BIOCOMP 2006: Las Vegas, Nevada, USA
Hamid R. Arabnia, Homayoun Valafar (Eds.): Proceedings of the 2006 International Conference on Bioinformatics & Computational Biology, BIOCOMP'06, Las Vegas, Nevada, USA, June 26-29, 2006. CSREA Press 2006 ISBN 1-60132-002-7
Sequence and Structure Alignment of Macro Molecules
- Xijiang Miao, Michael Bryson, Homayoun Valafar: TALI: Protein Structure Alignment Using Backbone Torsion Angles. 3-9
- Dan He, Abdullah N. Arslan: Space-Efficient Parallel Algorithms for the Constrained Multiple Sequence Alignment Problem. 10-16
- Hanno Hinsch, Artemis G. Hatzigeorgiou: Simple Methods of Finding Short Protein Coding Sequences. 17-23
- Achuthsankar S. Nair, Koshy P. Vaidyan: Homology Modeling of Myoglobin using Adaptive Neurofuzzy Systems. 24-30
Biomolecular Pathways and System Biology
- Yu Zhang, Zhidong Deng, Hongshan Jiang, Peifa Jia: Dynamic Bayesian Network (DBN) with Structure Expectation Maximization (SEM) for Modeling of Gene Network from Time Series Gene Expression Data. 41-47
- Feng Cui, Michael Sirotin, Victor Zhurkin: Comparative Sequence Analysis of the p53 Response Elements Associated with Apoptosis and Cell Cycle Arrest. 48-55
- Srinidhi Jayasuryan, Anil Bamezai, Vijay Gehlot: Petri Net Based Model Of The T Cell Receptor Signaling Pathway. 56-62
- Keyuan Jiang: Data Integration with BioPAX Pathway Datasets for Automated Navigation. 63-68
Phylogenetic Reconstruction and Molecular Evolution
- Liying Cui, Feng Yue, Claude W. dePamphilis, Bernard M. E. Moret, Jijun Tang: Inferring Ancestral Chloroplast Genomes with Inverted Repea. 75-81
- John Rose, Rishi Mukhopadhyay: Evidence for Functional Protein Fragment Homology in Viral Genome Types. 82-86
- Bing Bing Zhou, Monther Tarawneh, Daniel Chu, Francis Wang, Chen Wang, Albert Y. Zomaya, Richard P. Brent: On a New Quartet-Based Phylogeny Reconstruction Algorithm. 87-93
- Luis Fernández, Fernando Arroyo, Juan Castellanos, Jorge A. Tejedor, Ivan Garcia: New Algorithms for Application of Evolution Rules based on Applicability Benchmarks. 94-102
Microarray Data Analysis and Gene Expression
- Vetria Byrd, Tarynn Witten: Needs Assessment for Scientific Visualization of Multivariate, High-Dimensional Microarray Data. 103-109
- Rafal Kustra: Reduced-rank Multivariate Model for Time-course Microarray Data. 110-116
- Meral Unal, Ismail Cakmak, Yildiz Aydin, Aysen Yumurtaci, Ahu Altinkut, Emel Yesil, Sema Karanlik, Hikmet Budak: Data Mining of ESTs for Genetic Improvement of Salt Tolerance in Wheat. 117-124
- Hiroyuki Kuwahara, Chris J. Myers, Michael S. Samoilov: Abstracted Stochastic Analysis of Type 1 Pili Expression in E.coli. 125-134
Gene Identification and Clustering
- Scott F. Smith: Acceleration of Covariance Models for Non-coding RNA Search. 148-153
- Jing Zhao, Tian Xue, Boyu Yang, Kelly Williams, Alice R. Wattam, Rebecca Will, Bruce Sharp, Ron Kenyon, Oswald Crasta, Bruno W. S. Sobral: Genome Annotation and Comparison System. 154-160
- Atiq Islam, Khan M. Iftekharuddin, David J. Russomanno: Marker Gene Selection Evaluation in Brain Tumor Patients Using Parallel Coordinates. 172-176
Medical Diagnostic and Software Tools
- Beomjin Kim: Automated Blood Volume Quantification from Color Doppler Images while Tracking the Conduit Motion. 177-181
- Baris Andirinli, Ali Tekin, Yasin Kapucu, I. Ilkay Boduroglu: A Machine Learning Prototype for the Identification of Patients who are Not Likely to Respond to Medical Treatment of BPH with alpha-Blockers. 187-193
- Dinesh P. Mital, Shankar Srinivasan, Syed Haque, Radhika Uppalapati: An Artificial Neural Network based Model to Analyze Malarial Data and Predict Organ Failure. 194-200
- Sebastian Guzmán, Juan Fernando Ospina: Basic Reproductive Rate of a Spatial Epidemic Seir Model using Computer Algebra Software. 201-204
- Roman Andrushkiw, Yuriy Petunin, Lyudmila Ostapchenko, Natalya Boroday, Yulia Lozovskaya, Vasiliy Chekhun, Irina Dosenko: Computer-Aided Cytogenetic Method of Breast Cancer Diagnosis, Part I - Decision Rule. 205-209
- Roman Andrushkiw, Dmitry Klyushin, Ekaterina Golubeva, Mikhail Pokoyoviy, Andrey Romanov: Computer-Aided Cytogenetic Method of Breast Cancer Diagnosis, Part II - Test Criteria. 210-216
Application of Engineering Techniques and Mathematics in Medicine
- Dawei Hong, Shushuang Man, Daniel Shain, Joseph V. Martin: Development of Maximized Total Capillary Surface: the quater power scaling law from developmental biology perspective. 217-221
- Mikaël Bourhis, Vincent Rodin, Gabriel Querrec: SPiC-MAS: A Multiagent Simulation of Stochastic pi-calculus Models. 229-235
- Sara Sharifi Sedeh, Reza Sharifi Sedeh, Keivan Navi: Reducing Harmful Effects Of Road Excitations On Human Health By Designing Car Active Suspension Systems. 236-241
- Reza Sharifi Sedeh, Sara Sharifi Sedeh, Keivan Navi: Using Car Semi-Active Suspension Systems To Decrease Undesirable Effects Of Road Excitations On Human Health. 242-250
Bioinformatics and Medical Informatics Software Tools
- Simon M. C. Yuen, Fu-Lai Chung, Robert Wing Pong Luk: Fast Dictionary Lookup in Genomic Information Retrieval. 251-257
- Boyu Yang, Tian Xue, Jing Zhao, Chaitanya Kommidi, Jeetendra Soneja, Jian Li, Rebecca Will, Bruce Sharp, Ron Kenyon, Oswald Crasta, Bruno W. S. Sobral: Bioinformatics Web Services. 258-264
- Patrick Bobbie, Renee Reams, Sandra Suther, C. Perry Brown: Finding Molecular Signature of Prostate Cancer: An Algorithmic Approach. 265-269
- Karol Szafranski, Molly Megraw, Martin Reczko, Artemis G. Hatzigeorgiou: Support Vector Machines for Predicting microRNA Hairpins. 270-276
- Gillian Pearce, Peter Wilson, Gill Jones, David Smith: A Design for Software to Assist in the Rehabilitation of Stroke Patients. 277-284
Prediction of Structure and Dynamics of Macro Molecules
- Jinmiao Chen, Narendra S. Chaudhari: Statistical Analysis of Long-Range Interactions in Proteins. 296-302
- Mary Qu Yang, Jack Y. Yang: Identification of Intrinsically Unstructured Regions in Proteins Using Primary Structure. 303-309
- John Manor, Peter Salamon, James Nulton, Joseph Mahaffy, Arlette Baljon, Terrence Frey: Membrane Remodeling and Diffusion of Cytochrome C from a Geometrically Idealized Mitochondrial Crista. 310-314
- Aytug Tuncel, I. Halil Kavakli, Ozlem Keskin: Structure Prediction of Potato Large Subunit ADP - Glucose Pyrophosphorylase. 315-321
- H. Eugene Stanley, David Teplow, Noel Lazo, Jose Borreguero, Brigita Urbanc, Alfonso Lam: Discrete Molecular Dynamics Study of Alzheimer Amyloid B-protein (AB) Folding. 322-328
- Latifa Douali, Matt Ernst, John Miller, Michel Dupuis: Melting Free Energies of DNA Duplexes with oxidized Base Residues and Abasic sites: A Molecular Dynamics Characterization. 329-337
- Keum-Young Sung: The Use of Context-Sensitive Grammar For Modeling RNA Pseudoknots. 338-344
Metablomics, Proteomic and Protein Function Prediction
- Jack Y. Yang, Mary Qu Yang: Learning from Sequences with Determining Correlation between Transmembrane and Protein Disorder. 345-351
- George C. Runger, Kelly Canter, John Twist, David Rossi, Clifford Kirkham: X-Ray Powder Diffraction Metrics. 352-359
- Jian Zhi Hu, Donald N. Rommereim, Robert A. Wind, Kevin R. Minard, Jesse A. Sears: A Simple Approach for Obtaining High Resolution, High Sensitivity 1H NMR Metabolite Spectra of Biofluids with Limited Mass Supply. 360-366
- Sunshin Kim, Chung Rhee, Jungdo Choi, Yong Je Chung, Keun Ho Ryu: A New Algorithm to Predict the Active Sites Using Amino Acid Vectors and Biochemical features of Surface Patches. 367-372
Intelligent Drug Design
- Meena K. Sakharkar, Kishore R. Sakharkar, Vincent T. K. Chow: Fusion genes as putative microbial drug targets in H. pylori. 373-377
- Muhittin Emre Ozdemir, I. Halil Kavakli, Metin Türkay: Structure-Based Design and Analysis of Cytochrome P450 Inhibitors for the Treatment of Prostate Cancer. 378-384
- Xiaohua Douglas Zhang, Amy S. Espeseth, Namjin Chung, Marc Ferrer: Evaluation of a Novel Metric for Quality Control in an RNA Interference High Throughput Screening Assay. 385-390
- Marek Freindorf, Yihan Shao, Jing Kong, Thomas R. Furlani: Combined QM/MM Studies of Binding Effect of Cytochrome P450cam to Putidaredoxin. 391-398
Ontology, Semantics and Data Management Software
- Jack Horner: Sensivitity of the maximum parsimony algorithm to missing data. 399-405
- Yijie Han: Improving the Efficiency of Sorting by Reversals. 406-409
- Nicolás Guarín, Juan Ospina: Analytical Solution of a Spatial Sir Epidemic Model with Memory Inside a Circular Habitat with Endemic Memory using CAS. 410-413
- Rana Hashmy: Mapping Biological XML DTDs Using Ontology. 414-420
Algorithms and Models
- I. Derakhshan: Nonconvulsive Status Epilepticus with an Unusual EEG: Another Look at Lateralities of Motor Control and Awareness. 421-433
- Valery V. Gritsak-Groener, Julia Gritsak-Groener, Hamid R. Arabnia: Algorithms for Computational Viral Extension - Direct and Inverse Problems. 434-444
Gene Networks: Theory and Application
- Ai Li, Steve Horvath: The Multi-Node Topological Overlap Measure For Gene Neighborhood Analysis. 445-450
- Andy M. Yip, Steve Horvath: The Generalized Topological Overlap Matrix for Detecting Modules in Gene Networks. 451-457
- Wei Zhao, Paul Mischel, Marc Carlson, Bin Zhang, Stanley Nelson, Steve Horvath: A Network-Based Gene Screening Approach For Improving the Validation Success of Microarrays. 458-464
- Steve Horvath, Jun Dong, Andy M. Yip: The Relationship Between Intramodular Connectivity and Gene Significance in Co-Expression Networks. 465-471
- Frank Emmert-Streib, Matthias Dehmer: Theoretical Bounds for the Number of Inferable Edges in Sparse Random Networks. 472-476
- Frank Emmert-Streib, Matthias Dehmer, Chris Seidel: Influence of Prior Information on the Reconstruction of the Yeast Cell Cycle from Microarray Data. 477-482
- Jason E. Aten: Learning Genetic and Gene Bayesian Networks with Hidden Variables: Bilayer Verification Algorithm. 483-489
- Jing Yu, Gabriel Helmlinger, Muriel Saulnier, Anna Georgieva: Computational Inference of Compound-induced Anti-inflammatory Effects Across Time in an Adjuvant-induced Arthritis Rat Model. 490-495
- Alexander Mehler: In Search of a Bridge Between Network Analysis in Computational Linguistics and Computational Biology - A Conceptual Note. 496-502
Late Papers
- Min He, Blythe H. Devlin, Mary Markert, Marcella Sarzotti, Thomas B. Kepler: SpA: Web-accessible Spectratype Analysis: Application to Investigate the Development of TCR Diversity in a Patient with Complete DiGeorge Syndrome. 503-510
- Prashant Junankar, Dinesh P. Mital, Syed Haque, Shankar Srinivasan: A Clinical Decision Support System For Managing Flexor Tendon Injuries. 525-528
- Sukanya Manna, Cheng-Yuan Liou: Reverse Engineering Approach in Molecular Evolution: Simulation and Case Study with Enzyme Proteins. 529-533
- Bob Myers, Trevor I. Dix, Ross L. Coppel, David G. Green: Polyome: A Learning System for Extracting Bioinformatic Data. 534-540
- Cao Wei, Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, Kentaro Shimizu: Insight of the Signal Motif of GPI-(like)-anchored Proteins by using SVM. 541-546
- Joseph Gill, Legand L. Burge III, Zengjian Hu, William M. Southerland: WebDock: A Structure-Based Drug Discovery Web Service. 547-548
- Madhumita Mahalanabis, Jason Blue, Nancy Haigwood: AminoTrack: Automating the Entry and Analysis of Mutations in Multiple Protein Sequences Using a Spreadsheet Format. 549-555
- Pradeep Nair, Eugene John: Performance of Sequence Alignment Bioinformatics Applications on General Purpose Processors: A Case Study. 556-559
- Mohammad Anwar, Marcel Turcotte: An Approach to Selecting Putative RNA Motifs Using MDL Principle. 560-569
- Padmanabhan Mahadevan, Donald Seto: Comparative genomics using web-based GeneOrder to determine synteny and to function as an annotation tool. 566-570
- Robert Fraser, Janice I. Glasgow: Introducing Hippy: A Visualization Tool for Understanding the alpha-Helix Pair Interface. 571-
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