Professor Yi-Ping Phoebe Chen

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

Professor and Chair & Director of Research

Department of Computer Science and Computer Engineering

La Trobe University

Melbourne Bundoora, Victoria 3086,Australia,

Office: Melbourne Campus

Building/Room: Beth Gleason/BG239

Phone: +61-3-9479 6768; Fax: +61 3 9479 3060; Email: phoebe.chen@latrobe.edu.au

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

• 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.

• 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, 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.

• 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.

• 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.

• Kalyaanamoorthy S, Chen YPP*, Structure-based drug design to augment hit discovery, Drug Discovery Today, 16(17-18):831-839, 2011.

• 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.

• Knapp K, Chonka A, and Chen YPP*, POEM, a 3-Dimensional Exon Taxonomy and Patterns in Untranslated Exons, BMC Genomics 2008, 9:428. 

• Lee CC, Lo WC, Lai SM, Chen YPP, Tang CY and Lyu PC, Metabolic classification of microbial genomes using functional probes, BMC Genomics, 2012, 13:157.

• 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]

• 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.

• ZHU W, HOU J, and CHEN YPP, Exploiting Multi-Layered Information to Iteratively Predict Protein Functions, Mathematical Biosciences, 236 (2): 108–116, 2012.

• 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. 

• 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 Systems / Databases / Data Mining / Intelligent System / Simulation and Scientific Visualization

• BEGLEY S, ZHEN H, CHEN YPP (2012) “MCJoin: A memory-constrained join for column-based main-memory databases”, the ACM 39th International Conference on Management of Data, ACM SIGMOD 2012 (accepted as a full paper)
• An J, Chen YPP*, Chen H, DDR: An Index Method for Large Time Series Datasets, Information Systems, 30:333-348 (2005).
• NGUYEN, T; ZHEN H, CHEN YPP, SeTPR*-tree: Efficient Buffering for Spatiotemporal Indexes Via Shared Execution, The Computer Journal, in press.
• 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.
• 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.
• 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]
• CHEN Q, CHEN YPP, Mining Inhibition Pathways for Protein Kinases on Skeletal Muscle, IEEE Intelligent Systems, in press.
• 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.

• [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.

• [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 Eleventh Asia Pacific Bioinformatics Conference (APBC2013), Vancouver, BC, Canada, 21-24 January 2013.
• [SC-Chair] STEERING COMMITTEE CHAIR of the International Multimedia Modelling Conference, (2003 - .....), coming: The 19th International Conference on Multimedia Modelling (MMM2013), Huangshan, China, 7-9 January, 2013.
• [Conference Co-Chair] Third International Workshop on Conceptual Modelling for Life Sciences Applications (CMLSA2010), November 1-4, 2010 Vancouver, BC, Canada.
• [Conference-Chair] The Bioinformatics Australia 2009 (BA2009), Melbourne, Australia, 29-30 Oct. 2009.
• [PC Member] The 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2012), 15-17 July, Long Beach, California.
• [PC Member] The 23rd International Conference on Database and Expert Systems Applications (DEXA2012), 3-7 September, Vienna, Austria.
• [PC Member] The 16th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD2012), May 29- 1 June 2012, Kuala Lumpur, Malaysia.
• [PC Member] The 12th Pacific Rim International Conference on Artificial Intelligence (PRICAI2012), 3-7 September, Sarawak, Malaysia.
• [PC Member] 2012 IEEE/ICME International Conference on Complex Medical Engineering (CME2012), 1-4 July, Kobe, Japan.
• [PC Member] The 8th International Conference on Advanced Data Mining and Applications (ADMA2012), 15-18 December, Nangjing, China.
• [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

• What Google has on me?

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