Grants & Projects
Australian Research Council (ARC) Grants:

  • 2008-2010, Prof. Phoebe Chen, Chief Investigator, ARC Centre in Excellent in Bioinformatics, $3.3 million, funded by the Australian Research Council Centre in Excellent (with Professor MA Ragan (UQ) and others).

  • 2003-2007, Prof. Phoebe Chen, Chief Investigator, ARC Centre in Bioinformatics, $3.96 million, funded by the Australian Research Council (with Prof Ragan (UQ) and others).
     

  • Title: Exploiting Database Technologies for the Visualization and Analysis of Measured and Simulated Plant Structures in Bioinformatics
    Grant Awarded: ARC Discovery (Previous ARC Large), AU$150,000, 2005-2007
    Chief Investigators: Prof. Y. Phoebe Chen

  • Title: Development of Knowledge Discovery for High Dimensional Biomedical Data 
    Grant Awarded: ARC Linkage-International, AU$28,500, 2005-2007
    Chief Investigator: Prof. Y Phoebe Chen
    Overseas Investigators: Prof. L. Wong, Dr. J Li

  • Title: Integrating Database Technologies and Visual Analysis in Bioinformatics for Genome Data.
    Grant Awarded: ARC Discovery (Previous ARC Large), AU$334,000, 2003-2005. 
    Chief Investigators: Prof. Phoebe Chen (Project Leader) (Deakin), Prof Kevin Burrage (UQ), Prof Mark Ragan (UQ), Prof Xiaofang Zhou (UQ)
    PostDoc Fellow: Dr. Jiyuan An (Deakin)

  • Title: Computational Infrastructure for High-Throughput Genome Bioinformatics 
    Grant Awarded: ARC Linkage - Infrastructure, AU$400,000, 2003.
    Chief Investigators: Prof MA Ragan, Prof. Y Phoebe Chen, Dr TL Bailey, Dr SM Grimmond, A/Prof P Timms
     

  • 2003-2004, participants of the following successful ARC Research Network Seed-Funding Grant (under ARC Special Research Initiatives):
    • ARC Australian Bioinformatics Grid Network. 
    • ARC Research Network in Microarray Technology 
Industry Grants
  • 2005, Title:Development of Data Mining Tools for the Prediction of Genomic Linked Clinical Outcomes in a Genetic Disease State Cystic Fibrosis
    Grant Awarded: VPAC's e-Research Grant Program  AU$18,000
    Chief Investigator: Associate Professor Phoebe Chen (Deakin)
Internal Grants

  • 2006, Title: Microarray Data Analysis for Genetic Disease

    Grant Awarded: Deakin Central Research Grant Scheme (CRGS) AU$10,000

    Chief Investigator: Associate Professor Phoebe Chen and Dr. Jiyuan An (Deakin)

  • 2006, Title: New mathematical methods for minimising intensity-modulated radiotherapy treatment times

    Grant Awarded: Deakin Central Research Grant Scheme (CRGS) Grant AU$15,000

    Chief Investigators: Dr. Vicky Mak, Associate Professor Phoebe Chen (Deakin)

  • 2005, Title: Virtual Plant Applications in Bioinformatics for Branching Structure
    Grant Awarded: Deakin Central Research Grant Scheme (CRGS) AU$15,000, 2005. 
    Chief Investigator: Associate Professor Phoebe Chen (Deakin)

  • 2005, Title: Bioinformatics to Uncover New Mitochondrial Division Proteins 
    Grant Awarded: Deakin Central Research Grant Scheme (CRGS) Grant AU$18,000, 2005.  
    Chief Investigators: Dr. Peter Beech, Associate Professor Phoebe Chen (Deakin)

Bioinformatics Recent Selected Publications (1999 ~ ....)

Book Editor

  • CHEN, Y.-P. P., Ed.(2005), “Bioinformatics Technologies”, Springer - Jan 2005.

  • JIANG T., YANG U.-C., CHEN, YP, and WANG L. Editors. Proceedings of the 4th Asia-Pacific Bioinformatics Conference, Imperial College Press, London, February 2006. Advances in Bioinformatics & Computational Biology Vol 3 Feb 2006, by Imperial College Press.

  • CHEN, Y.-P. P., and L. Wang Editors, (2005), Proceedings of the Third Asia-Pacific Bioinformatics Conference, January 2005, Vol XX, Advances in Bioinformatics & Computational Biology by Imperial College Press.

  • CHEN, Y.-P. P., Editor (2004) “Bioinformatics 2004”, Proceedings of the Second Asia-Pacific Bioinformatics Conference, January 2004, Vol 29 in the Conferences in Research and Practice in Information Technology Series, published by the Australian Computer Society, in Association with the ACM Digital Library.

  • CHEN, Y.-P. P., Editor (2003) “Bioinformatics 2003”, Proceedings of the First Asia-Pacific Bioinformatics Conference, February 2003, Vol 19 in the Conferences in Research and Practice in Information Technology Series, published by the Australian Computer Society, in Association with the ACM Digital Library.

Journal Special Issue Editor

  • CHEN, Y.-P. P., Editor, (2004), The Journal of Bioinformatics & Computational Biology, Special Issue on "Advanced Techniques for Bioinformatics". In Press.
  • CHEN, Y.-P. P., Editor (2003) “Bioinformatics in Asia Pacific”, Special Issue of Asia-Pacific Biotech News, published by World Scientific, Vol. 7, No. 3, 3 February 2003.
  • CHEN, Y.-P. P., Editor (2003) “Biomedical Visualization”, Special Issue of Journal of Visualization Language and Computing, 2003, Elsevier Science,, in Press.
  • CHEN, Y.-P. P., Editor (2003) “Data Mining in Bioinformatics”, Special Issue of International Journal of Software Engineering and Knowledge Engineering, 2003, World Scientific, in Press.

Journal Articles

  • Chen F and Chen YPP*, Exploring cross-species related miRNAs based on Sequence and secondary structure. IEEE Transactions on Biomedical Engineering (Accepted on Jan 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.
  • KNAPP K. CHEN YPP (2007) "An Evaluation of Contemporary Hidden Markov Model Genefinders with a Predicted Exon Taxonomy", Nucleic Acids Research 2007 35: 317-324.
  • MANN S., LI J., CHEN YPP (2007) "A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts", Nucleic Acids Research. 2007 35: e12 1-7.
  • CHEN Q. CHEN YPP*, Discovery of Structural and Functional Features in RNA Pseudoknots, IEEE Transactions on Knowledge and Data Engineering (accepted).
  • 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.
  • JIANG D, ZHOU S, CHEN YPP, Compensatory ability to null mutation in metabolic networks, Biotechnology and Bioengineering (accepted).
  • AN J, CHEN YPP* (2009), Finding rule groups to classify high dimensional gene expression datasets, Computational Biology and Chemistry (accepted on Aug 2008).
  • RONG J, LI G and CHEN YPP* (2009) Acoustic Feature Selection for Automatic Emotion Recognition from Speech. Information Processing & Management (Elsevier), Accepted Sep 2008.
  • AN J, CHEN YPP* (2009), Finding Coverage Using Incremental Attribute Combinations, International Journal of Innovative Computing, Information and Control (Accepted on July 2008).
  • JIANG D, ZHOU S, CHEN YPP, (2009) Inferring minimal feasible metabolic networks of Escherichia coli, Applied Biochemistry and Biotechnology (accepted 17 Feb 2009).
  • CHEN YPP, CHEN F (2008) Targets for Drug Discovery using Bioinformatics, Expert Opinion on Therapeutic Targets, 12(4): 383-389, 2008.
  • KNAPP K, CHONKA A, and CHEN YPP (2008), POEM, a 3-Dimensional Exon Taxonomy and Patterns in Untranslated Exons, BMC Genomics 2008, 9:428.
  • AN J, CHEN YPP (2008), Finding Edging Genes From Microarray Data, Journal of Biotechnology, 135(3):233-240, 2008.
  • CHEN Q. CHEN, YP (2006) "Mining Frequent Patterns for AMP-activated Protein Kinase Regulation on Skeletal Muscle", BMC Bioinformatics 2006, 7:394.
  • CHEN Q, CHEN YPP and ZHANG C. (2007) Detecting Inconsistency in Biological Molecular Databases using Ontology, Data Mining and Knowledge Discovery 2007 15:275-296.
  • CHEN Y, TIMMS, P and CHEN YPP (2007) CIDB: Chlamydia Interactive Database for cross-querying genomics, transcriptomics and proteomics data, Biomolecular Engineering. 24(6):603-608, 2007.
  • NAHAR J., ALI S. CHEN YPP (2007) Microarray Data Classification Using Automatic SVM Kernel Selection, DNA and Cell Biology, 26(10):707-712, 2007.
  • AN J. YU J. X. RATANAMAHATANA C. A. CHEN YPP. (2007) A Dimensionality Reduction Algorithm and Its Application for Interactive Visualization, Visual Languages and Computing, Elsevier Science 18 (2007) 48-70.
  • NAHAR J., CHEN YPP, ALI S. (2007) Kernel Based Naive Bayes Classifier for Breast Cancer Prediction, Journal of Biological Systems, 15(1): 17-25.
  • CHEN, YP, PROMPRAMOTE S., MAIRE F. (2006) "MDSM: Microarray Database Schema Matching By Using Hungarian Method", Information Science, Vol 176, pp2771-2790.
  • SHI W., ZHOU W, CHEN, YP. (2006), Statistical Analysis of TATA Box and Its Extensions in the Promoters of Human Genes, Current Bioinformatics, Volume 1, Number 3, August 2006, Pp. 337-345
  • CHEN, YP. Ed. (2005), “Bioinformatics Technologies”, Springer - Jan 2005. p396. SCI.
  • GARCIA A., CHEN YP, RAGAN MA., (2005), “Information Integration in Molecular Bioscience”, Applied Bioinformatics, 2005; 4 (3): 157-173.
  • CHEN, YP. (2005), "Advanced Techniques for Bioinformatics". Journal of Bioinformatics & Computational Biology, Vol. 3, No. 1 (2005) 99-102.
  • AN J., CHEN, YP., CHEN, H. (2005) "DDR: An Index Method for Large Time Series Datasets", Information Systems, Volume 30, Issue 5, (July 2005), Elsevier Science. pp333-348.
  • CHEN, Y.-P. P. and COLOMB, B.M. (2003) "Database Technologies for L-system Simulations in Virtual Plant Applications on Bioinformatics", International Journal of Knowledge and Information Systems, Volume 5, Number 3 (July 2003), Springer-Verlag, pp288-314.
  • CHEN, Y.-P. P., and HANAN J. (2002) "Partial Automation of Database Processing of Simulation Outputs from L-systems Models of Plant Morphogenesis", BioSystems. (Journal of Biological and Information Processing Sciences), Volume/Issue 65/2-3 pp. 187-197, Elsevier Science. 2002-2.
  • CHEN, Y.-P. P. and McLachlan G., (2003) “Bioinformatics Research in Australia”, Special Issue of Asia-Pacific Biotech News, published by World Scientific, Vol. 7, No. 3, 3 February 2003.

Book Chapters

  • CHEN YPP, IVANOVA E, CARLONI P and WANG F (2009) Bioinformatics and its applications, in "Comprehensive Natural Products Chemistry II", Vol 9, Eds. L. Mander and H. Liu, Elesevier (in press. 2009).
  • CHEN YPP, RONG J, LI G (2009). Advanced Graph Mining Methods for Protein Analysis. Biological Data Mining. Chapman & Hall/CRC Press (Book Chapter, Accepted)
  • CHEN, Y.-P. P. (2005), "Introduction to Bioinformatics". Bioinformatics Technologies, edited by Y.-P. Phoebe Chen, Chapter 1, pages 1-14, Springer, Jan 2005.
  • PROMPRAMOTE S.,CHEN, Y., CHEN, Y.-P. P. (2005), "Machine Learning in Bioinformatics", Bioinformatics Technologies, edited by Y.-P. Phoebe Chen, Chapter 5, pages 117-154, Springer, Jan 2005.
  • SHI W., ZHOU W, CHEN, Y.-P. P. (2005), "Biological Sequence Assembly and Alignment", Bioinformatics Technologies, edited by Y.-P. Phoebe Chen, chapter 8, pages 243-262, Springer, Jan 2005.
  • MANN S, CHEN, Y.-P. P. (2005), "Modeling for Bioinformatics", Bioinformatics Technologies, edited by Y.-P. Phoebe Chen, Chapter 9, pages 263-298, Springer, Jan 2005.
  • TSE B., HUME D. CHEN, Y.-P. P. (2005), "Pattern Matching for Motifs", Bioinformatics Technologies, edited by Y.-P. Phoebe Chen, Chapter 10, pages 299-312, Springer, Jan 2005.

  • YU Z.-G., ANH V. CHEN Y.-P. P. (2005) "Visualization and Fractal Analysis of Biological Sequences", Bioinformatics Technologies, edited by Y.-P. Phoebe Chen, Chapter 11, pages 313-352, Springer, Jan 2005.

  • LIEW A. W.-C., YAN H., YANG M., CHEN Y.-P. P. (2005) "Microarray Data Analysis", Bioinformatics Technologies, edited by Y.-P. Phoebe Chen, Chapter 12, pages 353-388, Springer, Jan 2005.

  • CHEN, Y.-P. P. and COLOMB, R.M. (1999) "Generic Process Solution in Database Systems and L-systems for Bioinformatics Research", in Zhang Y., Rusinkiewicz M. and Kambayashi Y. (eds), Cooperative Databases and Applications’99, Springer-Verlag, pp.328-339.

Conference Publications

  • SCHMIDT S, LI G, CHEN YPP (2008) Medical Knowledge Discovery from a Regional Asthma Dataset (ICIC2008), Lecture Notes in Computer Science 5227: 888-895.
  • LUKMAN S, SIM K, LI J and CHEN YPP (2008) Interacting Amino Acid Preferences of 3D Pattern Pairs at the Binding Sites of Transient and Obligate Protein Complexes, The Sixth Asia Pacific Bioinformatics Conference (APBC2008), 14-17 January 2008 Kyoto, Japan.
  • NAHAR J., CHEN, YPP, ALI S.(2007) "Microarray Classification and Rule Based Cancer Identification", International Conference on Information and Communication Technology (ICICT 2007), March 7-9, 2007, Dhaka.
  • AN J. CHEN, YPP. (2006) “A similarity search algorithm to predict protein structures”, 10th International Conference on Knowledge-Based & Intelligent Information & Engineering Systems (KES2006) 9-11 October 2006, UK. Lecture Notes in Computer Science, LNCS 4252 Springer-Verlag, pp. 1305-1312.
  • CHEN Q. CHEN YPP., ZHANG C.and LI L.(2006), "Mining Frequent Itemsets for Protein Kinase Regulation" Lecture Notes in Computer Science, LNCS4099, The 9th Pacific Rim International Conference on Artificial Intelligence, Springer-Verlag, pp222-230.
  • AN J. CHEN, YPP (2006) "Finding Rule Groups to Classify High Dimensional Gene Expression Datasets", The 18th International Conference on Pattern Recognition 2006 (ICPR2006), 20 - 24 August 2006, Hong Kong, IEEE CS Press, pp1196-1199.
  • AN J. CHEN, YPP (2006) "Finding Short Patterns to Classify Text Documents", The 2006 IEEE/WIC/ACM International Conference on Web Intelligence (WI-06), 18 - 22 Dec 2006, Hong Kong, IEEE CS Press.
  • CHEN YPP,CHEN, Q (2006) “Analyzing Inconsistency Toward Enhancing Integration of Biological Molecular Databses”, Proceedings of the fourth Asia-Pacific Bioinformatics Conference (APBC2006), Taipei Taiwan 13-16 Feb 2006, pp197-206.

  • AN J., CHEN, YPP (2006) "Depth First Rule Generation for Text Categorization", Proceedings of The Fourth International Conference on Active Media Technology (AMT 2006) June 7-9, 2006, Brisbane Australia, pp.302-306.

  • SUBRAMANIAM C. AN J., CHEN, YPP (2006), "Microarray Analysis for Gene Expression that involves Trace Metals", Proceedings of The Fourth International Conference on Active Media Technology (AMT 2006) June 7-9, 2006, Brisbane Australia pp211-216.

  • AN J., CHEN Y.-P. P., XU Q. and ZHOU X., (2005) "A New Indexing Method for High Dimensional Dataset", Proceedings of The 10th International Conference on Database Systems for Advanced Applications (DASFAA 2005) April 18-20, 2005, Beijing, China. (Accepted).

  • MANN S., CHEN Y.-P. P. and EATON L. (2004) "A Computational Framework for Nucleic Acid Sub-Sequence Identification", Proceedings of IEEE Fourth Symposium on Bioinformatics and Bioengineering (BIBE2004) (Accepted).

  • CHEN Y., CHEN, Y.-P. P. and ZHU, J. (2004) "Real-Time Gene-Expression Extraction with Fast Classification (FC) Networks", Proceedings of The 2004 International Conference on Machine Learning, Models, Technologies and Applications (MLMTA'04), June 21-24, 2004, Las Vegas, Nevada, USA, pp883-889.
  • AN J., CHEN, Y.-P. P. and KEOGH E. (2004) "A Grid-based Index Method for Time Warping Distance", The Fifth International Conference on Web-Age Information Management (WAIM2004), 15 -17 July 2004, Dalian, China, Lecture Notes in Computer Science, Springer-Verlag, pp65-75.
  • AN J., CHEN, Y.-P. P. and XU Q. (2004) "Surface Spatial Index Structure of High-Dimensional Space", Fifth International Conference on Intelligent Data Engineering and Automated Learning (IDEAL'04) August 25-27, 2004, Exeter, UK, Lecture Notes in Computer Science, Springer-Verlag, pp272-278.
  • AN J. and CHEN Y.-P. P. (2004) "Concept Learning of Text Documents", IEEE/WIC/ACM WI-2004, Sep 20-24 2004, Beijing China, IEEE CS Press, pp698-701.
  • PROMPRAMOTE S., CHEN, Y.-P. P.(2004) "Rough Set Based Similarity Metrics for Mixed Data Set: A Case Study of Heart Disease Diagnosis", the 7th International Conference on Information Technology (CIT2004), 12/20/2004 - 12/23/2004, Hyderabad, Andhra Pradesh, India (Accepted).
  • PROMPRAMOTE S., CHEN, Y.-P. P. and MAIRE F. (2003) "Information Management for Microarray Experimental Data ", 5th IFAC Symposium on Modelling and Control in Biomedical Systems, IFAC2003, Elsevier Science.
  • LEE F. S. and CHEN, Y.-P. P.(2003), "BioWebFinder – Searching Biological Websites", Proceedings of the APAC'03, The APAC Conference and Exhibition on Advanced Computing, Grid Applications and eResearch, 29 September - 2 October, 2003, Royal Pines Resort Gold Coast, Queensland Australia.
  • RUNQIANG B., CHEN, Y.-P. P., BURRAGE K., HANAN J., ROOM P., BELWARD J. (2002), “Derivation of L-system models from measurements of biological branching structures using genetic algorithms”, Proceedings of the Fifteenth International Conference on Industrial & Engineering Application of Artificial Intelligence & Expert Systems, June 17-20, 2002. Cairns, Australia, Lecture Notes in Artifical Intelligence, pp.514-524, Springer-Verlag.
  • CHEN, Y.-P. P. and COLOMB, R.M. (2000) "Querying Recursive Structures Without Recursive Queries", the 11th Australian Database Conference, ADC-2000, IEEE CS Press, 31 January - 2 February, 2000, Canberra, Australia. pp.21-27.
  • CHEN, Y.-P. P. and COLOMB, R.M. (1999) "Generic Process Solution in Database Systems and L-systems for Bioinformatics Research" Proc of The Second International Symposium on Cooperative Database Systems for Advanced Applications (CODAS'99), March 27-28, 1999, Wollongong, Australia.
  • CHEN, Y.-P. P. (1999) "DML: A Bridge between Database Systems and L-Systems for Biological Research", The 11th International Conference on Scientific and Statistical Database Management (SSDBM'99), ACM SIGMOD and VLDB Endowment, IEEE press, July 28-30, 1999, Cleveland, Ohio, U.S.A.
  • CHEN, Y.-P. P. and COLOMB, R.M. (1999) "Decision Support in Bioninformatics Research", Proc: The Fifth International Conference of The International Society for Decision Support Systems (ISDSS'99), 20-23 July 1999, Melbourne, Australia.

International Conference Poster Session:

  • CHEN, Y.-P. P. (2003) “Generating Database Technologies and Simulations for Branching Structure Applications”, Presented in the 11th International conference on Intelligent Systems for Molecular Biology (ISMB2003). (Poster Session). Brisbane Australia June 29 to July 3, 2003.
  • AN J., and CHEN, Y.-P. P. (2003) “An Effective Query Method for DNA Sequence”, Presented in the 11th International conference on Intelligent Systems for Molecular Biology (ISMB2003). (Poster Session). Brisbane Australia June 29 to July 3, 2003.
  • PROMPRAMOTE S., CHEN, Y.-P. P., MAIRE F. (2003) “Integrated Storage for Microarray Experimental Data”, Presented in the 11th International conference on Intelligent Systems for Molecular Biology (ISMB2003). (Poster Session). Brisbane Australia June 29 to July 3, 2003.
  • CHEN Y. and CHEN, Y.-P. P. (2003) “BioInfoCallboratory: Towards an Agent-Assisted Web-Based Collaboration Environment for Bioinformatics”, Presented in the 11th International conference on Intelligent Systems for Molecular Biology (ISMB2003). (Poster Session). Brisbane Australia June 29 to July 3, 2003.
  • TSE B., WELLS C., RAVASI T., CHEN Y.-P. P., HUME D., (2003) “Computational prediction of macrophage specific regulatory network”, Presented in the 11th International conference on Intelligent Systems for Molecular Biology (ISMB2003). (Poster Session). Brisbane Australia June 29 to July 3, 2003.
  • GARCIA A., JOHN C., RAGAN M. A., CHEN Y.-P. P.. (2003), “SEMA, A semantic literature annotator”, Presented in the 11th International conference on Intelligent Systems for Molecular Biology (ISMB2003). (Win Australian Student Poster Prize). Brisbane Australia June 29 to July 3, 2003.
  • GARCIA A., LEYLA J. GARCIA L. J., RAGAN M. A., CHEN Y.-P. P. (2003) “JPIPE, A pipeline module for JEMBOSS”, Presented in the 11th International conference on Intelligent Systems for Molecular Biology (ISMB2003). (Poster Session). Brisbane Australia June 29 to July 3, 2003.
  • LEE F., CHEN, Y.-P. P. (2003) “BioWebFinder: Searching Biological Websites”, Presented in the 11th International conference on Intelligent Systems for Molecular Biology (ISMB2003). (Poster Session). Brisbane Australia June 29 to July 3, 2003.
 
 
 

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©Professor Phoebe Chen,

Bioinformatics

Department of Computer Science and Computer Engineering,

La Trobe University, Melbourne, Australia