8. PSB 2003:
Lihue,
Hawaii,
USA
Proceedings of the 8th Pacific Symposium on Biocomputing (PSB 2003),
Lihue,
Hawaii,
USA,
January 3-7,
2003
Gene Regulation
- Serafim Batzoglou, Lior Pachter:
Gene Regulation - Session Introduction.
3-4
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- Daniel P. Berrar, C. Stephen Downes, Werner Dubitzky:
Multiclass Cancer Classification Using Gene Expression Profiling and Probabilistic Neural Networks.
5-16
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- 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
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- Eleazar Eskin, Uri Keich, Mikhail S. Gelfand, Pavel A. Pevzner:
Genome-Wide Analysis of Bacterial Promoter Regions.
29-40
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- R. Ganesh, Deborah A. Siegele, Thomas R. Ioerger:
MOPAC: MOtif Finding by Preprocessing and Agglomerative Clustering from Microarrays.
41-52
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- J. Jaeger, Rimli Sengupta, Walter L. Ruzzo:
Improved Gene Selection for Classification of Microarrays.
53-64
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- Hongzhe Li, Yihui Luan:
Kernel Cox Regression Models for Linking Gene Expression Profiles to Censored Survival Data.
65-76
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- T. M. Murali, Simon Kasif:
Extracting Conserved Gene Expression Motifs from Gene Expression Data.
77-88
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- Eran Segal, Alexis Battle, Daphne Koller:
Decomposing Gene Expression into Cellular Processes.
89-100
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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
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- Ryan E. Altenbaugh, Kenneth J. Kauffman, Jeremy S. Edwards:
Suitability and Utility of Computational Analysis Tools: Characterization of Erythrocyte Parameter Variation.
104-115
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- 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
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- Lonnie Chrisman, Pat Langley, Stephen D. Bay:
Incorporating Biological Knowledge into Evaluation of Causal Regulatory Hypotheses.
128-139
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- Minghua Deng, Fengzhu Sun, Ting Chen:
Assessment of the reliability of protein-protein interactions and protein function prediction.
140-151
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- 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
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- V. Anne Smith, Erich D. Jarvis, Alexander J. Hartemink:
Influence of Network Topology and Data Collection on Network Inference.
164-175
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Informatics Approaches in Structural Genomics
- Sean D. Mooney, Patricia C. Babbitt:
Informatics Approaches in Structural Genomics - Session Introduction.
176-179
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- Robert C. Edgar, Kimmen Sjölander:
Simultaneous Sequence Alignment and Tree Construction Using Hidden Markov Models.
180-191
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- Kristian Kersting, Tapani Raiko, Stefan Kramer, Luc De Raedt:
Towards Discovering Structural Signatures of Protein Folds Based on Logical Hidden Markov Models.
192-203
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- Mike P. Liang, Douglas L. Brutlag, Russ B. Altman:
Automated Construction of Structural Motifs for Predicting Functional Sites on Protein Structures.
204-215
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- Predrag Radivojac, Zoran Obradovic, Celeste J. Brown, A. Keith Dunker:
Prediction of Boundaries Between Intrinsically Ordered and Disordered Protein Regions.
216-227
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- Rohit Singh, Mitul Saha:
Identifying Structural Motifs in Proteins.
228-239
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- 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
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- Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer:
Profile-Profile Alignment: A Powerful Tool for Protein Structure Prediction.
252-263
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- Jinbo Xu, Ming Li, Guo-Hui Lin, Dongsup Kim, Ying Xu:
Protein Threading by Linear Programming.
264-275
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Genome-wide Analysis and Comparative Genomics
- Liping Wei, Inna Dubchak, Victor V. Solovyev:
Genome-wide Analysis and Comparative Genomics - Session Introduction.
276-278
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- Louigi Addario-Berry, Michael T. Hallett, Jens Lagergren:
Towards Identifying Lateral Gene Transfer Events.
279-290
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- Evgeny Cheremushkin, Alexander E. Kel:
Whole Genome Human/Mouse Phylogenetic Footprinting of Potential Transcription Regulatory Signals.
291-302
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- Tamer Kahveci, Ambuj K. Singh:
MAP: Searching Large Genome Databases.
303-314
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- Luay Nakhleh, Jerry Sun, Tandy Warnow, C. Randal Linder, Bernard M. E. Moret, Anna Tholse:
Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods.
315-326
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- Victor Olman, Dong Xu, Ying Xu:
Identification of Regulatory Binding Sites Using Minimum Spanning Trees.
327-338
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- Sascha Ott, Yoshinori Tamada, Hideo Bannai, Kenta Nakai, Satoru Miyano:
Intrasplicing - Analysis of Long Intron Sequences.
339-350
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- 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
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- Shiquan Wu, Xun Gu:
Algorithms for Multiple Genome Rearrangement by Signed Reversals.
363-374
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- Tetsushi Yada, Yasushi Totoki, Y. Takaeda, Yasubumi Sakaki, Toshihisa Takagi:
DIGIT: A Novel Gene Finding Program by Combining Gene-Finders.
375-387
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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
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- Patrick Glenisson, Peter Antal, Janick Mathys, Yves Moreau, Bart De Moor:
Evaluation of the Vector Space Representation in Text-Based Gene Clustering.
391-402
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- Daniel Hanisch, Juliane Fluck, Heinz-Theodor Mevissen, Ralf Zimmer:
Playing Biology's Name Game: Identifying Protein Names in Scientific Text.
403-414
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- Hongfang Liu, Carol Friedman:
Mining Terminological Knowledge in Large Biomedical Corpora.
415-426
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- Meenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker:
A Biological Named Entity Recognizer.
Electronic Edition (link) BibTeX
- Indra Neil Sarkar, M. 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
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- Ariel S. Schwartz, Marti A. Hearst:
A Simple Algorithm for Identifying Abbreviation Definitions in Biomedical Text.
451-462
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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
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- 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
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- 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
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- 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
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- Mikko Koivisto, Markus Perola, T. Varilo, W. Hennah, J. Ekelund, M. 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
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- 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
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- Bruce Rannala, Jeff P. Reeve:
Joint Bayesian Estimation of Mutation Location and Age Using Linkage Disequilibrium.
526-534
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- 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
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- Anna Tsalenko, Amir Ben-Dor, Nancy Cox, Zohar Yakhini:
Methods for Analysis and Visualization of SNP Genotype Data for Complex Diseases.
548-561
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Biomedical Ontologies
- Olivier Bodenreider, Joyce A. Mitchell, Alexa T. McCray:
Biomedical Ontologies - Session Introduction.
562-564
Electronic Edition (link) BibTeX
- Liviu Badea:
Functional Discrimination of Gene Expression Patterns in Terms of the Gene Ontology.
565-576
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- Udo Hahn, Stefan Schulz:
Towards a Broad-Coverage Biomedical Ontology Based on Description Logics.
577-588
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- Patrick Lambrix, Anna Edberg:
Evaluation of Ontology Merging Tools in Bioinformatics.
589-600
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- Phillip W. Lord, Robert D. Stevens, Andy Brass, Carole A. Goble:
Semantic Similarity Measures as Tools for Exploring the Gene Ontology.
601-612
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- P. Karina Tulipano, William S. Millar, James J. Cimino:
Linking Molecular Imaging Terminology to the Gene Ontology (GO).
613-623
Electronic Edition (link) BibTeX
- 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
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Special Paper
Copyright © Sat May 16 23:35:19 2009
by Michael Ley (ley@uni-trier.de)
