W. Jim Zheng
Orcid: 0000-0001-7411-6047
According to our database1,
W. Jim Zheng
authored at least 51 papers
between 2004 and 2024.
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Bibliography
2024
SAFER: sub-hypergraph attention-based neural network for predicting effective responses to dose combinations.
BMC Bioinform., December, 2024
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, 2024
J. Am. Medical Informatics Assoc., 2024
GPTON: Generative Pre-trained Transformers enhanced with Ontology Narration for accurate annotation of biological data.
CoRR, 2024
Geneverse: A Collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research.
Proceedings of the Findings of the Association for Computational Linguistics: EMNLP 2024, 2024
2023
Extracting Drug-Protein Relation from Literature Using Ensembles of Biomedical Transformers.
Proceedings of the MEDINFO 2023 - The Future Is Accessible, 2023
2022
GPU accelerated estimation of a shared random effect joint model for dynamic prediction.
Comput. Stat. Data Anal., 2022
Bioinform., 2022
An evidence-based lexical pattern approach for quality assurance of Gene Ontology relations.
Briefings Bioinform., 2022
Conversational Bots for Psychotherapy: A Study of Generative Transformer Models Using Domain-specific Dialogues.
Proceedings of the 21st Workshop on Biomedical Language Processing, 2022
2021
Deep representation learning of patient data from Electronic Health Records (EHR): A systematic review.
J. Biomed. Informatics, 2021
J. Am. Medical Informatics Assoc., 2021
Segmenting thoracic cavities with neoplastic lesions: a head-to-head benchmark with fully convolutional neural networks.
Proceedings of the BCB '21: 12th ACM International Conference on Bioinformatics, 2021
2020
A content-based literature recommendation system for datasets to improve data reusability - A case study on Gene Expression Omnibus (GEO) datasets.
J. Biomed. Informatics, 2020
A transformation-based method for auditing the IS-A hierarchy of biomedical terminologies in the Unified Medical Language System.
J. Am. Medical Informatics Assoc., 2020
Int. J. Comput. Biol. Drug Des., 2020
An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries.
Database J. Biol. Databases Curation, 2020
Deep Representation Learning of Patient Data from Electronic Health Records: A Systematic Review.
Proceedings of the AMIA 2020, 2020
2019
Time-sensitive clinical concept embeddings learned from large electronic health records.
BMC Medical Informatics Decis. Mak., 2019
Gene fingerprint model for literature based detection of the associations among complex diseases: a case study of COPD.
BMC Medical Informatics Decis. Mak., 2019
Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis.
Database J. Biol. Databases Curation, 2019
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.
J. Biomed. Informatics, 2018
J. Biomed. Informatics, 2018
2017
The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work.
BMC Syst. Biol., 2017
The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools.
BMC Bioinform., 2017
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017
2016
Developing Combination Cancer Therapy from Ontology Fingerprint Derived Gene Network.
Proceedings of the Summit on Clinical Research Informatics, 2016
2015
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case.
BMC Syst. Biol., 2015
A comparative study of disease genes and drug targets in the human protein interactome.
BMC Bioinform., 2015
Colorectal cancer drug target prediction using ontology-based inference and network analysis.
Database J. Biol. Databases Curation, 2015
Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature.
Database J. Biol. Databases Curation, 2015
2014
Proceedings of the 7th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2014
Drug Target Prediction for Colorectal Cancer by Combining Ontology and Network Approaches.
Proceedings of the 5th International Conference on Biomedical Ontology, 2014
Using Ontology Fingerprints to Disambiguate Gene Name Entities in the Biomedical Literature.
Proceedings of the 5th International Conference on Biomedical Ontology, 2014
Proceedings of the AMIA 2014, 2014
2013
Proceedings of the 8th International Conference on the Foundations of Digital Games, 2013
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013
2012
BMC Syst. Biol., 2012
Ranking Gene-Drug Relationships in Biomedical Literature Using Latent Dirichlet Allocation.
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012
2011
Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior.
BMC Bioinform., 2011
Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome.
Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011
2010
Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome.
BMC Bioinform., 2010
2009
J. Biomed. Informatics, 2009
Evaluation of genome-wide association study results through development of ontology fingerprints.
Bioinform., 2009
2007
2006
Combining comparative genomics with <i>de novo </i>motif discovery to identify human transcription factor DNA-binding motifs.
BMC Bioinform., 2006
Combining Comparative Genomics with de novo Motif Discovery to Identify Human Transcription Factor DNA-Binding Motifs.
Proceedings of the Interdisciplinary and Multidisciplinary Research in Computer Science, 2006
2005
BMC Bioinform., 2005
Bioinform., 2005
Bioinform., 2005
2004
A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction.
Comput. Biol. Chem., 2004