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)

• 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]

• 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. [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, 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.

• Xi Y, Chen YPP, Cao M, Wang W and Wang F, Analysis on relationship between extreme pathways and correlated reaction sets. BMC Bioinformatics, 10(S1):S58, 2009.

• Jiang D, Zhou S, Chen YPP, Compensatory ability to null mutation in metabolic networks, Biotechnology and Bioengineering, 103(2):361-369, 2009. [pdf]

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

• An J and Chen YPP, Finding Edging Genes From Microarray Data, Journal of Biotechnology, 135(3):233-240, 2008.

• Chen YPP, Chen F, Targets for Drug Discovery using Bioinformatics, Expert Opinion on Therapeutic Targets, 12(4): 383-389, 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.

• Chen Y. Timms P, Chen YPP, CIDB: Chlamydia Interactive Database for cross-querying genomics, transcriptomics and proteomics data, Biomolecular Engineering 24(6):603-608, 2007.[pdf].

• Chen Q. Chen YPP, Mining Frequent Patterns for AMP-activated Protein Kinase Regulation on Skeletal Muscle, BMC Bioinformatics, 7:394, 2006.

• 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” [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. 40(5):1009-1024, 2010.
• 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.
• 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, 4(2):13:1-13:40, 2008.
• 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]
• 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].
• An J, Chen YPP, Chen H, DDR: An Index Method for Large Time Series Datasets, Information Systems, 30:333-348, 2005.
• Tjondronegoro, D, Chen, YPP, Content-based Indexing and Retrieval using MPEG-7 and X-Query in Video Data Management Systems, World Wide Web Journal, 5(3):207-227, 2002.

• [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.

• [ARC LIEF $400K] Computational Infrastructure for High-Throughput Genome Bioinformatics, 2003.

• [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 Twelfth Asia Pacific Bioinformatics Conference (APBC2014), Shanghai, China, 17-19 January 2014.
• [SC-Chair] STEERING COMMITTEE CHAIR of the International Multimedia Modelling Conference, (2003 - .....), coming: The 20th International Conference on Multimedia Modelling (MMM2014), Dublin, Ireland January 8-10, 2014.
• [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 Eleventh Asia Pacific Bioinformatics Conference (APBC 2013), Vancouver, BC, Canada 21-23 January 2013.
• [PC Member] the 17th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2013), Beijing, China, April 7-10, 2013.
• [PC Member] The 17th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD2013), 14-17 April 2013, Gold Coast, Australia.
• [PC Member] The 13th SIAM International Conference on Data Mining (SDM 2013), May 02-04, 2013, Austin, TX, USA.
• [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.