Table of Contents

• TALI: Protein Structure Alignment Using Backbone Torsion AnglesXijiang Miao, Michael Bryson, Homayoun Valafar. 3-9
• Space-Efficient Parallel Algorithms for the Constrained Multiple Sequence Alignment ProblemDan He, Abdullah N. Arslan. 10-16
• Simple Methods of Finding Short Protein Coding SequencesHanno Hinsch, Artemis G. Hatzigeorgiou. 17-23
• Homology Modeling of Myoglobin using Adaptive Neurofuzzy SystemsAchuthsankar S. Nair, Koshy P. Vaidyan. 24-30
• Parameterized Computation of LCS for Two SequencesYuan Lin, Jeff Jenness, Xiuzhen Huang. 31-40
• Dynamic Bayesian Network (DBN) with Structure Expectation Maximization (SEM) for Modeling of Gene Network from Time Series Gene Expression DataYu Zhang, Zhidong Deng, Hongshan Jiang, Peifa Jia. 41-47
• Comparative Sequence Analysis of the p53 Response Elements Associated with Apoptosis and Cell Cycle ArrestFeng Cui, Michael Sirotin, Victor Zhurkin. 48-55
• Petri Net Based Model Of The T Cell Receptor Signaling PathwaySrinidhi Jayasuryan, Anil Bamezai, Vijay Gehlot. 56-62
• Data Integration with BioPAX Pathway Datasets for Automated NavigationKeyuan Jiang. 63-68
• A Relational Genomics Search EngineJay Urbain, Nazli Goharian. 69-74
• Inferring Ancestral Chloroplast Genomes with Inverted RepeaLiying Cui, Feng Yue, Claude W. dePamphilis, Bernard M. E. Moret, Jijun Tang. 75-81
• Evidence for Functional Protein Fragment Homology in Viral Genome TypesJohn Rose, Rishi Mukhopadhyay. 82-86
• On a New Quartet-Based Phylogeny Reconstruction AlgorithmBing Bing Zhou, Monther Tarawneh, Daniel Chu, Francis Wang, Chen Wang, Albert Y. Zomaya, Richard P. Brent. 87-93
• New Algorithms for Application of Evolution Rules based on Applicability BenchmarksLuis Fernández, Fernando Arroyo, Juan Castellanos, Jorge A. Tejedor, Ivan Garcia. 94-102
• Needs Assessment for Scientific Visualization of Multivariate, High-Dimensional Microarray DataVetria Byrd, Tarynn Witten. 103-109
• Reduced-rank Multivariate Model for Time-course Microarray DataRafal Kustra. 110-116
• Data Mining of ESTs for Genetic Improvement of Salt Tolerance in WheatMeral Unal, Ismail Cakmak, Yildiz Aydin, Aysen Yumurtaci, Ahu Altinkut, Emel Yesil, Sema Karanlik, Hikmet Budak. 117-124
• Abstracted Stochastic Analysis of Type 1 Pili Expression in E.coliHiroyuki Kuwahara, Chris J. Myers, Michael S. Samoilov. 125-134
• A Heuristic Approach to Scoring Gene Clustering AlgorithmsLongde Yin, Chun-Hsi Huang. 135-141
• Finishing Repetitive Regions Automatically with DupfinisherCliff Han, Patrick Chain. 142-147
• Acceleration of Covariance Models for Non-coding RNA SearchScott F. Smith 0002. 148-153
• Genome Annotation and Comparison SystemJing Zhao, Tian Xue, Boyu Yang, Kelly Williams, Alice R. Wattam, Rebecca Will, Bruce Sharp, Ron Kenyon, Oswald Crasta, Bruno W. S. Sobral. 154-160
• Filtering Tandem Repeats in DNA SequencesDina Sokol, Justin Tojeira. 161-167
• Fast and Complete Search of siRNA Off-target SequencesHong Zhou, Yufang Wang, Xiao Zeng. 168-171
• Marker Gene Selection Evaluation in Brain Tumor Patients Using Parallel CoordinatesAtiq Islam, Khan M. Iftekharuddin, David J. Russomanno. 172-176
• Automated Blood Volume Quantification from Color Doppler Images while Tracking the Conduit MotionBeomjin Kim. 177-181
• Toward In Vivo Disease Diagnosis and Treatment Using DNAYuriy Brun, Manoj Gopalkrishnan. 182-186
• A Machine Learning Prototype for the Identification of Patients who are Not Likely to Respond to Medical Treatment of BPH with alpha-BlockersBaris Andirinli, Ali Tekin, Yasin Kapucu, I. Ilkay Boduroglu. 187-193
• An Artificial Neural Network based Model to Analyze Malarial Data and Predict Organ FailureDinesh P. Mital, Shankar Srinivasan, Syed Haque, Radhika Uppalapati. 194-200
• Basic Reproductive Rate of a Spatial Epidemic Seir Model using Computer Algebra SoftwareSebastian Guzmán, Juan Fernando Ospina. 201-204
• Computer-Aided Cytogenetic Method of Breast Cancer Diagnosis, Part I - Decision RuleRoman Andrushkiw, Yuriy Petunin, Lyudmila Ostapchenko, Natalya Boroday, Yulia Lozovskaya, Vasiliy Chekhun, Irina Dosenko. 205-209
• Computer-Aided Cytogenetic Method of Breast Cancer Diagnosis, Part II - Test CriteriaRoman Andrushkiw, Dmitry Klyushin, Ekaterina Golubeva, Mikhail Pokoyoviy, Andrey Romanov. 210-216
• Development of Maximized Total Capillary Surface: the quater power scaling law from developmental biology perspectiveDawei Hong, Shushuang Man, Daniel Shain, Joseph V. Martin. 217-221
• Surgeon s Magic Wand: A Screen Pointing Interactive MethodNaren Vira, Shaleen Vira. 222-228
• SPiC-MAS: A Multiagent Simulation of Stochastic pi-calculus ModelsMikaël Bourhis, Vincent Rodin, Gabriel Querrec. 229-235
• Reducing Harmful Effects Of Road Excitations On Human Health By Designing Car Active Suspension SystemsSara Sharifi Sedeh, Reza Sharifi Sedeh, Keivan Navi. 236-241
• Using Car Semi-Active Suspension Systems To Decrease Undesirable Effects Of Road Excitations On Human HealthReza Sharifi Sedeh, Sara Sharifi Sedeh, Keivan Navi. 242-250
• Fast Dictionary Lookup in Genomic Information RetrievalSimon M. C. Yuen, Fu-Lai Chung, Robert Wing Pong Luk. 251-257
• Bioinformatics Web ServicesBoyu Yang, Tian Xue, Jing Zhao, Chaitanya Kommidi, Jeetendra Soneja, Jian Li, Rebecca Will, Bruce Sharp, Ron Kenyon, Oswald Crasta, Bruno W. S. Sobral. 258-264
• Finding Molecular Signature of Prostate Cancer: An Algorithmic ApproachPatrick Bobbie, Renee Reams, Sandra Suther, C. Perry Brown. 265-269
• Support Vector Machines for Predicting microRNA HairpinsKarol Szafranski, Molly Megraw, Martin Reczko, Artemis G. Hatzigeorgiou. 270-276
• A Design for Software to Assist in the Rehabilitation of Stroke PatientsGillian Pearce, Peter Wilson, Gill Jones, David Smith. 277-284
• A Multi-strategy Approach to Protein Structural Alphabet DesignShih-Yen Ku, Yuh-Jyh Hu. 285-291
• Study on Properties of Protein Folding Conformation NetworkNengchao Wang, Zhongjun Wang. 292-295
• Statistical Analysis of Long-Range Interactions in ProteinsJinmiao Chen, Narendra S. Chaudhari. 296-302
• Identification of Intrinsically Unstructured Regions in Proteins Using Primary StructureMary Qu Yang, Jack Y. Yang. 303-309
• Membrane Remodeling and Diffusion of Cytochrome C from a Geometrically Idealized Mitochondrial CristaJohn Manor, Peter Salamon, James Nulton, Joseph Mahaffy, Arlette Baljon, Terrence Frey. 310-314
• Structure Prediction of Potato Large Subunit ADP - Glucose PyrophosphorylaseAytug Tuncel, I. Halil Kavakli, Ozlem Keskin. 315-321
• Discrete Molecular Dynamics Study of Alzheimer Amyloid B-protein (AB) FoldingH. Eugene Stanley, David Teplow, Noel Lazo, Jose Borreguero, Brigita Urbanc, Alfonso Lam. 322-328
• Melting Free Energies of DNA Duplexes with oxidized Base Residues and Abasic sites: A Molecular Dynamics CharacterizationLatifa Douali, Matt Ernst, John Miller, Michel Dupuis. 329-337
• The Use of Context-Sensitive Grammar For Modeling RNA PseudoknotsKeum-Young Sung. 338-344
• Learning from Sequences with Determining Correlation between Transmembrane and Protein DisorderJack Y. Yang, Mary Qu Yang. 345-351
• X-Ray Powder Diffraction MetricsGeorge Runger, Kelly Canter, John Twist, David Rossi, Clifford Kirkham. 352-359
• A Simple Approach for Obtaining High Resolution, High Sensitivity 1H NMR Metabolite Spectra of Biofluids with Limited Mass SupplyJian Zhi Hu, Donald N. Rommereim, Robert A. Wind, Kevin R. Minard, Jesse A. Sears. 360-366
• A New Algorithm to Predict the Active Sites Using Amino Acid Vectors and Biochemical features of Surface PatchesSunshin Kim, Chung Rhee, Jungdo Choi, Yongje Chung, Keun Ho Ryu. 367-372
• Fusion genes as putative microbial drug targets in H. pyloriMeena K. Sakharkar, Kishore R. Sakharkar, Vincent T. K. Chow. 373-377
• Structure-Based Design and Analysis of Cytochrome P450 Inhibitors for the Treatment of Prostate CancerMuhittin Emre Ozdemir, I. Halil Kavakli, Metin Türkay. 378-384
• Evaluation of a Novel Metric for Quality Control in an RNA Interference High Throughput Screening AssayXiaohua Douglas Zhang, Amy S. Espeseth, Namjin Chung, Marc Ferrer. 385-390
• Combined QM/MM Studies of Binding Effect of Cytochrome P450cam to PutidaredoxinMarek Freindorf, Yihan Shao, Jing Kong, Thomas R. Furlani. 391-398
• Sensivitity of the maximum parsimony algorithm to missing dataJack Horner. 399-405
• Improving the Efficiency of Sorting by ReversalsYijie Han. 406-409
• Analytical Solution of a Spatial Sir Epidemic Model with Memory Inside a Circular Habitat with Endemic Memory using CASNicolás Guarín, Juan Ospina. 410-413
• Mapping Biological XML DTDs Using OntologyRana Hashmy. 414-420
• Nonconvulsive Status Epilepticus with an Unusual EEG: Another Look at Lateralities of Motor Control and AwarenessI. Derakhshan. 421-433
• Algorithms for Computational Viral Extension - Direct and Inverse ProblemsValery V. Gritsak-Groener, Julia Gritsak-Groener, Hamid R. Arabnia. 434-444
• The Multi-Node Topological Overlap Measure For Gene Neighborhood AnalysisAi Li, Steve Horvath. 445-450
• The Generalized Topological Overlap Matrix for Detecting Modules in Gene NetworksAndy M. Yip, Steve Horvath. 451-457
• A Network-Based Gene Screening Approach For Improving the Validation Success of MicroarraysWei Zhao, Paul Mischel, Marc Carlson, Bin Zhang, Stanley Nelson, Steve Horvath. 458-464
• The Relationship Between Intramodular Connectivity and Gene Significance in Co-Expression NetworksSteve Horvath, Jun Dong, Andy M. Yip. 465-471
• Theoretical Bounds for the Number of Inferable Edges in Sparse Random NetworksFrank Emmert-Streib, Matthias Dehmer. 472-476
• Influence of Prior Information on the Reconstruction of the Yeast Cell Cycle from Microarray DataFrank Emmert-Streib, Matthias Dehmer, Chris Seidel. 477-482
• Learning Genetic and Gene Bayesian Networks with Hidden Variables: Bilayer Verification AlgorithmJason E. Aten. 483-489
• Computational Inference of Compound-induced Anti-inflammatory Effects Across Time in an Adjuvant-induced Arthritis Rat ModelJing Yu, Gabriel Helmlinger, Muriel Saulnier, Anna Georgieva. 490-495
• In Search of a Bridge Between Network Analysis in Computational Linguistics and Computational Biology - A Conceptual NoteAlexander Mehler. 496-502
• SpA: Web-accessible Spectratype Analysis: Application to Investigate the Development of TCR Diversity in a Patient with Complete DiGeorge SyndromeMin He, Blythe H. Devlin, Mary Markert, Marcella Sarzotti, Thomas B. Kepler. 503-510
• Using Neural Nets to Estimate Evolutionary ParametersChi-Chiang Lee, Paul Marjoram. 511-517
• PAC: Progressive Alignment with Consensus SequencesKe Liu, Mansur H. Samadzadeh. 518-524
• A Clinical Decision Support System For Managing Flexor Tendon InjuriesPrashant Junankar, Dinesh P. Mital, Syed Haque, Shankar Srinivasan. 525-528
• Reverse Engineering Approach in Molecular Evolution: Simulation and Case Study with Enzyme ProteinsSukanya Manna, Cheng-Yuan Liou. 529-533
• Polyome: A Learning System for Extracting Bioinformatic DataBob Myers, Trevor I. Dix, Ross L. Coppel, David G. Green. 534-540
• Insight of the Signal Motif of GPI-(like)-anchored Proteins by using SVMWei Cao, Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, Kentaro Shimizu. 541-546
• WebDock: A Structure-Based Drug Discovery Web ServiceJoseph Gill, Legand L. Burge III, Zengjian Hu, William M. Southerland. 547-548
• AminoTrack: Automating the Entry and Analysis of Mutations in Multiple Protein Sequences Using a Spreadsheet FormatMadhumita Mahalanabis, Jason Blue, Nancy Haigwood. 549-555
• Performance of Sequence Alignment Bioinformatics Applications on General Purpose Processors: A Case StudyPradeep Nair, Eugene John. 556-559
• An Approach to Selecting Putative RNA Motifs Using MDL PrincipleMohammad Anwar, Marcel Turcotte. 560-569
• Comparative genomics using web-based GeneOrder to determine synteny and to function as an annotation toolPadmanabhan Mahadevan, Donald Seto. 566-570
• Introducing Hippy: A Visualization Tool for Understanding the alpha-Helix Pair InterfaceRobert Fraser, Janice I. Glasgow. 571