Abstract is missing.
- PrefaceRuss B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein. [doi]
- A Biological Named Entity RecognizerMeenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker. [doi]
- Gene Regulation - Session IntroductionSerafim Batzoglou, Lior Pachter. 3-4 [doi]
- Multiclass Cancer Classification Using Gene Expression Profiling and Probabilistic Neural NetworksDaniel P. Berrar, C. Stephen Downes, Werner Dubitzky. 5-16 [doi]
- Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential EquationsMichiel J. L. de Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano. 17-28 [doi]
- Genome-Wide Analysis of Bacterial Promoter RegionsEleazar Eskin, Uri Keich, Mikhail S. Gelfand, Pavel A. Pevzner. 29-40 [doi]
- MOPAC: MOtif Finding by Preprocessing and Agglomerative Clustering from MicroarraysR. Ganesh, Deborah A. Siegele, Thomas R. Ioerger. 41-52 [doi]
- Improved Gene Selection for Classification of MicroarraysJ. Jaeger, Rimli Sengupta, Walter L. Ruzzo. 53-64 [doi]
- Kernel Cox Regression Models for Linking Gene Expression Profiles to Censored Survival DataHongzhe Li, Yihui Luan. 65-76 [doi]
- Extracting Conserved Gene Expression Motifs from Gene Expression DataT. M. Murali, Simon Kasif. 77-88 [doi]
- Decomposing Gene Expression into Cellular ProcessesEran Segal, Alexis Battle, Daphne Koller. 89-100 [doi]
- Genome, Pathway, and Interaction Bioinformatics - Session IntroductionPeter D. Karp, Eric P. Neumann, Alexander J. Hartemink, Pedro Romero. 101-103 [doi]
- Suitability and Utility of Computational Analysis Tools: Characterization of Erythrocyte Parameter VariationRyan E. Altenbaugh, Kenneth J. Kauffman, Jeremy S. Edwards. 104-115 [doi]
- Foundations of a Query and Simulation System for the Modeling of Biochemical and Biological ProcessesMarco Antoniotti, F. Park, Alberto Policriti, Nadia Ugel, Bud Mishra. 116-127 [doi]
- Incorporating Biological Knowledge into Evaluation of Causal Regulatory HypothesesLonnie Chrisman, Pat Langley, Stephen D. Bay. 128-139 [doi]
- Assessment of the reliability of protein-protein interactions and protein function predictionMinghua Deng, Fengzhu Sun, Ting Chen. 140-151 [doi]
- Boundary Formation by Notch Signaling in Drosophila Multicellular Systems: Experimental Observations and Gene Network Modeling by Genomic Object NetHiroshi Matsuno, Ryutaro Murakani, Rie Yamane, Naoyuki Yamasaki, Sachie Fujita, Haruka Yoshimori, Satoru Miyano. 152-163 [doi]
- Influence of Network Topology and Data Collection on Network InferenceV. Anne Smith, Erich D. Jarvis, Alexander J. Hartemink. 164-175 [doi]
- Informatics Approaches in Structural Genomics - Session IntroductionSean D. Mooney, Patricia C. Babbitt. 176-179 [doi]
- Simultaneous Sequence Alignment and Tree Construction Using Hidden Markov ModelsRobert C. Edgar, Kimmen Sjölander. 180-191 [doi]
- Towards Discovering Structural Signatures of Protein Folds Based on Logical Hidden Markov ModelsKristian Kersting, Tapani Raiko, Stefan Kramer, Luc De Raedt. 192-203 [doi]
- Automated Construction of Structural Motifs for Predicting Functional Sites on Protein StructuresMike P. Liang, Douglas L. Brutlag, Russ B. Altman. 204-215 [doi]
- Identifying Structural Motifs in ProteinsRohit Singh, Mitul Saha. 228-239 [doi]
- A Path Planning-Based Study of Protein Folding with a Case Study of Hairpin Formation in Protein G and LGuang Song, Shawna L. Thomas, Ken A. Dill, J. Martin Scholtz, Nancy M. Amato. 240-251 [doi]
- Profile-Profile Alignment: A Powerful Tool for Protein Structure PredictionNiklas von Öhsen, Ingolf Sommer, Ralf Zimmer. 252-263 [doi]
- Protein Threading by Linear ProgrammingJinbo Xu, Ming Li, Guo-Hui Lin, Dongsup Kim, Ying Xu. 264-275 [doi]
- Genome-wide Analysis and Comparative Genomics - Session IntroductionLiping Wei, Inna Dubchak, Victor V. Solovyev. 276-278 [doi]
- Towards Identifying Lateral Gene Transfer EventsLouigi Addario-Berry, Michael T. Hallett, Jens Lagergren. 279-290 [doi]
- Whole Genome Human/Mouse Phylogenetic Footprinting of Potential Transcription Regulatory SignalsEvgeny Cheremushkin, Alexander E. Kel. 291-302 [doi]
- MAP: Searching Large Genome DatabasesTamer Kahveci, Ambuj K. Singh. 303-314 [doi]
- Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction MethodsLuay Nakhleh, Jerry Sun, Tandy Warnow, C. Randal Linder, Bernard M. E. Moret, Anna Tholse. 315-326 [doi]
- Identification of Regulatory Binding Sites Using Minimum Spanning TreesVictor Olman, Dong Xu, Ying Xu. 327-338 [doi]
- Intrasplicing - Analysis of Long Intron SequencesSascha Ott, Yoshinori Tamada, Hideo Bannai, Kenta Nakai, Satoru Miyano. 339-350 [doi]
- Trajectory Clustering: A Non-Parametric Method for Grouping Gene Expression Time Courses with Applications to Mammary DevelopmentTzu L. Phang, Margaret C. Neville, Michael Rudolph, Lawrence Hunter. 351-362 [doi]
- Algorithms for Multiple Genome Rearrangement by Signed ReversalsShiquan Wu, Xun Gu. 363-374 [doi]
- DIGIT: A Novel Gene Finding Program by Combining Gene-FindersTetsushi Yada, Yasushi Totoki, Y. Takaeda, Yasubumi Sakaki, Toshihisa Takagi. 375-387 [doi]
- Linking Biomedical Language, Information and Knowledge - Session IntroductionLynette Hirschman, Carol Friedman, Robin McEntire, Cathy H. Wu. 388-390 [doi]
- Evaluation of the Vector Space Representation in Text-Based Gene ClusteringPatrick Glenisson, Peter Antal, Janick Mathys, Yves Moreau, Bart De Moor. 391-402 [doi]
- Playing Biology s Name Game: Identifying Protein Names in Scientific TextDaniel Hanisch, Juliane Fluck, Heinz-Theodor Mevissen, Ralf Zimmer. 403-414 [doi]
- Mining Terminological Knowledge in Large Biomedical CorporaHongfang Liu, Carol Friedman. 415-426 [doi]
- A Simple Algorithm for Identifying Abbreviation Definitions in Biomedical TextAriel S. Schwartz, Marti A. Hearst. 451-462 [doi]
- Human Genome Variation: Haplotypes, Linkage Disequilibrium, and Populations - Session IntroductionFrancisco M. de la Vega, Kenneth K. Kidd, Isaac S. Kohane. 463-465 [doi]
- Selection of Minimum Subsets of Single Nucleotide Polymorphisms to Capture Haplotype Block DiversityHadar I. Avi-Itzhak, Xiaoping Su, Francisco M. de la Vega. 466-477 [doi]
- On the Power to Detect SNP/Phenotype Association in Candidate Quantitative Trait Loci Genomic Regions: A Simulation StudyJosep M. Comeron, Martin Kreitman, Francisco M. de la Vega. 478-489 [doi]
- Errors and Linkage Disequilibrium Interact Multiplicatively When Computing Sample Sizes for Genetic Case-Control Association StudiesDerek Gordon, Mark A. Levenstien, Stephen J. Finch, Jürg Ott. 490-501 [doi]
- An MDL Method for Finding Haplotype Blocks and for Estimating the Strength of Haplotype Block BoundariesMikko Koivisto, Markus Perola, T. Varilo, W. Hennah, J. Ekelund, Margus Lukk, L. Peltonen, Esko Ukkonen, Heikki Mannila. 502-513 [doi]
- PyPop: A Software Framework for Population Genomics: Analyzing Large-Scale Multi-Locus Genotype DataAlex Lancaster, Mark P. Nelson, Diogo Meyer, Richard M. Single, Glenys Thomson. 514-525 [doi]
- SNP Analysis and Presentation in the Pharmacogenetics of Membrane Transporters ProjectDoug Stryke, Conrad C. Huang, Michiko Kawamoto, Susan J. Johns, Elaine J. Carlson, Joseph A. Deyoung, Maya K. Leabman, Ira Herskowitz, Kathleen M. Giacomini, Thomas E. Ferrin. 535-547 [doi]
- Methods for Analysis and Visualization of SNP Genotype Data for Complex DiseasesAnna Tsalenko, Amir Ben-Dor, Nancy Cox, Zohar Yakhini. 548-561 [doi]
- Functional Discrimination of Gene Expression Patterns in Terms of the Gene OntologyLiviu Badea. 565-576 [doi]
- Towards a Broad-Coverage Biomedical Ontology Based on Description LogicsUdo Hahn, Stefan Schulz. 577-588 [doi]
- Semantic Similarity Measures as Tools for Exploring the Gene OntologyPhillip W. Lord, Robert D. Stevens, Andy Brass, Carole A. Goble. 601-612 [doi]
- Linking Molecular Imaging Terminology to the Gene Ontology (GO)P. Karina Tulipano, William S. Millar, James J. Cimino. 613-623 [doi]
- A Methodology to Migrate the Gene Ontology to a Description Logic Environment Using DAML+OILChris Wroe, Robert Stevens, Carole A. Goble, Michael Ashburner. 624-635 [doi]
- Special Paper - IntroductionRuss B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein. 636-637 [doi]