Staff profile

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)

Qualifications

BEE NTUT, GradCert (HighEd) QUT, BInfTech UQ, BInfTech (Hon H1A) UQ, PhD UQ

Membership of professional associations

MACM, SMIEEE

Area of study

Computer Science
Computer Systems Engineering
Information Systems
Information Technology

Brief profile

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 30 research grants around 8 millions (include 13 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 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 195 refereed publications in recent years. These papers appeared in high standing publications such as Journal Papers include Molecular Systems Biology, 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 book Bioinformatics Technologies (Springer) has published on Jan 2005.

Research interests

Artificial intelligence research

- Artifical intelligence and siginal processing

Bioinformatics

- 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

Teaching units

CSE5BIO - Bioinformatics Technologies

CSE4DMI - Data Mining

Recent publications

homepage.cs.latrobe.edu.au/ypchen/publications.htm

2014

Journals:

205. Kalyaanamoorthy, S. CHEN YPP*, A steered molecular dynamics mediated hit discovery for histone deacetylases, Physical Chemistry Chemical Physics, 2014, 16 (8), 3777 - 3791.

204. Zhu W, CHEN YPP*, Computational developments in microRNA-regulated protein-protein interactions, BMC Systems Biology, 2014, 8:14.

203. Liu Q, CHEN YPP, Li J (2014), k-Partite Cliques of Protein Interactions: A Novel Subgraph Topology for Functional Coherence Analysis on PPI Networks, Journal of Theoretical Biology, 340(2014): 146–154.

202. Lee H, CHEN YPP* (2014) Cell Cycle Phase Detection with Cell Deformation Analysis, Expert Systems with Applications, 41(6): 2644–2651.

201. Lee H, CHEN YPP* (2014) Skin Cancer Extraction with Optimum Fuzzy Thresholding Technique, Applied Intelligence, accepted.

200. Chen F, Zhang Y, CHEN YPP* (2014) Subdividing Globally Important Zones Based on Data Distribution across Multiple Genome Fragments, Computers in Biology and Medicine, accepted.

199. Zhu W, Hou J, CHEN YPP* (2014), Select Cluster Features Effectively for Layered Protein Function Prediction, Current Bioinformatics. in press.

2013        

Journals:

198. 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.

197. Li Z, Bammann H, Li M, Liang H, Yan Z, CHEN YPP, Zhao M. and Khaitovich P, Evolutionary and ontogenetic changes in RNA editing in human, chimpanzee, and macaque brains, RNA 2013 19:1693-1702.

196. Yuan Y, Yang L, Shi M, Lu D, Lou H, CHEN YPP, Jin L, Xu S, Identification of Well-Differentiated Gene Expressions between Han Chinese and Japanese Using Genome-Wide Microarray Data Analysis, Journal of Medical Genetics, 50(8):534-42, 2013.

195. Cheng SC, Cheng KY, CHEN YPP, GHT-Based Associative Memory Learning and Its Application to Human Action Detection and Classification, Pattern Recognition, 46(11): 3117–3128.

194. Kalyaanamoorthy, S. CHEN YPP*, Ligand release mechanisms and channels in histone deacetylases. Journal of Computational Chemistry 34(26): 2270-2283 (2013).

193. Kalyaanamoorthy, S. CHEN YPP*, Energy based pharmacophore mapping of HDAC inhibitors against class I HDAC enzymes, BBA - Proteins and Proteomics, 1834(1):317-328, 2013.

192. Kalyaanamoorthy, S. CHEN YPP*,Quantum polarized ligand docking investigation to understand the significance of protonation states in histone deacetylase inhibitors, Journal of Molecular Graphics and Modelling, 44 (2013) 44–53.

191. Lee CC, CHEN YPP, Yao TJ, Lo, WC, Lyu PC, Tang CY and Ma CY, GI-POP: A combinational annotation and Genomic Island prediction Pipeline for Ongoing microbial genome Projects, Gene, 518(2013): 114-123.

190. Nahar, J., Imam, T., Tickle, K., and CHEN, YPP., "Computational Intelligence for Heart Disease Diagnosis: A Medical Knowledge Driven Approach", Expert Systems With Applications, 40(1):96-104, 2013.

189. Nahar, J., Imam, T., Tickle, K., and CHEN, YPP., "Association Rule Mining to Detect Factors which contribute to Heart Disease in Males and Females", Expert Systems With Applications, 40(4):1086-1093.

188. NGUYEN, T; ZHEN H, CHEN YPP, SeTPR*-tree: Efficient Buffering for Spatiotemporal Indexes Via Shared Execution, The Computer Journal, 56(1):115-137, 2013.

187. Zhu W, Hou J, CHEN YPP*, Semantically Predicting Protein Functions Based on Protein Functional Connectivity, Computational Biology and Chemistry, 44(2013): 9-14.

186. Song X, Wang M, CHEN YPP, Wang H, Han P, Sun H: Prediction of pre-miRNA with multiple stem-loops using pruning algorithm. Computers in Biology and Medicine. 43(5): 409-416 (2013).

185. Hou J., Zhu W, CHEN YPP* Dynamically predicting protein functions from semantic associations of proteins, Network Modeling Analysis in Health Informatics and Bioinformatics, 2(4):175-183, 2013.

 

2012

Journals:

184. 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.

183. 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.

182. 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.

181. CHIU JKH, CHEN YPP, Conformational Features of Topologically Classified RNA Secondary Structures, PLoS ONE, 7(7): e39907, 2012.

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

179. CHEN Q, CHEN YPP, Discovering Inhibition Pathways for Protein Kinases. IEEE Intelligent Systems, 27(5): 19-26, 2012.

178. SONG X., CHENG L, ZHOU T., GUO X., ZHANG X., CHEN YPP, HAN P., SHA J. Predicting miRNA-mediated gene silencing mode based on miRNA-target duplex features, Computers in Biology and Medicine, 42(1): 1–7, 2012.

177. Nahar, J., Imam, T., Tickle, K., Ali, S., and CHEN, YPP., "Computational Intelligence for Microarray Data and Biomedical Image Analysis for the Early Diagnosis of Breast Cancer", Expert Systems With Applications, 39 (2012) 12371–12377.

176. Rajasekaran R, CHEN YPP, Probing the structure of Leishmania major DHFR TS and structure based virtual screening of peptide library for the identification of anti-leishmanial leads, Journal of Molecular Modeling, 18(9): 4089-4100, 2012.

175. Y. Gotoh, T. Yoshihisa, H. Taniguchi, M. Kanazawa, W. Rahayu, and Chen YPP: "A Scheduling Method to Reduce Waiting Time for Close-range Broadcasting'', Mobile Information Systems Journal (MOBIS), Vol.8, Issue.4, pp.303-314, (Dec. 2012).

Refereed conference papers:

174. BEGLEY S, ZHEN H, CHEN YPP (2012) “MCJoin: A memory-constrained join for column-based main-memory databases”, Proceedings of the ACM SIGMOD 39th International Conference on Management of Data, SIGMOD 2012, 121-132. Scottsdale, Arizona, USA, 20-24 May 2012.

173. Y. Gotoh, T. Yoshihisa, H. Taniguchi, M. Kanazawa, W. Rahayu, and YPP CHEN "A Scheduling Method for Node Relay-based Webcast Considering Reconnection'' 26th IEEE International Conference on Advanced Information Networking and Applications (AINA-2012), 787-794, Fukuoka, Japan, 26-29 March 2012.

Older publications

               

2011

Journals:

172. CHEN Q, CHEN YPP (2011) Modeling Conserved Structure Patterns for Functional Noncoding RNA. IEEE Transactions on Biomedical Engineering, 58(6):1528-1533, 2011.

171. CHEN Q, LI G, CHEN YPP (2011) Interval-Based Distance Function for Identifying RNA Structure Candidates, Journal of Theoretical Biology, 269(8): 280-286, 2011.

170. 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.

169. 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.

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

167. XI Y, CHEN YPP, QIAN C., WANG F (2011), Comparative study of computational methods to detect the correlated reaction sets in biochemical networks, Briefings in Bioinformatics 12(2): 132-150, 2011.

166. NAHAR J., TICKLE, KS, ALI S. CHEN YPP* (2011), Significant Cancer Prevention Factor Extraction: An Association Rule Discovery Approach, Journal of Medical Systems 35(3): 353-367, 2011.

165. CHEN Q, CHEN YPP (2011). Mining Protein Kinase Regulation using Graphical Models. IEEE Transactions on NanoBioscience, 10(1):1-8, 2011.

164. SONG XF, HAN P, CHEN YPP (2011) Genetic variation of the hemagglutinin of H9N2 influenza viruses, Journal of Medical Virology, 83(5):838-46, 2011.

163. CHEN Q, CHEN YPP (2011), Function Annotation for Pseudoknot using Structure Similarity. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011 Nov-Dec ; 8(6):1535-1544.

162. WANG TT, CHEN F. CHEN YPP (2010) Ranking Inter-Relationships between Clusters, International Journal of Systems Science, 42(12):2071-2083, 2011.

161. KNAPP K. CHEN YPP*, Highly Variant Free Energy Levels in POEM Exons, Current Bioinformatics (Accepted).

Refereed conference papers:

160. Gotoh, Y., Yoshihisa, T., Taniguchi, H., Kanazawa, M., Rahayu, W. and Chen, YPP (2011), "A Method to Reduce Waiting Time for Close-range Broadcasting." The 9th International Conference on Advances in Mobile Computing and Multimedia (MoMM 2011), Ho Chi Minh City, Vietnam, vol. MoMM 2011, 116-122.

159. Song, X.-F., Wang, M., Chen YPP, and Ping, H. (2011), "Identifying multiple stem-loops pre-miRNA using support vector machine." The 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2011), Atlanta, Georgia, USA, vol. BIBMW 2011, 446-448.

158. Wang, H-W., Wu, W-K., Pai, T-W., Chen YPP, and Chang, M.D-T. (2011), "Impact of complex formation on predicting conformational epitopes." The 2nd IASTED International Conference on Computational Bioscience, CompBio 2011, Cambridge, United Kingdom, vol. CompBio 2011, 284-290.

 2010

Journals:

157. CHEN F, CHEN YPP (2010) Exploring Cross-species Related miRNAs Based on Sequence and Secondary Structure, IEEE Transactions on Biomedical Engineering 57(7) 1547 – 1553, 2010.

156. CHEN Q. CHEN YPP* (2010) Mining Characteristic Relations Bind to RNA Secondary Structures, IEEE Transactions on Information Technology in Biomedicine, 14(1):10-15, 2010.

155. ZHU W., HOU J., and CHEN YPP (2010) Semantic and layered protein function prediction from PPI networks, Journal of Theoretical Biology, 267(2): 129-136.

154. MANN S. CHEN YPP* (2010) Bacterial genomic G+C composition-eliciting environmental adaptation, Genomics, 95(1): 7-15, 2010.

153. MANN S, LI J, CHEN YPP* (2010) Insights into Bacterial Genome Composition through Variable Target GC Content Profiling, Journal of Computational Biology, 17(1): 79-96, 2010.

152. CHEN F, CHEN YPP (2010) Exploring the ncRNA-ncRNA patterns based on bridging rules. Journal of Biomedical Informatics 43(4): 569-577 (2010)

151. JIANG D, ZHOU S, LIU H, CHEN YPP* (2010) Inferring minimal feasible metabolic networks of Escherichia coli, Applied Biochemistry and Biotechnology, 160( 1): 222-231, 2010.

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

149. AN J, CHOI KP, WELLS CA, CHEN YPP* (2010), Identifying co-regulating microRNA Groups, Journal of Bioinformatics and Computational Biology. 8(1):99-115, 2010.

148. Sajjanhar A, Lu G, Zhang D, Hou J, Zhou w, CHEN YPP* (2010), Spectral Shape Descriptor using Spherical Harmonics, Integrated Computer-Aided Engineering 17 (2010) 1–7.

147. ZHANG Z, CHEN YPP (2010) Guest Editors' Introduction. International Journal of Software Engineering and Knowledge Engineering 20(8): 1043-1044 (2010)

Book Chapter

146. CHEN F, CHEN YPP* (2010), Pattern recognition for genomics context, Pattern Recognition and Machine Vision, Chapter 7, editor by Patrick S.P. Wang, River Publishers. 105-118.

145. CHEN YPP, IVANOVA E, CARLONI P, WANG F (2010), Bioinformatics and its applications, in Comprehensive Natural Products II: Chemistry and Biology, Eds., Lewis N. Mander and Hung-wen (Ben) Liu, pp569-593 (Elsevier, 2010).

 2009

Journals:

144. CHEN Q. CHEN YPP* (2009) Discovery of Structural and Functional Features in RNA Pseudoknots, IEEE Transactions on Knowledge and Data Engineering, 21(7):974-984, 2009.

143. XI Y, CHEN YPP, CAO M, WANG W and WANG F (2009) Analysis on relationship between extreme pathways and correlated reaction sets. BMC Bioinformatics 2009, 10(S1):S58.

143. JIANG D, ZHOU S, CHEN YPP* (2009) Compensatory ability to null mutation in metabolic networks, Biotechnology and Bioengineering, 103(2):361-369, 2009.

142. SONG XF, CHEN WM, CHEN YPP, JIANG B (2009) Candidate Working Set Strategy based SMO Algorithm in Support Vector Machine, Information Processing & Management 45(5): 584-592, 2009.

141. RONG J, LI G, CHEN YPP* (2009) Acoustic Feature Selection for Automatic Emotion Recognition from Speech. Information Processing & Management, 45(3):315-328, 2009.

140. AN J, CHEN YPP* (2009) Finding Coverage Using Incremental Attribute Combinations, International Journal of Innovative Computing, Information and Control, 5(5):1419-1428, 2009.

139. AN J, CHEN YPP* (2009) Finding rule groups to classify high dimensional gene expression datasets, Computational Biology and Chemistry 33(1):108-113, 2009.

Book Chapters

138. CHEN YPP, RONG J, LI G (2009) Advanced Graph Mining Methods for Protein Analysis. Biological Data Mining. Edited by Jake Y. Chen, Stefano Lonardi, Chapter 6, Chapman & Hall/CRC Press, 111-132.

Lecture Notes in Computer Science/Artificial Intelligence:

137. Sajjanhar A, Lu G, Zhang D, Hou J, Chen YPP (2009) Spherical Harmonics and Distance Transform for Image Representation and Retrieval, E. Corchado and H. Yin (Eds.), Lecture Notes in Computer Science, Volume 5788, pp. 309-316, 2009.

Refereed conference papers:

136. LIU Q, CHEN YPP, LI J (2009), High functional coherence in k-partite protein cliques of protein interaction networks, Proceedings of 2009 IEEE International conference on Bioinfomratics and Biomedicine, page 111-117. Washington D.C., USA. 1-4 November 2009.

135. NAHAR J., TICKLE, KS, ALI S. CHEN YPP (2009), Early Breast Cancer Identification: Which Way to Go? Microarray or Image Based Computer Aided Diagnosis!, 2009 Third International Conference on Network and System Security, pp456-461. 2009.

134. HOU J, CHEN YPP (2009) Data Pre-Processing for More Effective Gene Clustering, The 2009 International Joint Conference on Computational Sciences and Optimization (CSO 2009), Sanya, Hainan, China, April 24-26, 2009.

 2008

Journals:

133. CHEN YPP*, CHEN F (2008) Using Bioinformatics Techniques for Gene Identification in Drug Discovery and Development, Current Drug Metabolism, 9(6): 567-573, 2008.

132. KNAPP K, CHONKA A, and CHEN YPP* (2008) POEM, a 3-Dimensional Exon Taxonomy and Patterns in Untranslated Exons, BMC Genomics 2008, 9:428.

131. AN J, CHEN YPP* (2008) Finding Edging Genes From Microarray Data, Journal of Biotechnology, 135(3):233-240, 2008.

130. CHEN YPP*, CHEN F (2008) Targets for Drug Discovery using Bioinformatics, Expert Opinion on Therapeutic Targets, 12(4): 383-389, 2008.

129. TJONDRONEGORO, D., CHEN YPP*, JOLY A (2008) 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. [PDF].

128. CHEN Q, ZHANG S. CHEN YPP* (2008) Rule-based dependency models for security protocol analysis, Integrated Computer-Aided Engineering 15 (2008) 369-380.

Books:

127. Il-Yeol Song, Mario Piattini, Yi-Ping Phoebe Chen, Sven Hartmann, Fabio Grandi, Juan Trujillo, Andreas L. Opdahl, Fernando Ferri, Patrizia Grifoni, Maria Chiara Caschera, Colette Rolland, Carson Woo, Camille Salinesi, Esteban Zimányi, Christophe Claramunt, Flavius Frasincar, Geert-Jan Houben, Philippe Thiran: Advances in Conceptual Modeling - Challenges and Opportunities, ER 2008 Workshops CMLSA, ECDM, FP-UML, M2AS, RIGiM, SeCoGIS, WISM, Barcelona Spain, October 20-23, 2008. Proceedings Springer 2008

Lecture Notes in Computer Science/Artificial Intelligence:

126. SCHMIDT S, LI G, CHEN YPP (2008) Medical Knowledge Discovery from a Regional Asthma Dataset (ICIC2008), Lecture Notes in Computer Science 5227: 888-895.

Refereed conference papers:

125. 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.

124. SAJJANHAR A, LU G, ZHANG D, ZHOU W and CHEN YPP (2008) Image Retrieval Based On Semantics of Intra-Region Color Properties, IEEE 8th International Conference on Computer and Information Technology, 8-11 July 2008, Sydney Australia.

2007

Journals:

123. 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. [pdf]

122. 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. [pdf]

121. 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. [pdf]

120. 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. [pdf]

119. 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.[pdf]

118. NAHAR J., ALI S. CHEN YPP (2007) Microarray Data Classification Using Automatic SVM Kernel Selection, DNA and Cell Biology, 26(10):707-712, 2007. [pdf]

117. NAHAR J., CHEN YPP, ALI S. (2007) Kernel Based Naive Bayes Classifier for Breast Cancer Prediction, Journal of Biological Systems, 15(1): 17-25.

Lecture Notes in Computer Science/Artificial Intelligence:

116. CHEN YPP, QIN Q, CHEN Q (2007) Learning Dependency Model for AMP-activated Protein Kinase Regulation, Lecture Notes in Artificial Intelligence, 4798: 221-229.

115. CHEN Q, ZHANG S. CHEN YPP (2007) Identifying Dependency between Secure Messages for Protocol Analysis, Lecture Notes in Artificial Intelligence: 4798: 30-38.

Refereed conference papers:

114. NAHAR J., CHEN YPP, ALI S.(2007) Microarray Classification and Rule Based Cancer Identification, Proceedings of International Conference on Information and Communication Technology (ICICT 2007) March 7-9, 2007, Dhaka, IEEE, pp 43-46.

113. SUBRAMANIAM C. AN J., GUBBI J, CHEN YPP (2007) Finding Motifs in miRNA Sequences, Proceedings of The Sixth International Conference on Computer and Information Science (ICIS 2007) 11-13 July 2007, Melbourne, Australia. IEEE CS pp. 507-512.

112. RONG J, CHEN YPP, CHOWDHURY M, LI G (2007) Acoustic Features Extraction for Emotion Recognition, Proceedings of The Sixth International Conference on Computer and Information Science (ICIS 2007) 11-13 July 2007, Melbourne, Australia. IEEE CS, pp. 419-424.

111. CHEN Q, Zhang C. CHEN, YPP (2007) Probabilistic Reasoning of Inconsistent Belief in Protocol Analysis, Proceedings of 2007 International Conference on Intelligent Systems and Knowledge Engineering (ISKE2007), Chengdu, China.

110. KNAPP K, RAHAMAN A, CHEN YPP (2007) "Non-Quantized Minimum Free Energy in Untranslated Region Exons", Proceedings of Computational Structural Bioinformatics Workshop (CSBW) is held in conjunction with the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007) IEEE, pp. 32-37.

2006

Journals:

109. CHEN Q. CHEN YPP(2006) Mining Frequent Patterns for AMP-activated Protein Kinase Regulation on Skeletal Muscle, BMC Bioinformatics 7:394. [pdf]

108. CHEN YPP, PROMPRAMOTE S., MAIRE F. (2006) MDSM: Microarray Database Schema Matching By Using Hungarian Method , Information Sciences, Vol 176, pp2771-2790. [pdf]

107. LOPEZ C., CHEN YPP (2006) Using Object and Trajectory Analysis to Facilitate Indexing and Retrieval of Video, Knowledge-Based Systems Journal, Elsevier Science pp639-646. [pdf]

106. LAU R. Y. K., TANG M., WONG O., MILLINER S. W., CHEN YPP (2006) An evolutionary learning approach for adaptive negotiation agents , International Journal of Intelligent Systems, Volume 21, Issue 1 (January 2006) pp41-72. [pdf]

105. CHEN YPP, HWANG MJ, LEE S.K, WONG L (2006) Bioinformatics in Asia Pacific, Asia Pacific Biotech News, Vol. 10 . No. 24 19.

104. CHEN YPP , and WONG L. (2006) Algorithms and Computational Bioinformatics The Journal of Bioinformatics & Computational Biology.

103. SHI W., ZHOU W, CHEN YPP (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.

102. CHEN YPP and CHUA T.-S. (2006) Introduction: Multimedia Modelling . The Visual Computer, (2006) 22: 1–2.

Books:

101. JIANG T., YANG U.-C., CHEN YPP, and WONG 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.

Lecture Notes in Computer Science/Artificial Intelligence:

100. 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. [pdf]

99. 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.

98. CHEN Q. CHEN YPP., ZHANG C., ZHANG S. (2006) Detecting Collusion Attacks in Security Protocols, The Eighth Asia Pacific Web Conference January (APWeb2006) 16-18, 2006, Harbin, China. Lecture Notes in Computer Science, LNCS3841. pp297-306.

Refereed conference papers:

97. 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. (Tier A)

96. 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.

95. CHEN YPP, CHEN Q (2006) Analyzing Inconsistency Toward Enhancing Integration of Biological Molecular Databases, Proceedings of the fourth Asia-Pacific Bioinformatics Conference (APBC2006) Taipei Taiwan 13-16 Feb 2006, pp197-206.

94. TJONDRONEGORO, D. , CHEN YPP (2006) Using Decision-Tree to Automatically Construct Learned-Heuristics for Events Classification in Sports Video . IEEE International Conference on Multimedia & Expo (ICME2006) IEEE CS Press, July 9-12, 2006, Toronto, Canada, pp1465-1468.

93. TJONDRONEGORO, D. , CHEN YPP (2006) Towards Universal and Statistical-Driven Heuristics for Automatic Classification of Sports Video Events . the 12th International Multimedia Modelling Conference (MMM2006) IEEE Press, pp43-50.

92. TJONDRONEGORO, D. , CHEN YPP , PHAM B. (2006) Extensible Detection and Indexing of Highlight Events in Broadcast Sports Video Towards Universal and Statistical-Driven Heuristics for Automatic Classification of Sports Video Events . The 29th Australasian Computer Science Conference-2006 (ACSC2006) Hobart, TAS, Australia, pp237-246.

91. 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.

90. 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.

89. MORRISON D., SAIJANHAR A., HOU J., CHEN YPP (2005) Providing Real-Time Information Services for Public Bus Commuters , Proceedings of The Fourth International Conference on Active Media Technology (AMT 2006) June 7-9, 2006, Brisbane Australia pp384-387.

2005

Journals:

88. AN J., CHEN YPP CHEN H. (2005) DDR: An Index Method for Large Time Series Datasets , Information Systems, Volume 30, Issue 5, (July 2005) Elsevier Science. pp333-348. [pdf]

87, Zhang C., CHEN YPP, Zhang S. CHEN Q (2005) Mining Inconsistent Secure Messages Toward Analyzing Security Protocol, The International Journal of Intelligent Control and Systems (IJICS) Volume 10, Number 1, March 2005, pp77- 85.

86. GARCIA A., CHEN YPP, RAGAN MA (2005) Information Integration in Molecular Bioscience, Applied Bioinformatics, 2005; 4 (3): 157-173.

85, CHEN YPP (2005) Advanced Techniques for Bioinformatics . The Journal of Bioinformatics & Computational Biology, 3 (1): 99-102.

Books:

84. CHEN YPP, Ed., Bioinformatics Technologies, Springer - Jan 2005.

83. CHEN YPP, and WONG L. Editors, (2005) Proceedings of the Third Asia-Pacific Bioinformatics Conference, Advances in Bioinformatics & Computational Biology Vol 1 Jan 2005, by Imperial College Press.

82. CHEN YPP, Ed, (2005) Multimedia Modelling, Proceedings of the 11th International Multimedia Modelling Conference, IEEE CS Press.

Book Chapters

81. CHEN YPP (2005) Introduction to Bioinformatics. Bioinformatics Technologies, edited by Y.-P. Phoebe CHEN Chapter 1, pages 1-14, Springer, Jan 2005. pp1-13.

80. PROMPRAMOTE S., CHEN Y., CHEN YPP (2005) Machine Learning in Bioinformatics , Bioinformatics Technologies, edited by Y.-P. Phoebe CHEN Chapter 5, pages 117-154, Springer, Jan 2005, pp117-153.

79. SHI W., ZHOU W, CHEN YPP (2005) Biological Sequence Assembly and Alignment , Bioinformatics Technologies, edited by Y.-P. Phoebe CHEN chapter 8, pages 243-262, Springer, Jan 2005, pp241-261.

78. MANN S, CHEN YPP (2005) Modeling for Bioinformatics , Bioinformatics Technologies, edited by Y.-P. Phoebe CHEN Chapter 9, pages 263-298, Springer, Jan 2005, pp263-298.

77. TSE B., HUME D. CHEN YPP (2005) Pattern Matching for Motifs , Bioinformatics Technologies, edited by Y.-P. Phoebe CHEN Chapter 10, pages 299-312, Springer, Jan 2005, pp299-312.

76. YU Z.-G., ANH V. CHEN YPP (2005) Visualization and Fractal Analysis of Biological Sequences , Bioinformatics Technologies, edited by Y.-P. Phoebe CHEN Chapter 11, pages 313-352, Springer, Jan 2005, pp313-351.

75. LIEW A. W.-C., YAN H., YANG M., CHEN YPP (2005) Microarray Data Analysis , Bioinformatics Technologies, edited by Y.-P. Phoebe CHEN Chapter 12, pages 353-388, Springer, Jan 2005, pp353-388.

Lecture Notes in Computer Science/Artificial Intelligence:

74. AN J., CHEN YPP, XU Q. and ZHOU X., (2005) A New Indexing Method for High Dimensional Dataset , Database Systems for Advanced Applications (DASFAA2005) Lecture Notes in Computer Science, LNCS3453. Springer-Verlag, pp385-397. (Tier A)

73. TJONDRONEGORO, D. , CHEN YPP (2005) Multi-level Semantic Analysis for Sports Video . Knowledge-Based Intelligent Information and Engineering Systems (KES). Lecture Notes in Computer Science, LNCS3682 / 2005 , Springer pp24-30.

72. AN J., CHEN YPP (2005) Yet Another Induction Algorithm , Knowledge-Based & Intelligent Information & Engineering Systems (KES) Lecture Notes in Computer Science, LNCS3682 / 2005 , Springer, pp37-44. [PDF]

71. CHEN Q. CHEN YPP, (2005) Analyzing Security Protocols using Association Rule Mining, The 18th Australian Joint Conference on Artificial Intelligence, Sydney Australia, 5-9 December 2005, Lecture Notes in Artificial Intelligence LNAI3809. Springer-Verlag, pp 245-253.

Refereed conference papers:

70. TJONDRONEGORO, D. , CHEN YPP and PHAM B. (2005) Extraction and Classification of Self-consumable Sport Video Highlights , in Proceedings of The ACM MM2005, Singapore. (Tier A+)

69. GARCIA A., Thoraval S., GARCIA L.J. , CHEN YPP, RAGAN M. A., (2005) Bioinformatics workflows: G-PIPE as an implementation, Fifth workshop on Workflow Managements: new abailities for the biological information overview, Oct 5-7 2005 Naples, Italy. pp61-64.

68. TJONDRONEGORO, D. , CHEN YPP and PHAM B. (2005) A Statistical-driven Approach for Automatic Classification of Events in AFL Video Highlights. In Proc. Twenty-Eighth Australasian Computer Science Conference (ACSC2005) Newcastle, Australia. CRPIT, 38. Estivill-Castro, V., Ed. ACS. pp209-218.

67. AN J., CHEN YPP (2005) Keyword Extraction for Text Categorization , Proceedings of The Third International Conference on Active Media Technology (AMT 2005) May 19-21, 2005, Takamatsu, Kagawa, Japan, IEEE, pp556-561.

66. TJONDRONEGORO, D. , CHEN YPP and PHAM B. (2005) Content-based Video Indexing for Sports Applications using Integrated Multi-Modal Approach , in Proceedings of The 4th Asia Pacific International Symposium on Information Technology, Jan. 26-27, 2005, Gold Coast, Australia, pp200-203.

65. AN J., CHEN YPP SUBRAMANIAM C. (2005) Side Chain Conformational Preferences in Protein Structures , The 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS '05) June 20 - 23, 2005, Monte Carlo Resort, Las Vegas, Nevada, USA. pp48-52.

64. SAIJANHAR A., HOU J., CHEN YPP (2005) Content Exploration for e-Learning Using XML Web Services , Proceedings of The Third International Conference on Active Media Technology (AMT 2005) May 19-21, 2005, Takamatsu, Kagawa, Japan, IEEE, p266.

63, CHEN Q. CHEN YPP, Zhang C., Zhang S. (2005) A Framework for Merging Inconsistent Beliefs in Security Protocol Analysis, International Workshop on Data Engineering Issues in E-Commerce (DEEC2005) in conjunction with ICDE2005 conference Tokyo, Japan, 9 Apr 2005, Tokyo, Japan, IEEE, pp112-117.

62, PROMPRAMOTE S., CHEN YPP(2005) ANNODA: Tool for integrating Molecular-biological Annotation Data, in Proceedings of International Workshop on Biomedical Data Engineering (BMDE2005) in conjunction with ICDE2005, April 3-4, 2005, Tokyo, Japan. IEEE, pp113-120.

2004

Journals:

61. TJONDRONEGORO, D. , CHEN YPP and PHAM B. (2004) Integrating Highlights to Play-break Sequences for More Complete Sport Video Summarization , IEEE Multimedia, Oct-Dec, 2004, pp22-37.

60. SOON, L., CHEN YPP and UNDERWOOD, A. (2004) Knowledge Creation in Export Trading , Journal of Information & Knowledge Management (JIKM) World Scientific Vol. 3 No. 4 . pp. 297-316.

59. ZHANG, J., PHAM, B and CHEN YPP (2004) A Fuzzy Shape Database for Create Design , Control and Cybernetics, Issue 1/2004, pp. 141-172 .

Books:

58. CHEN YPP, 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

57. CHEN YPP, Editor, (2004) Multimedia Modelling, Proceedings of the 10th International Multimedia Modelling Conference, IEEE CS Press.

Lecture Notes in Computer Science/Artificial Intelligence:

56. AN J., CHEN YPP and KEOGH E. (2004) A Grid-based Index Method for Time Warping Distance , Web-Age Information Management, Lecture Notes in Computer Science, LNCS Vol 3129, Springer-Verlag, pp65-75. [

55. AN J., CHEN YPP and XU Q. (2004) Surface Spatial Index Structure of High-Dimensional Space , Intelligent Data Engineering and Automated Learning, Lecture Notes in Computer Science, LNCS Vol 3177, Springer-Verlag, pp272-278.

Refereed conference papers:

54, TJONDRONEGORO, D, CHEN YPP and PHAM B. (2004) The Power of Play-Break for Automatic Detection and Browsing of Self-consumable Sport Video Highlights , 6th ACM SIGMM International Workshop on Multimedia Information Retrieval October 15-16, 2004 (MIR2006), New York, NY USA, in conjunction with ACM Multimedia 2004, pp267-274. (Tier A)

53. MANN S., CHEN YPP and EATON L. (2004) A Computational Framework for Nucleic Acid Sub-Sequence Identification , Proceedings of IEEE Fourth Symposium on Bioinformatics and Bioengineering (BIBE2004) May 19-21, 2004, Taichung, Taiwan, ROC. IEEE CS Press, pp467-474.

52. CHEN Y., CHEN YPP 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.

51. TJONDRONEGORO, D. , CHEN YPP and PHAM B. (2004) Classification of Self-Consumable Highlights for Soccer Video Summaries , Proceedings of The 5th IEEE International Conference on Multimedia and Expo (ICME2004) The Grand Hotel, Taipei, Taiwan, June 27th – 30th, 2004. IEEE CS Press.

50, WU S.-T., LI Y., XU Y., PHAM B. and CHEN YPP, (2004) Automatic Pattern-Taxonomy Extraction for Web Mining , IEEE/WIC/ACM WI-2004, Sep 20-24 2004, Beijing China, IEEE CS Press, pp242-248.

49, AN J. and CHEN YPP (2004) Concept Learning of Text Documents , IEEE/WIC/ACM WI-2004, Sep 20-24 2004, Beijing China, IEEE CS Press, pp698-701.

48, PROMPRAMOTE S., CHEN YPP (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).

47, GOWARD P. and CHEN YPP (2004) Redesign of a Multimedia Course to reflect process not product , international conference E-Learn 2004, November 1-5, 2004, Washington, DC , pp660-665.

46, GOODMAN A. and CHEN YPP (2004) Maintaining Relevance in a Rapidly Changing Environment: Evolving a Multimedia Curriculum , Proceedings of 3rd Symposium on IT in Education, Kuala Lumpur, October 2004, pp9-13.

  

Before 2004 have around 45 publications.

 

 

Research projects

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.

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

  • [ARC RNSF 2003-2004] ARC Special Research Initiatives

    • ARC Australian Bioinformatics Grid Network

    • ARC Research Network in Microarray Technology

    • ARC Research Network in Multimedia Technology and Applications (MTA)