IEEE BIBE Plenary Keynote Lecture Notes (Part I)

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  A. Keith Dunker, Christopher J. Oldfield, Jingwei Meng, Pedro Romero, Jack Y. Yang, Zoran Obradovic, Vladimir N. Uversky: Intrinsically Disordered Proteins: Predictions and Applications. 1
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  John Quackenbush: Stochasticity and Networks in Genomic Data. 2
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  Mark Borodovsky: Decoding Novel Genomes: From Microbiomes to the Eukaryota. 3
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  Mary Qu Yang, Laura Elnitski: Promoter studies in the human genome: one perspective on an unfinished story. 4-6
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  Yi Pan: Protein Structure Prediction and Its Understanding Based on Machine Learning Methods. 7
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  Guo-Cheng Yuan, Jun S. Liu: Statistial Analysis of nucleosome occupancy and histone modification data. 8
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  Mary Qu Yang, Jack Y. Yang: An Investigation into the Feasibility of Detecting Microscopic Disease Using Machine Learning. 9-10
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  Linda K. Molnar: Nanobioinformatics: The Enabling Technology of Personalized Medicine. 11
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  Vladimir N. Uversky, Christopher J. Oldfield, A. Keith Dunker: Intrinsically Disordered Proteins in Human Diseases. 12
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  Xudong Huang: Metallobiochemistry of Alzheimer's Disease and Its Theranostic Agent Development. 13

Protein Structure and Function

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  Suk Hoon Jung, Hee-Young Hur, Desok Kim, Dong-Soo Han: Identification of Conserved Domain Combinations in S.cerevisiae Proteins. 14-20
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  Wei Zhong, Jieyue He, Yi Pan: Multiclass Fuzzy Clustering Support Vector Machines for Protein Local Structure Prediction. 21-26
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  Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski: A New Alignment-Independent Algorithm for Clustering Protein Sequences. 27-34
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  David J. John, Jacquelyn S. Fetrow, James L. Norris: Metropolis-Hastings Algorithm and Continuous Regression for finding Next-State Models of Protein Modification using Information Scores. 35-41
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  Valerio Freschi: Protein function prediction from interaction networks using a random walk ranking algorithm. 42-48
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  A. Keith Dunker, Christopher J. Oldfield, Jingwei Meng, Pedro Romero, Jack Y. Yang, Zoran Obradovic, Vladimir N. Uversky: Intrinsically Disordered Proteins: An Update. 49-58
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  Gil Alterovitz, Eugenia Lyashenko, Michael Xiang, Marco Ramoni: Linking Protein Mass with Function via Organismal Massome Networks. 59-65
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  Yuehui Chen, Xueqin Zhang, Mary Qu Yang, Jack Y. Yang: Ensemble of Probabilistic Neural Networks for Protein Fold Recognition. 66-70

Microarray Data and Applications (Part A)

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  Qiankun Zhao, Prasenjit Mitra, Dongwon Lee, Jaewoo Kang: HICCUP: Hierarchical Clustering Based Value Imputation using Heterogeneous Gene Expression Microarray Datasets. 71-78
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  Erliang Zeng, Chengyong Yang, Tao Li, Giri Narasimhan: On the Effectiveness of Constraints Sets in Clustering Genes. 79-86
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  Song Li: Integrate Qualitative Biological Knowledge to Build Gene Networks by Parallel Dynamic Bayesian Network Structure Learning. 87-92
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  Kerstin Koch, Stefan Schönauer, Ivy Jansen, Jan Van den Bussche, Tomasz Burzykowski: Finding Clusters of Positive and Negative Coregulated Genes in Gene Expression Data. 93-99
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  Noha A. Yousri, Mohamed S. Kamel, Mohamed A. Ismail: Pattern Cores And Connectedness in Cancer Gene Expression. 100-107
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  Peter Warren, Deanne Taylor, Paolo G. V. Martini, Jennifer Jackson, Jadwiga R. Bienkowska: PANP - a New Method of Gene Detection on Oligonucleotide Expression Arrays. 108-115

Microarray Data and Applications (Part B)

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  Rasha Kashef, Mohamed S. Kamel: Cooperative Partitional-Divisive Clustering and Its Application in Gene Expression Analysis. 116-122
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  Chris Thachuk, Anne Condon: On the Design of Oligos for Gene Synthesis. 123-130
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  Kenneth A. Marx, John Sharko, Georges G. Grinstein, Shannon Odelberg, Hans-Georg Simon: Evidence for Proximal to Distal Appendage Amputation Site Effects from Global Gene Expression Correlations Found in Newt Microarrays. 131-136
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  Nha Nguyen, Heng Huang, Soontorn Oraintara, Yuhang Wang: Denoising of Array-Based DNA Copy Number Data Using The Dual-tree Complex Wavelet Transform. 137-144
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  Brian E. Howard, Beate Sick, Imara Perera, Yang Ju Im, Heike Winter-Sederoff, Steffen Heber: Quality Assessment of Affymetrix GeneChip Data using the EM Algorithm and a Naive Bayes Classifier. 145-150
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  Yu-Chun Lin, Hsiang-Yuan Yeh, Shih-Wu Cheng, Von-Wun Soo: Comparing Cancer and Normal Gene Regulatory Networks Based on Microarray Data and Transcription Factor Analysis. 151-157

Microarray Data and Applications (Part C)

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  Chan-Hoon Park, Soo-Jin Kim, Sun Kim, Dong-Yeon Cho, Byoung-Tak Zhang: Finding Cancer-Related Gene Combinations Using a Molecular Evolutionary Algorithm. 158-163
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  Yi Zhang, Chris H. Q. Ding, Tao Li: A Two-Stage Gene Selection Algorithm by Combining ReliefF and mRMR. 164-171
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  John H. Phan, May D. Wang: Estimating Classification Error to Identify Biomarkers in Time Series Expression Data. 172-179
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  Minseo Park, Deane L. Falcone, Kil-Young Yun, Karen M. Daniels: Detection and Prediction of Alternative Splicing within Acceptor/Donor Sites in pre-mRNA of Arabidopsis thaliana. 180-186
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  Mehdi Pirooznia, Arun Rawat, Jack Y. Yang, Mary Qu Yang, Ping Gong, Edward J. Perkins, Youping Deng: An Effective Interwoven Loop Design Application for Two-Channel Microarray Experiments. 187-191
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  Fan Wang, Gagan Agrawal, Ruoming Jin, Helen Piontkivska: SNPMiner: A Domain-Specific Deep Web Mining Tool. 192-199

Biomedical Engineering

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  Iman Veisi, Naser Pariz, Ali Karimpour: Fast and Robust Detection of Epilepsy in Noisy EEG Signals Using Permutation Entropy. 200-203
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  Vishnu Mallapragada, Nilanjan Sarkar, Tarun Kanti Podder: A Robotic System for Real-time Tumor Manipulation During Image guided Breast Biopsy. 204-210
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  Li Shen, Andrew J. Saykin, Moo K. Chung, Heng Huang: Morphometric Analysis of Hippocampal Shape in Mild Cognitive Impairment: An Imaging Genetics Study. 211-217
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  Serdar Bozdag, Timothy J. Close, Stefano Lonardi: A Compartmentalized Approach to the Assembly of Physical Maps. 218-225
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  Lelin Zhang, Hongkai Xiong, Kai Zhang, Xiaobo Zhou: Graph Theory Application in Cell Nuleus Segmentation, Tracking and Identification. 226-232
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  Walker H. Land Jr., Daniel W. McKee, Tatyana Zhukov, Dansheng Song, Wei Qian: An End-to-End Process for Cancer Identification from Images of Lung Tissue. 233-239
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  Bin Wang, Jianhua Xuan, Matthew T. Freedman, Peter G. Shields, Yue Joseph Wang: Rat Mammary Fat Pad Segmentation and Growth Rate Evaluation in T1 Weighted MR Images. 240-245
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  Kai Zhang, Hongkai Xiong, Xiaobo Zhou: A Simulation-Based 3D Axon Axis Extraction in Confocal Fluorescence Microscopy Images. 246-250
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  Walker H. Land Jr., Alda Mizaku, Thomas Raway, John J. Heine, Claudia Berman, Nataliya Kovalchuk: Advancements in Automated Diagnostic Mammography. 251-256
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  Zhuangli Liang, W. Clem Karl, Synho Do, Udo Hoffmann, Thomas J. Brady, Homer H. Pien: Calcium De-blooming in Coronary CT Image. 257-262

Computational Methods in Bioinformatics

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  Hyunsoo Kim, Haesun Park, Hongyuan Zha: Distance Preserving Dimension Reduction Using the QR Factorization or the Cholesky Factorization. 263-269
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  Dumitru Brinza, Alexander Zelikovsky: Discrete Methods for Association Search and Status Prediction in Genotype Case-Control Studies. 270-277
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  Douglas W. Raiford, Dan E. Krane, Travis E. Doom, Michael L. Raymer: A Multi-Objective Genetic Algorithm that Employs a Hybrid Approach for Isolating Codon Usage Bias Indicative of Translational Efficiency. 278-285
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  Wamiq Manzoor Ahmed, Bulent Bayraktar, Arun K. Bhunia, E. Daniel Hirleman, J. Paul Robinson, Bartek Rajwa: Rapid Detection and Classification of Bacterial Contamination Using Grid Computing. 286-293
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  Sadaf R. Alam, Nikhil Bhatia, Jeffrey S. Vetter: Sensitivity Analysis of Biomolecular Simulations using Symbolic Models. 294-300

Sequence Analysis

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  Xiaoyong Fang, Zhigang Luo, Bo Yuan, Zhenghua Wang: Detecting and Assessing Conserved Stems for Accurate Structural Alignment of RNA Sequences. 301-306
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  Shibin Qiu, Terran Lane: The RNA String Kernel for siRNA Efficacy Prediction. 307-314
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  Stephanie Jimenez Irausquin, Liangjiang Wang: A Machine Learning Approach for Prediction of Lipid-Interacting Residues in Amino Acid Sequences. 315-319
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  Cornelia Caragea, Jivko Sinapov, Vasant Honavar, Drena Dobbs: Assessing the Performance of Macromolecular Sequence Classifiers. 320-326
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  Marina Barsky, Ulrike Stege, Alex Thomo, Chris Upton: Shortest Path Approaches for the Longest Common Subsequence of a Set of Strings. 327-333
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  Mugdha Khaladkar, Vivian Bellofatto, Jason Tsong-Li Wang, Vandanaben Patel, Marvin K. Nakayama: Constrained RNA Structural Alignment: Algorithms and Application to Motif Detection in the Untranslated Regions of Trypanosoma brucei mRNAs. 334-341

Systems Biology

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  Young-Rae Cho, Woochang Hwang, Aidong Zhang: Optimizing Flow-based Modularization by Iterative Centroid Search in Protein Interaction Networks. 342-349
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  Qiong Cheng, Robert W. Harrison, Alexander Zelikovsky: Homomorphisms of Multisource Trees into Networks with Applications to Metabolic Pathways. 350-357
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  Melissa Freedenberg, Chanchala Kaddi, Chang F. Quo, May D. Wang: Review of Systems Biology Simulation Tools for Translational Research. 358-365
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  Juliette Blanchet, Matthieu Vignes: Combined expression data with missing values and gene interaction network analysis: a Markovian integrated approach. 366-373
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  Gil Alterovitz, Taro Muso, Paresh Malalur, Marco Ramoni: A Systematic Approach to Quantifying Evolutionary Functional Trends Across the Universal Tree of Life. 374-378

Sequence and Structure

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  Bernard Chen, Stephen Pellicer, Phang C. Tai, Robert W. Harrison, Yi Pan: Super Granular Shrink-SVM Feature Elimination (Super GS-SVM-FE) Model for Protein Sequence Motif Information Extraction. 379-386
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  Osman Abul, Geir Kjetil Sandve, Finn Drabløs: False Discovery Rates in Identifying Functional DNA Motifs. 387-394
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  Gaofeng Huang, Peter Jeavons: A Geometrical Model for the SNP Motif Identification Problem. 395-402
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  Fei Xiong, Chris Bailey-Kellogg: A Hierarchical Grow-and-Match Algorithm for Backbone Resonance Assignments Given 3D Structure. 403-410
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  Xiang Chen, Simin He, Dongbo Bu, Runsheng Chen, Wen Gao: A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots. 411-417
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  Yu-Feng Huang, Yu-Shin Lin, Tian-Wei Hsu, Chien-Kang Huang: Mining Conserved Structures of Enzymes from Functional Hierarchical Classification. 418-424
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  Kreshna Gopal, James C. Sacchettini, Thomas R. Ioerger: Database Approaches and Data Representation in Structural Bioinformatics. 425-432

Bioinformatics Applications

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  Jung Hoon Woo, Tian Zheng, Ju Han Kim: Identifying Genomic Regulators of Set-Wise Co-Expression. 433-439
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  Mingwu Zhang, Daisuke Kihara, Sunil Prabhakar: Tracing Lineage in Multi-version Scientific Databases. 440-447
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  Nadia Yacoubi Ayadi, Zoé Lacroix: Resolving Scientific Service Interoperability With Schema Mapping. 448-455
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  M. L. Ujwal, Patrick Hoffman, Kenneth A. Marx: A Machine Learning Approach to Pharmacological Profiling of the Quinone Scaffold in the NCI Database: A Compound Class Enriched in Those Effective Against Melanoma and Leukemia Cell Lines. 456-463
• 
  Jung Hun Oh, Young Bun Kim, Prem Gurnani, Kevin P. Rosenblatt, Jean Gao: Biomarker Selection for Predicting Alzheimer Disease Using High-Resolution MALDI-TOF Data. 464-471
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  E. R. Muir, I. J. Ndiour, N. A. LeGoasduff, Richard A. Moffitt, Ying Liu, M. Cameron Sullards, Alfred H. Merrill, Yanfeng Chen, May D. Wang: Multivariate Analysis of Imaging Mass Spectrometry Data. 472-479
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  Jiaxing Xue, Jean Gao, Liping Tang: Phagocyte Transmigration Modeling Using System Dynamic Controls. 480-485

WORKSHOP on Bio-Nano-Info Integration for Personalized Medicine

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  David S. Paik: Toward a Nanobioinformatics Infrastructure for Nanotechnology-based Prostate Cancer Therapeutic Response Tracking. 486
• 
  Chenxi Shao, Hongli Deng: A Novel Approach for Signal Transduction Networks Simulation at a Mesoscopic Level. 487-494
• 
  Christopher Alberti, Jean-Philippe Villaréal, Delano Billingsley, Koon Yin Kong, Adam I. Marcus, Paraskevi Giannakakou, May D. Wang: Microtubule Dynamics Classification Using a Statistical Model of the Movement of Outer Tips. 495-502
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  Sohaib Waheed, Richard A. Moffitt, Qaiser Chaudry, Andrew N. Young, May D. Wang: Computer Aided Histopathological Classification of Cancer Subtypes. 503-508
• 
  John H. Phan, Richard A. Moffitt, Todd H. Stokes, May D. Wang: Evolving Biological Behavior in Gene-Based Cellular Simulations. 509-516
• 
  Mark Chen, Brian Huang, Eric Shin, Erik Robinson, Erik Pierstorff, Houjin Huang, Dean Ho: Engineering Multifunctional Biologically-Amenable Nanomaterials for Interfacial Therapeutic Delivery and Substrate-Based Cellular Interrogation. 517-523
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  Jack Y. Yang, Andrzej Niemierko, Mary Qu Yang, Youping Deng: Non-Monotonic Radio-Sensitivity over Tumor Volumes on Adjuvant Radio Therapy A New Insight on Cell Killing and Modeling. 524-531

WORKSHOP on Joint Research in the Southern Illinois University, University of Illinois, and Oak Ridge National Labortaroy, U.S. Department of Energy

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  Lisa Furby, Ravinder Gupta, Ajay Mahajan, Jarlen Don, Tsuchin Chu, Bakul Dave, Brad Schwartz: Novel Materials for the Direct Removal of Water and Ions from the Body for Patients with Dialysis Needs. 532-537
• 
  Min Xu, Louxin Zhang, Pei Li Joe Zhou: A Robust Method for Generating Discriminative Gene Clusters. 538-545
• 
  John R. Shell, Yonglian Wang, Nazeih M. Botros: Biological Mechanism on a Chip: Modeling and Realization of Growth Hormone Secretion Mechanism. 546-552
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  Manish Paliwal, D. Gordon Allan, Peter Filip: Retrieval Analysis of a Cementless Modular Total Hip Arthroplasty Prosthesis. 553-558
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  D. Gordon Allan, Manish Paliwal, Peter Filip: Trabecular Metal Patella Implanted into Soft-Tissue in a Post-Patellectomized Knee A Case Report. 559-562
• 
  Ying Chen, Joseph Y. Lo, James T. Dobbins: A comparison between traditional shift-and-add (SAA) and point-by-point back projection (BP) -- relevance to morphology of microcalcifications for isocentric motion in Digital Breast tomosynthesis (DBT). 563-569
• 
  Benfano Soewito, Ning Weng: Methodology for Evaluating DNA Pattern Searching Algorithms on Multiprocessor. 570-577
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  Qiang Shawn Cheng, Mehdi R. Zargham: An Efficient Compression Method for Multiplanar Reformulated Biomedical Images. 578-584
• 
  Jiazheng Yuan, Mengxia Zhu, M. Javed Iqbal, Jack Y. Yang, David A. Lightfoot: A Computational Approach to Understand Arabidopsis thaliana and Soybean Resistance to Fusarium solani (Fsg). 585-592
• 
  Yunfeng Yang, Michelle M. Zhu, Liyou Wu, Jizhong Zhou: Biostatistical Considerations of the Use of Genomic DNA Reference in Microarrays. 593-600
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  Salahuddin Mohammad Masum, Mohammed Yeasin: Dynamic Load Balancing for Mining of Molecular Structures using Genetic Algorithm. 601-608

WORKSHOP on Progress Toward Petascale Applications in Bioinformatics And Computational Biology

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  Robert Henschel, Matthias S. Müller: I/O Induced Scalability Limits of Bioinformatics Applications. 609-613
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  Marek Freindorf, Matthew D. Jones, Yihan Shao, Jing Kong, Thomas R. Furlani: Large-Scale QM/MM Calculations of Electronic Excitations in Yellow Protein: Toward Petascale Level of Protein Calculations. 614-619
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  Jeffrey L. Tilson, Gloria Rendon, Mao-Feng Ger, Eric Jakobsson: MotifNetwork: A Grid-enabled Workflow for High-throughput Domain Analysis of Biological Sequences: Implications for annotation and study of phylogeny, protein interactions, and intraspecies variation. 620-627
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  Scott B. Baden, Terrence J. Sejnowski, Thomas M. Bartol, Joel R. Stiles: Toward Petascale Simulation of Cellular Microphysiology. 628-634

Special Session on Computational Intelligence in Medical Informatics

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  Jacqueline Signorini, Patrick Greussay: Silent Killing: an Object-Oriented View of Hypertension and Kidney Failures Part I. 635-640
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  Wei Liu, Weidong Xu, Lihua Li: Medical Image Retrieval Based on Bidimensional Empirical Mode Decomposition. 641-646
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  Jun Kong, Wenjing Lu, Jianzhong Wang, Na Che, Yinghua Lu: A Modified Fuzzy Kohonen's Competitive Learning Algorithms Incorporating Local Information for MR Image Segmentation. 647-653
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  Siyuan Liu, Chao Liu, Yu Liu, Chunzhe Zhao: An Efficient Modeling and Simulation System on the Kidney Matching, Distribution and Exchange Problems. 654-661
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  Klaus H. Ecker, Lonnie R. Welch, Dazhang Gu: SiteSeeker - A Motif Discovery Tool. 662-664

Special Session on Evolutionary Systems Biology

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  Wen Zhou, Tian Xia, Jiansong Tong, Julie A. Dickerson, Bo Su, Xun Gu: Modeling protein interaction network and mechanisms in exocytosis. 665-672
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  Wenhai Chen, Tianzi Jiang, Tian Xia, Xun Gu: Toward a Realistic Model for Gene Network Evolution. 673-679
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  Pan Du, Simon M. Lin, Warren A. Kibbe, Haihui Wang: Application of Wavelet Transform to the MS-based Proteomics Data Preprocessing. 680-686
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  Jennifer L. Neary, Maribel Sanchez, Yufeng Wang, Timothy G. Lilburn: Pathway Complements of Four Yersinia. 687-692
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  Yi Zhang, Zhi-Li Pei, Jinhui Yang, Yanchun Liang: An Improved Ant Colony Optimization Algorithm Based on Route Optimization and Its Applications in Travelling Salesman Problem. 693-698
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  James F. Courage, Saurabh Gupta, Yufeng Wang: Characterization of MYC expression in gefitinib versus Acute Myeloid Leukemia reveals novel therapeutic targets. 699-706
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  Misha L. Rajaram, Vladimir N. Minin, Marc A. Suchard, Karin S. Dorman: Hot and Cold: Spatial Fluctuation in HIV-1 Recombination Rates. 707-714

Special Session 13: Speciall Sesssion on Research in Bioinformatics, Neuroinformatics, and Systems Biology in East Asia

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  Ryo Yoshida, Kazuyuki Numata, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Satoru Miyano: Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles. 715-722
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  Tae Ho Kang, Jae Soo Yoo, Hak Yong Kim: Mining Frequent Contiguous Sequence Patterns in Biological Sequences. 723-728
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  Shing-Kit Chan, Wai Lam: Efficient Methods for Biomedical Named Entity Recognition. 729-735
• 
  Dong-Soo Kahng, Yoonkey Nam, Doheon Lee: Stochastic Simulation Model for Patterned Neural Multi-Electrode Arrays. 736-740
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  Bum Ju Lee, Heon Gyu Lee, Jong Yun Lee, Keun Ho Ryu: Classification of Enzyme Function from Protein Sequence based on Feature Representation. 741-747
• 
  Yunkyu Sohn, Jaeseung Jeong: Inferring Behavioral-level Circuits of Caenorhabditis elegans from the Topology of its Wiring Diagram. 748-752
• 
  Huitao Sheng, Kishan Mehrotra, Chilukuri K. Mohan, Ramesh Raina: HAMMER Algorithm: Hashing with Arithmetic Modulo-4 for Motif Extraction of Regulatory Elements. 753-758
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  Meena K. Sakharkar, Kishore R. Sakharkar: A Tale of Intronless Genes in Eukaryotic Genomes. 759-765
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  Kishore R. Sakharkar, Meena K. Sakharkar: To fuse or not to fuse. 766-773

Special Session on Sequence Alignment and Phylogenetic Analysis

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  Kenneth Sundberg, Timothy O'Connor, Hyrum Carroll, Mark J. Clement, Quinn Snell: Using Parsimony to Guide Maximum Likelihood Searches. 774-779
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  Xu Zhang, Tamer Kahveci: QOMA2: Optimizing the alignment of many sequences. 780-787
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  Ken D. Nguyen, Yi Pan: A Reliable Metric for Quantifying Multiple Sequence Alignment. 788-795
• 
  Ahmet Sacan, Ismail Hakki Toroslu: Amino Acid Substitution Matrices Based on 4-Body Delaunay Contact Profiles. 796-801
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  Feng Yue, Meng Zhang, Jijun Tang: A Heuristic for Phylogenetic Reconstruction Using Transposition. 802-808
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  Abdullah N. Arslan, Peyman Bizargity: Phylogeny By Top Down Clustering Using a Given Multiple Alignment. 809-814
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  Patricia Buendia: Reconstructing Mutational Pathways from Serial Evolutionary Trees. 815-820

Special Session on Development of Algorithms for Solving Problems in Molecular Biology

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  Swapnoneel Roy, Ashok Kumar Thakur: Towards Construction of Optimal Strip-Exchanging Moves. 821-827
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  Ruizhi Wang, Duoqian Miao, Gang Li, Hongyun Zhang: Rough Overlapping Biclustering of Gene Expression Data. 828-834
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  Fa Zhang, Zhaoyun Ma, Zhiyong Liu, Bo Yuan: Using Domain-Based Structural Ensemble to Improve Structure Modeling. 835-841
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  Guo-Zheng Li, Hao-Hua Meng, Mary Qu Yang, Jack Y. Yang: Support Vector Regression with Feature Selection for the Multivariate Calibration of Spectrofluorimetric Determination of Aromatic Amino Acids. 842-848

Special Session on High-Throughput Data Analysis for Genomics and Proteomics

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  Hyung-Won Koh, Lars Hildebrand: Bottom-Up Multiple Row Addition Algorithms for the Biclustering-Problem. 849-856
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  Hongling Wang, Alberto Maria Segre, Yungui Huang, Jeffrey R. O'Connell, Veronica J. Vieland: Fast Computation of Human Genetic Linkage. 857-863
• 
  Afef Elloumi Oueslati, Noureddine Ellouze, Zied Lachiri: 3D Spectrum Analysis of DNA Sequence: Application to Caenorhabditis elegans Genome. 864-871
• 
  Jeffrey L. Tilson, Alan Blatecky, Gloria Rendon, Mao-Feng Ger, Eric Jakobsson: MotifNetwork: Genome-Wide Domain Analysis using Grid-enabled Workflows. 872-879
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  Elton José R. Vasconcelos, Ana Carolina L. Pacheco, Joao J. S. Gouveia, Fabiana F. Araújo, Michely C. Diniz, Michel T. Kamimura, Marcilia P. Costa, Rodrigo Maggioni, Raimundo Araujo-Filho, Raimundo B. Costa, Diana Magalhaes de Oliveira: Profilins, Formins and Katanins as Flagellar Proteins of Leishmania spp.: a Genome-based, Multi-step Bioinformatics-driven Description. 880-887

Special Session on Bio-Medical Soft Computing

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  Jason D. Bakos, Panormitis E. Elenis, Jijun Tang: FPGA Acceleration of Phylogeny Reconstruction for Whole Genome Data. 888-895
• 
  Elham Khabiri: A Preliminary Study of Correlation between Depth and Path Length of GO Nodes with Gene Sequence Similarity. 896-899
• 
  Siyuan Liu, Chao Liu, Chunzhe Zhao, Yu Liu: Mathematical Models and Optimization Discussion on EA System on AIDS/HIV Spread Estimating and Countermeasures Evaluating. 900-907

Special Session on Bio-Complexity

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  Radu Dobrescu, Loretta Ichim: Fractal Dimension of Mie Scattering Spectra for the Appraisal of Infected HeLa Cells in Cultures. 908-913
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  Jiejun Kong, Xiaoyan Hong, Dapeng Wu, Mario Gerla: Complexity-theoretic Modeling of Biological Cyanide Poisoning as Security Attack in Self-organizing Networks. 914-921
• 
  Alessandro Abate, Yu Bai, Nathalie Sznajder, Carolyn L. Talcott, Ashish Tiwari: Quantitative and Probabilistic Modeling in Pathway Logic. 922-929
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  Dimitrios Dakopoulos, Sanjay K. Boddhu, Nikolaos G. Bourbakis: A 2D Vibration Array as an Assistive Device for Visually Impaired. 930-937

Special Session on Machine Learning Methods in Structural and Functional Genomics

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  Leonardo Bobadilla, Fernando Niño, Edilberto Cepeda, Manuel A. Patarroyo: Characterizing and Predicting Catalytic Residues in Enzyme Active Sites Based on Local Properties: A Machine Learning Approach. 938-945
• 
  Tapan Patel, Li Liao: Predicting Protein-Protein Interaction Based on Fisher Scores Extracted from Domain Profiles. 946-951
• 
  Majid Masso, Iosif I. Vaisman: A Novel Sequence-Structure Approach for Accurate Prediction of Resistance to HIV-1 Protease Inhibitors. 952-958
• 
  Tho Hoan Pham, Tu Bao Ho, Dang Hung Tran, Kenji Satou: Prediction of Histone Modifications in DNA sequences. 959-966
• 
  Hua-Long Bu, Guo-Zheng Li, Xue-Qiang Zeng, Jack Y. Yang, Mary Qu Yang: Feature Selection and Partial Least Squares Based Dimension Reduction for Tumor Classification. 967-973
• 
  Hossam S. Sharara, Mohamed A. Ismail: aCORR: A novel algorithm for clustering gene expression data. 974-981
• 
  Vandana Gummuluru, Su-Shing Chen: An Intelligent System for Searching Genomic Sequences. 982-986
• 
  Michael L. Blinov, Ion I. Moraru: XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes. 987-994

Special Session on DNA Microarray Data Analysis

• 
  Kenneth Bryan, Padraig Cunningham: BALBOA: Extending Bicluster Analysis to Classify ORFs using Expression Data. 995-1002
• 
  Zhenyu Wang, Vasile Palade: A Comprehensive Fuzzy-Based Framework for Cancer Microarray Data Gene Expression Analysis. 1003-1010
• 
  Ángela Blanco, Manuel Martín-Merino, Javier De Las Rivas: Ensemble of Kernel Based Classifiers to Improve the Human Cancer Prediction using DNA Microarrays. 1011-1018
• 
  Li Teng, Laiwan Chan: Mining Order Preserving Patterns in Microarray Data by Finding Frequent Orders. 1019-1026
• 
  Nha Nguyen, Heng Huang, Soontorn Oraintara, An P. N. Vo: A New Smoothing Model for Analyzing Array CGH Data. 1027-1034
• 
  Sheehyun Kim, Dongsup Kim: Inference of Gene Regulatory Networks Using Time Sliding Comparison and Transcriptional Lagging Time from Time Series Gene Expression Profiles. 1035-1040

Microarray Gene Expression Analysis

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  Vidya P. Kamath, Lawrence O. Hall, Timothy Yeatman, Steven Eschrich: Multivariate Feature Selection using Random Subspace Classifiers for Gene Expression Data. 1041-1045
• 
  Fei Wang, Tao Li: Gene Selection via Matrix Factorization. 1046-1050
• 
  Fang Zhou, Jieyue He, Wei Zhong: Mutual Information based Minimum Spanning Trees Model for Selecting Discriminative Genes. 1051-1055
• 
  Elena Baralis, Elisa Ficarra, Alessandro Fiori, Enrico Macii: Gene-Markers Representation for Microarray Data Integration. 1056-1060
• 
  Yinyin Yuan, Chang-Tsun Li: Partial Mixture Model for Tight Clustering in Exploratory Gene Expression Analysis. 1061-1065
• 
  Yuhang Wang, Siling Wang, Andrew R. Zinn: rSWTi: A Robust Stationary Wavelet Denoising Method for Array CGH Data. 1066-1070
• 
  Jahangheer S. Shaik, E. Olusegun George, Mohammed Yeasin: An Empirical CDF Approach to Estimate the Significance of Gene Ranking for Finding Differentially Expressed Genes. 1071-1075
• 
  Monika Ray, Sekhar Dharmarajan, Johannes Freudenberg, G. Alexander Patterson, Weixiong Zhang: Gene expression profiling and machine learning to understand and predict primary graft dysfunction. 1076-1080
• 
  Jared Fox, Nik Brown: Sensitivity and Consistency of Affymetrix GeneChip Normalization Methods. 1081-1086

Bioengineering (Part A) -- Deformable and 3D Modeling

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  Qing He, Ye Duan, Judith Miles, Nicole Takahashi: Statistical Shape Analysis of the Corpus Callosum in Subtypes of Autism. 1087-1091
• 
  Ying Zhu: Simulation and Visualization of Menisci-Femur Contact Using Patient-Specific Deformable Models. 1092-1096
• 
  Foued Derraz, Abdelmalik Taleb-Ahmed, Azeddine Chikh, Fethi Bereksi-Reguig: Improved edge map of geometrical active contour model based on coupling to anisotropic diffusion filtering. 1097-1101
• 
  Soroor Behbahani, Keivan Magholi: Analysis of cardiac wall motion estimation methods. 1102-1107
• 
  Tarun Kanti Podder, Ivan Buzurovic, Yida Hu, James M. Galvin, Yan Yu: Partial transmission high-speed continuous tracking multi-leaf collimator for 4D adaptive radiation therapy. 1108-1112
• 
  Wamiq Manzoor Ahmed, Magdalena Jonczyk, Ali Shamsaie, Arif Ghafoor, J. Paul Robinson: Quantitative Analysis of Inter-object Spatial Relationships in Biological Images. 1113-1117

Bioengineering (Part B) -- Biomedical Image Processing I

• 
  Joerg Meyer: Histogram Transformation for Inter-Modality Image Registration. 1118-1123
• 
  Antonio Ruiz, Manuel Ujaldon, Jose Antonio Andrades, Jose Becerra, Kun Huang, Tony Pan, Joel H. Saltz: The GPU on biomedical image processing for color and phenotype analysis. 1124-1128
• 
  Santiago Aja-Fernández, Marcos Martín-Fernández, Carlos Alberola-López: Tissue Identification in Ultrasound Images using Rayleigh Local Parameter Estimation. 1129-1133
• 
  Amirali Shayan Arani, Yi Zhu, Yi-Ning Cheng, Chung-Kuan Cheng, Shien-Fong Lin, Peng-Sheng Chen: Exploring Cardioneural Signals from Noninvasive ECG Measurement. 1134-1138
• 
  Akmal A. Younis, Ahmed T. Soliman, Mansur R. Kabuka, Nigel M. John: MS Lesions Detection in MRI Using Grouping Artificial Immune Networks. 1139-1146
• 
  Hyunsoo Kim, Haesun Park, Lars Eldén: Non-negative Tensor Factorization Based on Alternating Large-scale Non-negativity-constrained Least Squares. 1147-1151

Bioengineering (Part C) -- Biomedical Image Processing II

• 
  Henry Carrillo, Jorge Villarreal, Miguel Sotaquira, Alvaro Goelkel, Ricardo Gutierrez: A Computer Aided Tool for the Assessment of Human Sperm Morphology. 1152-1157
• 
  Benedito G. Aguiar Neto, Joseana M. Fechine, Silvana Cunha Costa, Menaka Muppa: Feature Estimation for Vocal Fold Edema Detection Using Short-Term Cepstral Analysis. 1158-1162
• 
  Heng Huang, Paul R. Bergstresser: A New Hybrid Technique for Dermatological Image Registration. 1163-1167
• 
  Chengwei Li, Ruiqiang Hu: PID Control based on BP Neural Network for the Regulation of Blood Glucose Level in Diabetes. 1168-1172
• 
  César Pichardo-Almarza, Rod Smallwood, S. A. Billings: Spatiotemporal Analysis of an Agent-Based Model of a Colony of Keratinocytes: A First Approach for the Development of Validation Methods. 1173-1177

Sequence Analysis and Sequence Alignment

• 
  Hongwei Huo, Vojislav Stojkovic: A Suffix Tree Construction Algorithm for DNA Sequences. 1178-1182
• 
  Viktor Martyanov, Larkin Elderon, Amy Gladfelter, Dhanalakshmi R. Nair, Robert H. Gross: Identifying Fungal Regulatory Motif Patterns Using SCOPE, an Ensemble Learning Method Motif Finder. 1183-1187
• 
  Tieming Ji, Desh Ranjan, Jeanne Curry, Mary O'Connell: Computational Identification of Cis-regulatory Elements Associated with Pungency of Chili Peppers. 1188-1192
• 
  Yong Gao, Michael Henderson: Speeding Up Pairwise Sequence Alignments: A Scoring Scheme Reweighting Based Approach. 1194-1198
• 
  Dan He, Abdullah N. Arslan, Yu He, Xindong Wu: Iterative Refinement of Repeat Sequence Specification Using Constrained Pattern Matching. 1199-1203
• 
  Antonio E. de la Serna: Differential Scoring for Systolic Sequence Alignment. 1204-1208
• 
  Lisa M. Guntly, Jennifer L. Leopold, Anne M. Maglia: Determining Domain Similarity and Domain-Protein Similarity Using Functional Similarity Measurements of Gene Ontology Terms. 1209-1213
• 
  Paul Dan Cristea, Rodica Tuduce, Iulian Nastac, Jan Cornelis, Rudi Deklerck, Marius Andrei: Signal Representation and Processing of Nucleotide Sequences. 1214-1219
• 
  Huiru Zheng, Haiying Wang, Jinglu Hu: Cluster Analysis of Regulatory Sequences with a Log Likelihood Ratio Statistics-based Similarity Measure. 1220-1224

Bioengineering (Part D) -- Biomedical Applications

• 
  Yong-Jie Ni, Chan-Hyun Youn, Byoung-Jin Kim, Youngjoo Han, Peng Liu: A PQRM-based PACS System for Advanced Medical Services under Grid Environment. 1225-1229
• 
  Sung-huai Hsieh, Sheau-Ling Hsieh, Yung-Ching Weng, Tzu-Hsiang Yang, Feipei Lai, Po-Hsun Cheng, X. O. Ping, Mao-yu Jan, Jen-Chiun Lin, C. H. Peng, K. H. Huang, L. F. Ko, Chi-Huang Chen, Kai-Ping Hsu: Middleware based Inpatient Healthcare Information System. 1230-1234
• 
  Courtney Corley, Lindsey Brown, Armin R. Mikler, Diane J. Cook, Karan P. Singh: Generating social networks of intimate contacts for the study of public health intervention strategies. 1235-1239
• 
  Wen-Ran Zhang, Karl E. Peace: Yin Yang Mental Squares - An Equilibrium-Based System For Bipolar Neurobiological Pattern Classification and Analysis. 1240-1244
• 
  Jared Fox, Nik Brown: Automatically Extracting Acronyms from Biomedical Text. 1245-1248
• 
  Mingyuan Zhao, Mingtian Zhou, Qingxin Zhu, Ping Yang: Feature Extraction and Parameters Selection of Classification Model on Brain-Computer Interface. 1249-1253

Biological Networks

• 
  Rui Chang: Consistent Modeling, Integration and Simulation of Molecular Interaction Networks in Space-Time Dimension. 1254-1259
• 
  Mehmet Tan, Faruk Polat, Reda Alhajj: Feature Reduction for Gene Regulatory Network Control. 1260-1264
• 
  George Chin Jr., Grant C. Nakamura, Daniel G. Chavarría-Miranda, Heidi J. Sofia: Graph Mining of Networks from Genome Biology. 1265-1269
• 
  Martin S. R. Paradesi, Doina Caragea, William H. Hsu: Structural Prediction of Protein-Protein Interactions in Saccharomyces cerevisiae. 1270-1274
• 
  Mohieddine Missaoui, David R. C. Hill, Cécile Militon, Pierre Peyret: Complete Backtranslation of Oligopeptides for Metabolic Pathways Exploration of Complex Environments using Functional Microarrays. 1275-1279
• 
  Kazuyuki Numata, Seiya Imoto, Satoru Miyano: A Structure Learning Algorithm for Inference of Gene Networks from Microarray Gene Expression Data Using Bayesian Networks. 1280-1284

Algorithms in Bioinformatics

• 
  Zhang Lei, Li Ren-hou: An Algorithm for Mining Fuzzy Association Rules Based on Immune Principles. 1285-1289
• 
  Juan Shan, Yuxuan Wang, Changhui Yan: Toward The Recognition Code Of Protein-DNA Recognition. 1290-1293
• 
  Dragos Trinca, Sanguthevar Rajasekaran: Self-Optimizing Parallel Algorithms for Haplotype Reconstruction and Their Evaluation on the JPT and CHB Genotype Data. 1294-1298
• 
  Xiaolu Huang, Hesham H. Ali: Reducing Folding Scenario Candidates in Pseudoknots Detection Using PLMM_DPSS Algorithm Integrated With Energy Filters. 1299-1303
• 
  Paulius Micikevicius, Narsingh Deo: Exploring Topological Properties of NMR Graphs. 1304-1307
• 
  Yu-Ting Huang, Shih-Fang Lin, Chung-Cheng Chiu, Hsiang-Yuan Yeh, Von-Wun Soo: Probability Analysis on Associations of Adverse Drug Events with Drug-Drug Interactions. 1308-1312

Bioinformatics Tools

• 
  Jay Urbain, Nazli Goharian, Ophir Frieder: Combining Semantics, Context, and Statistical Evidence in Genomics Literature Search. 1313-1317
• 
  Fan Wang, Ruoming Jin, Gagan Agrawal, Helen Piontkivska: Graph and Topological Structure Mining on Scientific Articles. 1318-1322
• 
  Ying Liu, Yongjing Lin: Supervised HITS Algorithm for MEDLINE Citation Ranking. 1323-1327
• 
  Michel Kinsy, Zoé Lacroix: Storing Efficiently Bioinformatics Workflows. 1328-1332
• 
  Chen Lin, Wayne Mak, Pengyu Hong, Katharine J. Sepp, Norbert Perrimon: Intelligent Interfaces for Mining Large-Scale RNAi-HCS Image Databases. 1333-1337
• 
  Neha Nahar, Lutz Hamel, Maria S. Poptsova, J. Peter Gogarten: GPX: A Tool for the Exploration and Visualization of Genome Evolution. 1338-1342
• 
  Tom Milledge, Gaolin Zheng, Tim Mullins, Giri Narasimhan: SBLAST: Structural Basic Local Alignment Searching Tools using Geometric Hashing. 1343-1347

Protein Structural Prediction and Functional Analysis

• 
  Mudassir Fayyaz, Adnan Mujahid, Asifullah Khan, Tae-Sun Choi, Nadeem Iqbal: G-protein Coupled Receptor Subfamilies Prediction Based on Nearest Neighbor Approach. 1348-1354
• 
  Anjum Reyaz-Ahmed, Yan-Qing Zhang: Protein Secondary Structure Prediction Using Genetic Neural Support Vector Machines. 1355-1359
• 
  Xiaoli Li, Jun-Xiang Lee, Bharadwaj Veeravalli, See-Kiong Ng: An HV-SVM Classifier to Infer TF-TF Interactions Using Protein Domains and GO Annotations. 1360-1364
• 
  Fiona Browne, Haiying Wang, Huiru Zheng, Francisco Azuaje: Supervised Statistical and Machine Learning Approaches to Inferring Pairwise and Module-Based Protein Interaction Networks. 1365-1369
• 
  Jing Hu, Changhui Yan: Predicting Protein Subcelluar Localizations Using Weighted Euclidian Distance. 1370-1373
• 
  Alireza Hadj Khodabakhshi, Mehdi Mirzazadeh, Arvind Gupta: An efficient data structure for applying multiple seeds in homology search. 1374-1378
• 
  Ian MacDonald, George Berg: A Mixture of Experts Method for Predicting Domain Boundaries in Proteins. 1379-1383
• 
  Woochang Hwang, Taehyong Kim, Young-Rae Cho, Aidong Zhang, Murali Ramanathan: SIGN: reliable protein interaction identification by integrating the Similarity In GO and the similarity in protein interaction Networks. 1384-1388

Bioinformatics Applications

• 
  Elizabeth Rossin, Saumyadipta Pyne, Florian Hahne, Philip L. De Jager: Identification of Differential Flow Cytometry Expression. 1389-1393
• 
  Enis Afgan, Purushotham Bangalore: Performance Characterization of BLAST for the Grid. 1394-1398
• 
  Sihui Zhao, Jihye Kim, Steffen Heber: Large-scale Discovery of Regulatory Motifs Involved in Alternative Splicing. 1399-1403
• 
  Ionut Bebu, Françoise Seillier-Moiseiwitsch, Hongfang Liu: Semiparametric RMA Background-Correction for Oligonucleotide Arrays. 1404-1408
• 
  Anuradha Roy, Jennifer L. Leopold, Anne M. Maglia: Alternative Splicing: Associating Frequency with Isoforms. 1409-1413
• 
  Benjamin J. Kelly, Paul E. Anderson, Nicholas V. Reo, Nicholas J. DelRaso, Travis E. Doom, Michael L. Raymer: A Proposed Statistical Protocol for the Analysis of Metabolic Toxicological Data Derived from NMR Spectroscopy. 1414-1418
• 
  Fang-Xiang Wu, Jiarui Ding, Guy G. Poirier: A Framework for Mass Spectral Quality Assessment without Prior Information. 1419-1423
• 
  Tapani Utriainen, Graham J. L. Kemp: Using long fragments to reconstruct RNA backbones. 1424-1428
• 
  Jingwei Zhang, Layne T. Watson: A Modified Uniformization Method for the Chemical Master Equation. 1429-1433
• 
  Jonathan L. Jesneck, Sayan Mukherjee, Loren W. Nolte, Anna E. Lokshin, Jeffrey R. Marks, Joseph Y. Lo: Decision Fusion of Circulating Markers for Breast Cancer Detection in Premenopausal Women. 1434-1438

IEEE BIBE Plenary Keynote Lecture Notes (Part II)

• 
  Guo-Zheng Li, Xue-Qiang Zeng, Jack Y. Yang, Mary Qu Yang: Partial Least Squares Based Dimension Reduction with Gene Selection for Tumor Classification. 1439-1444
• 
  Steven Seltzer: Functional and Molecular Imaging: Key Components of Personalized Healthcare. 1445
• 
  Xiaohua Hu: Biomedical Literature Mining. 1446
• 
  Mary Qu Yang, Laura Elnitski: An Overview of Bidirectional Promoters. 1447
• 
  Ruzena Bajcsy: Distributed Wireless Sensors on the Human Body. 1448
• 
  Andreas D. Baxevanis: Transforming Medicine: Genomics, Bioinformatics, and Human Health. 1449
• 
  Brian D. Athey: Integrative Biomedical Informatics. 1450
• 
  Eric Jakobsson, May D. Wang, Linda Molnar: Bio-Nano-Info Integration for Personalized Medicine. 1452

Tutorial Lecture Notes

• 
  David A. Lightfoot, Mengxia Michelle Zhu: Using The Soybean Genome Database (SoyGD) To Display and Analyze a 1 Gbp Genome Sequence. 1453
• 
  Patrick S. P. Wang: Biometrics Intelligence Information Systems and Applications. 1454
• 
  Arif Ghafoor, J. Paul Robinson: Knowledge Modeling for High Content Screening of Multimedia Biological Data. 1455
• 
  Igor B. Zhulin: Reconstructing Signal Transduction from Raw Genomic Data. 1456
• 
  Tian Zheng: Studying Co-Regulation and Inter-Regulation of Genes via eQTL Mapping. 1457
• 
  Craig A. Stewart, Malinda Lingwall, David Bade: Lecture on Progress toward Petascale Applications in Bioinformatics and Computational Biology. 1458
• 
  Sadaf R. Alam, Pratul K. Agarwal, Jeffery A. Kuehn: Performance Evaluation of a Scalable Molecular Dynamics Simulation Framework on a Massively-Parallel System. 1459-1466

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