Professor Yi-Ping Phoebe Chen
Professor and Chair & Director of Research
Faculty of Science, Technology and Engineering
School of Engineering and Mathematical Sciences
Department of Computer Science and Computer Engineering
ARC Centre of Excellence in Bioinformatics
Beth Gleeson, Room 239, Melbourne (Bundoora)
BEE (NTUT), GradCert (HighEd) QUT, BInfTech (UQ), BInfTech (Hon H1A) UQ, PhD (CS) UQ
Membership of professional associations
Area of study
Professor Yi-Ping Phoebe Chen is Professor and Chair at the Department of Computer Science and Computer Engineering, La Trobe University, Melbourne Australia since April 2010. Prof. Chen is also the Director of Research, Department of Computer Science and Computer Engineering, La Trobe University. She was Head of Department from Sep 2010 to April 2012. Professor Phoebe Chen hosts the ARC Centre of Excellence in Bioinformatics from 2008-2010 and ARC Centre in Bioinformatics from 2003 to 2007. Prof Phoebe is a senior visiting professor of Fudan University Shanghai China, adjunct professor of National Chiao Tung University, Hsinchu, Taiwan and adjunct professor of National Taiwan Ocean University. Phoebe is a senior member of IEEE, member of ACM.
Phoebe finished her Bachelor of Information Technology degree in School of Information Technology and Electrical Engineering of the University of Queensland (UQ), in Brisbane, Australia. After that she finished Honours (First Class) in Information Technology in UQ. Phoebe received her Ph.D. degree in the area of Computer Science (Bioinformatics) in University of Queensland. Phoebe also finished Graduate Certificate in Higher Education from Queensland University of Technology (QUT).
Phoebe has been awarded 24 research grants around 8 millions (include 12 prestigious Australia Research Council (ARC) Grants) so far. Recently, Phoebe just received one ARC Discovery project from 2013 -2015. Phoebe received one ARC Centre of Excellence in Bioinformatics as project leader and chief investigator from 2008-2010, ARC Discovery - Exploiting Database Technologies for the Visualization and Analysis of Measured and Simulated Plant Structures in Bioinformatics as a sole Chief Investigator (CI) and one ARC Linkage-International - Development of Knowledge Discovery for High Dimensional Biomedical Data 2004 round and from 2005-2007. Phoebe is also the Principal Chief Investigator (CI) and Project Leader for an ARC large Discovery Grant (Previous ARC Large) on Integrating Database Technologies and Visual Analysis in Bioinformatics for Genome Data. Phoebe is also CI and QUT Manager of an ARC Large Linkage-Infrastructure grant on Computational infrastructure for high-throughput genome bioinformatics. She is a sole CI of ARC Linkage Project Grant on Design and Development of a Web-based Intelligent Multimedia Mining System. She is also a CI of successful ARC Centre in Bioinformatics. Prof. Chen is also three ARC Network Seeding Grants CIs. Most of them are in Bioinformatics and Multimedia field.
Phoebe published widely. She has presented her research at various international and national conferences. Phoebe have published more than 185 refereed publications in recent years. These papers appeared in high standing publications such as Journal Papers include Nucleic Acids Research, Aging Cell, BMC Genomics, BMC Bioinformatics, Current Drug Metabolism, Data Mining and Knowledge Discovery, IEEE Transactions on Knowledge and Data Engineering, Information Systems, IEEE Multimedia, ACM Transactions on Multimedia Computing, Communications and Applications etc. Phoebe is an editor for several journal issues and proceedings: Bioinformatics in Asia-Pacific, Bioinformatics 2003, Bioinformatics 2004, Bioinformatics 2005, Multimedia Modelling 2004, Multimedia Modelling 2005, Biomedical Visualization, Data Mining in Bioinformatics and Advanced Techniques for Bioinformatics. Phoebe's new book Bioinformatics Technologies (Springer) has just published on Jan 2005.
Artificial intelligence research
- Artifical intelligence and siginal processing
- computational infrastructure for high-throughput genome bioinformatics
Bioinformatics and biometric security
- Smart pattern recognition systems
Computational intelligence and multimedia technologies
- development of an integrated intelligent multimedia and game mining system
Databases and information system
- Exploiting Database Technologies for the Visualization and Analysis of Measured and Simulated Applications
CSE5BIO - Bioinformatics Technologies
CSE4DMI - Data Mining
Some Recent Selected Journal Publications: (more publications by year)
Bioinformatics / Computational Biology / System Biology
- Yuan Y, Chen YPP, Boyd-Kirkup J, Khaitovich P and Somel M, Accelerated aging-related transcriptome changes in the female prefrontal cortex, Aging Cell, 11(5):894-901, 2012. [link]
Mazin P, Xiong J, Liu X, Yan Z, Zhang X, Li M, He L, Somel M, Yuan Y, Chen YPP, Li N, Hu Y, Fu N, Ning Z, Zeng R, Yang H, Chen W, Gelfand M and Khaitovich P, Widespread splicing changes in human brain development and aging, Molecular Systems Biology, 9:633, 2013. [Link]
Kalyaanamoorthy, S. Chen YPP*, Exploring Inhibitor Release Pathways in Histone Deacetylase Using Random Acceleration Molecular Dynamics Simulation, Journal of Chemical Information and Modeling, 52 (2): 589–603, 2012. [link]
Lee CC, Lo WC, Lai SM, Chen YPP, Tang CY and Lyu PC, Metabolic classification of microbial genomes using functional probes, BMC Genomics, 13:157.2012. [Link]
Chiu JKH, Chen YPP*, Conformational Features of Topologically Classified RNA Secondary Structures, PLoS ONE, 7(7): e39907, 2012. [Link]
ZHU W, HOU J, and CHEN YPP*, Exploiting Multi-Layered Information to Iteratively Predict Protein Functions, Mathematical Biosciences, 236 (2): 108–116, 2012. [Link]
Kalyaanamoorthy S, Chen YPP*, Structure-based drug design to augment hit discovery, Drug Discovery Today, 16(17-18):831-839, 2011. [Link]
Chen Q, Chen YPP*, Modeling Conserved Structure Patterns for Functional Noncoding RNA. IEEE Transactions on Biomedical Engineering, 58(6):1528-1533, 2011.
Zhu W., Hou J., and Chen YPP*, Semantic and layered protein function prediction from PPI networks, Journal of Theoretical Biology, 267(2): 129-136, 2011.
Chen Q, Li G, Chen YPP*, Interval-Based Distance Function for Identifying RNA Structure Candidates, Journal of Theoretical Biology, 269(8): 280-286, 2011.
Yuan Y, Chen YPP*, Ni S, Xu AG, Tang L, Vingron M, Somel M, Khaitovich P, Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series, BMC Bioinformatics, 12:347, 2011.
Chen F and Chen YPP*, Exploring cross-species related miRNAs based on Sequence and secondary structure. IEEE Transactions on Biomedical Engineering, 57(7) 1547 – 1553, 2010.
- Chen Q. Chen YPP*, Mining Characteristic Relations Bind to RNA Secondary Structures, IEEE Transactions on Information Technology in Biomedicine 14(1):10-15, 2010.
- Chen YPP*, Chen F, Using Bioinformatics Techniques for Gene Identification in Drug Discovery and Development, Current Drug Metabolism 9(6): 567-573, 2008.
- An J, Chen YPP*, Chen H, DDR: An Index Method for Large Time Series Datasets, Information Systems, 30:333-348 (2005).
- Knapp K. Chen YPP* An Evaluation of Contemporary Hidden Markov Model Genefinders with a Predicted Exon Taxonomy, Nucleic Acids Research 35: 317-324 (2007) [pdf].
- Mann S, Li J, Chen YPP*, A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts, Nucleic Acids Research. 35: e12 1-7 (2007) [pdf].
- Chen Q. Chen YPP*, Discovery of Structural and Functional Features in RNA Pseudoknots, IEEE Transactions on Knowledge and Data Engineering, 21(7):974-984, 2009.
- Knapp K, Chonka A, and Chen YPP*, POEM, a 3-Dimensional Exon Taxonomy and Patterns in Untranslated Exons, BMC Genomics 2008, 9:428.
- Xi Y, Chen YPP, Cao M, Wang W and Wang F, Analysis on relationship between extreme pathways and correlated reaction sets. BMC Bioinformatics 2009, 10(S1):S58.
- Chen Q. Chen YPP*, Mining Frequent Patterns for AMP-activated Protein Kinase Regulation on Skeletal Muscle, BMC Bioinformatics 2006, 7:394. [pdf]
- Chen Q. Chen YPP*, and Zhang C., Detecting Inconsistency in Biological Molecular Databases using Ontology, Data Mining and Knowledge Discovery 15(2): 275-296. (2007) [pdf]
- Jiang D, Zhou S, Chen YPP, Compensatory ability to null mutation in metabolic networks, Biotechnology and Bioengineering, 103(2):361-369, 2009. [pdf]
- An J and Chen YPP*, Finding Edging Genes From Microarray Data, Journal of Biotechnology, 135(3):233-240, 2008.
- Xi Y, Chen YPP, Qian C. and Wang F, Comparative study of computational methods to detect the correlated reaction sets in biochemical networks, Briefings in Bioinformatics,1-19, 2010; doi: 10.1093/bib/bbp068.
- Chen YPP*, Chen F, Targets for Drug Discovery using Bioinformatics, Expert Opinion on Therapeutic Targets, 2008:12(4): 383-389.
- Chen Y. Timms P and Chen YPP*,CIDB: Chlamydia Interactive Database for cross-querying genomics, transcriptomics and proteomics data, Biomolecular Engineering 24(6):603-608, 2007.[pdf].
- Chen YPP, Prompramote S., Maire F. MDSM: Microarray Database Schema Matching By Using Hungarian Method , Information Sciences, 176:2771-2790 (2006).
- Nahar J., Ali S. Chen YPP*, Microarray Data Classification Using Automatic SVM Kernel Selection, DNA and Cell Biology, 26(10):707-712, 2007.[pdf]
- An J, Chen YPP*, Finding rule groups to classify high dimensional gene expression datasets, Computational Biology and Chemistry 33(1):108-113, 2009.
Chen, YPP. Ed., Bioinformatics Technologies, Springer - 2005. p396. SCI.
Multimedia Information Retrieval, Data Mining, Intelligent System and Scientific Visualization
- BEGLEY S, ZHEN H, CHEN YPP (2012) “MCJoin: A memory-constrained join for column-based main-memory databases” [PDF], the ACM 39th International Conference on Management of Data, ACM SIGMOD 2012, 121-132. Scottsdale, Arizona, USA, 20-24 May 2012. [Link]
- CHEN Q, CHEN YPP, Discovering Inhibition Pathways for Protein Kinases, IEEE Intelligent Systems, 27(5): 19-26, 2012.
- NGUYEN, T; ZHEN H, CHEN YPP, SeTPR*-tree: Efficient Buffering for Spatiotemporal Indexes Via Shared Execution, The Computer Journal, 56(1):115-137, 2013.
- Yang L, Zhen H, Chen YPP, Nguyen T, External Sorting on Flash Memory Via Natural Page Run Generation, The Computer Journal, 54(11): 1882-1990, 2011.
- Tjondronegoro, D, Chen, YPP*, Knowledge-discounted Event Detection in Sports Video, IEEE Transactions on Systems Man & Cybernetics, Part A. (in Press 2010).
- Rong J, Li G and Chen YPP*. Acoustic Feature Selection for Automatic Emotion Recognition from Speech. Information Processing & Management, 45(3):315-328, 2009.
- Song XF, Chen WM, Chen YPP, Jiang B, Candidate Working Set Strategy based SMO Algorithm in Support Vector Machine, Information Processing & Management, 45(5): 584-592, 2009
- Tjondronegoro, D, Chen, YPP*, Joly A, A Scalable and Extensible Segment-Event-Object based Sports Video Retrieval System: ACM Transactions on Multimedia Computing, Communications and Applications 2008: 4(2):13:1-13:40.
- An J. Yu JX. Ratanamahatana CA, Chen YPP* A Dimensionality Reduction Algorithm and Its Application for Interactive Visualization, Visual Languages and Computing, 18:48-70, 2007. [pdf].
- Tjondronegoro, D, Chen, YPP*. and Pham B.,Integrating Highlights to Play-break Sequences for More Complete Sport Video Summarization, IEEE Multimedia, IEEE, Oct-Dec, 2004, pp22-37. [pdf]
- Tjondronegoro, D, Chen, YPP*, Content-based Indexing and Retrieval using MPEG-7 and X-Query in Video Data Management Systems, World Wide Web Journal 2002 5(3):207-227.
Recent ARC Grants (more grants and research projects)
[ARC Discovery Project $270K] Advanced analytics utilising conjoint mining of data and content with applications in business, bio-medicine and electrical power systems, 2013-2015.
[ARC Centre of Excellence $3.3M] ARC Centre of Excellence in Bioinformatics (ACB), 2008-2010.
[ARC Centre of Excellence $3.96M] ARC Centre for Bioinformatics (ACB), 2003-2007.
[ARC Discovery Project $150K] Exploiting DB Technologies for the Visualization and Analysis of Measured and Simulated Plant Structures in Bioinformatics, 2005-2007.
[ARC Discovery Project $334K] Integrating Database Technologies and Visual Analysis in Bioinformatics for Genome Data, 2003-2005.
[ARC Linkage Project $28.5K] Design and Development of a Web-based Intelligent Multimedia Mining System, 2004-2007.
[ARC Linkage-International $69K] Development of Knowledge Discovery for High Dimensional Biomedical Data, 2005-2007.
[ARC LIEF $285K] A Haptically enabled Universal Motion Simulator Research Facility, 2008.
[ARC LIEF $430K] Micro/nano optomechatronics sensing, measurement, and control research, 2007.