Preface |
Organizing Committee |
Program Committee |
Referees |
Keynote Addresses |
Stepping up the Pace of Discovery: The Genomes to Life Program / M. Frazier ; D. Thomassen ; A. Patrinos ; G. Johnson ; C. Oliver ; E. Uberbacher |
The Role of Algorithmic Research in Computational Genomics / R. Karp |
Invited Speakers |
High Performance Computational Biology--Past Progress and Future Promise / P. Bourne |
Bridging Paradigm Gaps between Biology and Engineering / J. Bruck |
Microbial Functional Genomics: Pulling Together a Variety of Approaches and Concepts / J.-M. Claverie |
The Sea Urchin Endomesoderm Gene Regulatory Network, an Encoded Logic Map for Early Development / E. Davidson |
Epitope Prediction Algorithms for Peptide-Based Vaccine Design / L. Florea ; B. Halldorsson ; O. Kohlbacher ; R. Schwartz ; S. Hoffman ; S. Istrail |
Pathway Bioinformatics / P. Karp |
BPPS: An Algorithm for Analyzing Protein Sequence Alignments / J. Liu |
Eulerian Path Methods for Multiple Sequence Alignment / M. Waterman ; Y. Zhang |
Integrating Bioinformatics Advances into Disease Management Systems to Improve Quality of Care / S. Wong |
Genomes to Life |
Computing for the DOE Genomes to Life Program |
Motifs and Modules in Cellular Signal Processing: Applications to Microbial Stress Response Pathways / A. Arkin |
An Overview of the Sandia National Laboratories Genomes to Life Project, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling" / G. Heffelfinger |
Analysis of the Genetic Potential and Gene Expression of Microbial Communities Involved in the In Situ Bioremediation of Uranium and Harvesting Electrical Energy from Organic Matter / D. Lovley |
Microarray Data Analysis |
Clustering Binary Fingerprint Vectors with Missing Values for DNA Array Data Analysis / A. Figueroa ; J. Borneman ; T. Jiang |
Clustering Time-Varying Gene Expression Profiles Using Scale-Space Signals / T. Syeda-Mahmood |
Fast and Sensitive Probe Selection for DNA Chips Using Jumps in Matching Statistics / S. Rahmann |
Fast and Accurate Probe Selection Algorithm for Large Genomes / W.-K. Sung ; W.-H. Lee |
Degenerate Primer Design via Clustering / X. Wei ; D. Kuhn ; G. Narasimhan |
Group Testing with DNA Chips: Generating Designs and Decoding Experiments / A. Schliep ; D. Torney |
Pathways, Networks, and Systems Biology |
Can We Identify Cellular Pathways Implicated in Cancer Using Gene Expression Data? / N. Shah ; J. Lepre ; Y. Tu ; G. Stolovitzky |
Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks / S. Imoto ; T. Higuchi ; T. Goto ; K. Tashiro ; S. Kuhara ; S. Miyano |
Two Operative Concepts for the Post-Genomic Era: The "Memoire Vive" of the Cell and a Molecular Algebra / S. Bentolila |
Biomedical Research and Visualization |
Stochastic Stage-Structured Modeling of the Adaptive Immune System / D. Chao ; M. Davenport ; S. Forrest ; A. Perelson |
A Personalized and Automated dbSNP Surveillance System / S. Liu ; S. Lin ; M. Woon ; T. Klein ; R. Altman |
Fourier Harmonic Approach for Visualizing Temporal Patterns of Gene Expression Data / L. Zhang ; A. Zhang ; M. Ramanathan |
Towards Index-Based Similarity Search for Protein Structure Databases / O. Camoglu ; T. Kahveci ; A. Singh |
Local Similarity in RNA Secondary Structures / M. Hochsmann ; T. Toller ; R. Giegerich ; S. Kurtz |
CTSS: A Robust and Efficient Method for Protein Structure Alignment Based on Local Geometrical and Biological Features / T. Can ; Y.-F. Wang |
Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data / W. Krebs |
Statistical Inference for Well-Ordered Structures in Nucleotide Sequences / S.-Y. Le ; J.-H. Chen ; J. Maizel, Jr. |
Automated Protein NMR Resonance Assignments / X. Wan ; D. Xu ; C. Slupsky ; G. Lin |
3D Structural Homology Detection via Unassigned Residual Dipolar Couplings / C. Langmead ; B. Donald |
Data Mining |
Discovering Compact and Highly Discriminative Features or Feature Combinations of Drug Activities Using Support Vector Machines / H. Yu ; J. Yang ; W. Wang ; J. Han |
Initial Large-Scale Exploration of Protein-Protein Interactions in Human Brain / J. Chen ; A. Sivachenko ; R. Bell ; C. Kurschner ; I. Ota ; S. Sahasrabudhe |
An SVM-Based Algorithm for Identification of Photosynthesis-Specific Genome Features / G.-X. Yu ; G. Ostrouchov ; A. Geist ; N. Samatova |
Experimental Studies of the Universal Chemical Key (UCK) Algorithm on the NCI Database of Chemical Compounds / R. Grossman ; D. Hamelberg ; P. Kasturi ; B. Liu |
A Probabilistic Model for Identifying Protein Names and Their Name Boundaries / K. Seki ; J. Mostafa |
Pattern Recognition |
cWINNOWER Algorithm for Finding Fuzzy DNA Motifs / S. Liang |
LOGOS: A Modular Bayesian Model for de novo Motif Detection / E. Xing ; W. Wu ; M. Jordan |
SMASHing Regulatory Sites in DNA by Human-Mouse Sequence Comparisons / M. Zavolan ; N. Rajewsky ; N. Socci ; T. Gaasterlamd |
A Block Coding Method that Leads to Significantly Lower Entropy Values for the Proteins and Coding Sections of Haemophilus influenzae / G. Sampath |
A Pattern Matching Algorithm for Codon Optimization and CpG Motif-Engineering in DNA Expression Vectors / R. Satya ; A. Mukherjee ; U. Ranga |
Haplotype Motifs: An Algorithmic Approach to Locating Evolutionarily Conserved Patterns in Haploid Sequences |
Sequence Alignment |
Computing Highly Specific and Mismatch Tolerant Oligomers Efficiently / T. Yamada ; S. Morishita |
ANTICLUSTAL: Multiple Sequence Alignment by Antipole Clustering and Linear Approximate 1-Median Computation / C. Di Pietro ; V. Di Pietro ; G. Emmanuele ; A. Ferro ; T. Maugeri ; E. Modica ; G. Pigola ; A. Pulvirenti ; M. Purrello ; M. Ragusa ; M. Scalia ; D. Shasha ; S. Travali ; V. Zimmitti |
Efficient Constrained Multiple Sequence Alignment with Performance Guarantee / F. Chin ; N. Ho ; T. Lam ; P. Wong ; M. Chan |
A New Similarity Measure among Protein Sequences / K.-P. Wu ; H.-N. Lin ; T.-Y. Sung ; W.-L. Hsu |
A New Approach for Gene Annotation Using Unambiguous Sequence Joining / A. Tchourbanov ; D. Quest ; H. Ali ; M. Pauley ; R. Norgren |
Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination / D. Gusfield ; S. Eddhu ; C. Langley |
Prokaryote Phylogeny without Sequence Alignment: From Avoidance Signature to Composition Distance / B. Hao ; J. Qi |
Poster Papers |
Data Integration |
A Semantic Mediation Approach for Problems in Computational Molecular Biology / M. Chagoyen ; M. Kurul ; P. De-Alarcon ; S. Santini ; B. Ludascher ; J. Carazo ; A. Gupta |
A Query Language to Support Scientific Discovery / B. Eckman ; K. Deutsch ; M. Janer ; Z. Lacroix ; L. Raschid |
Application of Singular Value Decomposition and Functional Clustering to Analyzing Gene Expression Profiles of Renal Cell Carcinoma / Z.-H. Duan ; L. Liou ; T. Shi ; J. Di Donato |
Statistical Resynchronization and Detection of Periodic Transcripts / X. Lu ; W. Zhang ; Z. Qin |
A Method for Tight Clustering: With Application to Microarray / G. Tseng ; W. Wong |
Riptide: Fast Protein Identification from Mass Spectrometer Data / R. Carter |
Accelerating the Drug Design Process through Parallel Inductive Logic Programming Data Mining / J. Graham ; C. Page ; A. Kamal |
Estimating Recombination Rate Distribution by Optimal Quantization / M. Song ; S. Boissinot ; R. Haralick ; I. Phillips |
Statistical Issues in the Analysis of the Array CGH Data / J. Fridlyand ; A. Snijders ; D. Pinkel ; D. Albertson ; A. Jain |
Identification of Contaminants in Proteomics Mass Spectrometry Data / M. Duncan ; K. Fung ; H. Wang ; C. Yen ; K. Cios |
A Flexible Pipeline for Experimental Design, Processing, and Analysis of Microarray Data / S. Osborn ; S. Kennedy ; D. Chin |
A Computational Approach to Reconstructing Gene Regulatory Networks / X. Deng |
Probability Profiles--Novel Approach in Tandem Mass Spectrometry De Novo Sequencing / T. Fridman ; R. Day ; J. Razumovskaya ; A. Gorin |
A Symbolic Logic Strategy for Mapping Biological Concepts in the HERBE Prototype / E. Stephan ; G. Chin, Jr. ; K. Klicker ; A. Corrigan ; H. Sofia |
A Computational Method for Assessing Peptide-Identification Reliability in Tandem Mass Spectrometry Analysis with SEQUEST / V. Olman ; N. Verbermoes ; Y. Xu |
Functional Genomics |
Tomato Expression Database (TED)--An Interactive Management Tool for Tomato Expression Profiling Data / Z. Fei ; X. Tang ; R. Alba ; P. Payton ; J. Giovannoni |
Oncogenetics Tree Models--An Estimation / H. Gill |
The GeneCards Family of Databases: GeneCards, GeneLoc, GeneNote and GeneAnnot / M. Safran ; V. Chalifa-Caspi ; O. Shmueli ; N. Rosen ; H. Benjamin-Rodrig ; R. Ophir ; I. Yanai ; M. Shmoish ; D. Lancet |
Wavelet Transforms for the Analysis of Microarray Experiments / T. Tokuyasu |
MageBuilder: A Schema Translation Tool for Generating MAGE-ML from Tabular Microarray Data / W. Martin ; R. Horton |
OptiRNAi, A Web-Based Program to Select siRNA Sequences / W. Cui ; J. Ning ; U. Naik |
A Rule-Based Framework for Gene Regulation Pathways Discovery / B. Wilczynski ; T. Hvidsten ; A. Kryshtafovych ; L. Stubbs ; J. Komorowski ; K. Fidelis |
Gene Function, Metabolic Pathways and Comparative Genomics in Yeast / Q. Dong ; R. Balakrishnan ; G. Binkley ; K. Christie ; M. Costanzo ; K. Dolinski ; S. Dwight ; S. Engel ; D. Fisk ; J. Hirschman ; E. Hong ; R. Nash ; L. Issel-Tarver ; A. Sethuraman ; C. Theesfeld ; S. Weng ; D. Botstein ; J. Cherry |
Using Rule Induction Methods to Analyze Gene Expression Data / G. Li ; X. Li ; L. Hao ; J. Zhou |
Genomic Annotation |
Computational Prediction of DtxR Regulon--A Dissection of Physiological Process Controlled by DtxR in Corynebacterium Species / S. Yellaboina ; P. Chakhaiyar ; S. Hasnain ; A. Ranjan |
A New Approach to Gene Prediction Using the Self-Organizing Map / S. Mahony ; T. Smith ; J. McInerney ; A. Golden |
On Gene Prediction by Cross-Species Comparative Sequence Analysis / R. Chen |
CUBIC: Identification of Regulatory Binding Sites through Data Clustering |
Genotyping and SNPs |
SNP Analysis System for Detecting Complex Disease Associated Sites / Y. Higashi ; H. Higuchi ; T. Kido ; H. Matsumine ; M. Baba ; T. Morimoto ; M. Muramatsu |
Haplotype Pattern Mining and Classification for Detecting Disease Associated Site |
Molecular Simulation |
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 / S. Lee ; Y. Fujitsuka ; S. Takada ; D. Kim |
New Computational Methods for Electrostatics in Macromolecular Simulation / I. Tsukerman |
The Approximate Algorithm for Analysis of the Strand Separation Transition in Superhelical DNA Using Nearest Neighbor Energetics / C. Bi ; C. Benham |
Substrate Recognition by Enzymes: A Theoretical Study / K. Ueno-Noto ; K. Takano ; M. Hara-Yokoyama |
Computational Simulation of Lipid Bilayer Reorientation at Gaps / P. Kasson ; V. Pande |
Phylogeny and Evolution |
Search for Evolution-Related-Oligonucleotides and Conservative Words in rRNA Sequences / L. Luo ; L.-C. Hsieh ; F. Ji ; M. Jia ; H. Lee |
High Speed GAML-Based Phylogenetic Tree Reconstruction Using HW/SW Codesign / T. Mak ; K. Lam |
Evidence for Growth of Microbial Genomes by Short Segmental Duplications / H.-C. Lee |
PTC: An Interactive Tool for Phylogenetic Tree Construction / C. Yang ; S. Khuri |
Iterative Rank Based Methods for Clustering / S. Perrey ; H. Brinck ; A. Zielesny |
Analysis of Phylogenetic Profiles Using Bayesian Decomposition / G. Bidaut ; K. Suhre ; M. Ochs |
Automatic Recognition of Regions of Intrinsically Poor Multiple Alignment Using Machine Learning / Y. Shan ; E. Milios ; A. Roger ; C. Blouin ; E. Susko |
Reconstruction of Ancestral Gene Order after Segmental Duplication and Gene Loss / J. Huan ; J. Prins ; T. Vision |
Reconstruction of Ancient Operons from Complete Microbial Genome Sequences / Y. Wang ; J. Rose ; B.-C. Wang ; D. Lin |
Predictive Methods |
An Evolutionary Approach to Finding Schemas for 3-Class Protein Secondary Structure Prediction / H. Huang |
Gene Selection for Multi-Class Prediction of Microarray Data / D. Chen ; D. Hua ; J. Reifman ; X. Cheng |
Latent Structure Models for the Analysis of Gene Expression Data / A. Youssef |
Molecular Evaluation Using Comparative Molecular Interaction Profile Analysis System / Y. Hayashi ; K. Sakaguchi ; N. Iwata ; M. Kobayashi |
Probe Design for Large-Scale Molecular Biology Applications / V. VanBuren ; T. Yoshikawa ; T. Hamatani ; M. Ko |
Gene Selection for Cancer Classification Using Bootstrapped Genetic Algorithms and Support Vector Machines / X.-w. Chen |
A Statistical Model of Proteolytic Digestion / I.-J. Wang ; C. Diehl ; F. Pineda |
Preliminary Wavelet Analysis of Genomic Sequences / C. Moore ; J. Nelson |
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 / V. Stojkovic ; G. Steele ; W. Lupton |
Fold Recognition Using Sequence Fingerprints of Protein Local Substructures |
An Iterative Loop Matching Approach to the Prediction of RNA Secondary Structures with Pseudoknots / J. Ruan ; G. Stormo |
A New Method for Predicting RNA Secondary Structure / H. Taira ; T. Izumitani ; E. Maeda ; T. Suzuki |
Minimum Redundancy Feature Selection from Microarray Gene Expression Data / C. Ding ; H. Peng |
Sequence Comparison |
Automatic Parameter Selection for Sequence Similarity Search / G. Livingston ; G. Grinstein |
A Linear Programming Based Algorithm for Multiple Sequence Alignments / F. Hunt ; A. Kearsley ; A. O'Gallagher |
Alignment-Free Sequence Comparison with Vector Quantization and Hidden Markov Models / T. Pham |
Prediction of Protein Function Using Signal Processing of Biochemical Properties / K. Gopalakrishnan ; K. Najarian |
Genomic Sequence Analysis Using Gap Sequences and Pattern Filtering / S.-C. Su ; C. Yeh ; C.-C. Kuo |
An Optimal DNA Segmentation Based on the MDL Principle / W. Szpankowski ; W. Ren ; L. Szpankowski |
The Cybertory Sequence File System for Managing Large DNA Sequences / C. McMillin |
Implementing Parallel Hmm-pfam on the EARTH Multithreaded Architecture / W. Zhu ; Y. Niu ; J. Lu ; G. Gao |
Genome on Demand: Interactive Substring Searching |
CoMRI: A Compressed Multi-Resolution Index Structure for Sequence Similarity Queries / H. Sun ; O. Ozturk ; H. Ferhatosmanoglu |
Strings, Graphs, and Algorithms |
Genetic Algorithm Approach to the Closest String Problem / H. Mauch ; M. Melzer ; J. Hu |
GenericBioMatch: A Novel Generic Pattern Match Algorithm for Biological Sequences / Y. Pan ; A. Famili |
Aligning ESTs to Genome Using Multi-Layer Unique Makers / F. Hsu |
A Parallel Genetic Algorithm for Physical Mapping of Chromosomes / S. Bhandarkar ; J. Huang ; J. Arnold |
RCIS: A Common Interval Searching Algorithm for Amino Acid Sequences / X. Huang |
Algorithms for Bounded-Error Correlation of High Dimensional Data in Microarray Experiments / M. Koyuturk ; A. Grama |
Exact and Heuristic Algorithms for the DNA Fragment Assembly Problem / Y. Jing |
Finding Higher Order Motifs under the Levenshtein Measure / E. Adebiyi ; T. Dipe |
Mapping Discontinuous Antibody Epitopes to Reveal Protein Structure and Changes in Structure Related to Function / B. Mumey ; T. Angel ; B. Kirkpatrick ; B. Bailey ; P. Hargrave ; A. Jesaitis ; E. Dratz |
The SCP and Compressed Domain Analysis of Biological Sequences / D. Adjeroh ; J. Feng |
Identifying Regulatory Signals in DNA-Sequences with a Non-Statistical Approximation Approach / C.-Q. Zhang ; Y. Liu ; E. Eschen ; K. Wu |
A Genetic Algorithm for Simplifying the Amino Acid Alphabet / M. Palensky |
Structural Biology |
Spectral Decomposition of the Laplacian Matrix Applied to RNA Folding Predition / D. Barash |
Identification of Non-Random Patterns in Structural and Mutational Data: The Case of Prion Protein / I. Kuznetsov ; S. Rackovsky |
Multiple Protein Structure Alignment by Deterministic Annealing / L. Chen |
An Exact Algorithm for Determining Protein Backbone Structure from NH Residual Dipolar Couplings / L. Wang ; R. Mettu ; R. Lilien |
Automatic Construction of 3D Structural Motifs for Protein Function Prediction / M. Liang ; D. Brutlag |
Local Minima-Based Exploration for Off-Lattice Protein Folding / E. Santos ; K. Kim |
Systems Biology |
Pathway Logic Modeling of Protein Functional Domains in Signal Transduction / C. Talcott ; S. Eker ; M. Knapp ; P. Lincoln ; K. Laderoute |
Development of a Massively-Parallel, Biological Circuit Simulator / R. Schiek ; E. May |
Representing and Reasoning about Signal Networks: An Illustration Using NF[kappa]B Dependent Signaling Pathways / C. Baral ; K. Chancellor ; N. Tran |
Noise - Attenuation in Artificial Genetic Networks / Y. Morishita ; K. Aihara |
Computational Inference of Regulatory Pathways in Microbes: An Application to Phosphorus Assimilation Pathways in Synechococcus WH8102 / Z. Su ; P. Dam ; X. Chen ; B. Palenik |
Text Mining and Ontologies |
A Contradiction-Based Framework for Testing Gene Regulation Hypotheses / S. Racunas ; N. Fedoroff |
Identifying Gene and Protein Names from Biological Texts / W. Xuan ; S. Watson ; H. Akil ; F. Meng |
Refining the Extraction of Relevant Documents from Biomedical Literature to Create a Corpus for Pathway Text Mining / R. Harte ; Y. Lu ; D. Dehoney |
Using Natural Language Processing and the Gene Ontology to Populate a Structured Pathway Database |
Text Pattern Visalization for Analysis of Biology Full Text and Captions / A. Grimes ; R. Futrelle |
Miscellaneous |
Development and Assessment of Bioinformatics Tools for Species Conservation and Habitat Management and Habitat Management / M. Sutton ; L. Deneke ; J. Eme ; W. Bennett ; F. Wray |
MedfoLink: Bridging the Gap between IT and the Medical Community / J. Gerrein ; A. Kherlopian ; V. Wu ; M. Berman ; A. Wald |
TC-DB: An Architecture for Membrane Transport Protein Analysis / C. Tran ; N. Yang ; M. Saier, Jr. |
Author Index |