1. CSB 2002: Stanford, CA, USA
1st IEEE Computer Society Bioinformatics Conference (CSB 2002), 14-16 August 2002, Stanford, CA, USA. IEEE Computer Society 2002 ISBN 0-7695-1653-X
Invited Talk
- Dan Gusfield: Suffix Trees (and Relatives) Come of Age in Bioinformatics. 3
- Steven E. Brenner: Genome Annotation and Protein Structure. 4
- Michele Markstein, Angela Stathopoulos, Vicky Markstein, Peter W. Markstein, Naoe Harafuji, Dave Keys, Byung-in Lee, Paul Richardson, Dan Rokshar, Mike Levine: Decoding Noncoding Regulatory DNAs in Metazoan Genomes. 5
Phylogenetics
- Enrico Pontelli, Desh Ranjan, Brook Milligan, Gopal Gupta: F-LOG: A Domain Specific Language for Solving Phylogenetic Inference Problems. 9-20
- Alexandros Stamatakis, Thomas Ludwig, Harald Meier, Marty J. Wolf: AxML: A Fast Program for Sequential and Parallel Phylogenetic Tree Calculations Based on the Maximum Likelihood Method. 21-
Motif Finding
- Huimin Xie, Bailin Hao: Visualization of K -Tuple Distribution in Procaryote Complete Genomes and Their Randomized Counterparts. 31-42
- Jun Ogasawara, Shinichi Morishita: Fast and Sensitive Algorithm for Aligning ESTs to Human Genome. 43-53
- Sven Rahmann: Rapid Large-Scale Oligonucleotide Selection for Microarrays. 54-63
- Suchendra M. Bhandarkar, Jonathan Arnold: Parallel Monte Carlo Methods for Physical Mapping of Chromosones. 64-
Genotype-Phenotype
- Klaus Seidl: PheGe, the Platform for Exploring Genotype-Phenotype Relations on Cellular and Organism Level. 79-86
- Masazumi Takahashi, Fumihiko Matsuda, Nino Margetic, Mark G. Lathrop: Automated Identification of Single Nucleotide Polymorphisms from Sequencing Data. 87-
Database Mining
- Mathew J. Palakal, Matthew J. Stephens, Snehasis Mukhopadhyay, Rajeev R. Raje, Simon Rhodes: A Multi-Level Text Mining Method to Extract Biological Relationships. 97-108
- Lada A. Adamic, Dennis M. Wilkinson, Bernardo A. Huberman, Eytan Adar: A Literature Based Method for Identifying Gene-Disease Connections. 109-117
- Ann E. Loraine, Gregg A. Helt, Melissa S. Cline, Michael A. Siani-Rose: Protein-Based Analysis of Alternative Splicing in the Human Genome. 118-
Comparative Genomics
- Chuan 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: Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment. 127-137
Biological Networks
- Tetsuya Kobayashi, Luonan Chen, Kazuyuki Aihara: Design of Genetic Switches with Only Positive Feedback Loops. 151-
Proteomics
- Guo-Hui Lin, Dong Xu, Zhi-Zhong Chen, Tao Jiang, Jianjun Wen, Ying Xu: An Efficient Branch-and-Bound Algorithm for the Assignment of Protein Backbone NMR Peaks. 165-174
- Alessandro Vullo, Paolo Frasconi: A Bi-Recursive Neural Network Architecture for the Prediction of Protein Coarse Contact Maps. 187-196
- Minghua Deng, Kui Zhang, Shipra Mehta, Ting Chen, Fengzhu Sun: Prediction of Protein Function Using Protein-Protein Interaction Data. 197-206
- Jiong Yang, Wei Wang, Yi Xia, Philip S. Yu: Accelerating Approximate Subsequence Search on Large Protein Sequence Databases. 207-
Gene Expression
- Seiya Imoto, SunYong Kim, Takao Goto, Sachiyo Aburatani, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano: Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network. 219-227
- Lorie Dudoignon, Eric Glémet, Hendrik Cornelis Heus, Mathieu Raffinot: High Similarity Sequence Comparison in Clustering Large Sequence Databases. 228-236
- Christopher James Langmead, C. Robertson McClung, Bruce Randall Donald: A Maximum Entropy Algorithm for Rhythmic Analysis of Genome-Wide Expression Patterns. 237-245
- Jia Li, Hongyuan Zha: Simultaneous Classification and Feature Clustering Using Discriminant Vector Quantization with Applications to Microarray Data Analysis. 246-255
- Haixun Wang, Chang-Shing Perng, Wei Fan, Philip S. Yu: An Index Structure for Pattern Similarity Searching in DNA Microarray Dat. 256-267
- Yujing Zeng, Jianshan Tang, Javier Garcia-Frias, Guang R. Gao: An Adaptive Meta-Clustering Approach: Combining the Information from Different Clustering Results. 276-
Computer Science and Biology
- Shahid H. Bokhari, Matthew A. Glaser, Harry F. Jordan, Yves Lansac, Jon R. Sauer, Bart Van Zeghbroeck: Parallelizing a DNA Simulation Code for the Cray MTA-2. 291-302
- Donald A. Adjeroh, Yong Zhang, Amar Mukherjee, Matt Powell, Tim Bell: DNA Sequence Compression Using the Burrows-Wheeler Transform. 303-313
- Yumi Kawazoe, Toshikazu Shiba, Masahito Yamamoto, Azuma Ohuchi: A Security System for Personal Genome Information at DNA Level. 314-320
Poster Abstracts
- Shoko Miyake, Yukako Tohsato, Hideo Matsuda: An Application of a Pathway Alignment Method to Comparative Analysis between Genome and Pathways. 329-329
- Rishi Khan, Yujing Zeng, Javier Garcia-Frias, Guang R. Gao: A Bayesian Modeling Framework for Genetic Regulation. 330-332
- Daisuke Ogino, Shiro Mori, Masato Nose, Hideki Sawada: Complexity and Application of Pedigree Analysis Programme GTree. 333-335
- Luonan Chen, Tetsuya Kobayashi, Kazuyuki Aihara: Designing Oscillators in Synthetic Gene Networks Based on Multi-Scale Dynamics. 336
- Ryan T. Koehler, Nicolas Peyret: Distributions of Free Energy, Melting Temperature, and Hybridization Propensity for Genomic DNA Oligomers. 337
- Conrad Shyu, James A. Foster, Larry J. Forney: Electronic Polymerase Chain Reaction (EPCR) Search Algorithm. 338
- Marilyn 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: GeneCards? 2002: An Evolving Human Gene Compendium. 339
- Veerasamy Ravichandran, Jiri Vondrásek, Gary Gilliland, T. N. Bhat, Alexander Wlodawer: HIV Protease Structural Database. 340
- Conrad Shyu, James A. Foster, K. X. Liao, S. J. Bent, K. Sale, Larry J. Forney, Terence Soule: MiCA: Web-Based Computational Tools for the Analysis of Microbial Community Structure and Compisition Based on T-RFLP of 16S rRNA Gene. 341
- Shigeto Seno, Reiji Teramoto, Hideo Matsuda: P-quasi Complete Linkage Analysis for Gene-Expression Data. 342
- Dianjing Guo, Xingjing Li, Aejaaz Kamal, Olga Brazhnik, Pedro Mendes: A Reference Database for Medicago Truncatula Genes, Protiens, and Metabolites. 343
- Mashilamani Sambasivam: Selective Tree Growing: A Deterministic Constant-Space Linear-Time Algorithm for Pattern Discovery and for Computing Multiple Sequence Alignment. 344
- Nobuyuki Kawagashira, Yasuhiro Ohtomo, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi: Wavelet Profiles: Their Application in Oryza sativa DNA Sequence Analysis. 345-346
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