- Open Access
2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research
BMC Genomics volume 11, Article number: I1 (2010)
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.
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 ISIBM International 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 [1–8] were selected to the BMC Systems Biology and 16 papers were selected to the BMC Genomics[9–24] from 300+ submitted papers. About 120 papers were selected to the ISIBM IJCBS proceedings published by the IEEE Computer Society.
The BMC Genomics and BMC Systems Biology supplements for the ISIBM IJCBS consist of 24 research papers, amongst which 8 papers are in the BMC Systems Biology[1–8] and 16 papers [9–24] are in BMC Genomics research. Those papers include the following scopes.
1. Systems biology modeling in molecular biology
Wang et. al. presented dynamic network to model cellular interactions of different cell types  (http://www.biomedcentral.com/1752-0509/4/S1/S5). Chowdhary et. al.  presented a comprehensive computational analysis on genome wide promoter studies of human histone gene (http://www.biomedcentral.com/1752-0509/4/S1/S4). Wang et. al.  presented a novel modelling of protein - nucleic acid interactions on systems biology studies (http://www.biomedcentral.com/1752-0509/4/S1/S3), Chitankar et. al.  presented an algorithm for inferring gene regulatory networks from time series DNA microarray data (http://www.biomedcentral.com/1752-0509/4/S1/S7). To fulfil a model based drug development, Wang et. al.  proposed a new statistical approach for model based drug development (http://www.biomedcentral.com/1752-0509/4/S1/S8). Jiang et. al.  presented a network-based approach that can infer potential microRNAs with disease relevancy (http://www.biomedcentral.com/1752-0509/4/S1/S2). Wang et. al.  utilized machine learning to predict the siRNA potencies (http://www.biomedcentral.com/1471-2164/11/S3/S2). Meng et. al.  studied inference of the context specific structure and temporal dynamics of gene regulatory network (http://www.biomedcentral.com/1471-2164/11/S3/S11)
2. Systematic modelling and prediction of protein structure and function
Xue et. al.  presented a comprehensive studies of disordered proteins in archaea, (http://www.biomedcentral.com/1752-0509/4/S1/S1), Zhang et. al.  presented a hybrid genetic and tabu search algorithm to predict 3D structure of proteins. (http://www.biomedcentral.com/1752-0509/4/S1/S6). Huang  et. al. developed an algorithm for protein studies (http://www.biomedcentral.com/1471-2164/11/S3/S14). Wang et. al.  provided advances in clustering methods in proteins. (http://www.biomedcentral.com/1471-2164/11/S3/S10). Lo et. al.  presented a databases for proteins (http://www.biomedcentral.com/1471-2164/11/S3/S7).
3. Computational cancer studies and modeling
Land et. al.  developed new statistical learning approach to improve CT prediction of treatment in patients with metastatic colorectal carcinoma (http://www.biomedcentral.com/1471-2164/11/S3/S15). Dong et. al.  investigated genes and miRNAs in glioblastoma (http://www.biomedcentral.com/1471-2164/11/S3/S16). Sun et. al.  provided a comparative study of cancer proteins in human protein-protein interaction network (http://www.biomedcentral.com/1471-2164/11/S3/S5).
4. Bioinformatis and computational molecular biology studies
Xu et. al.  studied pathogens (http://www.biomedcentral.com/1471-2164/11/S3/S1). This paper is part of the plenary banquet keynote lecture of Dr. Dong Xu at the ISIBM IJCBS 2009. Ghosh et. al.  studied signal transduction systems (http://www.biomedcentral.com/1471-2164/11/S3/S3). Chowbia et. al.  studied rat liver pathways with DNT exposures. (http://www.biomedcentral.com/1471-2164/11/S3/S4). Tang et. al.  studied adipose separation of small animals (http://www.biomedcentral.com/1471-2164/11/S3/S9). Zhang et. al.  presented a peak detection algorithm for LC/MS (http://www.biomedcentral.com/1471-2164/11/S3/S8).
Promoting emerging cutting-edge research fields
Bioinformatics, Systems Biology and intelligent computing have been effectively used in the cutting edge translational biomedical research. The resonance and synergy of these fields are enormous, and are having profound impact on the advances of science and medicine. In cooperation with the International Society of Intelligent Biological Medicine http://www.isibm.org, International Journal of Computational Biology and Drug Design (IJCBDD), International Journal of Functional Informatics and Personalized Medicine (IJFIPM), the ISIBM IJCBS 2009 was designed dynamically to promote synergistic research and education. To this end, the ISBM IJCBS program committee especially appreciates the following keynote lecturers:
1) Dr. Dong Xu
James C. Dowell Distinguished Professor, Director of Digital Biology Laboratory and Chair of Computer Science Department, University of Missouri, USA.
Keynote Lecture Title: New Frontiers in Translational Research with Next-Generation Sequencing and Proteomics Analyses.
Recent advances in next-generation sequencing and proteomics further empowered translational research in medicine and agriculture. Based on new technologies, systematic approaches for personalized medicine, bioenergy, and transgenic crops are being developed. Dr. Xu showed that these developments have major social and economical impact. New technologies also pushed frontiers towards large-scale studies of more complex systems, such as non-coding RNA, post-translational modifications, and DNA methylations. These studies are typically data rich and require extensive bioinformatics developments. Dr. Xu was the plenary banquet keynote lecturer, he presented a number of examples showing the roles of computer science and bioinformatics in the related developments.
2) Dr. Joydeep Ghosh
Schlumberger Centennial Chair Professor of University of Texas at Austin, USA.
Keynote Lecture Title: Locating a Few Useful Clusters in Large Biological Datasets: A Tale of Two Viewpoints.
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.
4) Dr. Susan M. Bridges
Co-Director of the Institute for Digital Biology and Hearin Distinguished Professor,
Mississippi State University, USA.
Keynote Lecture Title: Algorithms for Structural Annotation of Genomes.
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. Bridges in her plenary keynote lecture.
5) Dr. Zhi-Hua Zhou
Cheung Kong Professor of Nanjing University, China.
Keynote Lecture Title: MIML: A New Machine Learning Framework with Application to Drosophila Gene Expression Pattern Annotation.
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. Pan.
8) Dr. Patrick Shen-Pei Wang
Professor of Northeastern University and MIT, USA.
Keynote Lecture Title: Intelligent Pattern Recognition and Applications to Similarity Measurement.
In his keynote talk, Dr Wang pointed out that time is money, saving time is saving money. Every penny saved is one penny earned as Dr. Wang stressed. His keynote discussed two major concerns that he can consider saving time: communication by post mails, and, transportation on roads, by intelligent pattern recognition, in terms of hierarchical structures and ambiguities. Dr. Wang along with Dr. Xu are the only 2 plenary banquet speakers. His keynote lecture have drawn a lot of interest among large audiences.
9) Dr. Sun Kim
Chair of Bioinformatics Program and Director of Center for Bioinformatics Research, Indiana University School of Informatics, USA.
Keynote Lecture Title: A Data-driven, Systems Biology Approach for Exploring the Role of Epigenetics in Drug-resistant Human Cancer.
Dr. Kim's keynote talk summarized a project to investigate the role of epigenetics in the development of the drug resistant phenotype in human cancer, a major research emphasis of the Indiana University and Ohio State University Integrated Cancer Biology. His keynote was a showcase of the translational genomics research at the OSU -IU alliance led by Dr. Tim Hui-ming Huang, a leading cancer biologist and PI of the NIH grants for their collaborative multi-university research projects.
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 General Chairs
Dr. Ruzena Bajcsy, Member of United States National Academy of Sciences, Institute of Medicine, Member of United States National Academy of Engineering, University Professor of the University of California at Berkeley, USA
Dr. Joydeep Ghosh, Fellow of IEEE, Chair Professor of the University of Texas at Austin, USA
Dr. Michael S Waterman, Member of United States National Academy of Sciences, Fellow of American Academy of Art and Sciences and Academician of French Académie des Sciences. University Professor of the University of Southern California at Los Angles, USA
Dr. Mark Borodovsky, President of ISIBM and Regents Professor of Georgia Institute of Technology, USA
Dr. Changjun Jiang, Dean of College of Engineering and Information Technology and University Professor of Tongji University, China
Steering Committee Members
1) Dr. Hamid R. Arabnia
Founding chair of WORLDCOMP Congress, Editor-in-Chief of The Journal of Supercomputing (Springer) and recipient of William F. Rockwell, Jr. Medal for promotion of multi-disciplinary research (Rockwell medal is International Technology Institute's highest honor). He is on the editorial and advisory boards of 25 other journals and science magazines.
2) Dr. Ruzena Bajcsy
Member of United States National Academy of Sciences, Institute of Medicine, Member of United States National Academy of Engineering, the 2003-2005 United States President’s Information Technology Advisory Committee (PITAC), 2001 ACM Allen Newell Award, Member of National Institute of Standards and Technology, Member of National Research Council Army Research Technical Assessment Board, Member of Computer Research Association for Women, Member of the Review Board of Stanford University Computer Science, Fellow of ACM and Fellow of IEEE, Distinguished Professor and Director of CITRIS, University of California at Berkeley, U.S.A.
3) Dr. Mark Borodovsky
President of International Society of Intelligent Biological Medicine, Founder of GeneMark and Pioneer of Bioinformatics Research, Founder of Georgia Tech Bioinformatics Ph.D. Programs, Distinguished Regents' Professor and Director Center for the Bioinformatics and Computational Genomics of the Georgia Institute of Technology and Emory University School of Medicine, both in Atlanta, Georgia, USA
4) Dr. Arif Ghafoor
Fellow of IEEE and Professor of School of Electrical and Computer Engineering of Purdue University. Dr. Ghafoor is a leading researcher in multimedia systems, databases, distributed computing systems, broadband multimedia networking and biomedical engineering. Areas of interest include communications, networking, signal & image processing, computer engineering and biomedical engineering.
5) Dr. Joydeep Ghosh
Distinguished Schlumberger Centennial Chair Professor of Engineering, Chair of IEEE DMTC and Fellow of IEEE, 1992 IEEE Darlington Award, Director of IDEAL (Intelligent Data Exploration and Analysis Lab), University of Texas at Austin, U.S.A.
6) Dr. Tony Xiaohua Hu
IEEE Computer Society Bioinformatics and Biomedicine Steering Committee Chair and the IEEE Computational Intelligence Society Granular Computing Technical Committee Chair, the founding Editor-in-Chief of the International Journal of Data Mining and Bioinformatics, an associate editor/editorial board member of four international journals (KAIS, IJDWM, IJSOI and JCIB). Dr. Hu has received a few prestigious awards including the 2005 National Science Foundation (NSF) Career award.
7) Dr. Yi Pan
Editor-in-Chief of the International Journal of Bioinformatics Research and Applications, series editor of Wiley Book Series on Bioinformatics, Associate Editor of 6 IEEE Transactions, winner of many awards, keynote speaker for over 10 conferences, and Chair of Department of Computer Science at Georgia State University, USA
8) Dr. Michael S. Waterman
Member of United States National Academy of Sciences, Fellow of American Academy of Art and Sciences and Academician of French Académie des Sciences. Co Editor-in-Chief of the Journal of Computational Biology, Editor-in-Chief of Lecture Notes in Bioinformatics, Lecture Notes in Computer Science (LNCS, Springer). Distinguished University Professor of University of Southern California, Los Angles, California, USA
9) Dr. Cathy H. Wu
Dr. Wu has conducted bioinformatics research since 1990 and developed several protein classification systems and databases. She has managed large software and database projects, led the bioinformatics effort of the Protein Information Resource (PIR) since 1999, and becoming the PIR Director in 2001. Her research interests include protein family classification and functional annotation, biological data integration, and literature mining.
10) Dr. Mary Qu Yang
Editor-in-Chief, International Journal of Computational Biology and Drug Design. Oak Ridge Institute for Science and Education, Oak Ridge National Lab. U.S. Department of Energy, USA, and National Human Genome Research Institute, National Institutes of Health (NIH) , U.S. Department of Health and Human Services, USA.
11) Dr. Aidong Zhang
Fellow of IEEE and Professor and Chair of Department of Computer Science and Engineering at the State University of New York at Buffalo and the director of the Buffalo Center for Biomedical Computing (BCBC). She is an author of more than 200 research publications and has served on many editorial boards of prestigious journals. Dr. Zhang is a recipient of the National Science Foundation CAREER Award and SUNY (State University of New York) Chancellor’s Research Recognition Award.
Dr. Joe Zhang,
Director of School of Computing, The University of Southern Mississippi, USA
Dr. Andreas Dress,
Professor and Director, Chinese Academy of Science, CAS-MPG Partner Institute for Computational Biology, Shanghai, China; Professor of University of Bielefeld and Max Planck Institute, Germany and Princeton Institute for Advanced Studies, Princeton, USA;
Dr. Guo-Zheng Li,
Tongji University, China
Prof. Heng Huang, University of Texas, Arlington, USA
Prof. Sumanth Yenduri , University of Southern Mississippi, USA
Prof. Zhongming Zhao, Vanderbilt University, USA
Workshop Principal Chairs and Coordinators
Prof. Abdullah N. Arslan, University of Vermont, USA
Dr. Ping Gong, Environmental Laboratory, U.S. Army Engineer Research and Development Center, and SpecPro Inc.
Professor Liangjiang Wang, Clemson University, USA.
Workshop on Bioinformatics Algorithms
Chair: Dr. Abdullah N. Arslan, University of Vermont, USA
Workshop on Bioinformatics in Radiation Oncology and Robotic Interventions in Cancer Diagnosis and Therapy
Chair: Dr. Yan Yu, Professor and Director of Medical Physics, Thomas Jefferson University, USA
Workshop on Machine Learning and Human Diseases
Chairs: Dr. Liangjiang Wang, Clemson University, USA
Dr. Susan M. Bridges, University Professor of the Mississippi State University, USA
Workshop on Bioinformatics and Systems Biology in Traditional Chinese Medicine Research.
Chairs: Dr. Dan Xi, NIH, U.S. Department of Health and Human Services, USA
Dr. Su-Shing Chen, University of Florida, USA.
Workshop on Methods and Applications of Systems Biology
Chairs: Dr. Yidong Chen, University of Texas,
Dr. Yufei Huang, University of Texas
Dr. Ji Zhang, Shanghai Jiao Tong University.
Special Panel on future directions of bioinformatics and systems biology
Chair: Professor Aidong Zhang, State University of New York at Buffalo, USA
Panelists: Professor Susan M. Bridges, Mississippi State University, USA.
Professor Sun Kim, Indiana University, USA.
Professor Yi Pan, Georgia State University, USA.
Professor Bo Yuan, Ohio State University, USA and Shanghai Jiao Tong University, China.
Special Session Principal Chairs and Coordinators
Prof. Jacqueline Signorini, Dean of the Faculty of Sciences, University Paris 8, France
Prof. Tianrui Li, Southwest Jiaotong University, China
Special Session on Evolutionary Systems Biology
Chairs: Prof. Yufeng Wang, University of Texas at San Antonio, USA.
Prof. Jianying Gu, City University of New York, USA.
Special Session on Biomedical Literature Mining and Bioontology
Chair: Dr. Hongfang Liu, Georgetown University, USA
Special Session on Data Mining in Protein Interaction Networks
Chairs: Dr. Xiaoli Li, Nanyang Technological University, Singapore
Dr. Erliang Zeng, University of Notre Dame, Indiana, USA
Special Session on Computational Epidemiology
Chairs: Prof. Armin R. Mikler, University of North Texas, USA
Dr. Courtney Corley, Pacific Northwest National Lab, DOE, USA
Special Session on Linear and Nonlinear Analysis of the EEG in Alzheimer's Disease
Chair: Dr. Jaeseung Jeong, Korea Advanced Institute of Science and Technology, Korea
Special Session on Genomics and Personalize Medicine
Chair: Dr. Leming Zhou, University of Pittsburgh, USA
Special Session on Gene Networks and Pathway Analysis
Chairs: Prof. Zhongming Zhao, Vanderbilt University, USA.
Prof. Danail Bonchev, Virginia Commonwealth University, USA
Prof. Shuigeng Zhou, Fudan University, China
Tutorial Lecture on Pattern Discovery in Genomics Context
Speaker: Professor Yi-Ping Phoebe Chen, Deakin University, Australia
Invited Lecture on Latent Structure Models and Diagnosis in Traditional Chinese Medicine
Invited Speaker: Professor Nevin L. Zhang, Hong Kong University of Science and Technology, Hong Kong.
Dr. Jiaoxiong Xia, Shanghai Municipal Education Commission, China
Prof. Yilong Yin, Shandong University, China
Dr. Mehdi Pirooznia, Johns Hopkins University, Baltimore, Maryland, USA
Dr. Yongqing Su, Tongji University, Shanghai, China
Prof. Youping Deng, University of Southern Mississippi and SpecPro Inc, USA
Prof. Fei Qiao, Tongji University, China
Dr. Weisheng Xu, Tongji University, China
Dr. Youling Yu, Tongji University, China
Dr. Mingyu You, Tongji University, China
Dr. Preetam Ghosh , University of Southern Mississippi, USA
Prof. Susan Bridges, Mississippi State University, USA
Prof. Hamid R. Arabnia , University of Georgia, USA
Prof. Yong-Sheng Ding , Donghua University, China
Prof. Jie Yang, Shanghai Jiao Tong University, China
Prof. Duoqian Miao, Tongji University, China
Dr. Jing Yao, Tongji University, China
Dr. Sadaf ALAM, Oak Ridge National Laboratory, USA
Prof. Laurence Rodrigues Do AMARAL, Federal University of Goias, Brazil
Dr. Purushotham BANGALORE, University of Alabama at Birmingham, USA
Dr. Pierre BEAUSEROY, University of Technology in Troyes, UTT, France
Dr. Mahua BHATTACHARYA, Indian Institute of Information Technology & Management, India
Dr. Hong CAI, University of Texas at San Antonio, USA
Rui CAMACHO, Porto University, Portugal
Prof. Zhiwei CAO, Tongji University, China
Cornelia CARAGEA, Iowa State University, USA
Dr. Doina CARAGEA, Kansas State University, USA
Dr. Rui CHANG, University of California, USA
Dr. Bernard CHEN , University of Central Arkansas, USA
Prof. Jake Y. CHEN, Indiana University Purdue University Indianapolis, USA
Dr. Yidong CHEN, University of Texas Health Science Center at San Antonio, USA
Dr. Jianlin (Jack) CHENG, University of Missouri, USA
Dr. Yanfeng CHENG, Georgia Institute of Technology, USA
Dr. Qiang CHENG, Southern Illinois University Carbondale, USA
Prof. Sung-Bae CHO, Yonsei University, Korea
Dr. Albert C. S. CHUNG , Hong Kong University of Science and Technology, Hong Kong
Dr. Mark CLEMENT, Brigham Young University, USA
Dr. Kevin DAIMI, University of Detroit Mercy, USA
Dr. Phuongan DAM , University of Georgia, USA
Prof. Yisheng DING, Donghua University, China
Dr. Qiwen DONG, Fudan University, China
Dr. Pan DU, Northwestern University, USA
Prof. Ye DUAN, University of Missouri - Columbia, USA
Dr. Werner DUBITZKY, University of Ulster at Coleraine, UK
Prof. Minrui FEI, Shanghai University, China
Dr. Elisa FICARRA, Politecnico di Torino, Italy
Christopher M. FRENZ, New York City College of Technology (CUNY)
Dr. Jean X. GAO , University of Texas at Arlington, USA
Prof. Yang GAO, Nanjing University, China
Dr. Xin GENG, South East University, China
Dr. Preetam GHOSH , University of Southern Mississippi, USA
Dr. Kreshna GOPAL, Texas A&M University, USA
Prof. Jianying GU , City University of New York, USA
Dr. Jun-tao GUO , The University of North Carolina at Charlotte, USA
Prof. Maozu GUO, Harbin Institute of Technology, China
Dr. Yufei Huang, University of Texas at San Antonio, USA
Prof. Wen-Lian HSU, Institute of Information Science, Academia Sinica, Taiwan
Dr. Hongwei HUO, Xidian University, China
Dr. Jaeseung JEONG, Korea Advanced Institute of Science and Technology, Korea
Dr. Liangxiao JIANG, University of Geosciences, China
Dr. Rui JIANG, Tsinghua University, China
Dr. Zhenran JIANG, East China Normal University, China
Prof. Jaewoo KANG , Korea University, Korea
Abdellali KELIL, University of Sherbrooke, Canada
Dr. Dongsup KIM , Korea Advanced Institute of Science and Technology, Korea
Dr. Hyunsoo KIM, Harvard University, USA
Dr. Sun KIM, Indiana University, USA
Dr. Jiejun KONG, University of California, USA
Dr. Wei KONG, Shanghai Maritime University, China
Prof. Rui KUANG , University of Minnesota, USA
Dr. Zoé LACROIX, Arizona State University, USA
Prof. Feipei LAI, National Taiwan University, Taiwan
Dr. Chang-Shing LEE , National University of Tainan, Taiwan
Dr. Haim LEVKOWITZ, University of Massachusetts at Lowell, USA
Dr. Chang-Tsun LI , University of Warwick, UK
Dr. Jia LI, Shanghai University, China
Dr. Kang LI, Queen's University Belfast, UK
Dr. Liao LI, University of Delaware, USA
Dr. Ming LI, Nanjing University, China
Prof. Shao LI, Tsinghua University, China
Prof. Shaozi LI, Shamen University, China
Dr. Shen LI, Indiana University, USA
Prof. Tianrui LI, Southwest Jiaotong University, China
Dr. Xiaoli LI, Nanyang Technological University, Singapore
Dr. Xiaolin LI, Nanjing University, China
Dr. Ying-Xin LI, Nanjing University, China
Dr. Tim. G. LILBURN, American Type Culture Collection, USA
Dr. Chun-Yuan LIN , Chang Gung University
Dr. Simon LIN, Northwestern University Biomedical Informatics Center, USA
Dr. Hongfang LIU, Georgetown University, USA
Dr. Jun LIU, Nanjing University of Aeronautics and Astronautics, China
Dr. Qingzhong LIU, New Mexico Tech, USA
Dr. Tianming LIU, The University of Georgia, USA
Prof. Gary LIVINGSTON, University of Massachusetts at Lowell, USA
Dr. Dang LONG, New York State Department of Health, USA
Prof. Hongtao LU, Shanghai JiaoTong University, China
Prof. Wencong LU, Shanghai University, China
Prof. Carol LUSHBOUGH, University of South Dakota, USA
Dr. Xiaotu MA, Shanghai Jiao Tong University, China
Dr. Ian M. MACDONALD, The College of Saint Rose, USA
Dr. Anant MADABHUSHI, Rutgers University, The State University of New Jersey, USA
Dr. Krzysztof MALCZEWSKI, Poznan University of Technology, Poland
Prof. Kezhi MAO, Nanyang Technological University, Singapore
Dr. Majid MASSO , George Mason University, USA
Dr. Vasilis MEGALOOIKONOMOU, Temple University, USA
Prof. Duoqian MIAO, Tongji University, China
Prof. Armin R. MIKLER, University of North Texas, USA
Dr. Nasir-ud-Din, Institute of Molecular Sciences & Bioinformatics, Pakistan
Dr. Jun NI , University of Iowa, USA
Dr. Giuseppe NICOSIA, University of Catania, Italy
Timothy O'CONNOR, University of Cambridge, UK
Prof. Manish PALIWAL, Southern Illinois University at Carbondale, USA
Minseo PARK, University of Massachusetts, USA
Dr. Vinhthuy PHAN , University Of Memphis, USA
Dr. Helen PIONTKIVSKA, Kent State University, USA
Dr. Aleksandar POLEKSIC, University of Northern Iowa, USA
Monika RAY, Washington University in St. Louis, USA.
Dr. Tong RUAN, East China University of Science and Technology, China
Dr. Ann RUNDELL, Purdue University, USA
Meena K. SAKHARKAR, Nanyang Technological University, Singapore
Prof. Jacqueline SIGNORINI, University Paris 8, France
Dr. Xiaofeng SONG, Nanjing University of Aeronautics and Astronautics, China
Dr. Vojislav STOJKOVIC, Morgan State University, USA
Dr. Jonathan SUN, University of Southern Mississippi, USA
Prof. Xiao SUN, Southeast University, China
Dr. Jay URBAIN, Illinois Institute of Technology, USA
Prof. Athanasios VASILAKOS, University of Peloponnese, Greece
Dr. Thanos VASILAKOS, University of Western Macedonia, Greece
Dr. Miguel A. VEGARODRIGUEZ, University of Extremadura, Spain
Dr. Jason T. L. WANG, New Jersey Institute of Technology, USA
Dr. Liangjiang WANG, Clemson University, USA
Dr. Min WANG, Hohai University, China
Dr. Nan Wang, University of Southern Mississippi, USA
Dr. Ruizhi WANG, Tongji University, China
Dr. Yufeng WANG, University of Texas at San Antonio, USA
Dr. Yuhang WANG, Southern Methodist University, USA
Dr. Yu-Ping WANG, University of Missouri-Kansas City, USA
Dr. Zhe WANG, East China University of Science and Technology, China
Dr. Qishi WU , University of Memphis, USA
Dr. Jiaoxiong XIA, Shanghai Municipal Education Commission, China
Dr. Min XU, University of Southern California, USA
Prof. Weisheng XU, Tongji University, China
Dr. Jianhua XUAN , Virginia Tech, USA
Dr. Kaiguo YAN, Thomas Jefferson University, USA
Prof. Jie YANG, Shanghai JiaoTong University, China
Prof. Laurence T. YANG , St Francis Xavier University, Canada
130, Prof. Yilong YIN, Shandong University, China
Dr. Jingkai YU, Wayne State University, USA
Dr. Yan YU, Thomas Jefferson University, USA
Dr. Erliang ZENG, University of Miami, USA
Prof. Aidong ZHANG, State University of New York at Buffalo, USA
Dr. Daoqiang ZHANG, Nanjing University of Aeronautics and Astronautics, China
Dr. Ji Zhang, Shanghai Jiao Tong University School of Medicine, China
Dr. Jun ZHANG, University of Kentucky, USA
Dr. Min-Ling ZHANG, Hohai University, China
Dr. Weixiong ZHANG, Washington University, USA
Dr. Yanqing ZHANG, Georgia State University, USA
Dr. Ying ZHAO, Tsinghua University, China
Dr. Huiru(Jane) ZHENG, University of Ulster, UK
Dr. W. Jim ZHENG, Medical University of South Carolina, USA
Prof. Yang ZHONG, Fudan University, China
Dr. Jie ZHOU, Northern Illinois University, USA
Dr. Leming ZHOU, University of Pittsburgh, USA
Prof. Shuigeng ZHOU, Fudan University, China
Dr. Xiaobo ZHOU, Cornell University, USA
Prof. Zhi-Hua ZHOU, Nanjing University, China
Dr. Hill ZHU, Florida Atlantic University, USA
Prof. Qingxin ZHU, University of Electronic Science and Technology, China,
Dr. Shanfeng ZHU, Fudan University
The International Society of Intelligent Biological Medicine awards 1-3 scholars for the Outstanding Achievement Awards each year based on following criteria: 1) Substantiated outstanding contributions to the field of intelligent biological medicine; 2) Research of the highest level; 3) Significant scientific impact; 4) Scientific leadership. At the banquet of the conference, the scientific 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 after their plenary keynote presentations. Since 2007 ISIBM has awarded 11 scholars for the Outstanding Achievement Awards: The 2007 awards were presented to Dr. Ruzena Bajcsy (UC Berkley), Dr. Mary Qu Yang (NIH) and Dr. Chin-Mingh Ho (UCLA) at the IEEE International Conference on Bioinformatics and Bioengineering at Harvard Medical School in Boston, Massachusetts USA, and the 2008 awards were presented to Dr. Brian D. Athey (Michigan) and Dr Jack Yang (Harvard) at the World Congress on Computer Science, Computer Engineering and Applied Computing in Las Vegas, Nevada USA. 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 non-profit 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.
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.
Conflict of Interest
The authors declared no conflict of interest.
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This article has been published as part of BMC Genomics Volume 11 Supplement 3, 2010:. The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2164/11?issue=S3.
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Yang, J.Y., Niemierko, A., Bajcsy, R. et al. 2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research. BMC Genomics 11 (Suppl 3), I1 (2010). https://doi.org/10.1186/1471-2164-11-S3-I1
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