Jake Yue Chen

According to our database, Jake Yue Chen authored at least 91 papers between 2003 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

Cross-Team Collaboration and Diversity in the Bridge2AI Project.

Huimin Xu, Chitrank Gupta, Zhandos Sembay, Swathi Thaker, Pamela Payne-Foster, Jake Y. Chen, Ying Ding

Proceedings of the Companion Proceedings of the ACM Web Conference 2023, 2023

22nd International Workshop on Data Mining in Bioinformatics (BIOKDD 2023).

Da Yan, Ariful Azad, Jie Hou, Jake Y. Chen, Mohammed J. Zaki

Proceedings of the 29th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2023

Accurate Identification of Human Emotional States from Images Using Deep Learning.

Emmy Yang, Jake Y. Chen

Proceedings of the IEEE EMBS International Conference on Biomedical and Health Informatics, 2023

Designing Helicobacter pylori as an Anticancer Bacterial Vector.

Selina Zhang, Jake Yue Chen

Proceedings of the 14th ACM International Conference on Bioinformatics, 2023

2022

Guest Editorial for Selected Papers From BIOKDD 2020.

Da Yan, Hong Qin, Hsiang-Yun Wu, Jake Y. Chen

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Guest Editorial for Selected Papers From BIOKDD 2021.

Da Yan, Zhaohui S. Qin, Debswapna Bhattacharya, Jake Y. Chen

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

WINNER: A network biology tool for biomolecular characterization and prioritization.

Thanh Nguyen, Zongliang Yue, Radomir Slominski, Robert Welner, Jianyi Zhang, Jake Y. Chen

Frontiers Big Data, 2022

21th International Workshop on Data Mining in Bioinformatics (BIOKDD 2022).

Da Yan, Catia Pesquita, Carsten Görg, Jake Y. Chen, Mohammed J. Zaki

Proceedings of the KDD '22: The 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, Washington, DC, USA, August 14, 2022

GraphWaGu: GPU Powered Large Scale Graph Layout Computation and Rendering for the Web.

Landon Dyken, Pravin Poudel, Will Usher, Steve Petruzza, Jake Y. Chen, Sidharth Kumar

Proceedings of the 22nd Eurographics Symposium on Parallel Graphics and Visualization, 2022

2021

Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams.

Thanh Nguyen, Tongbin Zhang, Geoffrey Fox, Sisi Zeng, Ni Cao, Chuandi Pan, Jake Y. Chen

BMC Medical Informatics Decis. Mak., February, 2021

Guest Editorial for Selected Papers From BIOKDD 2019.

Da Yan, Sharma V. Thankachan, Jake Y. Chen

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Scalable De Novo Genome Assembly Using a Pregel-Like Graph-Parallel System.

Guimu Guo, Hongzhi Chen, Da Yan, James Cheng, Jake Y. Chen, Zechen Chong

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies.

Zongliang Yue, Eric Zhang, Clark Xu, Sunny Khurana, Nishant Batra, Son Do Hai Dang, James J. Cimino, Jake Y. Chen

Nucleic Acids Res., 2021

Polar Gini Curve: A Technique to Discover Gene Expression Spatial Patterns from Single-cell RNA-seq Data.

Thanh Minh Nguyen, Jacob John Jeevan, Nuo Xu, Jake Y. Chen

Genom. Proteom. Bioinform., 2021

Editorial: Artificial Intelligence for Precision Medicine.

Jun Deng, Thomas Hartung, Enrico Capobianco, Jake Y. Chen, Frank Emmert-Streib

Frontiers Artif. Intell., 2021

Editorial: AI-Enabled Data Science for COVID-19.

Da Yan, Hong Qin, Hsiang-Yun Wu, Jake Y. Chen

Frontiers Big Data, 2021

Corrigendum: Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples.

Thanh Nguyen, Samuel Bharti, Zongliang Yue, Christopher D. Willey, Jake Y. Chen

Frontiers Big Data, 2021

Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples.

Thanh Nguyen, Samuel Bharti, Zongliang Yue, Christopher D. Willey, Jake Y. Chen

Frontiers Big Data, 2021

20th International Workshop on Data Mining in Bioinformatics (BIOKDD 2021).

Da Yan, Steve Qin, Debswapna Bhattacharya, Jake Y. Chen, Mohammed J. Zaki

Proceedings of the KDD '21: The 27th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2021

PAGER-CoV-Run: An online interactive analytical platform for COVID-19 functional genomic downstream analysis.

Zongliang Yue, Nishant Batra, Hui-Chen Hsu, John Mountz, Jake Y. Chen

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

2020

Guest Editorial for Selected Papers from BIOKDD 2018 and DMBIH 2018.

Da Yan, Xin Gao, Samah J. Fodeh, Jake Y. Chen

IEEE ACM Trans. Comput. Biol. Bioinform., 2020

Empowering Team Science Across the Translational Spectrum with the UAB Biomedical Research Infrastructure Technology Enhancement (U-BRITE).

James J. Cimino, Wayne H. Liang, Jelai Wang, Dongmei Sun, John David Osborne, Amy Y. Wang, S. Louis Bridges, Matthew C. Wyatt, Jake Y. Chen

Proceedings of the 21st International Conference on Information Reuse and Integration for Data Science, 2020

2019

WIPER: Weighted in-Path Edge Ranking for biomolecular association networks.

Zongliang Yue, Thanh Nguyen, Eric Zhang, Jianyi Zhang, Jake Y. Chen

Quant. Biol., 2019

BEERE: a web server for biomedical entity expansion, ranking and explorations.

Zongliang Yue, Christopher D. Willey, Anita B. Hjelmeland, Jake Y. Chen

Nucleic Acids Res., 2019

Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information.

Zaixiang Tang, Shufeng Lei, Xinyan Zhang, Zixuan Yi, Boyi Guo, Jake Y. Chen, Yueping Shen, Nengjun Yi

BMC Bioinform., 2019

2018

"Super Gene Set" Causal Relationship Discovery from Functional Genomics Data.

Zongliang Yue, Michael T. Neylon, Thanh Nguyen, Timothy Ratliff, Jake Y. Chen

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Multiscale and Multimodal Analysis for Computational Biology.

Xin Gao, Jake Y. Chen, Mohammed J. Zaki

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology.

Zongliang Yue, Qi Zheng, Michael T. Neylon, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, Jake Y. Chen

Nucleic Acids Res., 2018

2017

Repositioning drugs by targeting network modules: a Parkinson's disease case study.

Zongliang Yue, Itika Arora, Eric Y. Zhang, Vincent Laufer, S. Louis Bridges, Jake Y. Chen

BMC Bioinform., 2017

2016

DTMBIO 2016: The Tenth International Workshop on Data and Text Mining in Biomedical Informatics.

Sangwoo Kim, Jake Y. Chen, Vincenzo Cutello, Doheon Lee

Proceedings of the 25th ACM International Conference on Information and Knowledge Management, 2016

Towards constructing "Super Gene Sets" regulatory networks.

Jake Y. Chen, Zongliang Yue, Michael T. Neylon, Thanh Nguyen, Nafisa Bulsara, Itika Arora, Timothy Ratliff

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015

DMAP: a connectivity map database to enable identification of novel drug repositioning candidates.

Hui Huang, Thanh Nguyen, Sara Ibrahim, Sandeep Shantharam, Zongliang Yue, Jake Y. Chen

BMC Bioinform., December, 2015

Knowledge Discovery Using Big Data in Biomedical Systems.

Sarath Chandra Janga, Dongxiao Zhu, Jake Y. Chen, Mohammed J. Zaki

IEEE ACM Trans. Comput. Biol. Bioinform., 2015

PAGER: constructing PAGs and new PAG-PAG relationships for network biology.

Zongliang Yue, Madhura M. Kshirsagar, Thanh Nguyen, Chayaporn Suphavilai, Michael T. Neylon, Liugen Zhu, Timothy Ratliff, Jake Yue Chen

Bioinform., 2015

Predictive and preventive models for diabetes prevention using clinical information in electronic health record.

Ni Cao, Sisi Zeng, Feixia Shen, Chuandi Pan, Chengshui Chen, Thanh Nguyen, Jake Yue Chen

Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

2014

Seed-weighted random walk ranking for cancer biomarker prioritisation: a case study in leukaemia.

Tianxiao Huan, Xiaogang Wu, Zengliang Bai, Jake Y. Chen

Int. J. Data Min. Bioinform., 2014

SLDR: a computational technique to identify novel genetic regulatory relationships.

Zongliang Yue, Ping Wan, Hui Huang, Zhan Xie, Jake Yue Chen

BMC Bioinform., 2014

Computational Identification of De-Centric Genetic Regulatory Relationships from Functional Genomic Data.

Zongliang Yue, Ping Wan, Zhan Xie, Jake Y. Chen

Proceedings of the Bioinformatics Research and Applications - 10th International Symposium, 2014

Constructing regulatory gene set networks to reveal novel insights into biological systems.

Chayaporn Suphavilai, Liugen Zhu, Jake Y. Chen

Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, 2014

Computational Biomarker Discovery.

Fan Zhang, Xiaogang Wu, Jake Yue Chen

Proceedings of the Approaches in Integrative Bioinformatics - Towards the Virtual Cell, 2014

2013

Semantic Web meets Integrative Biology: a survey.

Huajun Chen, Tong Yu, Jake Y. Chen

Briefings Bioinform., 2013

2012

Biological knowledge discovery and data mining.

Mohammad Al Hasan, Jun Huan, Jake Yue Chen, Mohammed J. Zaki

Sci. Program., 2012

Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays.

Xiaogang Wu, Hui Huang, Tao Wei, Ragini Pandey, Christoph Reinhard, Shuyu D. Li, Jake Y. Chen

J. Integr. Bioinform., 2012

Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes.

Paul J. Hale, Alfredo M. López-Yunez, Jake Y. Chen

BMC Syst. Biol., 2012

Reordering based integrative expression profiling for microarray classification.

Xiaogang Wu, Hui Huang, Madhankumar Sonachalam, Sina Reinhard, Jeffrey Shen, Ragini Pandey, Jake Y. Chen

BMC Bioinform., 2012

PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries.

Hui Huang, Xiaogang Wu, Madhankumar Sonachalam, Sammed N. Mandape, Ragini Pandey, Karl F. MacDorman, Ping Wan, Jake Y. Chen

BMC Bioinform., 2012

An evaluation for merging signaling pathways by using protein-protein interaction data.

Xiaogang Wu, Jake Y. Chen

Proceedings of the Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, 2012

Multi-biomarker panel selection on a GPU.

David Johnson, Brandon Shafer, Jaehwan John Lee, Jake Y. Chen

Proceedings of the 2012 IEEE International Conference on Electro/Information Technology, 2012

2011

Computational Analysis of Drought Stress-Associated miRNAs and miRNA Co-Regulation Network in Physcomitrella patens.

Ping Wan, Jun Wu, Yuan Zhou, Junshu Xiao, Jie Feng, Weizhong Zhao, Shen Xiang, Guanglong Jiang, Jake Y. Chen

Genom. Proteom. Bioinform., 2011

An integrated proteomics analysis of bone tissues in response to mechanical stimulation.

Jiliang Li, Fan Zhang, Jake Y. Chen

BMC Syst. Biol., 2011

HOMER: a human organ-specific molecular electronic repository.

Fan Zhang, Jake Y. Chen

BMC Bioinform., 2011

New threats to health data privacy.

Fengjun Li, Xukai Zou, Peng Liu, Jake Y. Chen

BMC Bioinform., 2011

Personal genome privacy protection with feature-based hierarchical dual-stage encryption.

Xukai Zou, Peng Liu, Jake Y. Chen

Proceedings of the 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, 2011

Predicting drug efficacy based on the integrated breast cancer pathway model.

Hui Huang, Xiaogang Wu, Sara Ibrahim, Marianne McKenzie, Jake Y. Chen

Proceedings of the 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, 2011

A Network Biology Approach to Predicting Drug Cardiotoxicity.

Liang-Chin Huang, Jake Yue Chen

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

Ethics and Privacy Considerations for Systems Biology Applications in Predictive and Personalized Medicine.

Jake Y. Chen, Heng Xu, Pan Shi, Adam Culbertson, Eric M. Meslin

Proceedings of the Handbook of Research on Computational and Systems Biology, 2011

2010

Data Mining in Bioinformatics: Selected Papers from BIOKDD.

Stefano Lonardi, Jake Yue Chen

IEEE ACM Trans. Comput. Biol. Bioinform., 2010

GeneTerrain: Visual exploration of differential gene expression profiles organized in native biomolecular interaction networks.

Qian You, Shiaofen Fang, Jake Yue Chen

Inf. Vis., 2010

Discovering breast cancer drug candidates from biomedical literature.

Jiao Li, Xiaoyan Zhu, Jake Yue Chen

Int. J. Data Min. Bioinform., 2010

PEPPI: a peptidomic database of human protein isoforms for proteomics experiments.

Ao Zhou, Fan Zhang, Jake Y. Chen

BMC Bioinform., 2010

A GMM-IG framework for selecting genes as expression panel biomarkers.

Mingyi Wang, Jake Y. Chen

Artif. Intell. Medicine, 2010

Breast cancer plasma protein biomarker discovery by coupling LC-MS/MS proteomics and systems biology.

Fan Zhang, Mu Wang, Jake Y. Chen

Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

2009

Design of an Online Physician-Mediated Personal Health Record System.

Jake Y. Chen, Shailaja Taduri, Frank Lloyd

Proceedings of the Biomedical Data and Applications, 2009

Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts.

Jiao Li, Xiaoyan Zhu, Jake Yue Chen

PLoS Comput. Biol., 2009

Finding fractal patterns in molecular interaction networks: a case study in Alzheimer's disease.

Xiaogang Wu, Tianxiao Huan, Ragini Pandey, Tianshou Zhou, Jake Y. Chen

Int. J. Comput. Biol. Drug Des., 2009

HPD: an online integrated human pathway database enabling systems biology studies.

Sudhir R. Chowbina, Xiaogang Wu, Fan Zhang, Peter M. Li, Ragini Pandey, Harini N. Kasamsetty, Jake Y. Chen

BMC Bioinform., 2009

Semantic web for integrated network analysis in biomedicine.

Huajun Chen, Li Ding, Zhaohui Wu, Tong Yu, Lavanya Dhanapalan, Jake Yue Chen

Briefings Bioinform., 2009

Construct anticancer drug-drug correlation network.

Jiao Li, Pamela Crowell, Jake Yue Chen

Proceedings of the 2009 ACM Symposium on Applied Computing (SAC), 2009

Visualizing a Correlative Multi-level Graph of Biology Entity Interactions.

Qian You, Shiaofen Fang, Snehasis Mukhopadhyay, Harsha Gopal Goud Vaka, Jake Yue Chen

Proceedings of the NBiS 2009, 2009

Toward Ontology-Driven Omics Data Integration in Current Database Management Systems.

John A. Springer, Jake Y. Chen

Proceedings of the NBiS 2009, 2009

A neural network approach to multi-biomarker panel development based on LC/MS/MS proteomics profiles: A case study in breast cancer.

Fan Zhang, Jake Y. Chen

Proceedings of the Twenty-Second IEEE International Symposium on Computer-Based Medical Systems, 2009

RIC: Ranking with Interaction Chains and Its Application in Computational Clinical Proteomics Studies.

Jieun Jeong, Jake Y. Chen

Proceedings of the 2009 IEEE International Conference on Bioinformatics and Biomedicine, 2009

2008

BIOKDD 2008: a workshop report on data mining in bioinformatics.

Jake Y. Chen, Mohammed Javeed Zaki, Stefano Lonardi

SIGKDD Explor., 2008

ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.

Tianxiao Huan, Andrey Y. Sivachenko, Scott H. Harrison, Jake Yue Chen

BMC Bioinform., 2008

Mining disease-specific molecular association profiles from biomedical literature: a case study.

Jiao Li, Xiaoyan Zhu, Jake Yue Chen

Proceedings of the 2008 ACM Symposium on Applied Computing (SAC), 2008

Towards an integrative human pathway database for systems biology applications.

Harini N. Kasamsetty, Xiaogang Wu, Jake Yue Chen

Proceedings of the 2008 ACM Symposium on Applied Computing (SAC), 2008

Gene Selection using the GMM-IG Framework based Integrative Analysis.

Mingyi Wang, Jake Y. Chen

Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics, 2008

2007

DisProt: the Database of Disordered Proteins.

Megan Sickmeier, Justin A. Hamilton, Tanguy LeGall, Vladimir Vacic, Marc S. Cortese, Ágnes Tantos, Beáta Szabó, Peter Tompa, Jake Yue Chen, Vladimir N. Uversky, Zoran Obradovic, A. Keith Dunker

Nucleic Acids Res., 2007

A Systems Biology Approach to the Study of cisplatin Drug Resistance in Ovarian cancers.

Jake Yue Chen, Zhong Yan, Changyu Shen, Dawn P. G. Fitzpatrick, Mu Wang

J. Bioinform. Comput. Biol., 2007

A case study of integrating protein interaction data using semantic web technology.

Lavanya Dhanapalan, Jake Yue Chen

Int. J. Bioinform. Res. Appl., 2007

2006

An integrated computational proteomics method to extract protein targets for Fanconi Anemia studies.

Jake Yue Chen, Sarah L. Pinkerton, Changyu Shen, Mu Wang

Proceedings of the 2006 ACM Symposium on Applied Computing (SAC), 2006

Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome Data.

Jake Yue Chen, Changyu Shen, Andrey Y. Sivachenko

Proceedings of the Biocomputing 2006, 2006

2005

Oracle Database 10<i>g</i>: a platform for BLAST search and Regular Expression pattern matching in life sciences.

Susie Stephens, Jake Yue Chen, Marcel G. Davidson, Shiby Thomas, Barry M. Trute

Nucleic Acids Res., 2005

A complex biological database querying method.

Jake Yue Chen, John V. Carlis, Ning Gao

Proceedings of the 2005 ACM Symposium on Applied Computing (SAC), 2005

Discover True Association Rates in Multi-protein Complex Proteomics Data Sets.

Changyu Shen, Lang Li, Jake Yue Chen

Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005

2004

ODM BLAST: Sequence Homology Search in the RDBMS.

Susie Stephens, Jake Yue Chen, Shiby Thomas

IEEE Data Eng. Bull., 2004

Editorial message: special track on bioinformatics.

Warren T. Jones, Mathew J. Palakal, Jake Yue Chen

Proceedings of the 2004 ACM Symposium on Applied Computing (SAC), 2004

High-throughput Protein Interactome Data: Minable or Not?

Jake Yue Chen, Andrey Y. Sivachenko, Lang Li

Proceedings of the 4th ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2004), 2004

2003

Genomic data modeling.

Jake Yue Chen, John V. Carlis

Inf. Syst., 2003

Similar_Join: Extending DBMS with a Bio-specific Operator.

Jake Yue Chen, John V. Carlis

Proceedings of the 2003 ACM Symposium on Applied Computing (SAC), 2003

Initial Large-scale Exploration of Protein-protein Interactions in Human Brain.

Jake Yue Chen, Andrey Y. Sivachenko, Russell Bell, Cornelia Kurschner, Irene Ota, Sudhir Sahasrabudhe

Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003