) - [i2]Rongbin Li, Wenbo Chen, Jinbo Li, Hanwen Xing, Hua Xu, Zhao Li, W. Jim Zheng:
GPTON: Generative Pre-trained Transformers enhanced with Ontology Narration for accurate annotation of biological data. CoRR abs/2410.10899 (2024) - 2023
- [c15]Avisha Das, Zhao Li, Qiang Wei, Jianfu Li, Liang-Chin Huang, Yan Hu, Rongbin Li, Wenjin Jim Zheng, Hua Xu:
Extracting Drug-Protein Relation from Literature Using Ensembles of Biomedical Transformers. MedInfo 2023: 639-643 - 2022
- [j31]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) - [j30]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): 2096-2101 (2022) - [j29]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: 107528 (2022) - [c14]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: 285-297 - 2021
- [j28]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): 42-51 (2021) - [j27]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: 103671 (2021) - [c13]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: 33:1-33:8 - 2020
- [j26]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) - [j25]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): 124-143 (2020) - [j24]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): 1568-1575 (2020) - [j23]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: 103399 (2020) - [c12]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 - [i1]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 abs/2010.02809 (2020)
2010 – 2019
- 2019
- [j22]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: bay145 (2019) - [j21]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. 19-S(1): 20:1-20:9 (2019) - [j20]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. 19-S(2): 139-148 (2019) - 2018
- [j19]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: 11-16 (2018) - [j18]Guocai Chen, Alex Tsoi, Hua Xu, W. Jim Zheng:
Predict effective drug combination by deep belief network and ontology fingerprints. J. Biomed. Informatics 85: 149-154 (2018) - 2017
- [j17]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): 405:1-405:3 (2017) - [j16]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): 88:1-88:3 (2017) - [c11]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: 92-96 - 2016
- [c10]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 - 2015
- [j15]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) - [j14]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) - [j13]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): S1 (2015) - [j12]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): S2 (2015) - 2014
- [c9]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 - [c8]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: 66 - [c7]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: 67 - [c6]W. Jim Zheng, Jingcheng Du, Jijun Tang, Cui Tao:
GSO: A Semantic Web Ontology to Capture 3D Genome Structure. SWAT4LS 2014 - 2013
- [c5]Jeremiah J. Shepherd, Lingxi Zhou, Yan Zhang, W. Jim Zheng, Jijun Tang:
Exploring genomes with a game engine. BIBM 2013: 26-30 - [c4]Jeremiah J. Shepherd, Bill Arndt, W. Jim Zheng, Yun Zhu, Jijun Tang:
Exploring genomes with a game engine. FDG 2013: 447-448 - 2012
- [j11]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): S3 (2012) - [c3]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: 422-433 - 2011
- [j10]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: 438 (2011) - [c2]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: 936-938 - 2010
- [j9]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: 444 (2010)
2000 – 2009
- 2009
- [j8]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): 1314-1320 (2009) - [j7]Lam C. Tsoi, Ravi Patel, Wenle Zhao, W. Jim Zheng:
Text-mining approach to evaluate terms for ontology development. J. Biomed. Informatics 42(5): 824-830 (2009) - 2007
- [j6]Lam C. Tsoi, W. Jim Zheng:
A method of microarray data storage using array data type. Comput. Biol. Chem. 31(2): 143-147 (2007) - 2006
- [j5]Linyong Mao, W. Jim Zheng:
Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs. BMC Bioinform. 7(S-4) (2006) - [c1]Linyong Mao, W. Jim Zheng:
Combining Comparative Genomics with de novo Motif Discovery to Identify Human Transcription Factor DNA-Binding Motifs. IMSCCS (1) 2006: 158-163 - 2005
- [j4]Daniel Shegogue, W. Jim Zheng:
Capturing biological information with class?Cresponsibility?Ccollaboration cards. Bioinform. 21(3): 415-417 (2005) - [j3]Daniel Shegogue, W. Jim Zheng:
Object-oriented biological system integration: a SARS coronavirus example. Bioinform. 21(10): 2502-2509 (2005) - [j2]Daniel Shegogue, W. Jim Zheng:
Integration of the Gene Ontology into an object-oriented architecture. BMC Bioinform. 6: 113 (2005) - 2004
- [j1]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): 265-274 (2004)
Coauthor Index
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