BICoB 2009: New Orleans, LA, USA

Invited Talks

• Gowtham Atluri, Rohit Gupta, Gang Fang, Gaurav Pandey, Michael Steinbach, Vipin Kumar:
  Association Analysis Techniques for Bioinformatics Problems. 1-13
  
• Eric Banks, Elena Nabieva, Bernard Chazelle, Ryan Peterson, Mona Singh:
  Analyzing and Interrogating Biological Networks (Abstract). 14-15
  
• Vladimir Filkov:
  From Architecture to Function (and Back) in Bio-networks. 16-17
  
• Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen, Zoran Obradovic, A. Keith Dunker, Dong Xu:
  A New Machine Learning Approach for Protein Phosphorylation Site Prediction in Plants. 18-29
  
• Benjamin G. Jackson, Patrick S. Schnable, Srinivas Aluru:
  Assembly of Large Genomes from Paired Short Reads. 30-43
  
• Weiming Li, Bin Ma, Kaizhong Zhang:
  Amino Acid Classification and Hash Seeds for Homology Search. 44-51
  
• Ion I. Mandoiu:
  Genotype and Haplotype Reconstruction from Low-Coverage Short Sequencing Reads. 52-53
  
• Satoru Miyano, Rui Yamaguchi, Yoshinori Tamada, Masao Nagasaki, Seiya Imoto:
  Gene Networks Viewed through Two Models. 54-66
  
• Corban G. Rivera, T. M. Murali:
  Identifying Evolutionarily Conserved Protein Interaction Modules Using GraphHopper. 67-78
  
• Thomas K. F. Wong, Siu-Ming Yiu, Tak Wah Lam, Wing-Kin Sung:
  The 2-Interval Pattern Matching Problems and Its Application to ncRNA Scanning. 79-89
  

Refereed Papers

• Sahar Al Seesi, Sanguthevar Rajasekaran, Reda A. Ammar:
  RNA Pseudoknot Folding through Inference and Identification Using TAGRNA. 90-101
  
• Sébastien Angibaud, Damien Eveillard, Guillaume Fertin, Irena Rusu:
  Comparing Bacterial Genomes by Searching Their Common Intervals. 102-113
  
• Mukul S. Bansal, Wen-Chieh Chang, Oliver Eulenstein, David Fernández-Baca:
  Generalized Binary Tanglegrams: Algorithms and Applications. 114-125
  
• Felix Bollenbeck, Stephanie Kaspar, Hans-Peter Mock, Diana Weier, Udo Seiffert:
  Three-Dimensional Multimodality Modelling by Integration of High-Resolution Interindividual Atlases and Functional MALDI-IMS Data. 126-138
  
• Christina Boucher, Daniel G. Brown:
  Detecting Motifs in a Large Data Set: Applying Probabilistic Insights to Motif Finding. 139-150
  
• Doruk Bozdag, Jeffrey D. Parvin, Ümit V. Çatalyürek:
  A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets. 151-163
  
• Wei Cao, Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, Katsuhiko Kitamoto, Kentaro Shimizu:
  Computational Protocol for Screening GPI-anchored Proteins. 164-175
  
• Joseph E. Davis, Adnan Ozsoy, Sandeep Patel, Michela Taufer:
  Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors. 176-186
  
• Didier Dréau, Dimitre Stanimirov, Ted Carmichael, Mirsad Hadzikadic:
  An Agent-Based Model of Solid Tumor Progression. 187-198
  
• Difeng Dong, Chun-Ying Cui, Benjamin Mow, Limsoon Wong:
  Deciphering Drug Action and Escape Pathways: An Example on Nasopharyngeal Carcinoma. 199-210
  
• Shantanu Dutt, Yang Dai, Huan Ren, Joel Fontanarosa:
  Selection of Multiple SNPs in Case-Control Association Study Using a Discretized Network Flow Approach. 211-223
  
• Cesim Erten, Melih Sözdinler:
  Biclustering Expression Data Based on Expanding Localized Substructures. 224-235
  
• Alvaro J. González, Li Liao:
  Constrained Fisher Scores Derived from Interaction Profile Hidden Markov Models Improve Protein to Protein Interaction Prediction. 236-247
  
• Jianjun Hu, Fan Zhang:
  Improving Protein Localization Prediction Using Amino Acid Group Based Physichemical Encoding. 248-258
  
• Abu H. M. Kamal, Xingquan Zhu, Abhijit S. Pandya, Sam Hsu, Muhammad Shoaib:
  The Impact of Gene Selection on Imbalanced Microarray Expression Data. 259-269
  
• Matthieu Manceny, Marc Aiguier, Pascale Le Gall, Joan Hérisson, Ivan Junier, François Képès:
  Spatial Information and Boolean Genetic Regulatory Networks. 270-281
  
• Mylène Maurin, Morgan Magnin, Olivier H. Roux:
  Modeling of Genetic Regulatory Network in Stochastic pi-Calculus. 282-294
  
• Fangyuan Nan, Yaonan Wang, Xiaoping Ma:
  fMRI Activation Detection by MultiScale Hidden Markov Model. 295-306
  
• Carl Nettelblad, Sverker Holmgren, Lucy Crooks, Örjan Carlborg:
  cnF2freq: Efficient Determination of Genotype and Haplotype Probabilities in Outbred Populations Using Markov Models. 307-319
  
• Hatice Gulcin Ozer, Doruk Bozdag, Terry Camerlengo, Jiejun Wu, Yi-Wen Huang, Timothy D. R. Hartley, Jeffrey D. Parvin, Tim Hui-Ming Huang, Ümit V. Çatalyürek, Kun Huang:
  A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments. 320-330
  
• Hyun Jung Park, Tiffani L. Williams:
  A Fitness Distance Correlation Measure for Evolutionary Trees. 331-342
  
• Allison Regier, Michael Olson, Scott J. Emrich:
  Alignment and Analysis of Closely Related Genomes. 343-352
  
• Eric C. Rouchka, Xiangping Wang, James H. Graham, Nigel G. F. Cooper:
  Computational Prediction of Genes Translationally Regulated by Cytoplasmic Polyadenylation Elements. 353-361
  
• Fahad Saeed, Ashfaq A. Khokhar, Osvaldo Zagordi, Niko Beerenwinkel:
  Multiple Sequence Alignment System for Pyrosequencing Reads. 362-375
  
• Xinghua Shi, Rick L. Stevens:
  A Bayesian Approach to High-Throughput Biological Model Generation. 376-387
  
• Michael Slavik, Xingquan Zhu, Imad Mahgoub, Muhammad Shoaib:
  Parallel Selection of Informative Genes for Classification. 388-399
  
• Jaroslaw Smieja:
  Simulation Methods in Uncovering New Regulatory Mechanisms in Signaling Pathways. 400-408
  
• Stephen Tyree, Rayus Kuplicki, Trevor Sarratt, Scott Fujan, John Hale:
  GridSPiM: A Framework for Simple Locality and Containment in the Stochastic pi-Calculus. 409-423
  
• Duygu Ucar, Fatih Altiparmak, Hakan Ferhatosmanoglu, Srinivasan Parthasarathy:
  Mutual Information Based Extrinsic Similarity for Microarray Analysis. 424-436
  
• Hari Krishna Yalamanchili, Nita Parekh:
  Graph Spectral Approach for Identifying Protein Domains. 437-448