Some Recent Selected Journal Publications:
/ Computational Biology / System Biology / Biomedical Science
WANG T, CHEN
BOWMAN P, GODDARD M, HAYES B, A
hybrid expectation maximisation and MCMC sampling algorithm to
implement Bayesian mixture model based genomic prediction and QTL
17(1): 1-21, 2016.
CHIU JKH, CHEN
A Comprehensive Study of RNA Secondary Structure Alignment
Briefings in Bioinformatics,
CHIU JKH, CHEN YPP*,
Pairwise RNA Secondary Structure Alignment with Conserved Stem Pattern,
Bioinformatics, 31 (24):3914-3921, 2015.
Rajasekaran R, CHEN
Therapeutic Targets and Role of Technology in Developing Novel
Antileishmanial Drugs, Drug
20(8): 958-968, 2015.
CHIU JKH, CHEN YPP*,
Efficient conversion of RNA pseudoknots to knot-free structures using a
graphical model, IEEE Transactions on Biomedical Engineering,
62 (5), 1265-1271, 2015.
KOURFARIOTIS L, CHEN YPP, CHAMBERLIAN A, VANDERJAGT C, HAYES B
A catalogue of novel bovine long noncoding RNA across 18
tissues, PLoS ONE
10(10): e0141225, 2015.
S. Chen YPP*,
steered molecular dynamics mediated hit discovery for histone
deacetylases, Physical Chemistry Chemical Physics,
16 (8): 3777 - 3791, 2014.
Zhu W, Chen YPP*,
Computational developments in microRNA-regulated protein-protein
interactions, BMC Systems Biology, 8:14, 2014.
Koufariotis L., CHEN YPP,
Sunduimijid B, Hayes BJ,
Regulatory and coding genome regions are enriched for trait associated
variants in dairy and beef cattle, BMC Genomics, 2014, 15:436.
Liu Q, Chen YPP, Li J,
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, 2014.
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,
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,
Kalyaanamoorthy, S. CHEN YPP*,
Ligand release mechanisms and channels in histone deacetylases.
Journal of Computational Chemistry 34(26): 2270-2283, 2013.
Yuan Y, Chen YPP, Boyd-Kirkup
J, Khaitovich P and Somel M,
Accelerated aging-related transcriptome
changes in the female prefrontal cortex, Aging Cell,
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):
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.
Chiu JKH, Chen YPP*,
Conformational Features of Topologically Classified RNA Secondary
Structures, PLoS ONE, 7(7): e39907, 2012.
ZHU W, HOU J, and CHEN YPP*,
Exploiting Multi-Layered Information to Iteratively
Predict Protein Functions, Mathematical Biosciences,
236 (2): 108–116, 2012.
Kalyaanamoorthy S, Chen YPP*,
Structure-based drug design to augment hit discovery,
Xi Y, Chen YPP, Qian C.,
Comparative study of computational
methods to detect the correlated reaction sets in biochemical networks,
Briefings in Bioinformatics 12(2): 132-150, 2011.
Chen Q, Chen YPP*,
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,
Chen Q, Li G, Chen YPP*,
Interval-Based Distance Function for Identifying RNA Structure
Candidates, Journal of Theoretical Biology, 269(8):
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,
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*,
Characteristic Relations Bind to RNA Secondary Structures, IEEE
Transactions on Information Technology in Biomedicine 14(1):10-15,
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.
Using Bioinformatics Techniques for Gene
Identification in Drug Discovery and Development,
Current Drug Metabolism 9(6): 567-573, 2008.
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,
YPP, Chen F,
Targets for Drug Discovery using Bioinformatics,
Expert Opinion on
Therapeutic Targets, 12(4):
An Evaluation of Contemporary Hidden Markov Model Genefinders with a
Predicted Exon Taxonomy,
Nucleic Acids Research
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,
Timms P, Chen YPP,
CIDB: Chlamydia Interactive Database for
cross-querying genomics, transcriptomics and proteomics data, Biomolecular Engineering 24(6):603-608, 2007.
Chen Q. Chen YPP,
Patterns for AMP-activated Protein Kinase Regulation on Skeletal Muscle,
BMC Bioinformatics, 7:394, 2006.
Springer - 2005. p396. SCI.
Simulation and Scientific Visualization /
/ Information Systems
/ Databases / Data Mining / Intelligent System
- YANG HF, DILLON T, CHEN YPP*, Optimized Structure of the Traffic Flow Forecasting Model with a Deep Learning Approach, IEEE
Transactions on Neural Networks and Learning Systems, 2016 (in press). DOI: 10.1109/TNNLS.2016.2574840
ZHEN H, CHEN YPP,
PaMeCo Join: A Parallel Main Memory Compact Hash Join,
Information Systems, 58:105-125,2016.
ZHEN H, CHEN YPP*,
Workload-based Ordering of Multi-dimensional Data, IEEE
Transactions on Knowledge and Data Engineering,
CHEN Q, CHEN YPP,
Interval-Based Similarity for Classifying Conserved RNA Secondary Structures, IEEE Intelligent Systems,
Chen YPP*, Johnson C, Lalbakhsh P, Caelli T, Deng G, Tay D, Erickson
S, Broadbridge P, El Refaie A, Doube W, Morris
review of virtual speech therapists for speech disorders. Computer
Speech & Language ,
BEGLEY S, ZHEN H, CHEN YPP, “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]
Cheng SC, Cheng KY, CHEN
GHT-Based Associative Memory Learning and Its Application to Human
Action Detection and Classification, Pattern Recognition,
46(11): 3117–3128, 2013.
NGUYEN, T; ZHEN H, CHEN YPP,
Buffering for Spatiotemporal Indexes Via Shared Execution, The
Computer Journal, 56(1):115-137, 2013.
Q, CHEN YPP,
Discovering Inhibition Pathways for Protein
Kinases, IEEE Intelligent Systems, 27(5): 19-26, 2012.
Yang L, Zhen H,
Chen YPP, Nguyen T,
External Sorting on Flash Memory Via Natural Page
Run Generation, The Computer Journal, 54(11):
Knowledge-discounted Event Detection in Sports Video,
Transactions on Systems Man & Cybernetics, Part A.
Q. Chen YPP,
Discovery of Structural and Functional Features in RNA Pseudoknots,
IEEE Transactions on Knowledge and Data Engineering,
Rong J, Li
G and Chen YPP.
Acoustic Feature Selection for Automatic Emotion Recognition from Speech.
Information Processing & Management,
XF, Chen WM, Chen YPP,
Working Set Strategy based SMO Algorithm in Support Vector Machine,
Information Processing & Management,
45(5): 584-592, 2009.
and Extensible Segment-Event-Object based Sports Video Retrieval System:
ACM Transactions on Multimedia Computing, Communications and
Q. Chen YPP, and Zhang C.,
Inconsistency in Biological Molecular Databases using Ontology, Data
Mining and Knowledge Discovery
15(2): 275-296, 2007. [pdf]
J. Yu JX. Ratanamahatana
A Dimensionality Reduction Algorithm and Its Application for
Interactive Visualization, Visual Languages and Computing,
An J, Chen YPP, Chen H,
DDR: An Index Method for Large
Time Series Datasets, Information Systems, 30:333-348, 2005.
Content-based Indexing and Retrieval using MPEG-7 and X-Query in Video
Data Management Systems, World Wide Web Journal, 5(3):207-227,
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,
[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.
Exploiting DB Technologies for the
Visualization and Analysis of Measured and Simulated Plant Structures in
$334K] Integrating Database Technologies and Visual Analysis in
Bioinformatics for Genome Data, 2003-2005.
[ARC Linkage Project
Design and Development of a Web-based Intelligent Multimedia Mining
Development of Knowledge Discovery for High Dimensional Biomedical Data,
[ARC LIEF $285K] A
Haptically enabled Universal Motion Simulator Research Facility,
[ARC LIEF $430K]
optomechatronics sensing, measurement, and control research, 2007.
[ARC LIEF $400K]
Computational Infrastructure for High-Throughput Genome Bioinformatics,
Some Professional Activities: (more
conferences and others)
Associate Editor for the IEEE Transactions on Multimedia (T-MM)
Associate Editor for the Journal of Research and Practice in
Information Technology (JRPIT)
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 Fifteenth Asia Pacific Bioinformatics
Shenzhen, China, 16-18 January, 2017.
[SC-Chair] STEERING COMMITTEE CHAIR of the
Modelling Conference, (2003 -
.....), coming: The 23rd International Conference on
Multimedia Modelling (MMM2017),
Reykjavik, Iceland, January 4-6, 2017.
Third International Workshop on Conceptual Modelling for Life Sciences
November 1-4, 2010 Vancouver, BC, Canada.
The Bioinformatics Australia 2009 (BA2009),
29-30 Oct. 2009.
[Program Co-Chair] 25th ACM Multimedia
conference (ACM MM2017), 16-20 Oct 2017, Silicon Valley, California,
[Program Co-Chair] Fifteenth Asia
Pacific Bioinformatics Conference (APBC2017), 16-18 Jan, 2017, Shenzhen,
[Program Co-Chair] Fourteenth Asia
Pacific Bioinformatics Conference (APBC2016), 11-13 Jan, 2016, San
Francisco Bay Area, United States.
[Program Co-Chair] 27th International
Conference on Genome Informatics (GIW2016), October 3-5, 2016, Shanghai,
ACM Multimedia conference (ACM
MM2015), 26-30 Oct 2015, Brisbane, Australia.
[Australia Liaison] IEEE International Conference on Multimedia and
Expo( ICME 2017), 10-14 Jul
Member] The 21st Pacific-Asia Conference on Knowledge Discovery and Data
Mining (PAKDD 2017), 23-26 May
2017, Jeju, South Korea.
Member] The 19th Pacific-Asia Conference on Knowledge Discovery and Data
Mining (PAKDD 2015),
19-22 May, 2015, Ho Chi Minh City, Vietnam.
Member] 26th International Conference on Database and Expert Systems
Valencia, Spain September 1 - 4, 2015.
Member] The 18th Pacific-Asia Conference on Knowledge Discovery and Data
Mining (PAKDD 2014), 13-16
May, 2014, Tainan, Taiwan.
Member] 18th Annual International Conference on Research in
Computational Molecular Biology (RECOMB
2014), Pittsburgh, Pennsylvania, April 2-5, 2014.
Member] 25th International Conference on Database and Expert Systems
Applications (DEXA2014), September 1-5, 2014 in Munich, Germany.
Member] The 13th Pacific Rim International Conference on Artificial
Gold Coast, Queensland, Australia, 1-5 Dec 2014.
Member] The 14th SIAM International Conference on Data Mining (SDM2014),
Philadelphia, Pennsylvania, USA April 24 - 26, 2014.
Member] The Eleventh Asia Pacific Bioinformatics Conference (APBC
2013), Vancouver, BC, Canada 21-23 January 2013.
Member] the 17th Annual International Conference on Research in Computational
Molecular Biology (RECOMB
2013), Beijing, China, April 7-10, 2013.
The 17th Pacific-Asia Conference on Knowledge Discovery and Data Mining
(PAKDD2013), 14-17 April
2013, Gold Coast, Australia.
The 13th SIAM International Conference on Data Mining (SDM 2013),
May 02-04, 2013, Austin, TX, USA.
The 20th Annual International Conference on Intelligent Systems for
Molecular Biology (ISMB2012),
15-17 July, Long Beach, California.
The 23rd International Conference on Database and Expert Systems
Applications (DEXA2012), 3-7
September, Vienna, Austria.
The 16th Pacific-Asia Conference on Knowledge Discovery and Data Mining
(PAKDD2012), May 29- 1 June
2012, Kuala Lumpur, Malaysia.
The 12th Pacific Rim International Conference on Artificial Intelligence
September, Sarawak, Malaysia.
2012 IEEE/ICME International Conference on
Complex Medical Engineering (CME2012), 1-4 July, Kobe, Japan.
The 8th International Conference on Advanced
Data Mining and Applications (ADMA2012), 15-18 December, Nangjing,
International Conference on Data Engineering (ICDE2008), Cancun, Mexico,
April 7-12, 2008
International Conference on Pattern Recognition (ICPR 2008), Tampa,
Florida, USA, December 8-11, 2008
12th ACM International Conference on Information
and Knowledge Management (CIKM2003), November 3-8 2003, New Orleans, LA,
Member] The 11th
International conference on Intelligent Systems for Molecular Biology
(ISMB2003), Jun 29 - Jul 3, 2003,