Jake Y. Chen

80 papers A* 5A 1B 1Misc 2Journal 49Unranked 20
YearRankTypeTitle / Venue / Authors
2026 J jnl
NeSyDPP-4: discovering DPP-4 inhibitors for diabetes treatment with a neuro-symbolic AI approach.
Frontiers Bioinform.
Delower Hossain, Ehsan Saghapour, Jake Y. Chen
2026 J jnl
Temporal GeneTerrain: advancing precision medicine through dynamic gene expression visualization.
Frontiers Bioinform.
Ehsan Saghapour, Rahul Sharma, Delower Hossain, Kevin Song, Zhandos Sembay, Jake Y. Chen
2025 — conf
24
KDD (2)
Da Yan, Truong-Son Hy, Jake Y. Chen, Mohammed J. Zaki
2025 J jnl
A Hybrid Chaos-Based Cryptographic Framework for Post-Quantum Secure Communications.
CoRR
Kevin Song, Noorullah Imran, Jake Y. Chen, Allan C. Dobbins
2025 J jnl
A Study on Neuro-Symbolic Artificial Intelligence: Healthcare Perspectives.
CoRR
Delower Hossain, Jake Y. Chen
2025 — conf
BioRSP: Angular Scanning for Directional Gene Expression Enrichment in Single-Cell Embeddings.
BCB
Zeyu Yao, Jake Y. Chen
2025 J jnl
Editorial: Outbreak oracles: how AI's journey through COVID-19 shapes future epidemic strategy.
Frontiers Artif. Intell.
Dmytro Chumachenko, Jasleen Kaur, Jake Y. Chen
2025 — conf
Generating Novel Linker Structures in Antibody-Drug Conjugates with Diffusion Models.
AIME (2)
April Cao, Jake Y. Chen
2025 J jnl
Guest Editorial for Selected Papers From BIOKDD 2023.
IEEE Trans. Comput. Biol. Bioinform.
Da Yan, Ariful Azad, Jie Hou, Jake Y. Chen
2025 J jnl
Interactive Graph Visualization and TeamingRecommendation in an Interdisciplinary Project'sTalent Knowledge Graph.
CoRR
Jiawei Xu, Juichien Chen, Yilin Ye, Zhandos Sembay, Swathi Thaker, Pamela Payne-Foster, Jake Y. Chen, Ying Ding
2025 J jnl
LLM Agent Swarm for Hypothesis-Driven Drug Discovery.
CoRR
Kevin Song, Andrew Trotter, Jake Y. Chen
2025 J jnl
Llama-Affinity: A Predictive Antibody Antigen Binding Model Integrating Antibody Sequences with Llama3 Backbone Architecture.
CoRR
Delower Hossain, Ehsan Saghapour, Kevin Song, Jake Y. Chen
2025 J jnl
Spatial multi-omics characterizes neuronal mimicry as a coherent hybrid state in glioblastoma.
Briefings Bioinform.
Claire Yuan, Jake Y. Chen
2024 A* conf
23
KDD
Da Yan, Ahmed Abdeen Hamed, Jake Y. Chen, Mohammed J. Zaki
2024 — conf
Decoding Patterns of Data Generation Teams for Clinical and Scientific Success: Insights from the Bridge2AI Talent Knowledge Graph.
JCDL
Jiawei Xu, Qingnan Xie, Meijun Liu, Zhandos Sembay, Swathi Thaker, Pamela Payne-Foster, Jake Y. Chen, Ying Ding
2024 J jnl
Guest Editorial Selected Papers From BIOKDD 2022.
IEEE ACM Trans. Comput. Biol. Bioinform.
Da Yan, Catia Pesquita, Carsten Görg, Jake Y. Chen
2024 A* conf
Health Day: Building Health AI Ecosystem: From Data Harmonization to Knowledge Discovery.
KDD
Jake Y. Chen, Peipei Ping
2024 — conf
MLPA: A Multi-scale Digital Twin Framework for Personalized Cancer Simulation and Treatment Optimization.
BCB
James Gu, Jake Y. Chen
2024 — conf
Mondrian Abstraction and Language Model Embeddings for Differential Pathway Analysis.
BIBM
Fuad Al Abir, Jake Y. Chen
2024 J jnl
PAGER-scFGA: unveiling cell functions and molecular mechanisms in cell trajectories through single-cell functional genomics analysis.
Frontiers Bioinform.
Fengyuan Huang, Robert S. Welner, Jake Y. Chen, Zongliang Yue
2023 A* conf
22nd International Workshop on Data Mining in Bioinformatics (BIOKDD 2023).
KDD
Da Yan, Ariful Azad, Jie Hou, Jake Y. Chen, Mohammed J. Zaki
2023 — conf
Accurate Identification of Human Emotional States from Images Using Deep Learning.
BHI
Emmy Yang, Jake Y. Chen
2023 — conf
Cross-Team Collaboration and Diversity in the Bridge2AI Project.
WWW (Companion Volume)
Huimin Xu, Chitrank Gupta, Zhandos Sembay, Swathi Thaker, Pamela Payne-Foster, Jake Y. Chen, Ying Ding
2022 A* conf
21th International Workshop on Data Mining in Bioinformatics (BIOKDD 2022).
KDD
Da Yan, Catia Pesquita, Carsten Görg, Jake Y. Chen, Mohammed J. Zaki
2022 — conf
GraphWaGu: GPU Powered Large Scale Graph Layout Computation and Rendering for the Web.
EGPGV@EuroVis
Landon Dyken, Pravin Poudel, Will Usher, Steve Petruzza, Jake Y. Chen, Sidharth Kumar
2022 J jnl
Guest Editorial for Selected Papers From BIOKDD 2020.
IEEE ACM Trans. Comput. Biol. Bioinform.
Da Yan, Hong Qin, Hsiang-Yun Wu, Jake Y. Chen
2022 J jnl
Guest Editorial for Selected Papers From BIOKDD 2021.
IEEE ACM Trans. Comput. Biol. Bioinform.
Da Yan, Zhaohui S. Qin, Debswapna Bhattacharya, Jake Y. Chen
2022 J jnl
WINNER: A network biology tool for biomolecular characterization and prioritization.
Frontiers Big Data
Thanh Nguyen, Zongliang Yue, Radomir Slominski, Robert S. Welner, Jianyi Zhang, Jake Y. Chen
2021 A* conf
20th International Workshop on Data Mining in Bioinformatics (BIOKDD 2021).
KDD
Da Yan, Steve Qin, Debswapna Bhattacharya, Jake Y. Chen, Mohammed J. Zaki
2021 J jnl
Corrigendum: Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples.
Frontiers Big Data
Thanh Nguyen, Samuel Bharti, Zongliang Yue, Christopher D. Willey, Jake Y. Chen
2021 J jnl
Editorial: AI-Enabled Data Science for COVID-19.
Frontiers Big Data
Da Yan, Hong Qin, Hsiang-Yun Wu, Jake Y. Chen
2021 J jnl
Editorial: Artificial Intelligence for Precision Medicine.
Frontiers Artif. Intell.
Jun Deng, Thomas Hartung, Enrico Capobianco, Jake Y. Chen, Frank Emmert-Streib
2021 J jnl
Guest Editorial for Selected Papers From BIOKDD 2019.
IEEE ACM Trans. Comput. Biol. Bioinform.
Da Yan, Sharma V. Thankachan, Jake Y. Chen
2021 J jnl
Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams.
BMC Medical Informatics Decis. Mak.
Thanh Nguyen, Tongbin Zhang, Geoffrey Fox, Sisi Zeng, Ni Cao, Chuandi Pan, Jake Y. Chen
2021 Misc conf
PAGER-CoV-Run: An online interactive analytical platform for COVID-19 functional genomic downstream analysis.
AMIA
Zongliang Yue, Nishant Batra, Hui-Chen Hsu, John Mountz, Jake Y. Chen
2021 J jnl
PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies.
Nucleic Acids Res.
Zongliang Yue, Eric Zhang, Clark Xu, Sunny Khurana, Nishant Batra, Son Do Hai Dang, James J. Cimino, Jake Y. Chen
2021 J jnl
Polar Gini Curve: A Technique to Discover Gene Expression Spatial Patterns from Single-cell RNA-seq Data.
Genom. Proteom. Bioinform.
Thanh Minh Nguyen, Jacob John Jeevan, Nuo Xu, Jake Y. Chen
2021 J jnl
Scalable De Novo Genome Assembly Using a Pregel-Like Graph-Parallel System.
IEEE ACM Trans. Comput. Biol. Bioinform.
Guimu Guo, Hongzhi Chen, Da Yan, James Cheng, Jake Y. Chen, Zechen Chong
2021 J jnl
Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples.
Frontiers Big Data
Thanh Nguyen, Samuel Bharti, Zongliang Yue, Christopher D. Willey, Jake Y. Chen
2020 Misc conf
Empowering Team Science Across the Translational Spectrum with the UAB Biomedical Research Infrastructure Technology Enhancement (U-BRITE).
IRI
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
2020 J jnl
Guest Editorial for Selected Papers from BIOKDD 2018 and DMBIH 2018.
IEEE ACM Trans. Comput. Biol. Bioinform.
Da Yan, Xin Gao, Samah J. Fodeh, Jake Y. Chen
2019 J jnl
BEERE: a web server for biomedical entity expansion, ranking and explorations.
Nucleic Acids Res.
Zongliang Yue, Christopher D. Willey, Anita B. Hjelmeland, Jake Y. Chen
2019 J jnl
Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information.
BMC Bioinform.
Zaixiang Tang, Shufeng Lei, Xinyan Zhang, Zixuan Yi, Boyi Guo, Jake Y. Chen, Yueping Shen, Nengjun Yi
2019 J jnl
WIPER: Weighted in-Path Edge Ranking for biomolecular association networks.
Quant. Biol.
Zongliang Yue, Thanh Nguyen, Eric Zhang, Jianyi Zhang, Jake Y. Chen
2018 J jnl
"Super Gene Set" Causal Relationship Discovery from Functional Genomics Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Zongliang Yue, Michael T. Neylon, Thanh Nguyen, Timothy Ratliff, Jake Y. Chen
2018 J jnl
Multiscale and Multimodal Analysis for Computational Biology.
IEEE ACM Trans. Comput. Biol. Bioinform.
Xin Gao, Jake Y. Chen, Mohammed J. Zaki
2018 J jnl
PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology.
Nucleic Acids Res.
Zongliang Yue, Qi Zheng, Michael T. Neylon, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, Jake Y. Chen
2017 J jnl
Repositioning drugs by targeting network modules: a Parkinson's disease case study.
BMC Bioinform.
Zongliang Yue, Itika Arora, Eric Y. Zhang, Vincent Laufer, S. Louis Bridges, Jake Y. Chen
2016 A conf
DTMBIO 2016: The Tenth International Workshop on Data and Text Mining in Biomedical Informatics.
CIKM
Sangwoo Kim, Jake Y. Chen, Vincenzo Cutello, Doheon Lee
2016 — conf
Towards constructing "Super Gene Sets" regulatory networks.
BIBM
Jake Y. Chen, Zongliang Yue, Michael T. Neylon, Thanh Nguyen, Nafisa Bulsara, Itika Arora, Timothy Ratliff
2015 J jnl
DMAP: a connectivity map database to enable identification of novel drug repositioning candidates.
BMC Bioinform.
Hui Huang, Thanh Nguyen, Sara Ibrahim, Sandeep Shantharam, Zongliang Yue, Jake Y. Chen
2015 J jnl
Knowledge Discovery Using Big Data in Biomedical Systems.
IEEE ACM Trans. Comput. Biol. Bioinform.
Sarath Chandra Janga, Dongxiao Zhu, Jake Y. Chen, Mohammed J. Zaki
2014 — conf
Computational Identification of De-Centric Genetic Regulatory Relationships from Functional Genomic Data.
ISBRA
Zongliang Yue, Ping Wan, Zhan Xie, Jake Y. Chen
2014 — conf
Constructing regulatory gene set networks to reveal novel insights into biological systems.
ICCABS
Chayaporn Suphavilai, Liugen Zhu, Jake Y. Chen
2014 J jnl
Seed-weighted random walk ranking for cancer biomarker prioritisation: a case study in leukaemia.
Int. J. Data Min. Bioinform.
Tianxiao Huan, Xiaogang Wu, Zengliang Bai, Jake Y. Chen
2013 J jnl
Semantic Web meets Integrative Biology: a survey.
Briefings Bioinform.
Huajun Chen, Tong Yu, Jake Y. Chen
2012 — conf
An evaluation for merging signaling pathways by using protein-protein interaction data.
GENSiPS
Xiaogang Wu, Jake Y. Chen
2012 J jnl
Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes.
BMC Syst. Biol.
Paul J. Hale, Alfredo M. López-Yunez, Jake Y. Chen
2012 — conf
Multi-biomarker panel selection on a GPU.
EIT
David Johnson, Brandon Shafer, Jaehwan John Lee, Jake Y. Chen
2012 J jnl
Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays.
J. Integr. Bioinform.
Xiaogang Wu, Hui Huang, Tao Wei, Ragini Pandey, Christoph Reinhard, Shuyu D. Li, Jake Y. Chen
2012 J jnl
PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries.
BMC Bioinform.
Hui Huang, Xiaogang Wu, Madhankumar Sonachalam, Sammed N. Mandape, Ragini Pandey, Karl F. MacDorman, Ping Wan, Jake Y. Chen
2012 J jnl
Reordering based integrative expression profiling for microarray classification.
BMC Bioinform.
Xiaogang Wu, Hui Huang, Madhankumar Sonachalam, Sina Reinhard, Jeffrey Shen, Ragini Pandey, Jake Y. Chen
2011 J jnl
An integrated proteomics analysis of bone tissues in response to mechanical stimulation.
BMC Syst. Biol.
Jiliang Li, Fan Zhang, Jake Y. Chen
2011 J jnl
Computational Analysis of Drought Stress-Associated miRNAs and miRNA Co-Regulation Network in Physcomitrella patens.
Genom. Proteom. Bioinform.
Ping Wan, Jun Wu, Yuan Zhou, Junshu Xiao, Jie Feng, Weizhong Zhao, Shen Xiang, Guanglong Jiang, Jake Y. Chen
2011 — ch.
Ethics and Privacy Considerations for Systems Biology Applications in Predictive and Personalized Medicine.
Handbook of Research on Computational and Systems Biology
Jake Y. Chen, Heng Xu, Pan Shi, Adam Culbertson, Eric M. Meslin
2011 J jnl
HOMER: a human organ-specific molecular electronic repository.
BMC Bioinform.
Fan Zhang, Jake Y. Chen
2011 J jnl
New threats to health data privacy.
BMC Bioinform.
Fengjun Li, Xukai Zou, Peng Liu, Jake Y. Chen
2011 — conf
Personal genome privacy protection with feature-based hierarchical dual-stage encryption.
GENSiPS
Xukai Zou, Peng Liu, Jake Y. Chen
2011 — conf
Predicting drug efficacy based on the integrated breast cancer pathway model.
GENSiPS
Hui Huang, Xiaogang Wu, Sara Ibrahim, Marianne McKenzie, Jake Y. Chen
2010 J jnl
A GMM-IG framework for selecting genes as expression panel biomarkers.
Artif. Intell. Medicine
Mingyi Wang, Jake Y. Chen
2010 — conf
Breast cancer plasma protein biomarker discovery by coupling LC-MS/MS proteomics and systems biology.
BCB
Fan Zhang, Mu Wang, Jake Y. Chen
2010 J jnl
PEPPI: a peptidomic database of human protein isoforms for proteomics experiments.
BMC Bioinform.
Ao Zhou, Fan Zhang, Jake Y. Chen
2009 B conf
A neural network approach to multi-biomarker panel development based on LC/MS/MS proteomics profiles: A case study in breast cancer.
CBMS
Fan Zhang, Jake Y. Chen
2009 — ch.
Design of an Online Physician-Mediated Personal Health Record System.
Biomedical Data and Applications
Jake Y. Chen, Shailaja Taduri, Frank Lloyd
2009 J jnl
Finding fractal patterns in molecular interaction networks: a case study in Alzheimer's disease.
Int. J. Comput. Biol. Drug Des.
Xiaogang Wu, Tianxiao Huan, Ragini Pandey, Tianshou Zhou, Jake Y. Chen
2009 J jnl
HPD: an online integrated human pathway database enabling systems biology studies.
BMC Bioinform.
Sudhir R. Chowbina, Xiaogang Wu, Fan Zhang, Peter M. Li, Ragini Pandey, Harini N. Kasamsetty, Jake Y. Chen
2009 — conf
RIC: Ranking with Interaction Chains and Its Application in Computational Clinical Proteomics Studies.
BIBM
Jieun Jeong, Jake Y. Chen
2009 — conf
Toward Ontology-Driven Omics Data Integration in Current Database Management Systems.
NBiS
John A. Springer, Jake Y. Chen
2008 J jnl
BIOKDD 2008: a workshop report on data mining in bioinformatics.
SIGKDD Explor.
Jake Y. Chen, Mohammed Javeed Zaki, Stefano Lonardi
2008 — conf
Gene Selection using the GMM-IG Framework based Integrative Analysis.
BMEI (1)
Mingyi Wang, Jake Y. Chen