Jake Y. Chen

Publication Activity (10 Years)

Years Active: 2008-2024
Publications (10 Years): 33

Top Topics

Functional Genomics

International Workshop

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Frontiers Big Data

Publications

Fengyuan Huang, Robert S. Welner, Jake Y. Chen, Zongliang Yue
PAGER-scFGA: unveiling cell functions and molecular mechanisms in cell trajectories through single-cell functional genomics analysis. Frontiers Bioinform. 4 (2024)
Da Yan, Ahmed Abdeen Hamed, Jake Y. Chen, Mohammed J. Zaki
International Workshop on Data Mining in Bioinformatics (BIOKDD 2024). KDD (2024)
Da Yan, Ariful Azad, Jie Hou, Jake Y. Chen, Mohammed J. Zaki
22nd International Workshop on Data Mining in Bioinformatics (BIOKDD 2023). KDD (2023)
Emmy Yang, Jake Y. Chen
Accurate Identification of Human Emotional States from Images Using Deep Learning. BHI (2023)
Da Yan, Hong Qin, Hsiang-Yun Wu, Jake Y. Chen
Guest Editorial for Selected Papers From BIOKDD 2020. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (5) (2022)
Landon Dyken, Pravin Poudel, Will Usher, Steve Petruzza, Jake Y. Chen, Sidharth Kumar
GraphWaGu: GPU Powered Large Scale Graph Layout Computation and Rendering for the Web. EGPGV@EuroVis (2022)
Da Yan, Catia Pesquita, Carsten Görg, Jake Y. Chen, Mohammed J. Zaki
21th International Workshop on Data Mining in Bioinformatics (BIOKDD 2022). KDD (2022)
Thanh Nguyen, Zongliang Yue, Radomir Slominski, Robert Welner, Jianyi Zhang, Jake Y. Chen
WINNER: A network biology tool for biomolecular characterization and prioritization. Frontiers Big Data 5 (2022)
Da Yan, Zhaohui S. Qin, Debswapna Bhattacharya, Jake Y. Chen
Guest Editorial for Selected Papers From BIOKDD 2021. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (6) (2022)
Thanh Nguyen, Tongbin Zhang, Geoffrey Fox, Sisi Zeng, Ni Cao, Chuandi Pan, Jake Y. Chen
Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams. BMC Medical Informatics Decis. Mak. (3) (2021)
Jun Deng, Thomas Hartung, Enrico Capobianco, Jake Y. Chen, Frank Emmert-Streib
Editorial: Artificial Intelligence for Precision Medicine. Frontiers Artif. Intell. 4 (2021)
Da Yan, Hong Qin, Hsiang-Yun Wu, Jake Y. Chen
Editorial: AI-Enabled Data Science for COVID-19. Frontiers Big Data 4 (2021)
Zongliang Yue, Nishant Batra, Hui-Chen Hsu, John Mountz, Jake Y. Chen
PAGER-CoV-Run: An online interactive analytical platform for COVID-19 functional genomic downstream analysis. AMIA (2021)
Thanh Nguyen, Samuel Bharti, Zongliang Yue, Christopher D. Willey, Jake Y. Chen
Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples. Frontiers Big Data 4 (2021)
Zongliang Yue, Eric Zhang, Clark Xu, Sunny Khurana, Nishant Batra, Son Do Hai Dang, James J. Cimino, Jake Y. Chen
PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies. Nucleic Acids Res. 49 (Database-Issue) (2021)
Thanh Minh Nguyen, Jacob John Jeevan, Nuo Xu, Jake Y. Chen
Polar Gini Curve: A Technique to Discover Gene Expression Spatial Patterns from Single-cell RNA-seq Data. Genom. Proteom. Bioinform. 19 (3) (2021)
Guimu Guo, Hongzhi Chen, Da Yan, James Cheng, Jake Y. Chen, Zechen Chong
Scalable De Novo Genome Assembly Using a Pregel-Like Graph-Parallel System. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (2) (2021)
Da Yan, Steve Qin, Debswapna Bhattacharya, Jake Y. Chen, Mohammed J. Zaki
20th International Workshop on Data Mining in Bioinformatics (BIOKDD 2021). KDD (2021)
Thanh Nguyen, Samuel Bharti, Zongliang Yue, Christopher D. Willey, Jake Y. Chen
Corrigendum: Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples. Frontiers Big Data 4 (2021)
Da Yan, Sharma V. Thankachan, Jake Y. Chen
Guest Editorial for Selected Papers From BIOKDD 2019. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (3) (2021)
Da Yan, Xin Gao, Samah J. Fodeh, Jake Y. Chen
Guest Editorial for Selected Papers from BIOKDD 2018 and DMBIH 2018. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (6) (2020)
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
Empowering Team Science Across the Translational Spectrum with the UAB Biomedical Research Infrastructure Technology Enhancement (U-BRITE). IRI (2020)
Zongliang Yue, Thanh Nguyen, Eric Zhang, Jianyi Zhang, Jake Y. Chen
WIPER: Weighted in-Path Edge Ranking for biomolecular association networks. Quant. Biol. 7 (4) (2019)
Zongliang Yue, Christopher D. Willey, Anita B. Hjelmeland, Jake Y. Chen
BEERE: a web server for biomedical entity expansion, ranking and explorations. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Zaixiang Tang, Shufeng Lei, Xinyan Zhang, Zixuan Yi, Boyi Guo, Jake Y. Chen, Yueping Shen, Nengjun Yi
Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information. BMC Bioinform. 20 (1) (2019)
Zongliang Yue, Qi Zheng, Michael T. Neylon, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, Jake Y. Chen
PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. Nucleic Acids Res. 46 (Database-Issue) (2018)
Zongliang Yue, Michael T. Neylon, Thanh Nguyen, Timothy Ratliff, Jake Y. Chen
"Super Gene Set" Causal Relationship Discovery from Functional Genomics Data. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (6) (2018)
Xin Gao, Jake Y. Chen, Mohammed J. Zaki
Multiscale and Multimodal Analysis for Computational Biology. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (6) (2018)
Zongliang Yue, Itika Arora, Eric Y. Zhang, Vincent Laufer, S. Louis Bridges, Jake Y. Chen
Repositioning drugs by targeting network modules: a Parkinson's disease case study. BMC Bioinform. 18 (14) (2017)
Sangwoo Kim, Jake Y. Chen, Vincenzo Cutello, Doheon Lee
DTMBIO 2016: The Tenth International Workshop on Data and Text Mining in Biomedical Informatics. CIKM (2016)
Jake Y. Chen, Zongliang Yue, Michael T. Neylon, Thanh Nguyen, Nafisa Bulsara, Itika Arora, Timothy Ratliff
Towards constructing "Super Gene Sets" regulatory networks. BIBM (2016)
Sarath Chandra Janga, Dongxiao Zhu, Jake Y. Chen, Mohammed J. Zaki
Knowledge Discovery Using Big Data in Biomedical Systems. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (4) (2015)
Hui Huang, Thanh Nguyen, Sara Ibrahim, Sandeep Shantharam, Zongliang Yue, Jake Y. Chen
DMAP: a connectivity map database to enable identification of novel drug repositioning candidates. BMC Bioinform. 16 (S13) (2015)
Chayaporn Suphavilai, Liugen Zhu, Jake Y. Chen
Constructing regulatory gene set networks to reveal novel insights into biological systems. ICCABS (2014)
Tianxiao Huan, Xiaogang Wu, Zengliang Bai, Jake Y. Chen
Seed-weighted random walk ranking for cancer biomarker prioritisation: a case study in leukaemia. Int. J. Data Min. Bioinform. 9 (2) (2014)
Zongliang Yue, Ping Wan, Zhan Xie, Jake Y. Chen
Computational Identification of De-Centric Genetic Regulatory Relationships from Functional Genomic Data. ISBRA (2014)
Huajun Chen, Tong Yu, Jake Y. Chen
Semantic Web meets Integrative Biology: a survey. Briefings Bioinform. 14 (1) (2013)
David Johnson, Brandon Shafer, Jaehwan John Lee, Jake Y. Chen
Multi-biomarker panel selection on a GPU. EIT (2012)
Xiaogang Wu, Hui Huang, Tao Wei, Ragini Pandey, Christoph Reinhard, Shuyu D. Li, Jake Y. Chen
Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays. J. Integr. Bioinform. 9 (2) (2012)
Paul J. Hale, Alfredo M. López-Yunez, Jake Y. Chen
Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes. BMC Syst. Biol. 6 (S-3) (2012)
Xiaogang Wu, Hui Huang, Madhankumar Sonachalam, Sina Reinhard, Jeffrey Shen, Ragini Pandey, Jake Y. Chen
Reordering based integrative expression profiling for microarray classification. BMC Bioinform. 13 (S-2) (2012)
Hui Huang, Xiaogang Wu, Madhankumar Sonachalam, Sammed N. Mandape, Ragini Pandey, Karl F. MacDorman, Ping Wan, Jake Y. Chen
PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries. BMC Bioinform. 13 (S-15) (2012)
Xiaogang Wu, Jake Y. Chen
An evaluation for merging signaling pathways by using protein-protein interaction data. GENSiPS (2012)
Jiliang Li, Fan Zhang, Jake Y. Chen
An integrated proteomics analysis of bone tissues in response to mechanical stimulation. BMC Syst. Biol. 5 (S-3) (2011)
Fengjun Li, Xukai Zou, Peng Liu, Jake Y. Chen
New threats to health data privacy. BMC Bioinform. 12 (S-12) (2011)
Hui Huang, Xiaogang Wu, Sara Ibrahim, Marianne McKenzie, Jake Y. Chen
Predicting drug efficacy based on the integrated breast cancer pathway model. GENSiPS (2011)
Fan Zhang, Jake Y. Chen
HOMER: a human organ-specific molecular electronic repository. BMC Bioinform. 12 (S-10) (2011)
Ping Wan, Jun Wu, Yuan Zhou, Junshu Xiao, Jie Feng, Weizhong Zhao, Shen Xiang, Guanglong Jiang, Jake Y. Chen
Computational Analysis of Drought Stress-Associated miRNAs and miRNA Co-Regulation Network in Physcomitrella patens. Genom. Proteom. Bioinform. 9 (1-2) (2011)
Xukai Zou, Peng Liu, Jake Y. Chen
Personal genome privacy protection with feature-based hierarchical dual-stage encryption. GENSiPS (2011)
Ao Zhou, Fan Zhang, Jake Y. Chen
PEPPI: a peptidomic database of human protein isoforms for proteomics experiments. BMC Bioinform. 11 (S-6) (2010)
Mingyi Wang, Jake Y. Chen
A GMM-IG framework for selecting genes as expression panel biomarkers. Artif. Intell. Medicine 48 (2-3) (2010)
Fan Zhang, Mu Wang, Jake Y. Chen
Breast cancer plasma protein biomarker discovery by coupling LC-MS/MS proteomics and systems biology. BCB (2010)
John A. Springer, Jake Y. Chen
Toward Ontology-Driven Omics Data Integration in Current Database Management Systems. NBiS (2009)
Jieun Jeong, Jake Y. Chen
RIC: Ranking with Interaction Chains and Its Application in Computational Clinical Proteomics Studies. BIBM (2009)
Fan Zhang, Jake Y. Chen
A neural network approach to multi-biomarker panel development based on LC/MS/MS proteomics profiles: A case study in breast cancer. CBMS (2009)
Xiaogang Wu, Tianxiao Huan, Ragini Pandey, Tianshou Zhou, Jake Y. Chen
Finding fractal patterns in molecular interaction networks: a case study in Alzheimer's disease. Int. J. Comput. Biol. Drug Des. 2 (4) (2009)
Sudhir R. Chowbina, Xiaogang Wu, Fan Zhang, Peter M. Li, Ragini Pandey, Harini N. Kasamsetty, Jake Y. Chen
HPD: an online integrated human pathway database enabling systems biology studies. BMC Bioinform. 10 (S-11) (2009)
Mingyi Wang, Jake Y. Chen
Gene Selection using the GMM-IG Framework based Integrative Analysis. BMEI (1) (2008)
Jake Y. Chen, Mohammed Javeed Zaki, Stefano Lonardi
BIOKDD 2008: a workshop report on data mining in bioinformatics. SIGKDD Explor. 10 (2) (2008)