Professor Phoebe Chen - La Trobe Home Page

Professor Dr Phoebe Chen

BInfTech (Hons 1st), PhD (Computer Science) UQ, GradCertEd (HigherEd) QUT, SIEEE, MACM

Professor and Chair & Head of Department

Department of Computer Science and Computer Engineering

School of Engineering and Mathematical Sciences

Faculty of Science, Technology and Engineering, La Trobe University

Bundoora 3086, Melbourne Australia, Beth Gleason Building Room 239,

Phone: +61-3-9479 6768; Email: phoebe.chen@latrobe.edu.au

Professor Yi-Ping Phoebe Chen is Professor and Chair & Head of Department at the Department of Computer Science and Computer Engineering, School of Engineering and Mathematical Sciences, Faculty of Science, Technology and Engineering, La Trobe University, Melbourne Australia. Prof Chen is the Chief Investigator of ARC Centre of Excellence in Bioinformatics. Phoebe received her BInfTech degree with First Class Honours and PhD in Computer Science (Bioinformatics) from the University of Queensland. Before she joined La Trobe, Phoebe was Associate Professor (Reader) in Deakin University from Dec 2003 to April 2010. She worked as a Associate Lecturer/Lecturer/Senior Lecturer in Queensland University of Technology from Jul 1999 to Nov 2003. She is currently working on knowledge discovery technologies and is especially interested in their application to genomics and biomedical science. Her research focus is to find best solutions for mining, integrating and analyzing complex data structure and functions for scientific and biomedical applications. She has been working in the area of bioinformatics, health informatics, multimedia databases, query system and systems biology, co-authored over 150 research papers with many published in top journals and conferences such as IEEE Transactions on Biomedical Engineering, IEEE Transactions on Information Technology in Biomedicine, Nucleic Acids Research, BMC Genomics, BMC Bioinformatics, Current Drug Metabolism, Data Mining and Knowledge Discovery, IEEE Transactions on Knowledge and Data Engineering, Information Systems and ACM Transactions. She is steering committee chair of Asia-Pacific Bioinformatics Conference (founder) and International conference on Multimedia Modelling. She has been on the program committees of over 100 international conferences, including top ranking conferences such as ICDE, ICPR, ISMB, CIKM etc. Phoebe is a senior member of IEEE, member of ACM. More.....

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Some Recent Selected Journal Publications: (more publications by year)

Bioinformatics / Computational Biology / System Biology

Chen Q, Chen YPP, Modeling Conserved Structure Patterns for Functional Noncoding RNA. IEEE Transactions on Biomedical Engineering, 58(6):1528-1533, 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.
An J, Chen YPP*, Chen H, DDR: An Index Method for Large Time Series Datasets, Information Systems, 30:333-348 (2005).
Yang L, Zhen H, Chen YPP, Nguyen T, External Sorting on Flash Memory Via Natural Page Run Generation, The Computer Journal, in press.
Chen Q. Chen YPP*, Mining Characteristic Relations Bind to RNA Secondary Structures, IEEE Transactions on Information Technology in Biomedicine 14(1):10-15, 2010.
Zhu W., Hou J., and Chen YPP*, Semantic and layered protein function prediction from PPI networks, Journal of Theoretical Biology, 267(2): 129-136.
Chen Q, Li G, Chen YPP, Interval-Based Distance Function for Identifying RNA Structure Candidates, Journal of Theoretical Biology, 269(8): 280-286, 2011.
Chen YPP*, Chen F, Using Bioinformatics Techniques for Gene Identification in Drug Discovery and Development, Current Drug Metabolism 9(6): 567-573, 2008.
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].
Kalyaanamoorthy S, Chen YPP*, Structure-based drug design to augment hit discovery, Drug Discovery Today, 16(17-18):831-839, 2011.
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.
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, 2011, 12:347.
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.
Chen Q, Chen YPP, Mining Inhibition Pathways for Protein Kinases on Skeletal Muscle. IEEE Intelligent Systems, in press.
Xi Y, Chen YPP, Qian C., Wang F, Comparative study of computational methods to detect the correlated reaction sets in biochemical networks, Briefings in Bioinformatics 12(2): 132-150, 2011.
Chen YPP*, Chen F, Targets for Drug Discovery using Bioinformatics, Expert Opinion on Therapeutic Targets, 2008:12(4): 383-389.
Mann S, Li J, Chen YPP*, Insights into Bacterial Genome Composition through Variable Target GC Content Profiling, Journal of Computational Biology, 17(1): 79-96, 2010.
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. Ed., Bioinformatics Technologies, Springer - 2005. p396. SCI.

Multimedia Information Retrieval, Databases, Data Mining, Intelligent System, Simulation and Scientific Visualization

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].
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*, 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.
Tjondronegoro, D, Chen, YPP*, Knowledge-discounted Event Detection in Sports Video, IEEE Transactions on Systems Man & Cybernetics, Part A. 40(5):1009-1024, 2010.
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.

Recent ARC Grants (more grants and research projects)

[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.

Some Professional Activities: (more conferences and others)

[EB] Editorial Advisory Board for the Journal of Current Bioinformatics (CBIO)
[AE] Associate Editor for the IEEE Transactions on Multimedia (T-MM)
[AE] Associate Editor for the Journal of Research and Practice in Information Technology (JRPIT)
[AE] Associate Editor for the International Journal of Intelligent Computing in Medical Sciences and Image Processing (IC-MED）
[SC-Chair] STEERING COMMITTEE CHAIR (FOUNDER) of the Asia-Pacific Bioinformatics Conference, (2003 - ....), coming: The Tenth Asia Pacific Bioinformatics Conference (APBC2012), Melbourne, Australia, 17-19 January 2012.
[SC-Chair] STEERING COMMITTEE CHAIR of the International Multimedia Modelling Conference, (2003 - .....), coming: The 18th International Conference on Multimedia Modelling (MMM2012), Klagenfurt, Austria, 4-6 January, 2012.
[Conference Co-Chair] Third International Workshop on Conceptual Modelling for Life Sciences Applications (CMLSA 2010), November 1-4, 2010 Vancouver, BC, Canada.
[Conference-Chair] The Bioinformatics Australia 2009 (BA2009), Melbourne, Australia, 29-30 Oct. 2009.
[PC Member] The 14th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD2010), Hyderabad, India, June 21-24, 2010.
[PC Member] The 21th International Conference on Database and Expert Systems Applications (DEXA 2010), Bilbao, Spain, August 30-September 3 2010.
[PC Member] The 7th Asia-Pacific Bioinformatics Conference (APBC2009), 13-16 Jan 2009, Beijing China.
[PC Member] The 20th International Conference on Database and Expert Systems Applications (DEXA 2009), Aug 31-Sep 4, 2009, Linz, Austria.
[PC Member] The 14th International Conference on Database Systems for Advanced Applications (DASFAA 2009), April 21-23, 2009, Brisbane, Australia.
[PC Member] The 13th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD2009), 27-30 April 2009.Bangkok, Thailand.
[PC Member] The 10th IEEE International Conference on Multimedia and Expo (ICME 2009), June 28 - July 3, 2009, Cancun, Mexico.
[PC Member] The 24th International Conference on Data Engineering (ICDE2008), Cancun, Mexico, April 7-12, 2008
[PC Member] The 19th International Conference on Pattern Recognition (ICPR 2008), Tampa, Florida, USA, December 8-11, 2008
[PC Member] The 12th ACM International Conference on Information and Knowledge Management (CIKM2003), November 3-8 2003, New Orleans, LA, USA
[PC Member] The 11th International conference on Intelligent Systems for Molecular Biology (ISMB2003), Jun 29 - Jul 3, 2003, Brisbane Australia

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Recent Book

CHEN, YPP., Ed., Bioinformatics Technologies, Springer - 2005 p396. SCI.

(C) Professor Phoebe Chen

This page was last updated on 12/4/2010