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ORCIDBIBM 2008: Philadephia, Pennsylvania, USA
- Xue-wen Chen, Xiaohua Hu, Sun Kim:
2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008, Philadephia, Pennsylvania, USA, November 3-5, 2008. IEEE Computer Society 2008, ISBN 978-0-7695-3452-7
Regular Papers: Bioinformatics of Diseases
- Young Bun Kim, Jean Gao, Ying Dong, Chin-Rang Yang:
Functional Proteomic Pattern Identification under Low Dose Ionizing Radiation. 3-8
Regular Papers: Biological Databases and Ontologies
- Hong Yang, Rajshekhar Sunderraman, Hao Tian:
bcnQL: A Query Language for Biochemical Network. 11-16 - Xiaohua Zhou, Xiaohua Hu, Xiaodan Zhang, Daniel Duanqing Wu, Tingting He, Aijing Luo:
A Mixture Language Model for Class-Attribute Mining from Biomedical Literature Digital Library. 17-22 - Li An, Hongbo M. Xie
, Mark H. Chin, Zoran Obradovic, Desmond J. Smith, Vasileios Megalooikonomou:
Analysis of Multiplex Gene Expression Maps Obtained by Voxelation. 23-28
Regular Papers: Biological Data Mining and Visualization
- Hong Zhou, Xiao Zeng:
Energy Profile and Secondary Structure Impact shRNA Efficacy. 31-36 - Saira Ali Kazmi, Yoo-Ah Kim, Baikang Pei, Ravi Nori, David W. Rowe, Hsin-Wei Wang, Alan Wong, Dong-Guk Shin:
Meta Analysis of Microarray Data Using Gene Regulation Pathways. 37-42 - Anca I. D. Bucur, Jasper van Leeuwen, Nevenka Dimitrova, Chetan Mittal:
Frequency Sorting Method for Spectral Analysis of DNA Sequences. 43-50 - John Hayward, Sergio A. Alvarez, Carolina Ruiz, Mary Sullivan, Jennifer Tseng, Giles Whalen:
Knowledge Discovery in Clinical Performance of Cancer Patients. 51-58 - Young-Rae Cho, Aidong Zhang:
Discovering Frequent Patterns of Functional Associations in Protein Interaction Networks for Function Prediction. 59-65 - Zheng Chen, Jian Tang:
Using Gene Ontology to Enhance Effectiveness of Similarity Measures for Microarray Data. 66-71 - Rachel Caldwell, Yan-Xia Lin, Ren Zhang:
Correlations of Length Distributions between Non-coding and Coding Sequences of Arabidopsis thaliana. 72-77 - Christine Martin, Antoine Cornuéjols:
Identifying Interface Elements Implied in Protein-Protein Interactions Using Statistical Tests and Frequent Item Sets. 78-83 - Patrick C. H. Ma, Keith C. C. Chan:
Mining Fuzzy Association Patterns in Gene Expression Data for Gene Function Prediction. 84-89 - Jeffrey D. Leblond, Andrew D. Lasiter, Cen Li, Ramiro Logares, Karin Rengefors, Terence J. Evens:
Applying Clustering and Phylogeny Analysis to Study Dinoflagellates Based on Sterol Composition. 90-97 - Bernard Chen, Jieyue He, Stephen Pellicer, Yi Pan:
Protein Sequence Motif Super-Rule-Tree (SRT) Structure Constructed by Hybrid Hierarchical K-Means Clustering Algorithm. 98-103 - Cornelia Caragea, Jivko Sinapov, Drena Dobbs, Vasant G. Honavar:
Using Global Sequence Similarity to Enhance Biological Sequence Labeling. 104-111
Regular Papers: Comparative Genomics
- Md. Nurul Haque Mollah, Shinto Eguchi:
Robust Composite Interval Mapping for QTL Analysis by Minimum beta-Divergence Method. 115-120 - Jia Zeng, Reda Alhajj, Douglas J. Demetrick:
Effectiveness of Applying Codon Usage Bias for Translational Initiation Sites Prediction. 121-126
Regular Papers: Computational Systems Biology
- Baikang Pei, David W. Rowe, Dong-Guk Shin:
Reverse Engineering of Gene Regulatory Network by Integration of Prior Global Gene Regulatory Information. 129-134 - Jamil Ahmad, Olivier F. Roux:
Invariance Kernel of Biological Regulatory Networks. 135-140 - Vinhthuy Phan, Sudip Saha, Ashutosh Pandey, Tit-Yee Wong:
Synthetic Gene Design with a Large Number of Hidden Stop Codons. 141-146 - Qiong Cheng, Piotr Berman, Robert W. Harrison, Alexander Zelikovsky:
Fast Alignments of Metabolic Networks. 147-152
Regular Papers: Microarray Data Analysis
- Alex Kosorukoff, Saurabh Sinha:
Heart of the Matter: Discovering the Consensus of Multiple Clustering Results. 155-162 - Wei Dai, Olgica Milenkovic, Mona A. Sheikh, Richard G. Baraniuk:
Probe Design for Compressive Sensing DNA Microarrays. 163-169 - Fang-Xiang Wu:
Detecting Significantly Expressed Genes from Their Time-Course Expression Profiles and Its Validation. 170-175
Regular Papers: Protein Structure, Function, and Interactions
- Thomas Grindinger, Feng Luo, Xiu-Feng Wan, Richard H. Scheuermann:
Exploring Core/Periphery Structures in Protein Interaction Networks Provides Structure-Property Relation Insights. 179-186 - Xiaotong Lin, Mei Liu, Xue-wen Chen:
Protein-Protein Interaction Prediction and Assessment from Model Organisms. 187-192 - Seak Fei Lei, Jun Huan:
Towards Site-Based Protein Functional Annotations. 193-198 - Deepak Bandyopadhyay, Jun Huan, Jinze Liu, Jan F. Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha:
Functional Neighbors: Inferring Relationships between Non-Homologous Protein Families Using Family-Specific Packing Motifs. 199-206 - Andrew C. Doxey, Zhenyu Cheng, Brendan J. McConkey:
Discrimination of Insoluble-Carbohydrate Binding Proteins and Their Binding Sites Using a 3D Motif Detection Method. 207-213
Regular Papers: Sequence Analysis, Evolution and Phylogeny
- Pavel P. Kuksa, Pai-Hsi Huang, Vladimir Pavlovic:
On the Role of Local Matching for Efficient Semi-supervised Protein Sequence Classification. 217-222 - Niranjan Nagarajan, Carl Kingsford:
Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques. 223-230 - Jing Xia, Doina Caragea, Susan J. Brown:
Exploring Alternative Splicing Features Using Support Vector Machines. 231-238 - Seung-Jin Sul, Suzanne J. Matthews, Tiffani L. Williams:
New Approaches to Compare Phylogenetic Search Heuristics. 239-245
Regular Papers: Healthcare Informatics
- Jung Hun Oh, Jean Gao, Kevin P. Rosenblatt:
Biological Data Outlier Detection Based on Kullback-Leibler Divergence. 249-254
Regular Papers: Biomedical Text Mining and Ontologies
- Snehasis Mukhopadhyay, Mathew J. Palakal, Kalyan Maddu:
Multi-way Association Extraction from Biological Text Documents Using Hyper-Graphs. 257-262 - Natsu Ishii, Asako Koike, Yasunori Yamamoto, Toshihisa Takagi:
Figure Classification in Biomedical Literature towards Figure Mining. 263-269
Short Papers: Bioinformatics of Diseases
- Udi Rubinstein, Yifat Felder, Nana Ginzbourg, Michael Gurevich, Tamir Tuller:
Editing Bayesian Networks: A New Approach for Combining Prior Knowledge and Gene Expression Measurements for Researching Diseases. 273-277 - Antonina Mitrofanova, Samantha Kleinberg, Jane Carlton, Simon Kasif, Bud Mishra:
Systems Biology via Redescription and Ontologies (III): Protein Classification Using Malaria Parasite's Temporal Transcriptomic Profiles. 278-283 - Maja Hadzic, Meifania Chen, Tharam S. Dillon:
Towards the Mental Health Ontology. 284-288 - Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar:
Predicting Protective Linear B-Cell Epitopes Using Evolutionary Information. 289-292
Short Papers: Biological Databases and Ontologies
- Shahriyar Hossain, Munirul Islam, Jesmin, Hasan M. Jamil:
PhyQL: A Web-Based Phylogenetic Visual Query Engine. 295-298
Short Papers: Biological Data Mining and Visualization
- Qiang Wang, Yunming Ye, Joshua Zhexue Huang:
A Changing Window Approach to Exploring Gene Expression Patterns. 301-304 - Lin Liu, Li Xiong, James J. Lu, Kim M. Gernert, Vicki Hertzberg:
Comparing and Clustering Flow Cytometry Data. 305-309 - Jiarui Ding, Jin-Hong Shi, An-Min Zou, Fang-Xiang Wu:
Feature Selection for Tandem Mass Spectrum Quality Assessment. 310-313 - Antonina Mitrofanova, Vladimir Pavlovic, Bud Mishra:
Integrative Protein Function Transfer Using Factor Graphs and Heterogeneous Data Sources. 314-318
Short Papers: Computational Systems Biology
- Winnie W. M. Lam, Keith C. C. Chan:
A Graph Mining Algorithm for Classifying Chemical Compounds. 321-324 - Perry Evans, Ted Sandler, Lyle H. Ungar:
Protein-Protein Interaction Network Alignment by Quantitative Simulation. 325-328 - Peng Yu, Xi Chen, David Z. Pan, Andrew D. Ellington:
Synthetic Biology Design and Analysis: A Case Study of Frequency Entrained Biological Clock. 329-334 - Taehyong Kim, Woochang Hwang, Aidong Zhang, Surajit Sen, Murali Ramanathan:
Multi-agent Model Analysis of the Containment Strategy for Avian Influenza (AI) in South Korea. 335-338 - Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen:
Reconstruction of Regulator Activity in E. coli Post-Transcription Processes. 339-342 - Erliang Zeng, Giri Narasimhan, Lisa Schneper, Kalai Mathee:
A Functional Network of Yeast Genes Using Gene Ontology Information. 343-346
Short Papers: Gene Regulation and Transcriptomics
- Jung Hoon Woo, Eunjee Lee, Sung-Bum Cho, Ju Han Kim:
Estimating Regulatory Associations of Genomic Loci and Biological Pathways in Lymphoblastoid Cells. 349-352 - Hyojin Kang, Eunkyoo Oh, Giltsu Choi, Doheon Lee:
Genome-Wide DNA-Binding Specificity of PIL5, a Arabidopsis Basic Helix-Loop-Helix (bHLH) Transcription Factor. 353-356 - Kazuyuki Numata, Seiya Imoto, Satoru Miyano:
Partial Order-Based Bayesian Network Learning Algorithm for Estimating Gene Networks. 357-360
Short Papers: Microarray Data Analysis
- Junwan Liu, Zhoujun Li, Feifei Liu, Yiming Chen:
Multi-objective Particle Swarm Optimization Biclustering of Microarray Data. 363-366 - Gyan Prakash Srivastava, Jing Qiu, Dong Xu:
Functional Annotation from Meta-analysis of Microarray Datasets. 367-371 - Siyuan Ren, Zoran Obradovic:
Improvement of Survival Prediction from Gene Expression Profiles by Mining of Prior Knowledge. 372-375 - Gaurav Pandey, Lakshmi Naarayanan Ramakrishnan, Michael S. Steinbach, Vipin Kumar:
Systematic Evaluation of Scaling Methods for Gene Expression Data. 376-381 - Azadeh Mohammadi, Mohammad Hossein Saraee:
Estimating Missing Value in Microarray Data Using Fuzzy Clustering and Gene Ontology. 382-385 - Xin Zhou, Xinyu Wu, Ke Zhi Mao, David P. Tuck:
Fast Gene Selection for Microarray Data Using SVM-Based Evaluation Criterion. 386-389
Short Papers: Protein Structure, Function, and Interactions
- Yazhene Krishnaraj, Chandan K. Reddy:
Boosting Methods for Protein Fold Recognition: An Empirical Comparison. 393-396 - Ivan Merelli, Paolo Cozzi, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi:
Images Based System for Surface Matching in Macromolecular Screening. 397-401 - Majid Masso, Ewy A. Mathé, Nida Parvez, Kahkeshan Hijazi, Iosif I. Vaisman:
Structure Based Functional Analysis of Bacteriophage f1 Gene V Protein. 402-406 - Hui Liu, Hai Deng:
Identifying Calcium-Binding Sites with Oxygen-Carbon Shell Geometric and Chemic Criteria-A Graph-Based Approach. 407-410 - Xiaoyu Jiang, Naoki Nariai, Martin Steffen, Simon Kasif, David Gold, Eric D. Kolaczyk:
Combining Hierarchical Inference in Ontologies with Heterogeneous Data Sources Improves Gene Function Prediction. 411-416 - Osamu Maruyama, Hideki Hirakawa, Takao Iwayanagi, Yoshiko Ishida, Shizu Takeda, Jun Otomo, Satoru Kuhara:
Evaluating Protein Sequence Signatures Inferred from Protein-Protein Interaction Data by Gene Ontology Annotations. 417-420 - Vítor Santos Costa, Nuno A. Fonseca, Rui Camacho:
LogCHEM: Interactive Discriminative Mining of Chemical Structure. 421-426
Short Papers: Sequence Analysis, Evolution and Phylogeny
- Vishal Thapar, Sanguthevar Rajasekaran:
Sampling Based Meta-algorithms for Accurate Multiple Sequence Alignment. 429-432 - Ankit Agrawal, Xiaoqiu Huang:
Conservative, Non-conservative and Average Pairwise Statistical Significance of Local Sequence Alignment. 433-436 - Ruinan Zhang, Huzefa Rangwala, George Karypis:
Genome Alignments Using MPI-LAGAN. 437-440
Short Papers: Healthcare Informatics
- Tian Mi, Robert H. Aseltine, Sanguthevar Rajasekaran:
Data Integration on Multiple Data Sets. 443-446
Short Papers: Biomedical Text Mining and Ontologies
- Vasileios Kandylas, Lyle H. Ungar, Ted Sandler, Shane T. Jensen:
Multiway Clustering for Creating Biomedical Term Sets. 449-452 - Lawrence H. Reeve, Hyoil Han, Ari D. Brooks:
Online Biomedical Concept Annotation Using Language Model Mapping. 453-456 - Min Song, Alex Rudniy:
Detecting Duplicate Biological Entities Using Markov Random Field-Based Edit Distance. 457-460 - Guixian Xu, Lanlan Yin, Manabu Torii, Zhendong Niu, Cathy H. Wu, Zhang-Zhi Hu, Hongfang Liu:
Document Classification for Mining Host Pathogen Protein-Protein Interactions. 461-466 - Zhang-Zhi Hu, K. Bretonnel Cohen, Lynette Hirschman, Alfonso Valencia, Hongfang Liu, Michelle G. Giglio, Cathy H. Wu:
iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology. 467-472 - Syed Toufeeq Ahmed, Hasan Davulcu, Chitta Baral:
Extracting Protein-Protein Interactions from MEDLINE Using Syntactic Roles. 473-476
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