CALL FOR CHAPTERS
Submission Deadline: March 31, 2008
Biological Data Mining in Protein Interaction Networks
A book edited by X.-L. Li and S.-K. Ng, Institute for Infocomm Research, Singapore
Introduction
The cellular machinery is a complex system with a multitude of bio-molecular
interactions. Most of the cellular processes are mediated by protein-protein interactions
(PPIs). Recently, high-throughput methods for detecting PPIs have revealed global
pictures of protein interactions on a genomic scale, making it possible to interrogate the
interplay of the bio-molecules in carrying out critical life processes at the networked cooperative level. As a result, modern biology’s focus has shifted from scrutinizing single
molecules to analyzing large complex networks.
The Overall Objective of the Book
Genome-wide screenings of PPIs can be represented as large protein interaction networks
(PINs) in which the nodes represent individual proteins, and the links represent the
existence of biological interactions between the corresponding pairs of proteins. In this
book, we will present bioinformatics methods that are designed for the computational
analyses of the PINs. Each of the chapters will serve as a tutorial for network-based
computational analysis PINs. The objective of this book is to disseminate the research
results and best practice from researchers and practitioners working on bioinformatics,
data mining, and proteomics. We aim to present the various methodologies in an
accessible way to our inter-disciplinary audience, through which we hope to bring better
awareness of this interesting and challenging problem to inspire new solutions and
applications.
Recommended topics include, but are not limited to, the following:
1. Introduction
a. Data mining overview
b. Data mining applications in Biology
c. Data mining applications in Healthcare (evaluation of treatment
effectiveness, management of healthcare, customer relationship
management, and the detection of fraud and abuse.) (Prof Hian Chye Koh)
2. Data preprocessing
a. Biological and medical data collection, cleansing, and integration
b. Biological and medical data visualization
c. Data pre-processing to handle noisy, missing biological and medical data
3. Association rule mining and applications
a. Introduction to Association Rule Mining
b. Identifying HotSpots in Lung Cancer Data Using Association Rule Mining
(Alok Choudhary, IEEE Fellow, Northwestern University)
c. Discovering Relational-Based Association Rules with Multiple Minimum
Supports on Microarray Datasets (Vincent S. Tseng)
4. Clustering and applications
a. Introduction to Clustering
b. FTCluster: Efficient Mining Fault-Tolerant Biclusters in Microarray
Dataset
5. Classification and applications
a. Introduction to Classification
b. Health informatics ( Prof. Raymond Ng, University of British Columbia)
c. Medical Data Mining for Early Deterioration Warning in General Hospital
Wards (Prof Thomas C. Bailey , MD)
d. Biological markers detection
e. Disease genes prediction
f. Disease bioinformatics
g. Computational methods for drug discovery
6. Graph mining and applications
a. Introduction to Graph Mining
b. Graph Based Classification of MRI Data Based on the Ventricular System
(Prof Lawrence Holder, Washington State University)
c. Mining epidemiology/ diseases networks
d. Biological network analysis (protein interaction network, metabolic
network, transcription factor network, signalling network, etc.)
7. Image mining and applications
a. Introduction to Image Mining
b. Non-conventional approach to stem cell image classification (Prof Ming
Li, IEEE & ACM Fellow, University of Waterloo)
c. Brain tumor pathological area delimitation through Non-negative Matrix
Factorization (Prof Paulo Lisboa )
d. Biomedical image analysis
8. Text mining and applications
a. Introduction to Text Mining
b. From sequences to Papers: an Information Retrieval Exercise (Prof
Eugenio Oliveira)
c. Text mining algorithms for biological and healthcare applications (Prof
Wen-Lian Hsu)
9. Sequence mining and applications
a. Introduction to Sequence Mining
b. Mining protein sequence databases for remote homologues that can
display considerable domain length variations (Dr. Ramanathan
Sowdhamini, The National Centre for Biological Sciences (NCBS)
10. Trend Analysis
a. Introduction to Trend Analysis
b. Analyzing trends of hospital length of stay using Phase-type distributions
(Prof Chee-Keong Kwoh)
c. Analysis of complex disorders
11. Semantic web and knowledge acquisition in biology and healthcare
a. Introduction to Semantic Web
b. Using semantic web to revolutionizing data mining in the life sciences
(Prof. Christopher Baker, University of New Brunswick, Canada)
12. Semi-supervised learning
a. Introduction to Semi-supervised learning
b. Transduction of Semi-Supervised Regression Targets in Survival Analysis
for Medical Prognosis (Dr. Qiuhua Liu)
13. Ensemble Learning
a. Introduction to Ensemble Learning
b. Confident Surgical Decision Making in Temporal Lobe Epilepsy by
Heterogeneous Classifier Ensembles (Prof Farshad Fotouhi)
14. Hybrid Learning
a. Introduction to Hydrid Learning
b. In Vivo and In Silico Evidence: Hippocampal Cholesterol Metabolism
Decreases with Aging and Increases with Alzheimer Disease (Prof George
Perry, The University of Texas at San Antonio)
c. Integration of biological and clinical data for translational research
15. Online resources: Database and repositories
a. Electronic health records and biomedical repositories
b. Bioinformatics databases and resources
Submission Procedure
Important Dates
Aug 5, 2011: Due date for paper submission
September 20, 2011: Notification of paper acceptance
October 11, 2011: Camera-ready versions of accepted papers
December 11, 2011: Workshop date
Researchers and practitioners are invited to submit on or before March 31, 2008, a 2-5
page manuscript proposal clearly explaining the mission and concerns of the proposed
chapter. Authors of accepted proposals will be notified by April 10, 2008 about the status
of their proposals and sent chapter organizational guidelines. Full chapters are expected
to be submitted by May 31, 2008. All submitted chapters will be reviewed on a doubleblind review basis.
The
book
is
scheduled
http://www.worldscientific.com/.
to
be
published
by
World
Scientific
Inquiries and submissions can be forwarded electronically (Word document) or by mail to:
Dr. Xiao-Li Li
Data Mining Department
Institute for Infocomm Research
21 Heng Mui Keng Terrace, Singapore 119613
Tel: 65 68748452 • Fax: 65 67768109
E-mail: xlli@i2r.a-star.edu.sg
Website: http://www1.i2r.a-star.edu.sg/~xlli/PPI_BOOK.html