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ORCID2. CSB 2003: Stanford, CA, USA
- 2nd IEEE Computer Society Bioinformatics Conference, CSB 2003, Stanford, CA, USA, August 11-14, 2003. IEEE Computer Society 2003, ISBN 0-7695-2000-6
Keynote Addresses
- Marvin Frazier, David Thomassen, Aristides Patrinos, Gary Johnson, Carl Edward Oliver, Edward C. Uberbacher:
Stepping Up the Pace of Discovery: the Genomes to Life Program. 2-9 - Richard M. Karp:
The Role of Algorithmic Research in Computational Genomics. 10-12
Invited Speaker
- Philip E. Bourne:
High Performance Computational Biology - Past Progress and Future Promise. 13 - Jehoshua Bruck
:
Bridging Paradigm Gaps Between Biology and Engineering. 14 - Jean-Michel Claverie:
Microbial Functional Genomics: Pulling Together a Variety of Approaches and Concepts. 15 - Eric H. Davidson:
The Sea Urchin Endomesoderm Gene Regulatory Network, an Encoded Logic Map for Early Development. 16 - Liliana Florea, Bjarni V. Halldórsson, Oliver Kohlbacher, Russell Schwartz, Stephen Hoffman, Sorin Istrail:
Epitope Prediction Algorithms for Peptide based Vaccine Design. 17-26 - Peter D. Karp:
Pathway Bioinformatics. 27 - Jun S. Liu:
BPPS: An Algorithm for Analyzing Protein Sequence Alignments. 28 - Michael S. Waterman, Yu Zhang:
Eulerian Path Methods for Multiple Sequence Alignment. 29 - Stephen T. C. Wong:
Integrating Bioinformatics Advances into Disease Management Systems to Improve Quality of Care. 30
Genomes to Life
- Edward C. Uberbacher, David Thomassen, Aristides Patrinos, Gary Johnson, Carl Edward Oliver, Marvin Frazier:
Computing for the DOE Genomes to Life Program. 32 - Adam P. Arkin:
Motifs and Modules in Cellular Signal Processing: Applications to Microbial Stress Response Pathways. 33 - Grant Heffelfinger:
An Overview of the Sandia National Laboratories Genomes to Life Project, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling". 34 - Derek Lovley:
Analysis of the Genetic Potential and Gene Expression of Microbial Communities Involved in the In Situ Bioremediation of Uranium and Harvesting ElectricalEnergy from Organic Matter. 35-37
Microarray Data Analysis
- Andres Figueroa, James Borneman, Tao Jiang:
Clustering Binary Fingerprint Vectors with Missing Values for DNA Array Data Analysis. 38-47 - Tanveer Fathima Syeda-Mahmood:
Clustering Time-Varying Gene Expression Profiles using Scale-space Signals. 48-56 - Sven Rahmann:
Fast and Sensitive Probe Selection for DNA Chips Using Jumps in Matching Statistics. 57-64 - Wing-Kin Sung, Wah-Heng Lee:
Fast and Accurate Probe Selection Algorithm for Large Genomes. 65-74 - Xintao Wei, David N. Kuhn, Giri Narasimhan:
Degenerate Primer Design via Clustering. 75-83 - Alexander Schliep, David C. Torney, Sven Rahmann:
Group Testing With DNA Chips: Generating Designs and Decoding Experiments. 84-93
Pathways, Networks, and Systems Biology
- Nigam Shah, Jorge Lepre, Yuhai Tu, Gustavo Stolovitzky:
Can We Identify Cellular Pathways Implicated in Cancer Using Gene Expression Data? 94-103 - Seiya Imoto, Tomoyuki Higuchi, Takao Goto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano:
Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks. 104-113 - Simone Bentolila:
Two operative concepts for the post-genomic era: the "me'moire vive" of the cell and a molecular algebra. 114-123
Biomedical Research and Visualization
- Dennis L. Chao, Miles P. Davenport, Stephanie Forrest, Alan S. Perelson:
Stochastic Stage-structured Modeling of the Adaptive Immune System. 124-131 - Shuo Liu, Steve Lin, Mark Woon, Teri E. Klein, Russ B. Altman:
A Personalized and Automated dbSNP Surveillance System. 132-136 - Li Zhang, Aidong Zhang, Murali Ramanathan:
Fourier Harmonic Approach for Visualizing Temporal Patterns of Gene Expression Data. 137-147 - Orhan Çamoglu, Tamer Kahveci, Ambuj K. Singh:
Towards Index-based Similarity Search for Protein Structure Databases. 148-158 - Matthias Höchsmann, Thomas Töller, Robert Giegerich, Stefan Kurtz:
Local Similarity in RNA Secondary Structures. 159-168 - Tolga Can, Yuan-Fang Wang:
CTSS: A Robust and Efficient Method for Protein Structure Alignment Based on Local Geometrical and Biological Feature. 169-179 - Werner G. Krebs, Philip E. Bourne:
Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. 180-189 - Shu-Yun Le, Jih-Hsiang Chen, Jacob V. Maizel:
Statistical Inference for Well-ordered Structures in Nucleotide Sequences. 190-196 - Xiang Wan, Dong Xu, Carolyn M. Slupsky, Guohui Lin:
Automated Protein NMR Resonance Assignments. 197-208 - Christopher James Langmead, Bruce Randall Donald:
3D Structural Homology Detection via Unassigned Residual Dipolar Couplings. 209-219
Data Mining
- Hwanjo Yu, Jiong Yang, Wei Wang, Jiawei Han:
Discovering Compact and Highly Discriminative Features or Feature Combinations of Drug Activities Using Support Vector Machines. 220-228 - Jake Yue Chen, Andrey Y. Sivachenko, Russell Bell, Cornelia Kurschner, Irene Ota, Sudhir Sahasrabudhe:
Initial Large-scale Exploration of Protein-protein Interactions in Human Brain. 229-234 - Gong-Xin Yu, George Ostrouchov, Al Geist, Nagiza F. Samatova:
An SVM-based Algorithm for Identification of Photosynthesis-specific Genome Features. 235-243 - Robert L. Grossman, Pavan Kasturi, Donald Hamelberg, Bing Liu:
Experimental Studies of the Universal Chemical Key (UCK)Algorithm on the NCI Database of Chemical Compounds. 244-250 - Kazuhiro Seki, Javed Mostafa:
A Probabilistic Model for Identifying Protein Names and their Name Boundaries. 251-259
Pattern Recognition
- Shoudan Liang:
cWINNOWER Algorithm for Finding Fuzzy DNA Motifs. 260-265 - Eric P. Xing, Wei Wu, Michael I. Jordan, Richard M. Karp:
LOGOS: a modular Bayesian model for de novo motif detection. 266-276 - Mihaela Zavolan, Nicholas D. Socci, Nikolaus Rajewsky, Terry Gaasterland:
SMASHing regulatory sites in DNA by human. 277-287 - G. Sampath:
A Block Coding Method that Leads to Significantly Lower Entropy Values for the Proteins and Coding Sections of Haemophilus influenzae. 287-293 - Ravi Vijaya Satya, Amar Mukherjee, Udaykumar Ranga:
A Pattern Matching Algorithm for Codon Optimization and CpG Motif-Engineering in DNA Expression Vectors. 294-305 - Russell Schwartz:
Haplotype Motifs: An Algorithmic Approach to Locating Evolutionarily Conserved Patterns in Haploid Sequences. 306-315
Sequence Alignment
- Tomoyuki Yamada, Shinichi Morishita:
Computing Highly Specific and Mismatch Tolerant Oligomers Efficiently. 316-325 - Cinzia Di Pietro, Valentina Di Pietro, Giovanni Emmanuele, Alfredo Ferro, T. Maugeri, E. Modica, Giuseppe Pigola, Alfredo Pulvirenti, Michele Purrello, Marco Ragusa, Marina Scalia, Dennis E. Shasha, Salvo Travali, V. Zimmitti:
ANTICLUSTAL: Multiple Sequence Alignment by Antipole Clustering and Linear Approximate 1-Median Computation. 326-336 - Francis Y. L. Chin, Ngai Lam Ho, Tak Wah Lam, Prudence W. H. Wong, Mee Yee Chan:
Efficient Constrained Multiple Sequence Alignment with Performance Guarantee. 337-346 - Kuen-Pin Wu, Hsin-Nan Lin, Ting-Yi Sung, Wen-Lian Hsu:
A New Similarity Measure among Protein Sequences. 347-352 - Alexandre Tchourbanov, Daniel Quest, Hesham H. Ali, Mark A. Pauley, Robert B. Norgren:
A New Approach for Gene Annotation Using Unambiguous Sequence Joining. 353-362 - Dan Gusfield, Satish Eddhu, Charles H. Langley:
Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. 363-374 - Bailin Hao, Ji Qi:
Prokaryote Phylogeny without Sequence Alignment: From Avoidance Signature to Composition Distance. 375-385
Poster Papers
Data Integration
- Monica Chagoyen, M. Erdem Kurul, Pedro A. de Alarcón, Simone Santini, Bertram Ludäscher, José María Carazo, Amarnath Gupta:
A Semantic Mediation Approach for Problems in Computational Molecular Biology. 386-387 - Barbara A. Eckman, Kerry Deutsch, Marta Janer, Zoé Lacroix, Louiqa Raschid:
A Query Language to Support Scientific Discovery. 388-391
Data Mining
- Zhong-Hui Duan, Louis S. Liou, Ting Shi, Joseph A. DiDonato:
Application of Singular Value Decomposition and Functional Clustering to Analyzing Gene Expression Profiles of Renal Cell Carcinoma. 392-393 - Xin Lu, Wen Zhang, Zhaohui S. Qin, Jun S. Liu:
Statistical Resynchronization and Detection of Periodic Transcripts. 394-395 - George C. Tseng, Wing Hung Wong:
A Method for Tight Clustering: with Application to Microarray. 396-397 - Richard J. Carter:
Riptide: Fast Protein Identification from Mass Spectrometer Data. 398-399 - James H. Graham, C. David Page Jr., Ahmed H. Kamal:
Accelerating the Drug Design Process through Parallel Inductive Logic Programming Data Mining. 400-402 - Mingzhou Song, Stéphane Boissinot, Robert M. Haralick, Ihsin T. Phillips:
Estimating Recombination Rate Distribution by Optimal Quantization. 403-406 - Jane Fridlyand, Antoine Snijders, Dan Pinkel, Donna Albertson, Ajay N. Jain:
Statistical issues in the analysis of the array CGH data. 407-408 - Mark W. Duncan, Kim Fung, Heng Wang, Chia-Yu Yen, Krzysztof J. Cios:
Identification of Contaminants in Proteomics Mass Spectrometry Data. 409-410 - Stephen Osborn, Scot Kennedy, Daniel Chin:
A Flexible Pipeline for Experimental Design, Processing, and Analysis of Microarray Data. 411-412 - Xutao Deng, Hesham H. Ali:
A Computational Approach to Reconstructing Gene Regulatory Networks. 413-414 - Tema Fridman, Robert M. Day, Jane Razumovsbya, Dong Xu, Andrey Gorin:
Probability Profiles - Novel Approach in Tandem Mass Spectrometry De Novo Sequencing. 415-418 - Eric G. Stephan, George Chin Jr., Kyle R. Klicker, Abigail L. Corrigan, Heidi J. Sofia:
A Symbolic Logic Strategy For Mapping Biological Concepts in the HERBE Prototype. 419-420 - Jane Razumovskaya, Victor Olman, Dong Xu, Edward C. Uberbacher, Nathan Verberkmoes, Ying Xu:
A Computational Method for Assessing Peptide-Identification Reliability in Tandem Mass Spectrometry Analysis with SEQUEST. 421-423
Functional Genomics
- Zhangjun Fei, Xuemei Tang, Rob Alba, Paxton Payton, James J. Giovannoni:
Tomato Expression Database (TED) - An Interactive Management Tool for Tomato Expression Profiling Data. 424-425 - Harpreet Kaur Gill:
Oncogenetics Tree Models - An Estimation. 426 - Marilyn Safran, Vered Chalifa-Caspi, Orit Shmueli, Naomi Rosen, Hila Benjamin-Rodrig, Ron Ophir, Itai Yanai, Michael Shmoish, Doron Lancet:
The GeneCardsTM Family of Databases: GeneCards, GeneLoc, GeneNote and GeneAnnot. 427-428 - Taku A. Tokuyasu, Donna Albertson, Dan Pinkel, Ajay N. Jain:
Wavelet Transforms for the Analysis of Microarray Experiments. 429-430 - Bill Martin, Robert M. Horton:
MageBuilder: A Schema Translation Tool for Generating MAGE-ML from Tabular Microarray Data. 431-432 - Wenwu Cui, Jianchang Ning, Ulhas P. Naik, Melinda K. Duncan:
OptiRNai, a Web-based Program to Select siRNA Sequences. 433-434 - Bartosz Wilczynski, Torgeir R. Hvidsten, Andriy Kryshtafovych, Lisa Stubbs, Henryk Jan Komorowski, Krzysztof Fidelis:
A rule-based framework for gene regulation pathways discovery. 435-436 - Qing Dong, Rama Balakrishnan, Gail Binkley, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Robert S. Nash, Laurie Issel-Tarver, Anand Sethuraman, Chandra L. Theesfeld, Shuai Weng, David Botstein, J. Michael Cherry:
Gene Function, Metabolic Pathways and Comparative Genomics in Yeast. 437-438 - Gary Livingston, Xiao Li, Guangyi Li, Liwu Hao, Jianping Zhou:
Using Rule Induction Methods to Analyze Gene Expression Data. 439-441
Genomic Annotation
- Sailu Yellaboina, Prachee Chakhaiyar, Seyed Ehetsham Hasnain, Akash Ranjan:
Computational prediction of DtxR regulon-A Dissection of physiological process controlled by DtxR in Corynebacterium species. 442-443 - Shaun Mahony, Terry J. Smith, James O. McInerney, Aaron Golden:
A New Approach to Gene Prediction Using the Self-Organizing Map. 444-445 - Rong Chen, Hesham H. Ali:
On Gene Prediction by Cross-Species Comparative Sequence Analysis. 446-447 - Victor Olman, Dong Xu, Ying Xu:
CUBIC: Identification of Regulatory Binding Sites Through Data Clustering. 448-449
Genotyping and SNPs
- Yoko Higashi, Hirotaka Higuchi, Takashi Kido, Hirohito Matsumine, Masanori Baba, Toshihiko Morimoto, Masaaki Muramatsu:
SNP Analysis System for Detecting Complex Disease Associated Sites. 450-451 - Takashi Kido, Masanori Baba, Hirohito Matsumine, Yoko Higashi, Hirotaka Higuchi, Masaaki Muramatsu:
Haplotype Pattern Mining & Classification for detecting disease associated Site. 452-455
Molecular Simulation
- Seung Yup Lee, Yoshimi Fujitsuka, Shoji Takada, Do Hyun Kim:
What makes IgG binding domain of protein L fold up to native state: a simulation study with physical oriented energy functions coupled to topology induced terms. 456-457 - Igor Tsukerman:
New Computational Methods for Electrostatics in Macromolecular Simulation. 458-459 - Chengpeng Bi, Craig J. Benham:
The Approximate Algorithm for Analysis of the Strand Separation Transition in Super helical DNA Using Nearest Neighbor Energetics. 460-461 - Kaori Ueno-Noto, Keiko Takano, Miki Hara-Yokoyama:
Substrate Recognition by Enzymes: a Theoretical Study. 462-463 - Peter M. Kasson, Vijay S. Pande:
Computational Simulation of Lipid Bilayer Reorientation at Gaps. 464-467
Phylogeny and Evolution
- Liaofu Luo, Li-Ching Hsieh, Fengmin Ji, Mengwen Jia, H. C. Lee:
Search for Evolution-Related-Oligonucleotides and Conservative Words in rRNA Sequences. 468-469 - Terrence S. T. Mak, Kai-Pui Lam:
High Speed GAML-based Phylogenetic Tree Reconstruction Using HW/SW Codesign. 470-473 - Li-Ching Hsieh, Liaofu Luo, H. C. Lee:
Evidence for Growth of Microbial Genomes by Short Segmental Duplications. 474-475 - Chen Yang, Sami Khuri:
PTC: An Interactive Tool for Phylogenetic Tree Construction. 476-477 - Sören W. Perrey, Heinrich Brinck, Achim Zielesny:
Iterative Rank based Methods for Clustering. 478-479 - Ghislain Bidaut, Karsten Suhre, Jean-Michel Claverie, Michael F. Ochs:
Analysis of Phylogenetic Profiles Using Bayesian Decomposition. 480-481 - Yunfeng Shan, Evangelos E. Milios, Andrew J. Roger, Christian Blouin, Edward Susko:
Automatic Recognition of Regions of Intrinsically Poor Multiple Alignment Using Machine Learning. 482-483 - Jun Huan, Jan F. Prins, Wei Wang, Todd J. Vision:
Reconstruction of Ancestral Gene Order after Segmental Duplication and Gene Loss. 484-485 - Yuhong Wang, John P. Rose, Bi-Cheng Wang, Dawei Lin:
Reconstruction of Ancient Operons From Complete Microbial Genome Sequences. 486-487
Predictive Methods
- Hsiang Chi Huang:
An Evolutionary Approach to Finding Schemas for 3-Class Protein Secondary Structure Prediction. 488-491 - Dechang Chen, Dong Hua, Jaques Reifman, Xiuzhen Cheng:
Gene Selection for Multi-Class Prediction of Microarray Data. 492-495 - Dong Hua, Dechang Chen, Xiuzhen Cheng, Abdou Youssef:
Latent Structure Models for the Analysis of Gene Expression Data. 496-499 - Yoshiharu Hayashi, Katsuyoshi Sakaguchi, Nao Iwata, Masaki Kobayashi:
Molecular Evaluation using Comparative Molecular Interaction Profile Analysis system. 500-501 - Vincent Van Buren, Toshiyuki Yoshikawa, Toshio Hamatani, Minoru S. H. Ko:
Probe Design for Large-Scale Molecular Biology Applications. 502-503 - Xue-wen Chen:
Gene Selection for Cancer Classification Using Bootstrapped Genetic Algorithms and Support Vector Machines. 504-505 - I-Jeng Wang, Christopher P. Diehl, Fernando J. Pineda:
A Statistical Model of Proteolytic Digestion. 506-508 - Jianchang Ning, Charles N. Moore, J. Clare Nelson:
Preliminary Wavelet Analysis of Genomic Sequences. 509-510 - Vojislav Stojkovic, Grace Steele, William Lupton:
Using Easel for Modeling and Simulating the Interactions of Cells in Order to Better Understand the Basics of Biological Processes and to Predict Their Likely Behaviors. 511-516 - Andriy Kryshtafovych, Torgeir R. Hvidsten, Henryk Jan Komorowski, Krzysztof Fidelis:
Fold Recognition Using Sequence Fingerprints of Protein Local Substructures. 517-518 - Jianhua Ruan, Gary D. Stormo, Weixiong Zhang:
An Iterative Loop Matching Approach to the Prediction of RNA Secondary Stru. 519-520 - Hirotoshi Taira, Tomonori Izumitani, Eisaku Maeda, Takeshi Suzuki:
A New Method for Predicting RNA Secondary Structure. 521-522 - Chris H. Q. Ding, Hanchuan Peng:
Minimum Redundancy Feature Selection from Microarray Gene Expression Data. 523-529
Sequence Comparison
- Jianping Zhou, Gary Livingston, Georges G. Grinstein:
Automatic Parameter Selection for Sequence Similarity Search. 530-531 - Fern Y. Hunt, Anthony J. Kearsley, Agnes O'Gallagher:
A Linear Programming Based Algorithm for Multiple Sequence Alignments. 532-533 - Tuan D. Pham:
Alignment-Free Sequence Comparison with Vector Quantization and Hidden Markov Models. 534-535 - Krishna Gopalakrishnan, Kayvan Najarian:
Prediction of Protein Function Using Signal Processing of Biochemical Properties. 536-538 - Shih-Chieh Su, Chia-Hung Yeh, C.-C. Jay Kuo:
Genomic Sequence Analysis Using Gap Sequences and Pattern Filtering. 539-540 - Wojciech Szpankowski, Wenhui Ren, Lukasz Szpankowski:
An Optimal DNA Segmentation Based on the MDL Principle. 541-546