Table of Contents

• Suffix Trees (and Relatives) Come of Age in BioinformaticsDan Gusfield. 3 [doi]
• Genome Annotation and Protein StructureSteven E. Brenner. 4 [doi]
• Decoding Noncoding Regulatory DNAs in Metazoan GenomesMichele Markstein, Angela Stathopoulos, Vicky Markstein, Peter W. Markstein, Naoe Harafuji, Dave Keys, Byung-in Lee, Paul Richardson, Dan Rokshar, Mike Levine. 5 [doi]
• F-LOG: A Domain Specific Language for Solving Phylogenetic Inference ProblemsEnrico Pontelli, Desh Ranjan, Brook Milligan, Gopal Gupta. 9-20 [doi]
• AxML: A Fast Program for Sequential and Parallel Phylogenetic Tree Calculations Based on the Maximum Likelihood MethodAlexandros Stamatakis, Thomas Ludwig 0002, Harald Meier, Marty J. Wolf. 21 [doi]
• Visualization of K -Tuple Distribution in Procaryote Complete Genomes and Their Randomized CounterpartsHuimin Xie, Bailin Hao. 31-42 [doi]
• Fast and Sensitive Algorithm for Aligning ESTs to Human GenomeJun Ogasawara, Shinichi Morishita. 43-53 [doi]
• Rapid Large-Scale Oligonucleotide Selection for MicroarraysSven Rahmann. 54-63 [doi]
• Parallel Monte Carlo Methods for Physical Mapping of ChromosonesSuchendra M. Bhandarkar, Jonathan Arnold. 64 [doi]
• PheGe, the Platform for Exploring Genotype-Phenotype Relations on Cellular and Organism LevelKlaus Seidl. 79-86 [doi]
• Automated Identification of Single Nucleotide Polymorphisms from Sequencing DataMasazumi Takahashi, Fumihiko Matsuda, Nino Margetic, Mark G. Lathrop. 87 [doi]
• A Multi-Level Text Mining Method to Extract Biological RelationshipsMathew J. Palakal, Matthew Stephens, Snehasis Mukhopadhyay, Rajeev R. Raje, Simon Rhodes. 97-108 [doi]
• A Literature Based Method for Identifying Gene-Disease ConnectionsLada A. Adamic, Dennis M. Wilkinson, Bernardo A. Huberman, Eytan Adar. 109-117 [doi]
• Protein-Based Analysis of Alternative Splicing in the Human GenomeAnn E. Loraine, Gregg A. Helt, Melissa S. Cline, Michael A. Siani-Rose. 118 [doi]
• Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family AlignmentChuan Yi Tang, Chin Lung Lu, Margaret Dah-Tsyr Chang, Yin-Te Tsai, Yuh-Ju Sun, Kun-Mao Chao, Jia-Ming Chang, Yu-Han Chiou, Chia-Mao Wu, Hao-Teng Chang, Wei-I Chou. 127-137 [doi]
• Fast and Sensitive Alignment of Large Genomic SequencesMichael Brudno, Burkhard Morgenstern. 138 [doi]
• Design of Genetic Switches with Only Positive Feedback LoopsTetsuya Kobayashi, Luonan Chen, Kazuyuki Aihara. 151 [doi]
• An Efficient Branch-and-Bound Algorithm for the Assignment of Protein Backbone NMR PeaksGuo-Hui Lin, Dong Xu, Zhi-Zhong Chen, Tao Jiang, Jianjun Wen, Ying Xu. 165-174 [doi]
• Towards Automatic Clustering of Protein SequencesJiong Yang, Wei Wang 0010. 175-186 [doi]
• A Bi-Recursive Neural Network Architecture for the Prediction of Protein Coarse Contact MapsAlessandro Vullo, Paolo Frasconi. 187-196 [doi]
• Prediction of Protein Function Using Protein-Protein Interaction DataMinghua Deng, Kui Zhang, Shipra Mehta, Ting Chen, Fengzhu Sun. 197-206 [doi]
• Accelerating Approximate Subsequence Search on Large Protein Sequence DatabasesJiong Yang, Wei Wang 0010, Yi Xia, Philip S. Yu. 207 [doi]
• Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic NetworkSeiya Imoto, SunYong Kim, Takao Goto, Sachiyo Aburatani, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano. 219-227 [doi]
• High Similarity Sequence Comparison in Clustering Large Sequence DatabasesLorie Dudoignon, Eric Glémet, Hendrik Cornelis Heus, Mathieu Raffinot. 228-236 [doi]
• A Maximum Entropy Algorithm for Rhythmic Analysis of Genome-Wide Expression PatternsChristopher James Langmead, C. Robertson McClung, Bruce Randall Donald. 237-245 [doi]
• Simultaneous Classification and Feature Clustering Using Discriminant Vector Quantization with Applications to Microarray Data AnalysisJia Li, Hongyuan Zha. 246-255 [doi]
• An Index Structure for Pattern Similarity Searching in DNA Microarray DatHaixun Wang, Chang-Shing Perng, Wei Fan, Philip S. Yu. 256-267 [doi]
• A New Clustering Method for Microarray Data AnalysisLouxin Zhang, Song Zhu. 268-275 [doi]
• An Adaptive Meta-Clustering Approach: Combining the Information from Different Clustering ResultsYujing Zeng, Jianshan Tang, Javier Garcia-Frias, Guang R. Gao. 276 [doi]
• Parallelizing a DNA Simulation Code for the Cray MTA-2Shahid H. Bokhari, Matthew A. Glaser, Harry F. Jordan, Yves Lansac, Jon R. Sauer, Bart Van Zeghbroeck. 291-302 [doi]
• DNA Sequence Compression Using the Burrows-Wheeler TransformDonald A. Adjeroh, Yong Zhang, Amar Mukherjee, Matt Powell, Tim Bell. 303-313 [doi]
• A Security System for Personal Genome Information at DNA LevelYumi Kawazoe, Toshikazu Shiba, Masahito Yamamoto, Azuma Ohuchi. 314-320 [doi]
• Visualization Techniques for Genomic DataAnn E. Loraine, Gregg A. Helt. 321 [doi]
• An Application of a Pathway Alignment Method to Comparative Analysis between Genome and PathwaysShoko Miyake, Yukako Tohsato, Hideo Matsuda. 329-329 [doi]
• A Bayesian Modeling Framework for Genetic RegulationRishi Khan, Yujing Zeng, Javier Garcia-Frias, Guang R. Gao. 330-332 [doi]
• Complexity and Application of Pedigree Analysis Programme GTreeDaisuke Ogino, Shiro Mori, Masato Nose, Hideki Sawada. 333-335 [doi]
• Designing Oscillators in Synthetic Gene Networks Based on Multi-Scale DynamicsLuonan Chen, Tetsuya Kobayashi, Kazuyuki Aihara. 336 [doi]
• Distributions of Free Energy, Melting Temperature, and Hybridization Propensity for Genomic DNA OligomersRyan T. Koehler, Nicolas Peyret. 337 [doi]
• Electronic Polymerase Chain Reaction (EPCR) Search AlgorithmConrad Shyu, James A. Foster, Larry J. Forney. 338 [doi]
• GeneCards? 2002: An Evolving Human Gene CompendiumMarilyn Safran, Irina Solomon, Orit Shmueli, Michal Lapidot, Shai Shen-Orr, Avital Adato, Uri Ben-Dor, Nir Esterman, Naomi Rosen, Inga Peter, Tsviya Olender, Vered Chalifa-Caspi, Doron Lancet. 339 [doi]
• HIV Protease Structural DatabaseVeerasamy Ravichandran, Jiri Vondrásek, Gary Gilliland, T. N. Bhat, Alexander Wlodawer. 340 [doi]
• MiCA: Web-Based Computational Tools for the Analysis of Microbial Community Structure and Compisition Based on T-RFLP of 16S rRNA GeneConrad Shyu, James A. Foster, K. X. Liao, S. J. Bent, K. Sale, Larry J. Forney, Terence Soule. 341 [doi]
• P-quasi Complete Linkage Analysis for Gene-Expression DataShigeto Seno, Reiji Teramoto, Hideo Matsuda. 342 [doi]
• A Reference Database for Medicago Truncatula Genes, Protiens, and MetabolitesDianjing Guo, Xingjing Li, Aejaaz Kamal, Olga Brazhnik, Pedro Mendes. 343 [doi]
• Selective Tree Growing: A Deterministic Constant-Space Linear-Time Algorithm for Pattern Discovery and for Computing Multiple Sequence AlignmentMashilamani Sambasivam. 344 [doi]
• Wavelet Profiles: Their Application in Oryza sativa DNA Sequence AnalysisNobuyuki Kawagashira, Yasuhiro Ohtomo, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi. 345-346 [doi]