BIBM 2009: Washington, DC, USA

Genomics and Molecular Structure, Function, and Evolution

• Guan Ning Lin, Zheng Wang, Dong Xu, Jianlin Cheng:
  Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines. 3-8
  
• Jeffrey L. Ram, Yi Lu:
  Bioinformatics Pipeline for Identification of Binding Motifs of Flexible Protein Tethers. 9-14
  
• Hengyun Lu, Genke Yang, Lam Fat Yeung:
  Extremal Optimization for the Protein Structure Alignment. 15-19
  
• Wei-Yao Chou, Shu-Chuan Lin, Rong-Yuan Huang, Ting-Ying Jiang, Chien-Jung Chen, Chia-Mao Wu, Chuan Yi Tang, Margaret Dah-Tsyr Chang, Wei-I Chou, Hao-Teng Chang:
  Biological Feature Incorporated Alignment for Cross Species Analysis on Carbohydrate Binding Modules. 20-25
  
• Majid Masso, Tariq Alsheddi, Iosif I. Vaisman:
  Accurate Prediction of Stability Changes in Bacteriophage T4 Lysozyme upon Single Amino Acid Replacements. 26-30
  
• Tak Wah Lam, Ruiqiang Li, Alan Tam, Simon C. K. Wong, Edward Wu, Siu-Ming Yiu:
  High Throughput Short Read Alignment via Bi-directional BWT. 31-36
  
• Eddie Y. T. Ma, Stefan C. Kremer:
  Neural Grammar Networks in QSAR Chemistry. 37-42
  
• Bo Li, Feng Luo:
  Predicting Yeast Synthetic Lethal Genetic Interactions Using Protein Domains. 43-47
  
• Fadi Towfic, M. Heather West Greenlee, Vasant Honavar:
  Detection of Gene Orthology Based on Protein-Protein Interaction Networks. 48-53
  
• Jeffrey Martin, Wenhan Zhu, Nicholas H. Bergman, Mark Borodovsky:
  Assessment of Gene Annotation Accuracy by Inferring Transcripts from RNA-Seq. 54-59
  
• Matthew C. Schmidt, Nagiza F. Samatova:
  An Algorithm for the Discovery of Phenotype Related Metabolic Pathways. 60-65
  
• Bin Liu, Lei Lin, Xiaolong Wang, Xuan Wang, Yi Shen:
  Protein Long Disordered Region Prediction Based on Profile-Level Disorder Propensities and Position-Specific Scoring Matrixes. 66-69
  
• Hyrum Carroll, Mark J. Clement, Quinn Snell, David A. McClellan:
  ChemAlign: Biologically Relevant Multiple Sequence Alignment Using Physicochemical Properties. 70-73
  
• Min Xu, Shi-Hua Zhang, Frank Alber:
  3D Rotation Invariant Features for the Characterization of Molecular Density Maps. 74-78
  
• Pavel P. Kuksa, Vladimir Pavlovic:
  Fast Motif Selection for Biological Sequences. 79-82
  
• Mohammadreza Ghodsi, Mihai Pop:
  Inexact Local Alignment Search over Suffix Arrays. 83-87
  
• Mehmet Tan, Faruk Polat, Reda Alhajj:
  Derivation of Transcriptional Regulatory Relationships by Partial Least Squares Regression. 88-91
  
• M. Chaley, N. Nazipova, E. Teplukhina, G. Tyulbasheva, V. Kutyrkin:
  Statistical Methods for Detecting Latent Periodicity in Biological Sequences: Solving a Problem of Small-Size Samples. 92-96
  

Computational Systems Biology

• Timur Fayruzov, Martine De Cock, Chris Cornelis, Dirk Vermeir:
  Modeling Protein Interaction Networks with Answer Set Programming. 99-104
  
• Young-Rae Cho, Aidong Zhang:
  Restructuring Protein Interaction Networks to Reveal Structural Hubs and Functional Organizations. 105-110
  
• Qian Liu, Yi-Ping Phoebe Chen, Jinyan Li:
  High Functional Coherence in k-Partite Protein Cliques of Protein Interaction Networks. 111-117
  
• Daniel Duanqing Wu, Xiaohua Hu, Tingting He:
  Exploratory Analysis of Protein Translation Regulatory Networks Using Hierarchical Random Graphs. 118-123
  
• Zina M. Ibrahim, Ahmed Y. Tawfik, Alioune Ngom:
  Qualitative Motif Detection in Gene Regulatory Networks. 124-129
  
• Brian E. Howard, Steffen Heber:
  Towards Reliable Isoform Quantification Using RNA-Seq Data. 130-135
  
• Yoon Soo Pyon, Jing Li:
  Identifying Gene Signatures from Cancer Progression Data Using Ordinal Analysis. 136-141
  
• Mutsumi Fukuzaki, Mio Seki, Hisashi Kashima, Jun Sese:
  Side Effect Prediction Using Cooperative Pathways. 142-147
  
• Bing Han, Meeyoung Park, Xue-wen Chen:
  DASSO-MB: Detection of Epistatic Interactions in Genome-Wide Association Studies Using Markov Blankets. 148-153
  
• Sejoon Lee, Eunjung Lee, Kwang Hyung Lee, Doheon Lee:
  Disease Classification Based on the Activities of Interacting Molecular Modules with Condition-Responsive Correlation. 154-159
  
• Liang Lan, Slobodan Vucetic:
  A Multi-task Feature Selection Filter for Microarray Classification. 160-165
  
• Akther Shermin, Mehmet A. Orgun:
  A 2-Stage Approach for Inferring Gene Regulatory Networks Using Dynamic Bayesian Networks. 166-169
  
• Junwan Liu, Zhoujun Li, Xiaohua Hu, Yiming Chen:
  Microarray Biclustering with Crowding Based MOACO. 170-173
  
• Pankaj Chopra, Jaewoo Kang, Jinseung Lee:
  Using Gene Pair Combinations to Improve the Accuracy of the PAM Classifier. 174-177
  
• Yi Jia, Jun Huan:
  The Analysis of Arabidopsis thaliana Circadian Network Based on Non-stationary DBNs Approach with Flexible Time Lag Choosing Mechanism. 178-181
  

Medical Informatics and Translational Bioinformatics

• Darío Rojas, Luis Rueda, Alioune Ngom, Homero Urrutia, Gerardo Carcamo:
  Biofilm Image Segmentation Using Optimal Multi-level Thresholding. 185-190
  
• Yan Lu, Jingyu Yan, Yeung Yam:
  Model-Based ECG Denoising Using Empirical Mode Decomposition. 191-196
  
• Sardar Ansari, Kayvan Najarian, Kevin Ward, Mohamad Hakam Tiba:
  Extraction of Respiratory Rate from Impedance Signal Measured on Arm: A Portable Respiratory Rate Measurement Device. 197-202
  
• Stan Pounds, Xueyuan Cao, Cheng Cheng, Jun J. Yang, Dario Campana, William E. Evans, Ching-Hon Pui, Mary Relling:
  Integrated Analysis of Pharmacokinetic, Clinical, and SNP Microarray Data Using Projection onto the Most Interesting Statistical Evidence with Adaptive Permutation Testing. 203-209
  
• Stuart J. Nelson, Kelly Zeng, John Kilbourne:
  Building a Standards-Based and Collaborative E-Prescribing Tool. 210-215
  
• Jieun Jeong, Jake Y. Chen:
  RIC: Ranking with Interaction Chains and Its Application in Computational Clinical Proteomics Studies. 216-221
  
• Jeffrey Q. Jiang, Andreas W. M. Dress, Ming Chen:
  Towards Identification of Human Disease Phenotype-Genotype Association via a Network-Module Based Method. 222-227
  
• Ala Qabaja, Mohammed Al-Shalalfa, Reda Alhajj, Jon G. Rokne:
  Multiagent Approach for Identifying Cancer Biomarkers. 228-233
  
• Haixia Yan, Yiqin Wang, Zhaorong Liu, Rui Guo, Fufeng Li, Fengying Run, Yujian Hong:
  Feature Extraction for Pulse Waveform in Traditional Chinese Medicine by Hemodynamic Analysis. 234-238
  
• Indranil Palit, Chandan K. Reddy, Kendra L. Schwartz:
  Differential Predictive Modeling for Racial Disparities in Breast Cancer. 239-245
  
• Sara Nasser, Aarati R. Ranade, Shravan Sridhart, Lisa Haney, Ronald L. Korn, Michael B. Gotway, Glen J. Weiss, Seungchan Kim:
  Identifying MiRNA and Imaging Features Associated with Metastasis of Lung Cancer to the Brain. 246-251
  
• Alberto Cavallo, Cocetta Dodaro, Andrea Renda:
  Evolution of the Probability of an MPM (Multiple Primary Malignancy) after a First Colon Tumor. 252-256
  
• Mohammad Zia Ur Rahman, Rafi Ahamed Shaik, D. V. Rama Koti Reddy:
  An Efficient Noise Cancellation Technique to Remove Noise from the ECG Signal Using Normalized Signed Regressor LMS Algorithm. 257-260
  
• Gene Shuman:
  Using Forearm Electromyograms to Classify Hand Gestures. 261-264
  
• Yujie Dong, Adam Hoover, Eric Muth:
  A Device for Detecting and Counting Bites of Food Taken by a Person during Eating. 265-268
  
• Rafal Ladysz:
  Nonlinear Dynamical and Entropic Complexity Measures as Indicators of Nonstationarities in Short-Term ECG Signals. 269-278
  
• Abhisek Kundu, Hatice Gulcin Ozer, Tara Borlawsky, Kristin C. Circle, Kun Huang, Philip R. O. Payne:
  Clinical Attribute Network for Chronic Lymphocytic Leukemia. 279-282
  
• Jiexun Li, Lifan Guo, Neal Handly:
  Hospital Admission Prediction Using Pre-hospital Variables. 283-286
  
• Aniruddha J. Joshi, Sharat Chandran, Vaidyanathan K. Jayaraman, Bhaskar D. Kulkarni:
  Hybrid SVM for Multiclass Arrhythmia Classification. 287-290
  
• Wenan Chen, Rebecca Smith, Simina Vasilache, Kayvan Najarian, Kevin Ward, Charles Cockrell, Jonathan Ha:
  Traumatic Pelvic Injury Outcome Prediction by Extracting Features from Relevant Medical Records and X-Ray Images. 291-294
  

Cross-Cutting Computational Methods and Bioinformatics Infrastructure

• Kevin Karsch, Qing He, Ye Duan:
  A Fast, Semi-automatic Brain Structure Segmentation Algorithm for Magnetic Resonance Imaging. 297-302
  
• Dayu Lv, Bill Goodwine:
  Pancreas Modeling from IVGTT Data Using a Deterministic Optimal Search Method. 303-308
  
• Kai-Cheng Hsu, Yen-Fu Chen, Jinn-Moon Yang:
  GemAffinity: A Scoring Function for Predicting Binding Affinity and Virtual Screening. 309-314
  
• Amit Sabnis, Robert W. Harrison:
  A Novel Deterministic-Stochastic Crossover Method for Simulating Biochemical Networks. 315-320
  
• Alberto Casagrande, Cristian Del Fabbro, Simone Scalabrin, Alberto Policriti:
  GAM: Genomic Assemblies Merger: A Graph Based Method to Integrate Different Assemblies. 321-326
  
• Mark J. O'Connor, Anja E. Hauser, Ann M. Haberman, Steven H. Kleinstein:
  Activated Germinal-Center B Cells Undergo Directed Migration. 327-331
  
• Guoqiang Yu, Bai Zhang, Jianfeng Xu, Ie-Ming Shih, Yue Joseph Wang:
  Accurate Estimation of Genomic Deletions and Normal Cell Contamination by Bayesian Analysis of Mixtures. 332-337
  
• Minoo Aminian, Amina Shabbeer, Kristin P. Bennett:
  Determination of Major Lineages of Mycobacterium tuberculosis Complex Using Mycobacterial Interspersed Repetitive Units. 338-343
  
• Xiaoshi Yin, Xiangji Huang, Zhoujun Li:
  Towards a Better Ranking for Biomedical Information Retrieval Using Context. 344-349
  
• Min Su Lee, Sangyoon Oh, Byoung-Tak Zhang:
  Ensemble Learning Based on Active Example Selection for Solving Imbalanced Data Problem in Biomedical Data. 350-355
  
• Xiaohong Wang, Jun Huan, Aaron M. Smalter, Gerald H. Lushington:
  Application of Kernel Functions for Accurate Similarity Search in Large Chemical Databases. 356-361
  
• Yue W. Webster, Ranga Chandra Gudivada, Ernst R. Dow, Jacob Koehler, Mathew J. Palakal:
  A Hybrid Method to Discover and Rank Cross-Disciplinary Associations. 362-365
  
• Jayasimha Reddy Katukuri, Ying Xie, Vijay V. Raghavan:
  Biomedical Relationship Extraction from Literature Based on Bio-semantic Token Subsequences. 366-370
  
• Woo-Hyuk Jang, Suk Hoon Jung, Bo-ra Hyun, Dong-Soo Han:
  A Protein-Protein Interaction Prediction Method Embracing Intra-protein Domain Cohesion Information. 371-374
  
• Xiaoshi Yin, Xiangji Huang, Zhoujun Li:
  BioCLink: A Probabilistic Approach for Improving Genomics Search with Citation Links. 375-378
  
• Md. Muksitul Haque, Ananth Kalyanaraman, Amit Dhingra, Nehal Abu-Lail, Kaori Graybeal:
  DNAjig: A New Approach for Building DNA Nanostructures. 379-383
  
• Sook S. Ha, Inyoung Kim, Jianhua Xuan:
  Enhancing Pathway Based Analysis Using Different Weighting Schemes. 384-387
  
• Yuanjian Feng, Guoqiang Yu, Tian-Li Wang, Ie-Ming Shih, Yue Joseph Wang:
  Analyzing DNA Copy Number Changes Using Fused Margin Regression. 388-391
  
• Terry Camerlengo, Hatice Gulcin Ozer, Pearlly Yan, Jeffrey D. Parvin, Tim Hui-Ming Huang, Kun Huang, Mingxiang Teng, Lang Li, Yunlong Liu, Francisco Perez, Tahsin M. Kurç:
  Enabling Data Analysis on High-Throughput Data in Large Data Depository Using Web-Based Analysis Platform - A Case Study on Integrating QUEST with GenePattern in Epigenetics Research. 392-395
  
• Yanpeng Li, Hongfei Lin, Zhihao Yang:
  Applying Feature Coupling Generalization for Protein-Protein Interaction Extraction. 396-400
  
• Yixun Liu, Andriy Fedorov, Ron Kikinis, Nikos Chrisochoides:
  Real-Time Non-rigid Registration of Medical Images on a Cooperative Parallel Architecture. 401-404
  
• Dongxiao Zhu, Guorong Xu, Lipi R. Acharya:
  A Generalized Multivariate Approach for Correlation-Based Pattern Discovery from Replicated Molecular Profiling Data. 405-410
  
• Bi-Hua Cheng, Harsha Gopal Goud Vaka, Snehasis Mukhopadhyay:
  A Genetic Association Study between Breast Cancer and Osteoporosis Using Transitive Text Mining. 411-414
  
• Linlin Shao, Yuehui Chen:
  Bacterial Foraging Optimization Algorithm Integrating Tabu Search for Motif Discovery. 415-418
  
• Hashmat Rohian, Aijun An, Jiashu Zhao, Xiangji Huang:
  Discovering Temporal Associations among Significant Changes in Gene Expression. 419-423
  
• Fan Zhang, Jianjun Hu:
  Bayesian Classifier for Anchored Protein Sorting Discovery. 424-428
  

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