BIBM 2007: Silicon Valley, CA, USA

Kenotes

• Russ B. Altman:
  Combining Simulation and Machine Learning to Recognize Function in 4D. 3
  
• Michael I. Jordan:
  Statistical Machine Learning and Computational Biology. 4
  
• Richard M. Karp:
  Computer Science as a Lens on the Sciences: The Example of Computational Molecular Biology. 5
  

Biological Data Mining

• Lei Yu, Hao Li:
  Feature Cluster Selection for High-Throughput Data Analysis. 9-14
  
• Ricardo Martínez, Claude Pasquier, Nicolas Pasquier:
  GenMiner: Mining Informative Association Rules from Genomic Data. 15-22
  
• Sun Kim, Ankita Bhan, Bharath K. Maryada, Kwangmin Choi, Yves V. Brun:
  EGGS: Extraction of Gene Clusters Using Genome Context Based Sequence Matching Techniques. 23-28
  
• Mutlu Mete, Xiaowei Xu, Chun-Yang Fan, Gal Shafirstein:
  A Machine Learning Approach for Identification of Head and Neck Squamous Cell Carcinoma. 29-34
  
• Feihong Wu, Fadi Towfic, Drena Dobbs, Vasant Honavar:
  Analysis of Protein Protein Dimeric Interfaces. 35
  
• Min Song, Illhoi Yoo:
  A Hybrid Abbreviation Extraction Technique for Biomedical Literature. 42-47
  
• Dharmesh Thakkar, Carolina Ruiz, Elizabeth F. Ryder:
  Hypothesis-Driven Specialization of Gene Expression Association Rules. 48-55
  
• Razvan Andonie, Levente Fabry-Asztalos, Lukas Magill, Sarah Abdul-Wahid:
  A New Fuzzy ARTMAP Approach for Predicting Biological Activity of Potential HIV-1 Protease Inhibitors. 56-61
  
• Yutaka Sasaki, Brian Rea, Sophia Ananiadou:
  Multi-topic Aspects in Clinical Text Classification. 62-70
  

High Performance Bio-computing

• Jaegul Choo, Hyunsoo Kim, Haesun Park, Hongyuan Zha:
  A Comparison of Unsupervised Dimension Reduction Algorithms for Classification. 71-77
  
• Antonio Ruiz, Olcay Sertel, Manuel Ujaldon, Ümit V. Çatalyürek, Joel H. Saltz, Metin N. Gurcan:
  Pathological Image Analysis Using the GPU: Stroma Classification for Neuroblastoma. 78-88
  

Genomics, Comparative Genomics

• Winnie W. M. Lam, Keith C. C. Chan, David K. Y. Chiu, Andrew K. C. Wong:
  MAGMA: An Algorithm for Mining Multi-level Patterns in Genomic Data. 89-94
  
• Arnaud Fontaine, Hélène Touzet:
  Computational Identification of Protein-Coding Sequences by Comparative Analysis. 95-102
  
• Jia Zeng, Reda Alhajj:
  Multi-agent System for Translation Initiation Site Prediction. 103-110
  

Biological Databases, Data Integration and Visualization

• Denise Jones, Ying Jin, Huaqin Xu:
  An Active Rule-Based Approach for Constraint Management of Biological Data in XML Documents. 111-116
  
• Paul M. K. Gordon, Edward Kawas, Mark D. Wilkinson, Christoph W. Sensen:
  Using a Novel Data Transformation Technique to Provide the EMBOSS Software Suite as Semantic Web Services. 117-124
  
• Dragana Veljkovic, Kay A. Robbins, Doug Rubino, Nicholas G. Hatsopoulos:
  Exploring and Organizing Spatiotemporal Features such as Waves in High Throughput Brain Recordings by Lifting to Feature Space. 125-134
  

Molecular Sequence Analysis

• Shengyin Gu, Olivier Poch, Bernd Hamann, Patrice Koehl:
  A Geometric Representation of Protein Sequences. 135-142
  
• Feng Yue, Jijun Tang:
  A Divide-and-Conquer Implementation of Three Sequence Alignment and Ancestor Inference. 143-150
  
• Dan He, Xindong Wu, Xingquan Zhu:
  SAIL-APPROX: An Efficient On-Line Algorithm for Approximate Pattern Matching with Wildcards and Length Constraints. 151-158
  
• Lenwood S. Heath, Amrita Pati:
  Predicting Markov Chain Order in Genomic Sequences. 159-164
  
• Abanish Singh, Cédric Feschotte, Nikola Stojanovic:
  Micro-repetitive Structure of Genomic Sequences and the Identification of Ancient Repeat Elements. 165-171
  
• Shihyen Chen, Bin Ma, Kaizhong Zhang:
  The Normalized Similarity Metric and Its Applications. 172-180
  

Healthcare Informatics

• Kimiko Matsuoka, Shigeki Yokoyama, Kunitomo Watanabe, Shusaku Tsumoto:
  Mining Rules for Risk Factors on Blood Stream Infection in Hospital Information System. 181-187
  
• Soo-Yeon Ji, Toan Huynh, Kayvan Najarian:
  A Comparative Medical Informatics Approach to Traumatic Pelvic Injuries. 188-193
  
• Oliver Amft, Martin Kusserow, Gerhard Tröster:
  Automatic Identification of Temporal Sequences in Chewing Sounds. 194-201
  
• Sai T. Moturu, William G. Johnson, Huan Liu:
  Predicting Future High-Cost Patients: A Real-World Risk Modeling Application. 202-208
  
• Aaron Smalter, Seak Fei Lei, Xue-wen Chen:
  Human Disease-Gene Classification with Integrative Sequence-Based and Topological Features of Protein-Protein Interaction Networks. 209-216
  

Proteomics, Computational Proteomics

• Tingting Li, Hu Fu, Xuegong Zhang:
  Prediction of Kinase-Specific Phosphorylation Sites by One-Class SVMs. 217-222
  
• Byung-Hoon Park, Bing Zhang, Tatiana V. Karpinets, Nagiza F. Samatova:
  Multi-stage Framework to Infer Protein Functional Modules from Mass Spectrometry Pull-Down Data with Assessment of Biological Relevance. 223-229
  
• Karin Noy, Daniel P. Fasulo:
  Robust Estimation and Graph-Based Meta Clustering for LC-MS Feature Extraction. 230-236
  
• Jung Hun Oh, Young Bun Kim, Jean Gao:
  A Novel Classification Method for Analysis of Multi-stage Diseases via Mass Spectrometric Data. 237-244
  

Protein Structure

• Satu Jääskeläinen, Pentti Riikonen, Tapio Salakoski, Mauno Vihinen:
  Evaluation of Protein Hydropathy Scales. 245-251
  
• Christophe Nicolas Magnan, Cécile Capponi, François Denis:
  A Protocol to Detect Local Affinities Involved in Proteins Distant Interactions. 252-257
  
• Frank DiMaio, Ameet Soni, George N. Phillips, Jude W. Shavlik:
  Improved Methods for Template-Matching in Electron-Density Maps Using Spherical Harmonics. 258-265
  
• Yhi Shiau, Jia-Nan Wang, Yu-Feng Huang, Chien-Kang Huang:
  Heuristic Strategy for Geometric Hashing Based Protein Structure Comparison of Ellipsoidal Representation. 266-274
  

Computational Systems Biology

• Doan Dai Duong, Patricia A. Evans:
  A Haplotyping Algorithm for Non-recombinant Pedigree Data Containing Missing Members. 275-281
  
• Dumitru Brinza, Alexander Zelikovsky:
  Risk Factor Searching Heuristics for SNP Case-Control Studies. 282-287
  
• Luca Bortolussi, Simone Fonda, Alberto Policriti:
  Constraint-Based Simulation of Biological Systems Described by Molecular Interaction Maps. 288-293
  
• Yudong Sun, Steve McKeever, Kia Balali-Mood, Mark S. P. Sansom:
  A Multiscale Model for Efficient Simulation of a Membrane Bound Viral Fusion Peptide. 294-301
  
• Jiaxing Xue, Jean Gao, Liping Tang:
  Mathematical Modeling of Phagocyte Chemotaxis toward and Adherence to Biomaterial Implants. 302-307
  
• Samik Ghosh, Preetam Ghosh, Kalyan Basu, Sajal K. Das:
  Modeling the Stochastic Dynamics of Gene Expression in Single Cells: A Birth and Death Markov Chain Analysis. 308-316
  

Microarray Design and Data Analysis

• Fatih Altiparmak, Selnur Erdal, Ozgur Ozturk, Hakan Ferhatosmanoglu:
  A Multi-metric Similarity Based Analysis of Microarray Data. 317-324
  
• Brandon J. Smith, Bruce R. Southey, Sandra L. Rodriguez-Zas:
  Smoothing Spline Mixed Effects Modeling of Multifactorial Gene Expression Profiles. 325-332
  

BioOntologies

• Sachin Mathur, Deendayal Dinakarpandian:
  A New Metric to Measure Gene Product Similarity. 333-338
  
• Oliver Ruebenacker, Ion I. Moraru, James C. Schaff, Michael L. Blinov:
  Kinetic Modeling Using BioPAX Ontology. 339-348
  

Gene Networks, Pathways, Networks, Systems Biology

• Leonardo Bobadilla, Fernando Niño, Edilberto Cepeda, Manuel A. Patarroyo:
  A Novel Methodology for Characterizing and Predicting Protein Functional Sites. 349-354
  
• Valeria Fionda, Luigi Palopoli, Simona Panni, Simona E. Rombo:
  GRAPPIN: Bipartite GRAph Based Protein-Protein Interaction Network Similarity Search. 355-361
  
• Younhee Ko, Chengxiang Zhai, Sandra L. Rodriguez-Zas:
  Inference of Gene Pathways Using Gaussian Mixture Models. 362-367
  
• Xin Li, Zhu Zhang, Hsinchun Chen, Jiexun Li:
  Graph Kernel-Based Learning for Gene Function Prediction from Gene Interaction Network. 368-373
  
• Fang Fang, Robert L. Grossman, Xiangjun Liu:
  An Algorithm for Assigning Unique Keys to Metabolic Pathways. 374-382
  

Signal and Image Processing in BioMedicine

• Hara Stefanou, Thanasis Margaritis, Dimitris Kafetzopoulos, Konstantinos Marias, Panagiotis Tsakalides:
  Microarray Image Denoising Using a Two-Stage Multiresolution Technique. 383-389
  
• Santa Di Cataldo, Elisa Ficarra, Enrico Macii:
  Selection of Tumor Areas and Segmentation of Nuclear Membranes in Tissue Confocal Images: A Fully Automated Approach. 390-398
  

BioMedical Databases and Information Systems, BioMedical Information

• Chetan Mittal, Nevenka Dimitrova, Vijaykumar Channakeshava:
  MDDM: A Resource for Differential Methylation in Cancer. 399-405
  
• James Zijun Wang, Zhidian Du, Philip S. Yu, Chin-Fu Chen:
  An Efficient Online Tool to Search Top-N Genes with Similar Biological Functions in Gene Ontology Database. 406-411
  
• Fusheng Wang, Cornelius Rabsch, Peiya Liu:
  Using SVG to Model and Query Image Annotations and Their History. 412-422
  

Intelligent Biomedical Knowledge Discovery

• Thanh Phuong Nguyen, Tu Bao Ho:
  A Semi-supervised Learning Approach to Disease Gene Prediction. 423-428
  
• Michele Berlingerio, Francesco Bonchi, Fosca Giannotti, Franco Turini:
  Mining Clinical Data with a Temporal Dimension: A Case Study. 429-436
  
• Quan Wen, Jean Gao, Kate Luby-Phelps:
  Multiple Interacting Subcellular Structure Tracking by Sequential Monte Carlo Method. 437-442