3. ISBRA 2007: Atlanta, GA, USA

• Xubo Fei, Shiyong Lu, Horia F. Pop, Lily R. Liang:
  GFBA: A Biclustering Algorithm for Discovering Value-Coherent Biclusters. 1-12
  
• Fang-Xiang Wu:
  Significance Analysis of Time-Course Gene Expression Profiles. 13-24
  
• Juntao Li, Jianhua Liu, Karuturi R. Krishna Murthy:
  Data-Driven Smoothness Enhanced Variance Ratio Test to Unearth Responsive Genes in 0-Time Normalized Time-Course Microarray Data. 25-36
  
• Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz:
  Efficiently Finding the Most Parsimonious Phylogenetic Tree Via Linear Programming. 37-48
  
• Róbert Busa-Fekete, András Kocsor, Csaba Bagyinka:
  A Multi-Stack Based Phylogenetic Tree Building Method. 49-60
  
• Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller:
  A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. 61-72
  
• Qihua Tan, Jesper Dahlgaard, Basem M. Abdallah, Werner Vach, Moustapha Kassem, Torben Arvid Kruse:
  A Bootstrap Correspondence Analysis for Factorial Microarray Experiments with Replications. 73-84
  
• Roy Varshavsky, David Horn, Michal Linial:
  Clustering Algorithms Optimizer: A Framework for Large Datasets. 85-96
  
• Jahangheer S. Shaik, Mohammed Yeasin:
  Ranking Function Based on Higher Order Statistics (RF-HOS) for Two-Sample Microarray Experiments. 97-108
  
• Patricia Buendia, Giri Narasimhan:
  Searching for Recombinant Donors in a Phylogenetic Network of Serial Samples. 109-120
  
• Arvind Gupta, Ján Manuch, Ladislav Stacho, Xiaohong Zhao:
  Algorithm for Haplotype Inferring Via Galled-Tree Networks with Simple Galls. 121-132
  
• Frederick Cohan, Danny Krizanc, Yun Lu:
  Estimating Bacterial Diversity from Environmental DNA: A Maximum Likelihood Approach. 133-144
  
• Ming Li:
  Invited Talk: Modern Homology Search. 145
  
• Pramod K. Gupta, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Satoru Miyano:
  Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data. 146-157
  
• Italo Zoppis, Daniele Merico, Marco Antoniotti, Bud Mishra, Giancarlo Mauri:
  Discovering Relations Among GO-Annotated Clusters by Graph Kernel Methods. 158-169
  
• George Lee, Carlos Rodriguez, Anant Madabhushi:
  An Empirical Comparison of Dimensionality Reduction Methods for Classifying Gene and Protein Expression Datasets. 170-181
  
• Robert J. Calin-Jageman, Chao Xie, Yi Pan, Art Vandenberg, Paul S. Katz:
  NEURONgrid: A Toolkit for Generating Parameter-Space Maps Using NEURON in a Grid Environment. 182-191
  
• Leonid Zaslavsky, Yiming Bao, Tatiana A. Tatusova:
  An Adaptive Resolution Tree Visualization of Large Influenza Virus Sequence Datasets. 192-202
  
• Gordana Derado, F. DuBois Bowman, Rajan Patel, Mary Newell, Brani Vidakovic:
  Wavelet Image Interpolation (WII): A Wavelet-Based Approach to Enhancement of Digital Mammography Images. 203-214
  
• Yanchao Wang, Rajshekhar Sunderraman, Piyaphol Phoungphol:
  High Level Programming Environment System for Protein Structure Data. 215-226
  
• Kung-Hua Chang, Yong Kyun Kwon, Douglas Stott Parker Jr.:
  Finding Minimal Sets of Informative Genes in Microarray Data. 227-236
  
• Li Chen, Dmitry B. Goldgof, Lawrence O. Hall, Steven Eschrich:
  Noise-Based Feature Perturbation as a Selection Method for Microarray Data. 237-247
  
• Igor Trajkovski, Nada Lavrac:
  Efficient Generation of Biologically Relevant Enriched Gene Sets. 248-259
  
• Sudha Balla, Sanguthevar Rajasekaran:
  Space and Time Efficient Algorithms to Discover Endogenous RNAi Patterns in Complete Genome Data. 260-269
  
• Scott F. Smith:
  A Fast Approximate Covariance-Model-Based Database Search Method for Non-coding RNA. 270-281
  
• Raja Loganantharaj:
  Extensions of Naive Bayes and Their Applications to Bioinformatics. 282-292
  
• Marília D. V. Braga, Marie-France Sagot, Celine Scornavacca, Eric Tannier:
  The Solution Space of Sorting by Reversals. 293-304
  
• Matthias Bernt, Daniel Merkle, Martin Middendorf:
  A Fast and Exact Algorithm for the Perfect Reversal Median Problem. 305-316
  
• Lenwood S. Heath, Amrita Pati:
  Genomic Signatures from DNA Word Graphs. 317-328
  
• Erliang Zeng, Giri Narasimhan:
  Enhancing Motif Refinement by Incorporating Comparative Genomics Data. 329-337
  
• Hyunmin Kim, Katherina J. Kechris, Lawrence Hunter:
  Mining Discriminative Distance Context of Transcription Factor Binding Sites on ChIP Enriched Regions. 338-349
  
• Allison N. Tegge, Sandra L. Rodriguez-Zas, Jonathan V. Sweedler, Bruce R. Southey:
  Enhanced Prediction of Cleavage in Bovine Precursor Sequences. 350-360
  
• Mary Qu Yang, Laura Elnitski:
  Invited Talk: A Computational Study of Bidirectional Promoters in the Human Genome. 361-371
  
• Mark J. Lawson, Liqing Zhang:
  The Identification of Antisense Gene Pairs Through Available Software. 372-381
  
• Steinar Thorvaldsen, Elinor Ytterstad, Tor Flå:
  Inferring Weak Adaptations and Selection Biases in Proteins from Composition and Substitution Matrices. 382-393
  
• Michael E. Sparks, Volker Brendel, Karin S. Dorman:
  Markov Model Variants for Appraisal of Coding Potential in Plant DNA. 394-405
  
• Zheng Rong Yang:
  Predicting Palmitoylation Sites Using a Regularised Bio-basis Function Neural Network. 406-417
  
• Hao Yu, Minlie Huang, Xiaoyan Zhu, Yabin Guo:
  A Novel Kernel-Based Approach for Predicting Binding Peptides for HLA Class II Molecules. 418-429
  
• Margaret Dah-Tsyr Chang, Hao-Teng Chang, Rong-Yuan Huang, Wen-Shyong Tzou, Chih-Hong Liu, Wei-Jun Zhung, Hsien-Wei Wang, Chun-Tien Chang, Tun-Wen Pai:
  A Database for Prediction of Unique Peptide Motifs as Linear Epitopes. 430-440
  
• Dan He:
  A Novel Greedy Algorithm for the Minimum Common String Partition Problem. 441-452
  
• Mun-Ho Choi, In-Seon Jeong, Seung-Ho Kang, Hyeong-Seok Lim:
  An Efficient Algorithm for Finding Gene-Specific Probes for DNA Microarrays. 453-464
  
• Chengpeng Bi:
  Multiple Sequence Local Alignment Using Monte Carlo EM Algorithm. 465-476
  
• Hyunsoo Kim, Haesun Park:
  Cancer Class Discovery Using Non-negative Matrix Factorization Based on Alternating Non-negativity-Constrained Least Squares. 477-487
  
• Chen Liao, Shutao Li:
  A Support Vector Machine Ensemble for Cancer Classification Using Gene Expression Data. 488-495
  
• Xiujuan Chen, Yichuan Zhao, Yan-Qing Zhang, Robert W. Harrison:
  Combining SVM Classifiers Using Genetic Fuzzy Systems Based on AUC for Gene Expression Data Analysis. 496-505
  
• Dandan Song, Zhidong Deng:
  A BP-SCFG Based Approach for RNA Secondary Structure Prediction with Consecutive Bases Dependency and Their Relative Positions Information. 506-517
  
• Minghui Jiang, Martin Mayne, Joel Gillespie:
  Delta: A Toolset for the Structural Analysis of Biological Sequences on a 3D Triangular Lattice. 518-529
  
• Xuezheng Fu, Bernard Chen, Yi Pan, Robert W. Harrison:
  Statistical Estimate for the Size of the Protein Structural Vocabulary. 530-538
  
• Cui Lin, Shiyong Lu, Danqing Wu, Jing Hua, Otto Muzik:
  Coclustering Based Parcellation of Human Brain Cortex Using Diffusion Tensor MRI. 539-550
  
• Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu:
  An Algorithm for Hierarchical Classification of Genes of Prokaryotic Genomes. 551-563
  
• Mudassir Fayyaz, Asifullah Khan, Adnan Mujahid, Alex Kavokin:
  Using Multi Level Nearest Neighbor Classifiers for G-Protein Coupled Receptor Sub-families Prediction. 564-576
  
• Mark Borodovsky:
  Invited Talk: Ab Initio Gene Finding Engines: What Is Under the Hood. 577
  
• Marco Vassura, Luciano Margara, Filippo Medri, Pietro di Lena, Piero Fariselli, Rita Casadio:
  Reconstruction of 3D Structures from Protein Contact Maps. 578-589
  
• Gulsah Altun, Hae-Jin Hu, Stefan Gremalschi, Robert W. Harrison, Yi Pan:
  A Feature Selection Algorithm Based on Graph Theory and Random Forests for Protein Secondary Structure Prediction. 590-600
  
• Amin R. Mazloom, Kalyan Basu, Subhrangsu S. Mandal, Mehran Sorourian, Sajal K. Das:
  DNA Sites Buried in Nucleosome Become Accessible at Room Temperature: A Discrete-Event-Simulation Based Modeling Approach. 601-614
  
• Shiquan Wu, Jing Li:
  Comparative Analysis of Gene-Coexpression Networks Across Species. 615-626
  
• Jizhen Zhao, Dongsheng Che, Liming Cai:
  Comparative Pathway Prediction Via Unified Graph Modeling of Genomic Structure Information. 627-637
  
• Roberto Barbuti, Andrea Maggiolo-Schettini, Paolo Milazzo:
  Extending the Calculus of Looping Sequences to Model Protein Interaction at the Domain Level. 638-649
  

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