Table of Contents

• Functional Proteomic Pattern Identification under Low Dose Ionizing RadiationYoung Bun Kim, Jean Gao, Ying Dong, Chin-Rang Yang. 3-8 [doi]
• bcnQL: A Query Language for Biochemical NetworkHong Yang, Rajshekhar Sunderraman, Hao Tian. 11-16 [doi]
• A Mixture Language Model for Class-Attribute Mining from Biomedical Literature Digital LibraryXiaohua Zhou, Xiaohua Hu, Xiaodan Zhang, Daniel Duanqing Wu, Tingting He, Aijing Luo. 17-22 [doi]
• Analysis of Multiplex Gene Expression Maps Obtained by VoxelationLi An, Hongbo Xie, Mark H. Chin, Zoran Obradovic, Desmond J. Smith, Vasileios Megalooikonomou. 23-28 [doi]
• Energy Profile and Secondary Structure Impact shRNA EfficacyHong Zhou, Xiao Zeng. 31-36 [doi]
• Meta Analysis of Microarray Data Using Gene Regulation PathwaysSaira Ali Kazmi, Yoo Ah Kim, Baikang Pei, Ravi Nori, David W. Rowe, Hsin-Wei Wang, Alan Wong, Dong-Guk Shin. 37-42 [doi]
• Frequency Sorting Method for Spectral Analysis of DNA SequencesAnca Bucur, Jasper van Leeuwen, Nevenka Dimitrova, Chetan Mittal. 43-50 [doi]
• Knowledge Discovery in Clinical Performance of Cancer PatientsJohn Hayward, Sergio A. Alvarez, Carolina Ruiz, Mary Sullivan, Jennifer Tseng, Giles Whalen. 51-58 [doi]
• Discovering Frequent Patterns of Functional Associations in Protein Interaction Networks for Function PredictionYoung-Rae Cho, Aidong Zhang. 59-65 [doi]
• Using Gene Ontology to Enhance Effectiveness of Similarity Measures for Microarray DataZheng Chen, Jian Tang. 66-71 [doi]
• Correlations of Length Distributions between Non-coding and Coding Sequences of Arabidopsis thalianaRachel Caldwell, Yan-Xia Lin, Ren Zhang. 72-77 [doi]
• Identifying Interface Elements Implied in Protein-Protein Interactions Using Statistical Tests and Frequent Item SetsChristine Martin, Antoine Cornuéjols. 78-83 [doi]
• Mining Fuzzy Association Patterns in Gene Expression Data for Gene Function PredictionPatrick C. H. Ma, Keith C. C. Chan. 84-89 [doi]
• Applying Clustering and Phylogeny Analysis to Study Dinoflagellates Based on Sterol CompositionJeffrey D. Leblond, Andrew D. Lasiter, Cen Li, Ramiro Logares, Karin Rengefors, Terence J. Evens. 90-97 [doi]
• Protein Sequence Motif Super-Rule-Tree (SRT) Structure Constructed by Hybrid Hierarchical K-Means Clustering AlgorithmBernard Chen, Jieyue He, Stephen Pellicer, Yi Pan. 98-103 [doi]
• Using Global Sequence Similarity to Enhance Biological Sequence LabelingCornelia Caragea, Jivko Sinapov, Drena Dobbs, Vasant Honavar. 104-111 [doi]
• Robust Composite Interval Mapping for QTL Analysis by Minimum beta-Divergence MethodMd. Nurul Haque Mollah, Shinto Eguchi. 115-120 [doi]
• Effectiveness of Applying Codon Usage Bias for Translational Initiation Sites PredictionJia Zeng, Reda Alhajj, Douglas J. Demetrick. 121-126 [doi]
• Reverse Engineering of Gene Regulatory Network by Integration of Prior Global Gene Regulatory InformationBaikang Pei, David W. Rowe, Dong-Guk Shin. 129-134 [doi]
• Invariance Kernel of Biological Regulatory NetworksJamil Ahmad, Olivier Roux. 135-140 [doi]
• Synthetic Gene Design with a Large Number of Hidden Stop CodonsVinhthuy Phan, Sudip Saha, Ashutosh Pandey, Tit-Yee Wong. 141-146 [doi]
• Fast Alignments of Metabolic NetworksQiong Cheng, Piotr Berman, Robert W. Harrison, Alexander Zelikovsky. 147-152 [doi]
• Heart of the Matter: Discovering the Consensus of Multiple Clustering ResultsAlex Kosorukoff, Saurabh Sinha. 155-162 [doi]
• Probe Design for Compressive Sensing DNA MicroarraysWei Dai, Olgica Milenkovic, Mona A. Sheikh, Richard G. Baraniuk. 163-169 [doi]
• Detecting Significantly Expressed Genes from Their Time-Course Expression Profiles and Its ValidationFang-Xiang Wu. 170-175 [doi]
• Exploring Core/Periphery Structures in Protein Interaction Networks Provides Structure-Property Relation InsightsThomas Grindinger, Feng Luo, Xiu-Feng Wan, Richard H. Scheuermann. 179-186 [doi]
• Protein-Protein Interaction Prediction and Assessment from Model OrganismsXiaotong Lin, Mei Liu, Xue-wen Chen. 187-192 [doi]
• Towards Site-Based Protein Functional AnnotationsSeak Fei Lei, Jun Huan. 193-198 [doi]
• Functional Neighbors: Inferring Relationships between Non-Homologous Protein Families Using Family-Specific Packing MotifsDeepak Bandyopadhyay, Jun (Luke) Huan, Jinze Liu, Jan Prins, Jack Snoeyink, Wei Wang 0010, Alexander Tropsha. 199-206 [doi]
• Discrimination of Insoluble-Carbohydrate Binding Proteins and Their Binding Sites Using a 3D Motif Detection MethodAndrew C. Doxey, Zhenyu Cheng, Brendan J. McConkey. 207-213 [doi]
• On the Role of Local Matching for Efficient Semi-supervised Protein Sequence ClassificationPavel P. Kuksa, Pai-Hsi Huang, Vladimir Pavlovic. 217-222 [doi]
• Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal BicliquesNiranjan Nagarajan, Carl Kingsford. 223-230 [doi]
• Exploring Alternative Splicing Features Using Support Vector MachinesJing Xia, Doina Caragea, Susan Brown. 231-238 [doi]
• New Approaches to Compare Phylogenetic Search HeuristicsSeung-Jin Sul, Suzanne Matthews, Tiffani L. Williams. 239-245 [doi]
• Biological Data Outlier Detection Based on Kullback-Leibler DivergenceJung Hun Oh, Jean Gao, Kevin P. Rosenblatt. 249-254 [doi]
• Multi-way Association Extraction from Biological Text Documents Using Hyper-GraphsSnehasis Mukhopadhyay, Mathew J. Palakal, Kalyan Maddu. 257-262 [doi]
• Figure Classification in Biomedical Literature towards Figure MiningNatsu Ishii, Asako Koike, Yasunori Yamamoto, Toshihisa Takagi. 263-269 [doi]
• Editing Bayesian Networks: A New Approach for Combining Prior Knowledge and Gene Expression Measurements for Researching DiseasesUdi Rubinstein, Yifat Felder, Nana Ginzbourg, Michael Gurevich, Tamir Tuller. 273-277 [doi]
• Systems Biology via Redescription and Ontologies (III): Protein Classification Using Malaria Parasite s Temporal Transcriptomic ProfilesAntonina Mitrofanova, Samantha Kleinberg, Jane Carlton, Simon Kasif, Bud Mishra. 278-283 [doi]
• Towards the Mental Health OntologyMaja Hadzic, Meifania Chen, Tharam S. Dillon. 284-288 [doi]
• Predicting Protective Linear B-Cell Epitopes Using Evolutionary InformationYasser El-Manzalawy, Drena Dobbs, Vasant Honavar. 289-292 [doi]
• PhyQL: A Web-Based Phylogenetic Visual Query EngineShahriyar Hossain, Munirul Islam, Jesmin, Hasan M. Jamil. 295-298 [doi]
• A Changing Window Approach to Exploring Gene Expression PatternsQiang Wang, Yunming Ye, Joshua Zhexue Huang. 301-304 [doi]
• Comparing and Clustering Flow Cytometry DataLin Liu, Li Xiong, James J. Lu, Kim M. Gernert, Vicki Hertzberg. 305-309 [doi]
• Feature Selection for Tandem Mass Spectrum Quality AssessmentJiarui Ding, Jin-Hong Shi, An-Min Zou, Fang-Xiang Wu. 310-313 [doi]
• Integrative Protein Function Transfer Using Factor Graphs and Heterogeneous Data SourcesAntonina Mitrofanova, Vladimir Pavlovic, Bud Mishra. 314-318 [doi]
• A Graph Mining Algorithm for Classifying Chemical CompoundsWinnie W. M. Lam, Keith C. C. Chan. 321-324 [doi]
• Protein-Protein Interaction Network Alignment by Quantitative SimulationPerry Evans, Ted Sandler, Lyle H. Ungar. 325-328 [doi]
• Synthetic Biology Design and Analysis: A Case Study of Frequency Entrained Biological ClockPeng Yu, Xi Chen, David Z. Pan, Andrew D. Ellington. 329-334 [doi]
• Multi-agent Model Analysis of the Containment Strategy for Avian Influenza (AI) in South KoreaTaehyong Kim, Woochang Hwang, Aidong Zhang, Surajit Sen, Murali Ramanathan. 335-338 [doi]
• Reconstruction of Regulator Activity in E. coli Post-Transcription ProcessesRui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen. 339-342 [doi]
• A Functional Network of Yeast Genes Using Gene Ontology InformationErliang Zeng, Giri Narasimhan, Lisa Schneper, Kalai Mathee. 343-346 [doi]
• Estimating Regulatory Associations of Genomic Loci and Biological Pathways in Lymphoblastoid CellsJung Hoon Woo, Eunjee Lee, Sung-Bum Cho, Ju Han Kim. 349-352 [doi]
• Genome-Wide DNA-Binding Specificity of PIL5, a Arabidopsis Basic Helix-Loop-Helix (bHLH) Transcription FactorHyojin Kang, Eunkyoo Oh, Giltsu Choi, Doheon Lee. 353-356 [doi]
• Partial Order-Based Bayesian Network Learning Algorithm for Estimating Gene NetworksKazuyuki Numata, Seiya Imoto, Satoru Miyano. 357-360 [doi]
• Multi-objective Particle Swarm Optimization Biclustering of Microarray DataJunwan Liu, Zhoujun Li, Feifei Liu, Yiming Chen. 363-366 [doi]
• Functional Annotation from Meta-analysis of Microarray DatasetsGyan Prakash Srivastava, Jing Qiu, Dong Xu. 367-371 [doi]
• Improvement of Survival Prediction from Gene Expression Profiles by Mining of Prior KnowledgeSiyuan Ren, Zoran Obradovic. 372-375 [doi]
• Systematic Evaluation of Scaling Methods for Gene Expression DataGaurav Pandey, Lakshmi Naarayanan Ramakrishnan, Michael Steinbach, Vipin Kumar. 376-381 [doi]
• Estimating Missing Value in Microarray Data Using Fuzzy Clustering and Gene OntologyAzadeh Mohammadi, Mohammad Hossein Saraee. 382-385 [doi]
• Fast Gene Selection for Microarray Data Using SVM-Based Evaluation CriterionXin Zhou, X. Y. Wu, K. Z. Mao, David P. Tuck. 386-389 [doi]
• Boosting Methods for Protein Fold Recognition: An Empirical ComparisonYazhene Krishnaraj, Chandan K. Reddy. 393-396 [doi]
• Images Based System for Surface Matching in Macromolecular ScreeningIvan Merelli, Paolo Cozzi, Daniele D Agostino, Andrea Clematis, Luciano Milanesi. 397-401 [doi]
• Structure Based Functional Analysis of Bacteriophage f1 Gene V ProteinMajid Masso, Ewy Mathe, Nida Parvez, Kahkeshan Hijazi, Iosif I. Vaisman. 402-406 [doi]
• Identifying Calcium-Binding Sites with Oxygen-Carbon Shell Geometric and Chemic Criteria-A Graph-Based ApproachHui Liu, Hai Deng. 407-410 [doi]
• Combining Hierarchical Inference in Ontologies with Heterogeneous Data Sources Improves Gene Function PredictionXiaoyu Jiang, Naoki Nariai, Martin Steffen, Simon Kasif, David Gold, Eric D. Kolaczyk. 411-416 [doi]
• Evaluating Protein Sequence Signatures Inferred from Protein-Protein Interaction Data by Gene Ontology AnnotationsOsamu Maruyama, Hideki Hirakawa, Takao Iwayanagi, Yoshiko Ishida, Shizu Takeda, Jun Otomo, Satoru Kuhara. 417-420 [doi]
• LogCHEM: Interactive Discriminative Mining of Chemical StructureVítor Santos Costa, Nuno A. Fonseca, Rui Camacho. 421-426 [doi]
• Sampling Based Meta-algorithms for Accurate Multiple Sequence AlignmentVishal Thapar, Sanguthevar Rajasekaran. 429-432 [doi]
• Conservative, Non-conservative and Average Pairwise Statistical Significance of Local Sequence AlignmentAnkit Agrawal, Xiaoqiu Huang. 433-436 [doi]
• Genome Alignments Using MPI-LAGANRuinan Zhang, Huzefa Rangwala, George Karypis. 437-440 [doi]
• Data Integration on Multiple Data SetsTian Mi, Robert Aseltine, Sanguthevar Rajasekaran. 443-446 [doi]
• Multiway Clustering for Creating Biomedical Term SetsVasileios Kandylas, Lyle H. Ungar, Ted Sandler, Shane Jensen. 449-452 [doi]
• Online Biomedical Concept Annotation Using Language Model MappingLawrence H. Reeve, Hyoil Han, Ari D. Brooks. 453-456 [doi]
• Detecting Duplicate Biological Entities Using Markov Random Field-Based Edit DistanceMin Song, Alex Rudniy. 457-460 [doi]
• Document Classification for Mining Host Pathogen Protein-Protein InteractionsGuixian Xu, Lanlan Yin, Manabu Torii, Zhendong Niu, Cathy H. Wu, Zhang-Zhi Hu, Hongfang Liu. 461-466 [doi]
• iProLINK: A Framework for Linking Text Mining with Ontology and Systems BiologyZhang-Zhi Hu, K. Bretonnel Cohen, Lynette Hirschman, Alfonso Valencia, Hongfang Liu, Michelle G. Giglio, Cathy H. Wu. 467-472 [doi]
• Extracting Protein-Protein Interactions from MEDLINE Using Syntactic RolesSyed Toufeeq Ahmed, Hasan Davulcu, Chitta Baral. 473-476 [doi]