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ORCID8. PSB 2003: Lihue, Hawaii, USA
- Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein:
Proceedings of the 8th Pacific Symposium on Biocomputing, PSB 2003, Lihue, Hawaii, USA, January 3-7, 2003. 2003 - Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein:
Preface.
Gene Regulation
- Serafim Batzoglou, Lior Pachter:
Gene Regulation - Session Introduction. 3-4 - Daniel P. Berrar, C. Stephen Downes, Werner Dubitzky:
Multiclass Cancer Classification Using Gene Expression Profiling and Probabilistic Neural Networks. 5-16 - Michiel J. L. de Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano:
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations. 17-28 - Eleazar Eskin, Uri Keich, Mikhail S. Gelfand, Pavel A. Pevzner:
Genome-Wide Analysis of Bacterial Promoter Regions. 29-40 - R. Ganesh, Deborah A. Siegele, Thomas R. Ioerger:
MOPAC: MOtif Finding by Preprocessing and Agglomerative Clustering from Microarrays. 41-52 - Jochen Jaeger, Rimli Sengupta, Walter L. Ruzzo:
Improved Gene Selection for Classification of Microarrays. 53-64 - Hongzhe Li, Yihui Luan:
Kernel Cox Regression Models for Linking Gene Expression Profiles to Censored Survival Data. 65-76 - T. M. Murali, Simon Kasif:
Extracting Conserved Gene Expression Motifs from Gene Expression Data. 77-88 - Eran Segal, Alexis J. Battle, Daphne Koller:
Decomposing Gene Expression into Cellular Processes. 89-100
Genome, Pathway, and Interaction Bioinformatics
- Peter D. Karp, Eric P. Neumann, Alexander J. Hartemink, Pedro Romero:
Genome, Pathway, and Interaction Bioinformatics - Session Introduction. 101-103 - Ryan E. Altenbaugh, Kenneth J. Kauffman, Jeremy S. Edwards:
Suitability and Utility of Computational Analysis Tools: Characterization of Erythrocyte Parameter Variation. 104-115 - Marco Antoniotti, F. Park, Alberto Policriti, Nadia Ugel, Bud Mishra:
Foundations of a Query and Simulation System for the Modeling of Biochemical and Biological Processes. 116-127 - Lonnie Chrisman, Pat Langley, Stephen D. Bay:
Incorporating Biological Knowledge into Evaluation of Causal Regulatory Hypotheses. 128-139 - Minghua Deng, Fengzhu Sun, Ting Chen:
Assessment of the reliability of protein-protein interactions and protein function prediction. 140-151 - Hiroshi Matsuno, Ryutaro Murakani, Rie Yamane, Naoyuki Yamasaki, Sachie Fujita, Haruka Yoshimori, Satoru Miyano:
Boundary Formation by Notch Signaling in Drosophila Multicellular Systems: Experimental Observations and Gene Network Modeling by Genomic Object Net. 152-163 - V. Anne Smith, Erich D. Jarvis, Alexander J. Hartemink:
Influence of Network Topology and Data Collection on Network Inference. 164-175
Informatics Approaches in Structural Genomics
- Sean D. Mooney, Patricia C. Babbitt:
Informatics Approaches in Structural Genomics - Session Introduction. 176-179 - Robert C. Edgar, Kimmen Sjölander:
Simultaneous Sequence Alignment and Tree Construction Using Hidden Markov Models. 180-191 - Kristian Kersting, Tapani Raiko, Stefan Kramer, Luc De Raedt:
Towards Discovering Structural Signatures of Protein Folds Based on Logical Hidden Markov Models. 192-203 - Mike P. Liang, Douglas L. Brutlag, Russ B. Altman:
Automated Construction of Structural Motifs for Predicting Functional Sites on Protein Structures. 204-215 - Predrag Radivojac, Zoran Obradovic, Celeste J. Brown, A. Keith Dunker:
Prediction of Boundaries Between Intrinsically Ordered and Disordered Protein Regions. 216-227 - Rohit Singh, Mitul Saha:
Identifying Structural Motifs in Proteins. 228-239 - Guang Song, Shawna L. Thomas, Ken A. Dill, J. Martin Scholtz, Nancy M. Amato:
A Path Planning-Based Study of Protein Folding with a Case Study of Hairpin Formation in Protein G and L. 240-251 - Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer:
Profile-Profile Alignment: A Powerful Tool for Protein Structure Prediction. 252-263 - Jinbo Xu, Ming Li, Guo-Hui Lin, Dongsup Kim, Ying Xu:
Protein Threading by Linear Programming. 264-275
Genome-wide Analysis and Comparative Genomics
- Liping Wei, Inna Dubchak, Victor V. Solovyev:
Genome-wide Analysis and Comparative Genomics - Session Introduction. 276-278 - Louigi Addario-Berry, Michael T. Hallett, Jens Lagergren:
Towards Identifying Lateral Gene Transfer Events. 279-290 - Evgeny Cheremushkin, Alexander E. Kel:
Whole Genome Human/Mouse Phylogenetic Footprinting of Potential Transcription Regulatory Signals. 291-302 - Tamer Kahveci, Ambuj K. Singh:
MAP: Searching Large Genome Databases. 303-314 - Luay Nakhleh, Jerry Sun, Tandy J. Warnow, C. Randal Linder, Bernard M. E. Moret, Anna Tholse:
Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. 315-326 - Victor Olman, Dong Xu, Ying Xu:
Identification of Regulatory Binding Sites Using Minimum Spanning Trees. 327-338 - Sascha Ott, Yoshinori Tamada, Hideo Bannai, Kenta Nakai, Satoru Miyano:
Intrasplicing - Analysis of Long Intron Sequences. 339-350 - Tzu L. Phang, Margaret C. Neville, Michael Rudolph, Lawrence Hunter:
Trajectory Clustering: A Non-Parametric Method for Grouping Gene Expression Time Courses with Applications to Mammary Development. 351-362 - Shiquan Wu, Xun Gu:
Algorithms for Multiple Genome Rearrangement by Signed Reversals. 363-374 - Tetsushi Yada, Yasushi Totoki, Y. Takaeda, Yasubumi Sakaki, Toshihisa Takagi:
DIGIT: A Novel Gene Finding Program by Combining Gene-Finders. 375-387
Linking Biomedical Language, Information and Knowledge
- Lynette Hirschman, Carol Friedman, Robin McEntire, Cathy H. Wu:
Linking Biomedical Language, Information and Knowledge - Session Introduction. 388-390 - Patrick Glenisson, Peter Antal, Janick Mathys, Yves Moreau, Bart De Moor:
Evaluation of the Vector Space Representation in Text-Based Gene Clustering. 391-402 - Daniel Hanisch, Juliane Fluck, Heinz-Theodor Mevissen, Ralf Zimmer:
Playing Biology's Name Game: Identifying Protein Names in Scientific Text. 403-414 - Hongfang Liu, Carol Friedman:
Mining Terminological Knowledge in Large Biomedical Corpora. 415-426 - Meenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker:
A Biological Named Entity Recognizer. - Indra Neil Sarkar, Michael N. Cantor, R. Gelman, Frank W. Hartel, Yves A. Lussier:
Linking Biomedical Language Information and Knowledge Resources in the 21st Century: GO and UMLS. 427-450 - Ariel S. Schwartz, Marti A. Hearst:
A Simple Algorithm for Identifying Abbreviation Definitions in Biomedical Text. 451-462
Human Genome Variation: Haplotypes, Linkage Disequilibrium, and Populations
- Francisco M. de la Vega, Kenneth K. Kidd, Isaac S. Kohane:
Human Genome Variation: Haplotypes, Linkage Disequilibrium, and Populations - Session Introduction. 463-465 - Hadar I. Avi-Itzhak, Xiaoping Su, Francisco M. de la Vega:
Selection of Minimum Subsets of Single Nucleotide Polymorphisms to Capture Haplotype Block Diversity. 466-477 - Josep M. Comeron, Martin Kreitman, Francisco M. de la Vega:
On the Power to Detect SNP/Phenotype Association in Candidate Quantitative Trait Loci Genomic Regions: A Simulation Study. 478-489 - Derek Gordon, Mark A. Levenstien, Stephen J. Finch, Jürg Ott:
Errors and Linkage Disequilibrium Interact Multiplicatively When Computing Sample Sizes for Genetic Case-Control Association Studies. 490-501 - Mikko Koivisto, Markus Perola, T. Varilo, W. Hennah, J. Ekelund, Margus Lukk, L. Peltonen, Esko Ukkonen, Heikki Mannila:
An MDL Method for Finding Haplotype Blocks and for Estimating the Strength of Haplotype Block Boundaries. 502-513 - Alex Lancaster, Mark P. Nelson, Diogo Meyer, Richard M. Single, Glenys Thomson:
PyPop: A Software Framework for Population Genomics: Analyzing Large-Scale Multi-Locus Genotype Data. 514-525 - Bruce Rannala, Jeff P. Reeve:
Joint Bayesian Estimation of Mutation Location and Age Using Linkage Disequilibrium. 526-534 - Doug 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:
SNP Analysis and Presentation in the Pharmacogenetics of Membrane Transporters Project. 535-547 - Anya Tsalenko, Amir Ben-Dor, Nancy Cox, Zohar Yakhini:
Methods for Analysis and Visualization of SNP Genotype Data for Complex Diseases. 548-561
Biomedical Ontologies
- Olivier Bodenreider, Joyce A. Mitchell, Alexa T. McCray:
Biomedical Ontologies - Session Introduction. 562-564 - Liviu Badea:
Functional Discrimination of Gene Expression Patterns in Terms of the Gene Ontology. 565-576 - Udo Hahn, Stefan Schulz:
Towards a Broad-Coverage Biomedical Ontology Based on Description Logics. 577-588 - Patrick Lambrix, Anna Edberg:
Evaluation of Ontology Merging Tools in Bioinformatics. 589-600 - Phillip W. Lord, Robert D. Stevens, Andy Brass, Carole A. Goble:
Semantic Similarity Measures as Tools for Exploring the Gene Ontology. 601-612 - P. Karina Tulipano, William S. Millar, James J. Cimino:
Linking Molecular Imaging Terminology to the Gene Ontology (GO). 613-623 - Chris Wroe, Robert Stevens, Carole A. Goble, Michael Ashburner:
A Methodology to Migrate the Gene Ontology to a Description Logic Environment Using DAML+OIL. 624-635
Special Paper
- Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein:
Special Paper - Introduction. 636-637 - Howard D. Cash, Jonathan W. Hoyle, Amy J. Sutton:
Development Under Extreme Conditions: Forensic Bioinformatics in the Wake of the World Trade Center Disaster. Pacific Symposium on Biocomputing 2003: 638-653
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