Jake Yue Chen

According to our database1, Jake Yue Chen authored at least 66 papers between 2003 and 2019.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.



In proceedings 
PhD thesis 


On csauthors.net:


Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information.
BMC Bioinformatics, 2019

"Super Gene Set" Causal Relationship Discovery from Functional Genomics Data.
IEEE/ACM Trans. Comput. Biology Bioinform., 2018

Multiscale and Multimodal Analysis for Computational Biology.
IEEE/ACM Trans. Comput. Biology Bioinform., 2018

PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology.
Nucleic Acids Research, 2018

Repositioning drugs by targeting network modules: a Parkinson's disease case study.
BMC Bioinformatics, 2017

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

Towards constructing "Super Gene Sets" regulatory networks.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Knowledge Discovery Using Big Data in Biomedical Systems.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015

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

Seed-weighted random walk ranking for cancer biomarker prioritisation: a case study in leukaemia.
IJDMB, 2014

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

Computational Biomarker Discovery.
Proceedings of the Approaches in Integrative Bioinformatics - Towards the Virtual Cell, 2014

Semantic Web meets Integrative Biology: a survey.
Briefings in Bioinformatics, 2013

Biological knowledge discovery and data mining.
Scientific Programming, 2012

Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays.
J. Integrative Bioinformatics, 2012

Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes.
BMC Systems Biology, 2012

Reordering based integrative expression profiling for microarray classification.
BMC Bioinformatics, 2012

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

Multi-biomarker panel selection on a GPU.
Proceedings of the 2012 IEEE International Conference on Electro/Information Technology, 2012

Computational Analysis of Drought Stress-Associated miRNAs and miRNA Co-Regulation Network in Physcomitrella patens.
Genomics, Proteomics & Bioinformatics, 2011

An integrated proteomics analysis of bone tissues in response to mechanical stimulation.
BMC Systems Biology, 2011

HOMER: a human organ-specific molecular electronic repository.
BMC Bioinformatics, 2011

New threats to health data privacy.
BMC Bioinformatics, 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

Predicting drug efficacy based on the integrated breast cancer pathway model.
Proceedings of the 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, 2011

A Network Biology Approach to Predicting Drug Cardiotoxicity.
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

Data Mining in Bioinformatics: Selected Papers from BIOKDD.
IEEE/ACM Trans. Comput. Biology Bioinform., 2010

GeneTerrain: Visual exploration of differential gene expression profiles organized in native biomolecular interaction networks.
Information Visualization, 2010

Discovering breast cancer drug candidates from biomedical literature.
IJDMB, 2010

PEPPI: a peptidomic database of human protein isoforms for proteomics experiments.
BMC Bioinformatics, 2010

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

Design of an Online Physician-Mediated Personal Health Record System.
Proceedings of the Biomedical Data and Applications, 2009

Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts.
PLoS Computational Biology, 2009

Finding fractal patterns in molecular interaction networks: a case study in Alzheimer's disease.
I. J. Computational Biology and Drug Design, 2009

HPD: an online integrated human pathway database enabling systems biology studies.
BMC Bioinformatics, 2009

Semantic web for integrated network analysis in biomedicine.
Briefings in Bioinformatics, 2009

Construct anticancer drug-drug correlation network.
Proceedings of the 2009 ACM Symposium on Applied Computing (SAC), 2009

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

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

ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.
BMC Bioinformatics, 2008

Mining disease-specific molecular association profiles from biomedical literature: a case study.
Proceedings of the 2008 ACM Symposium on Applied Computing (SAC), 2008

Towards an integrative human pathway database for systems biology applications.
Proceedings of the 2008 ACM Symposium on Applied Computing (SAC), 2008

Gene Selection using the GMM-IG Framework based Integrative Analysis.
Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics, 2008

DisProt: the Database of Disordered Proteins.
Nucleic Acids Research, 2007

A Systems Biology Approach to the Study of cisplatin Drug Resistance in Ovarian cancers.
J. Bioinformatics and Computational Biology, 2007

A case study of integrating protein interaction data using semantic web technology.
IJBRA, 2007

An integrated computational proteomics method to extract protein targets for Fanconi Anemia studies.
Proceedings of the 2006 ACM Symposium on Applied Computing (SAC), 2006

Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome Data.
Proceedings of the Biocomputing 2006, 2006

Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences.
Nucleic Acids Research, 2005

A complex biological database querying method.
Proceedings of the 2005 ACM Symposium on Applied Computing (SAC), 2005

Discover True Association Rates in Multi-protein Complex Proteomics Data Sets.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005

ODM BLAST: Sequence Homology Search in the RDBMS.
IEEE Data Eng. Bull., 2004

Editorial message: special track on bioinformatics.
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

Genomic data modeling.
Inf. Syst., 2003

Similar_Join: Extending DBMS with a Bio-specific Operator.
Proceedings of the 2003 ACM Symposium on Applied Computing (SAC), 2003

Initial Large-scale Exploration of Protein-protein Interactions in Human Brain.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003