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CIBCB 2005: La Jolla, CA, USA
- Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2005, Embassy Suites Hotel La Jolla, La Jolla, CA, USA, November 14 & 15, 2005. IEEE 2005, ISBN 0-7803-9388-0
Microarray / Gene Expression Analysis
- Thorhildur Juliusdottir, David Corne, Ed Keedwell, Ajit Narayanan:
Two-Phase EA/k-NN for Feature Selection and Classification in Cancer Microarray Datasets. CIBCB 2005: 1-8 - E. Ke Tang, Ponnuthurai N. Suganthan, Xin Yao:
Feature Selection for Microarray Data Using Least Squares SVM and Particle Swarm Optimization. CIBCB 2005: 9-16 - Anupam Chakraborty, Hitashyam Maka:
Biclustering of Gene Expression Data Using Genetic Algorithm. CIBCB 2005: 17-24 - Yuchun Tang, Yuanchen He, Yan-Qing Zhang, Zhen Huang, Xiaohua Hu, Rajshekhar Sunderraman:
A Hybrid CI-Based Knowledge Discovery System on Microarray Gene Expression Data. CIBCB 2005: 25-30
RNA Sequence and Structure
- Mars Cheung, Gary B. Fogel:
Identification of Functional RNA Genes Using Evolved Neural Networks. CIBCB 2005: 31-37 - Daniel A. Ashlock, Justin Schonfeld:
Depth Annotation of RNA Folds for Secondary Structure Motif Search. CIBCB 2005: 38-45 - Sung-Kyu Kim, Jin-Wu Nam, Wha-Jin Lee, Byoung-Tak Zhang:
A Kernel Method for MicroRNA Target Prediction Using Sensible Data and Position-Based Features. CIBCB 2005: 46-52 - Daniel A. Ashlock, Sheridan K. Houghten:
A Novel Variation Operator for More Rapid Evolution of DNA Error Correcting Codes. CIBCB 2005: 53-60
Gene Regulatory Networks / Pathways
- Christian Spieth, Felix Streichert, Jochen Supper, Nora Speer, Andreas Zell:
Feedback Memetic Algorithms for Modeling Gene Regulatory Networks. CIBCB 2005: 61-67 - George Barreto Bezerra, Tiago V. Barra, Fernando J. Von Zuben, Leandro Nunes de Castro:
Handling Data Sparseness in Gene Network Reconstruction. CIBCB 2005: 68-75 - Alireza Darvish, Kayvan Najarian, Dong Hyun Jeong, William Ribarsky:
System Identification and Nonlinear Factor Analysis for Discovery and Visualization of Dynamic Gene Regulatory Pathways. CIBCB 2005: 76-81 - Chien-Feng Huang, Christian Forst, Madeline Tiee:
Pathway Optimization of Mycobacterium Tuberculosis Drug Response Networks. CIBCB 2005: 82-89 - Jennifer Hallinan, Paul T. Jackway:
Network Motifs, Feedback Loops and the Dynamics of Genetic Regulatory Networks. CIBCB 2005: 90-96
Phylogenetics and Small Molecules for Drug Design
- Clare Bates Congdon, Charles Fizer, Noah W. Smith, H. Rex Gaskins, Joseph C. Aman, Gerardo M. Nava, Carolyn J. Mattingly:
Preliminary Results for GAMI: A Genetic Algorithms Approach to Motif Inference. CIBCB 2005: 97-104 - Xiaomeng Wu, Guohui Lin:
Selected String Representation for Whole Genomes. CIBCB 2005: 105-112 - Razvan Andonie, Levente Fabry-Asztalos, Catharine Collar, Sarah Abdul-Wahid, Nicholas Salim:
Neuro-fuzzy Prediction of Biological Activity and Rule Extraction for HIV-1 Protease Inhibitors. CIBCB 2005: 113-120 - Bo Jin, Yan-Qing Zhang, Binghe Wang:
Evolutionary Granular Kernel Trees and Applications in Drug Activity Comparisons. CIBCB 2005: 121-126 - Tiffani L. Williams, Marc Smith:
Cooperative Rec-I-DCM3: A Population-Based Approach for Reconstructing Phylogenies. CIBCB 2005: 127-134
General Topics
- Daniel Duanqing Wu, Xiaohua Hu:
An Efficient Approach to Detect a Protein Community from a Seed. CIBCB 2005: 135-141 - Nora Speer, Holger Fröhlich, Christian Spieth, Andreas Zell:
Functional Distances for Genes Based on GO Feature Maps and their Application to Clustering. CIBCB 2005: 142-149 - Sven Siebert, Rolf Backofen:
A New Distance Measure of RNA Ensembles and Its Application to Phylogenetic Tree Construction. CIBCB 2005: 150-157 - Toshiko Matsumoto, Ryo Nakashige:
Evaluating Robustness of Algorithm for Microsatellite Marker Genotyping. CIBCB 2005: 158-164 - Noriyasu Homma, Koh Fuchigami, Madan M. Gupta:
Neural Spike Communication under Noisy Environments. CIBCB 2005: 165-171 - Marta Szachniuk, Lukasz Popenda, Zofia Gdaniec, Ryszard W. Adamiak, Jacek Blazewicz:
NMR Analysis of RNA Bulged structures: Tabu Search Application in NOE Signal Assignment. CIBCB 2005: 172-178 - Eleazar Eskin, Sagi Snir:
The Homology Kernel: A Biologically Motivated Sequence Embedding into Euclidean Space. CIBCB 2005: 179-186 - Jakkarin Suksawatchon, Chidchanok Lursinsap, Mikael Bodén:
Heuristic Algorithm for Computing Reversal Distance with MultiGene Families via Binary Integer Programming. CIBCB 2005: 187-193 - Pierre Geurts, Antia Blanco Cuesta, Louis Wehenkel:
Segment and Combine Approach for Biological Sequence Classification. CIBCB 2005: 194-201 - Valmik Desai, Purvesh Khatri, Arina Done, Aviva Friedman, Michael A. Tainsky, Sorin Draghici:
A Novel Bioinformatics Technique for Predicting Condition-specific Transcription Factor Binding Sites. CIBCB 2005: 202-207 - Young Bun Kim, Jean Gao:
A New Semi-Supervised Subspace Clustering Algorithm on Fitting Mixture Models. CIBCB 2005: 208-215 - Anthony Almudevar, Peter Salzman:
Using a Bayesian Posterior Density in the Design of Perturbation Experiments. CIBCB 2005: 216-222 - Ilias Tagkopoulos:
A Transcriptional Approach to Gene Clustering. CIBCB 2005: 223-229 - Abdullah N. Arslan:
Multiple Sequence Alignment Containing a Sequence of Regular Expressions. CIBCB 2005: 230-236 - Daniel A. Ashlock, Ruth Swanson, Patrick S. Schnable:
Selection of Genetically Diverse Recombinant Inbreds with an Ordered Gene Evolutionary Algorithm. CIBCB 2005: 237-242 - Luca Pireddu, Brett Poulin, Duane Szafron, Paul Lu, David S. Wishart:
Pathway Analyst--Automated Metabolic Pathway Prediction. CIBCB 2005: 243-250 - Runxuan Zhang, Narasimhan Sundararajan, Guang-Bin Huang, Paramasivan Saratchandran:
An Efficient Sequential RBF Network for Gene Expression-Based Multi-category Classification. CIBCB 2005: 251-256 - Scott F. Smith:
Truncated Profile Hidden Markov Models. CIBCB 2005: 257-261 - Kana Shimizu, Yoichi Muraoka, Shuichi Hirose, Tamotsu Noguchi:
Feature Selection Based on Physicochemical Properties of Redefined N-term Region and C-term Regions for Predicting Disorder. CIBCB 2005: 262-267 - Huilin Xiong, Xue-wen Chen:
Optimized Kernel Machine for Cancer Classification Using Gene Expression Data. CIBCB 2005: 268-274 - Leif E. Peterson, Mustafa Ozen, Halime Erdem, Andrew Amini, Lori Gomez, Colleen C. Nelson, Michael Ittmann:
Artificial Neural Network Analysis of DNA Microarray-based Prostate Cancer Recurrence. CIBCB 2005: 275-282 - Carla D. Lopes, Erik Schüler, Paulo Engel, Altamiro Amadeu Susin:
ERP signal identification of Individuals at Risk for Alcoholism using Learning Vector Quantization Network. CIBCB 2005: 283-287 - Yang Yang, Bao-Liang Lu:
Extracting Features from Protein Sequences Using Chinese Segmentation Techniques for Subcellular Localization. CIBCB 2005: 288-295 - Kok-Sin Toh, Minh Ngoc Nguyen, Jagath C. Rajapakse:
LVQ Approach Using AA Indices for Protein Subcellular Localisation Prediction. CIBCB 2005: 296-302 - Yi-Yuan Chiu, Jenn-Kang Hwang, Jinn-Moon Yang:
GEMSCORE: A New Empirical Energy Function for Protein Folding. CIBCB 2005: 303-310 - Yunlong Liu, Hiroki Yokota:
Modeling Transcriptional Regulation in Chondrogenesis Using Particle Swarm Optimization. CIBCB 2005: 311-317 - Jiankuan Ye, Casimir A. Kulikowski, Ilya B. Muchnik:
Protein-Protein Interaction Prediction Based on Sequence Data by Support Vector Machine with Probability Assignment. CIBCB 2005: 318-324 - Jochen Supper, Christian Spieth, Andreas Zell:
Reverse Engineering Non-Linear Gene Regulatory Networks Based on the Bacteriophage lambda cI Circuit. CIBCB 2005: 325-332 - Supoj Hengpraprohm, Prabhas Chongstitvatana:
Diffuse Large B-cell Lymphoma Classification Using Genetic Programming Classifier. CIBCB 2005: 333-338 - Jung Hun Oh, Jean Gao, Animesh Nandi, Prem Gurnani, Lynne Knowles, John Schorge, Kevin P. Rosenblatt:
Multicategory Classification using Extended SVM-RFE and Markov Blanket on SELDITOF Mass Spectrometry Data. CIBCB 2005: 339-345 - Xiaoxu Han:
A Machine Leaning Approach to Resolving Incongruence in Molecular Phylogenies and Visualization Analysis. CIBCB 2005: 346-353 - Roman Eisner, Brett Poulin, Duane Szafron, Paul Lu, Russell Greiner:
Improving Protein Function Prediction Using the Hierarchical Structure of the Gene Ontology. CIBCB 2005: 354-363 - Vasileios Megalooikonomou, Despina Kontos, Nicholas DeClaris, Pedro Cano:
Utilizing Domain Knowledge in Developing Robust Neural Network Models for Peptide-Allele Binding Prediction. CIBCB 2005: 364-371 - Yijuan Lu, Qi Tian, Maribel Sanchez, Yufeng Wang:
Hybrid PCA and LDA Analysis of Microarray Gene Expression Data. CIBCB 2005: 372-377
Mass Spectroscopy
- Habtom W. Ressom, Rency S. Varghese, Eduard Orvisky, Steven K. Drake, Glen L. Hortin, Mohamed Abdel-Hamid, Christopher A. Loffredo, Radoslav Goldman:
Analysis of MALDI-TOF Serum Profiles for Biomarker Selection and Sample Classification. CIBCB 2005: 378-384 - Elena Marchiori, Niels H. H. Heegaard, Connie R. Jimenez, Mikkel West-Nielsen:
Feature Selection for Classification with Proteomic Data of Mixed Quality. CIBCB 2005: 385-391 - David Schaffer, Angel Janevski, Mark Simpson:
A Genetic Algorithm Approach for Discovering Diagnostic Patterns in Molecular Measurement Data. CIBCB 2005: 392-399 - Joseph Kolibal, Daniel Howard:
Novel Algorithm for MALDI-TOF Baseline Drift Removal. CIBCB 2005: 400-405
Sequence Analysis
- Mansoor Doostfatemeh, Stefan C. Kremer:
Biological Sequence Prediction using General Fuzzy Automata. CIBCB 2005: 406-413 - Xiao Yang, Jagath C. Rajapakse:
Robust Algorithm for Finding Weak Motifs. CIBCB 2005: 414-419 - Carey Pridgeon, David Corne:
Hypermotifs: Novel Discriminatory Patterns for Nucleotide Sequences and their Application to Core Promoter Prediction in Eukaryotes. CIBCB 2005: 420-426 - Niranjan P. Bidargaddi, Madhu Chetty, Joarder Kamruzzaman:
Fuzzy Profile Hidden Markov Models for Protein Sequence Analysis. CIBCB 2005: 427-434 - Jianmin Ma, Minh Ngoc Nguyen, Gavyn Pang, Jagath C. Rajapakse:
Gene Classification Using Codon Usage Patterns and SVMs. CIBCB 2005: 435-442
Medical Informatics
- Hitoshi Iyatomi, Hiroshi Oka, Masahiro Hashimoto, Masaru Tanaka, Koichi Ogawa:
An Internet-based Melanoma Diagnostic System - Toward the Practical Application. CIBCB 2005: 443-446 - Nicolaos B. Karayiannis, Yaohua Xiong:
Training Reformulated Radial Basis Function Neural Networks Capable of Identifying Uncertainty in the Recognition of Videotaped Neonatal Seizures. CIBCB 2005: 447-454 - Lee Lancashire, Selma Ugurel, Colin Creaser, Dirk Schadendorf, Robert C. Rees, Graham R. Ball:
Utilizing Artificial Neural Networks to Elucidate Serum Biomarker Patterns Which Discriminate Between Clinical Stages in Melanoma. CIBCB 2005: 455-460 - Christian Spieth, Felix Streichert, Nora Speer, Christian Sinzger, Kathrin Eberhard, Andreas Zell:
Predicting Single Genes Related to Immune-Relevant Processes. CIBCB 2005: 461-468
Protein Structure Analysis I
- John Hawkins, Mikael Bodén:
Predicting Peroxisomal Proteins. CIBCB 2005: 469-474 - Kenneth Daily, Predrag Radivojac, A. Keith Dunker:
Intrinsic Disorder and Protein modifications: Building an SVM Predictor for Methylation. CIBCB 2005: 475-481 - Deborah Stoffer, L. Gwenn Volkert:
A Neural Network for Predicting Protein Disorder using Amino Acid Hydropathy Values. CIBCB 2005: 482-489
Protein Structure Analysis II
- Uros Midic, A. Keith Dunker, Zoran Obradovic:
Improving Protein Secondary-Structure Prediction by Predicting Ends of Secondary-Structure Segments. CIBCB 2005: 490-497 - Niranjan P. Bidargaddi, Madhu Chetty, Joarder Kamruzzaman:
An Architecture Combining Bayesian segmentation and Neural Network Ensembles for Protein Secondary Structure Prediction. CIBCB 2005: 498-505 - Lutz Hamel, Gongqin Sun, Jing Zhang:
Toward Protein Structure Analysis with Self-Organizing Maps. CIBCB 2005: 506-513 - Denis C. Bauer, Mikael Bodén, Ricarda Thier, Zheng Yuan:
Predicting Structural Disruption of Proteins Caused by Crossover (based on Amino Acid Sequence). CIBCB 2005: 514-520 - Larry Huang, Wen-Lin Huang, Shinn-Ying Ho, Shiow-Fen Hwang:
Interpretable Prediction of Protein Stability Changes upon Mutation by Using Decision Tree. CIBCB 2005: 521-525 - Peng Wai Meng, Jagath C. Rajapakse:
Multi-class Protein Subcellular Localization Classification Using Support Vector Machines. CIBCB 2005: 526-
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