Jake Yue Chen
Orcid: 0000-0001-8829-7504
According to our database1,
Jake Yue Chen
authored at least 96 papers
between 2003 and 2024.
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Online presence:
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Bibliography
2024
IEEE ACM Trans. Comput. Biol. Bioinform., 2024
PAGER-scFGA: unveiling cell functions and molecular mechanisms in cell trajectories through single-cell functional genomics analysis.
Frontiers Bioinform., 2024
23<sup>rd</sup> International Workshop on Data Mining in Bioinformatics (BIOKDD 2024).
Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2024
MLPA: A Multi-scale Digital Twin Framework for Personalized Cancer Simulation and Treatment Optimization.
Proceedings of the 15th ACM International Conference on Bioinformatics, 2024
2023
Proceedings of the Companion Proceedings of the ACM Web Conference 2023, 2023
Proceedings of the 29th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2023
Proceedings of the IEEE EMBS International Conference on Biomedical and Health Informatics, 2023
Proceedings of the 14th ACM International Conference on Bioinformatics, 2023
2022
IEEE ACM Trans. Comput. Biol. Bioinform., 2022
IEEE ACM Trans. Comput. Biol. Bioinform., 2022
Frontiers Big Data, 2022
DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features.
Bioinform., 2022
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.
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.
BMC Medical Informatics Decis. Mak., February, 2021
IEEE ACM Trans. Comput. Biol. Bioinform., 2021
IEEE ACM Trans. Comput. Biol. Bioinform., 2021
PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies.
Nucleic Acids Res., 2021
Polar Gini Curve: A Technique to Discover Gene Expression Spatial Patterns from Single-cell RNA-seq Data.
Genom. Proteom. Bioinform., 2021
Frontiers Artif. Intell., 2021
Corrigendum: Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples.
Frontiers Big Data, 2021
Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples.
Frontiers Big Data, 2021
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.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021
2020
IEEE ACM Trans. Comput. Biol. Bioinform., 2020
Empowering Team Science Across the Translational Spectrum with the UAB Biomedical Research Infrastructure Technology Enhancement (U-BRITE).
Proceedings of the 21st International Conference on Information Reuse and Integration for Data Science, 2020
2019
Quant. Biol., 2019
Nucleic Acids Res., 2019
Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information.
BMC Bioinform., 2019
2018
IEEE ACM Trans. Comput. Biol. Bioinform., 2018
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.
Nucleic Acids Res., 2018
2017
BMC Bioinform., 2017
2016
DTMBIO 2016: The Tenth International Workshop on Data and Text Mining in Biomedical Informatics.
Proceedings of the 25th ACM International Conference on Information and Knowledge Management, 2016
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.
BMC Bioinform., December, 2015
IEEE ACM Trans. Comput. Biol. Bioinform., 2015
Bioinform., 2015
Predictive and preventive models for diabetes prevention using clinical information in electronic health record.
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.
Int. J. Data Min. Bioinform., 2014
BMC Bioinform., 2014
Computational Identification of De-Centric Genetic Regulatory Relationships from Functional Genomic Data.
Proceedings of the Bioinformatics Research and Applications - 10th International Symposium, 2014
Constructing regulatory gene set networks to reveal novel insights into biological systems.
Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, 2014
Proceedings of the Approaches in Integrative Bioinformatics - Towards the Virtual Cell, 2014
2013
2012
Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays.
J. Integr. Bioinform., 2012
BMC Syst. Biol., 2012
BMC Bioinform., 2012
PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries.
BMC Bioinform., 2012
An evaluation for merging signaling pathways by using protein-protein interaction data.
Proceedings of the Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, 2012
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.
Genom. Proteom. Bioinform., 2011
An integrated proteomics analysis of bone tissues in response to mechanical stimulation.
BMC Syst. Biol., 2011
Personal genome privacy protection with feature-based hierarchical dual-stage encryption.
Proceedings of the 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, 2011
Proceedings of the 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, 2011
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011
Ethics and Privacy Considerations for Systems Biology Applications in Predictive and Personalized Medicine.
Proceedings of the Handbook of Research on Computational and Systems Biology, 2011
2010
IEEE ACM Trans. Comput. Biol. Bioinform., 2010
GeneTerrain: Visual exploration of differential gene expression profiles organized in native biomolecular interaction networks.
Inf. Vis., 2010
Int. J. Data Min. Bioinform., 2010
BMC Bioinform., 2010
Artif. Intell. Medicine, 2010
Breast cancer plasma protein biomarker discovery by coupling LC-MS/MS proteomics and systems biology.
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010
2009
Proceedings of the Biomedical Data and Applications, 2009
Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts.
PLoS Comput. Biol., 2009
Finding fractal patterns in molecular interaction networks: a case study in Alzheimer's disease.
Int. J. Comput. Biol. Drug Des., 2009
BMC Bioinform., 2009
Briefings Bioinform., 2009
Proceedings of the 2009 ACM Symposium on Applied Computing (SAC), 2009
Proceedings of the NBiS 2009, 2009
Toward Ontology-Driven Omics Data Integration in Current Database Management Systems.
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.
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.
Proceedings of the 2009 IEEE International Conference on Bioinformatics and Biomedicine, 2009
2008
SIGKDD Explor., 2008
ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.
BMC Bioinform., 2008
Mining disease-specific molecular association profiles from biomedical literature: a case study.
Proceedings of the 2008 ACM Symposium on Applied Computing (SAC), 2008
Proceedings of the 2008 ACM Symposium on Applied Computing (SAC), 2008
Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics, 2008
2007
A Systems Biology Approach to the Study of cisplatin Drug Resistance in Ovarian cancers.
J. Bioinform. Comput. Biol., 2007
Int. J. Bioinform. Res. Appl., 2007
2006
An integrated computational proteomics method to extract protein targets for Fanconi Anemia studies.
Proceedings of the 2006 ACM Symposium on Applied Computing (SAC), 2006
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.
Nucleic Acids Res., 2005
Proceedings of the 2005 ACM Symposium on Applied Computing (SAC), 2005
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005
2004
Proceedings of the 2004 ACM Symposium on Applied Computing (SAC), 2004
High-throughput Protein Interactome Data: Minable or Not?
Proceedings of the 4th ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2004), 2004
2003
Proceedings of the 2003 ACM Symposium on Applied Computing (SAC), 2003
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003