2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research

Significant interest exists in establishing synergistic research in bioinformatics, systems biology and intelligent computing. Supported by the United States National Science Foundation (NSF), International Society of Intelligent Biological Medicine (http://www.ISIBM.org), International Journal of Computational Biology and Drug Design (IJCBDD) and International Journal of Functional Informatics and Personalized Medicine, the ISIBM International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing (ISIBM IJCBS 2009) attracted more than 300 papers and 400 researchers and medical doctors world-wide. It was the only inter/multidisciplinary conference aimed to promote synergistic research and education in bioinformatics, systems biology and intelligent computing. The conference committee was very grateful for the valuable advice and suggestions from honorary chairs, steering committee members and scientific leaders including Dr. Michael S. Waterman (USC, Member of United States National Academy of Sciences), Dr. Chih-Ming Ho (UCLA, Member of United States National Academy of Engineering and Academician of Academia Sinica), Dr. Wing H. Wong (Stanford, Member of United States National Academy of Sciences), Dr. Ruzena Bajcsy (UC Berkeley, Member of United States National Academy of Engineering and Member of United States Institute of Medicine of the National Academies), Dr. Mary Qu Yang (United States National Institutes of Health and Oak Ridge, DOE), Dr. Andrzej Niemierko (Harvard), Dr. A. Keith Dunker (Indiana), Dr. Brian D. Athey (Michigan), Dr. Weida Tong (FDA, United States Department of Health and Human Services), Dr. Cathy H. Wu (Georgetown), Dr. Dong Xu (Missouri), Drs. Arif Ghafoor and Okan K Ersoy (Purdue), Dr. Mark Borodovsky (Georgia Tech, President of ISIBM), Dr. Hamid R. Arabnia (UGA, Vice-President of ISIBM), and other scientific leaders. The committee presented the 2009 ISIBM Outstanding Achievement Awards to Dr. Joydeep Ghosh (UT Austin), Dr. Aidong Zhang (Buffalo) and Dr. Zhi-Hua Zhou (Nanjing) for their significant contributions to the field of intelligent biological medicine.


Introduction
Bioinformatics, Systems Biology and Intelligent Computing have been extensively used in the advanced research in biomedical, agricultural, environmental, pharmaceutical and medical sciences as well as public health, drug design, genomics and so on. Research and development in these areas are impacting the advances of science and technology. Supported by the U.S. National Science Foundation (NSF), International Society of Intelligent Biological Medicine (ISIBM), International Journal of Computational Biology and Drug Design (IJCBDD) and International Journal of Functional Informatics and Personalized Medicine (IJFIPM), the ISIBMInternational Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (ISIBM IJCBS 2009) (http://www.isibm.org/IJCBS) was designed to promote synergistic research and education in bioinformatics, systems biology and intelligent computing. The ISIBM IJCBS 2009 has provided an integrated platform for the cross fertilization of ideas, and to help shape knowledge and scientific achievements by bridging the independent and complementary disciplines into an interactive and attractive forum. ISIBM IJCBS assembles a spectrum of affiliated research workshops, keynote and tutorial lectures and special interest research sessions into a coordinated research meeting held at Tongji University in Shanghai, China on 3-6 August, 2009. The ISIBM IJCBS 2009 was a showcase for integrative research and provided a platform of continuing education with presentations of a number of keynote sessions, workshops, special interest research sessions and tutorial sessions. The conference was also designed for students to learn advanced knowledge in bioinformatics and systems biology for their continued successes in conducting research. Among 300 papers received by the ISIBM IJCBS, a significant portion of the papers were first-authored by students. Each paper was reviewed and ranked by at least three experts in the program and scientific review committee which consists more than one hundred professors in USA, China and worldwide. Over one hundred scholars in the ISIBM IJCBS Program Committee have dedicated themselves to this great academic event in evaluating and selecting papers based on high publication standard. After a rigorous peer review process, 8 papers [1][2][3][4][5][6][7][8] were selected to the BMC Systems Biology and 16 papers were selected to the BMC Genomics [9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24] from 300+ submitted papers. About 120 papers were selected to the ISIBM IJCBS proceedings published by the IEEE Computer Society.

Bioinformatis and computational molecular biology studies
Xu et. al. [9] studied pathogens (http://www.biomedcentral.com/1471-2164/11/S3/S1). This paper is part of the plenary banquet keynote lecture of Dr A key application of clustering data obtained from sources such as microarrays, protein mass spectroscopy and phylogenetic profiles, is the detection of functionally related genes. Typically, only a small number of functionally related genes form meaningful groups, while the rest need to be ignored. Additional complications arise when there are several irrelevant experimental conditions, when the useful clusters occur at different resolutions/scales, and when genes participate in multiple biological processes, leading to multiple cluster memberships. Thus the corresponding data mining problem is to detect a small number of cohesive, possibly overlapping clusters in the data while ignoring irrelevant data portions. Dr. Ghosh discussed two broad approaches to this problem: (a) a generative approach where one determines and fits a suitable probabilistic model to the data, and (b) a non-parametric approach inspired by Wishart's remarkable but obscure mode analysis work from 1968. The pros and cons of the two approaches have been illustrated by Dr. Ghosh using results from gene expression data analysis. The 2009 ISIBM outstanding achievement award was presented by the committee to Dr. Ghosh right after his plenary keynote lecture.
3) Dr. Aidong Zhang Professor and Chair of Department of Computer Science and Engineering, University at Buffalo, The State University of New York, USA.
Keynote Lecture Title: Computational Analysis of Biological Networks.
The development of computational techniques for the effective analysis of biological datasets is a crucial step in the medical application of bioinformatics. This unique merging of computer science and biomedical expertise is expected to provide the synergy needed to advance biomedical research to the next level. When analyzing biological data, we face many new computational challenges. Algorithms that are specifically designed for biological data are required so that Dr. Zhang can take advantage of their unique features and address the unique problems they raised. In her keynote lecture, Dr. Zhang discussed new computational research issues and approaches to analysis of biological networks, especially protein interaction networks.
The 2009 ISIBM outstanding achievement award was presented to Dr. Zhang by the committee right after her plenary keynote lecture. Novel approaches for structural annotation of genomes are required. Dr. Bridges extracted the full value from the avalanche of genome sequence generated from new sequencing technologies. New approaches for annotating genomes using proteomics data and for defragmenting dispersed repeats on genomes were described by Dr A new machine learning framework, Multi-Instance Multi-Label Learning (MIML), was proposed recently by Dr. Zhou. In this framework, an object is represented by multiple feature vectors, and is allowed to be associated with multiple class labels simultaneously. His seminal framework was particularly helpful for learning with complicated objects, and has been found well useful in applications such as image categorization and text categorization. The Berkeley Drosophila Genome Project (BDGP) has generated a large amount of gene expression patterns during Drosophila embryogenesis. Automating the annotation process is very desired. However, there is a big challenge; that is, the anatomical and developmental ontology terms are body-part related and present in local regions of images, while in the BDGP, they are attached collectively to groups of images and it is unknown which term is assigned to which region of which image in the group. Dr. Zhou's MIML provided a promising way to address the challenge. His plenary keynote talk gave an introduction to his MIML as well as the application to Drosophila gene expression pattern annotation. The 2009 ISIBM outstanding achievement award was presented to Dr. Zhou by the committee right after his plenary keynote lecture. 6) Dr. Xiaohua Tony Hu College of Information Science and Technology, Drexel University, USA.
Keynote Lecture Title: Mining, Modelling and Evaluation of the Biomolecular Network.
Biomolecular networks dynamically respond to stimuli and implement cellular function, and understanding these dynamic changes is the key challenge for cell biologists. As biomolecular networks grow in size and complexity, the model of a biomolecular network must become more rigorous to keep track of all the components and their interactions, and in general this presents the need for computer simulation to manipulate and understand the biomolecular network model. In his keynote talk, Dr. Hu presented a novel method to mining, modeling and evaluating a regulatory system that executing cellular functions, which can be represented as a biomolecular network. His method consists of two steps. First, a novel scale-free network clustering approach is applied to such biomolecular network to obtain various sub-networks. Second, computational models are generated for the sub-networks and simulated to predict their behavior in the cellular context. He discussed and evaluated some of the advanced computational modeling approaches; in particular, state-space modeling, probabilistic Boolean network modeling, and fuzzy logic modeling. The modeling and simulation results represented hypotheses that were tested against high-throughput biological datasets (microarrays and/or genetic screens) under normal and perturbation conditions. Experimental results on time-series gene expression data for the human cell cycle indicated that Dr. Hu's approach was promising for the sub-network mining and simulation from large biomolecular networks. 7) Dr. Yi Pan Chair and Professor of Computer Science, Professor of Computer Information Systems, Georgia State University, USA.
Keynote Lecture Title: Protein Structure Prediction and its Understanding Based on Machine Learning Methods.
Understanding protein structures is vital to determining the function of a protein and its interaction with DNA, RNA and enzymes. The information about its conformation can provide essential information for drug design and protein engineering. While there are over a million known protein sequences, only a limited number of protein structures were experimentally determined. Hence, prediction of protein structures from protein sequences using computer programs is an important step to unveil proteins' three dimensional conformation and functions. As a result, prediction of protein structures has profound theoretical and practical influence over biological study. The explanation of how a decision is made during prediction is also important for improving protein structure prediction and guiding the experimental design. In his keynote talk, Dr. Pan showed how to use machine learning methods to improve the accuracy of protein structure prediction and to interpret prediction results. He reported the frontier research on using neural networks, Support Vector Machines combined with Decision Tree and Association Rule for protein structure prediction, rule extraction and prediction interpretation. Evaluation and comparisons of various prediction and rule extraction systems were presented and future research direction in the area were also presented by Dr Those keynote lectures showed that in order to understand the mechanisms of live organisms, information must be integrated at multiple levels. ISIBM IJCBS was designed for integrating information from bioinformatics, systems biology and intelligent computing points of views. The synergy of integrative research on both bioinformatics and systems biology using intelligent computing was very beneficial. The ISIBM IJCBS successfully assembled a spectrum of affiliated research workshops, keynote and tutorial lectures and special interest research sessions into a coordinated research meeting held at Tongji University in Shanghai, China on 3-6 August, 2009. The Program and Scientific Committee consists of more than a hundred professors and scholars world-wide and was organized as follows: Honorary Furthermore, by the time of this paper is published in November 2010, the scientific committee has also presented the 2010 ISIBM Outstanding Achievement Awards to Dr. Arif Ghafoor (Purdue), Dr. Mark Borodovsky (Georgia Tech) and Dr. Dong Xu (University of Missouri) for their significant contributions to the field of intelligent biological medicine. The nonprofit academic society welcomes the nominations for the 2011 awards. Please send your nominations to President of ISIBM T. K. Li Professor A. Keith Dunker, Vice-President Professor Hamid R. Arabnia and Secretary-General Professor Yunlong Liu. 1-3 winners will be announced by the president of the society after the rigorous evolution and selection process by the committee.

Conclusions
As upcoming emerging fields, bioinformatics, systems biology and intelligent computing integrate scientific and engineering knowledge to solve significant biomedical problems. It is important to train the next generation bioinformatics and systems biology experts with up-to-date technologies and advancements in the fields. ISIBM IJCBS 2009 provided an opportunity to promote inter/multidisciplinary scientific research and education for students, faculty, scientists, engineers and medical doctors, and help them better prepared for new initiatives and cutting-edge researches. Updated cutting-edge technologies and breaking through ideas were presented in the keynote and tutorial lectures, in the open discussion sessions, and in special interest and scientific exchange sessions to inspire innovations, novel ideas and scientific discoveries. The BMC Genomics and the BMC Systems Biology issues were products of part of the achievement of the ISIBM International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing in promoting emerging cutting-edge research fields with most updated research trends, novel technologies, breakthrough ideas and scientific discoveries. We hope that attendees' experiences with the professional society were, are and will be always pleasant, memorable and productive. The non-profit academic society strives to promote science and education and warmly welcomes suggestions world-wide.