Volume 7, Number S-1, 2006

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  Cornelis A. Albers, Martijn A. R. Leisink, Hilbert J. Kappen: The Cluster Variation Method for Efficient Linkage Analysis on Extended Pedigrees.
• 
  Asa Ben-Hur, William Stafford Noble: Choosing negative examples for the prediction of protein-protein interactions.
• 
  Tomer Hertz, Chen Yanover: PepDist: A New Framework for Protein-Peptide Binding Prediction based on Learning Peptide Distance Functions.
• 
  Tsuyoshi Kato, Yukio Murata, Koh Miura, Kiyoshi Asai, Paul Horton, Koji Tsuda, Wataru Fujibuchi: Network-based de-noising improves prediction from microarray data.
• 
  Anshul Kundaje, Manuel Middendorf, Mihir Shah, Chris Wiggins, Yoav Freund, Christina S. Leslie: A classification-based framework for predicting and analyzing gene regulatory response.
• 
  Michal Linial: The Secrets of a Functional Synapse - From a Computational and Experimental Viewpoint.
• 
  Adam A. Margolin, Ilya Nemenman, Katia Basso, Chris Wiggins, Gustavo Stolovitzky, Riccardo Dalla Favera, Andrea Califano: ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context.
• 
  Sean O'Rourke, Gal Chechik, Robin Friedman, Eleazar Eskin: Discrete profile comparison using information bottleneck.
• 
  Gunnar Rätsch, Sören Sonnenburg, Christin Schäfer: Learning Interpretable SVMs for Biological Sequence Classification.
• 
  Jason Weston, Rui Kuang, Christina S. Leslie, William Stafford Noble: Protein Ranking by Semi-Supervised Network Propagation.
• 
  Zizhen Yao, Walter L. Ruzzo: A Regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data.

Volume 7, Number S-2, 2006

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  Jonathan D. Wren, Yuriy Gusev, Andrey A. Ptitsyn, Stephen Winters-Hilt: Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society.
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  Vijayaraj Nagarajan, Navodit Kaushik, Beddhu Murali, Chaoyang Zhang, Sanyogita Lakhera, Mohamed O. Elasri, Youping Deng: A Fourier Transformation based Method to Mine Peptide Space for Antimicrobial Activity.
• 
  Jonathan D. Wren: A scalable machine-learning approach to recognize chemical names within large text databases.
• 
  Stephen Winters-Hilt, Anil Yelundur, Charlie McChesney, Matthew Landry: Support Vector Machine Implementations for Classification & Clustering.
• 
  Raja Loganantharaj, Satish Cheepala, John Clifford: Metric for Measuring the Effectiveness of Clustering of DNA Microarray Expression.
• 
  Venkata Thodima, Mehdi Pirooznia, Youping Deng: RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers.
• 
  Laila A. Nahum, Matthew T. Reynolds, Zhengyuan O. Wang, Jeremiah J. Faith, Rahul Jonna, Zhi J. Jiang, Thomas J. Meyer, David D. Pollock: EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity.
• 
  Tomasz G. Smolinski, Roger Buchanan, Grzegorz M. Boratyn, Mariofanna G. Milanova, Astrid A. Prinz: Independent Component Analysis-motivated Approach to Classificatory Decomposition of Cortical Evoked Potentials.
• 
  Tao Han, Jianyong Wang, Weida Tong, Martha M. Moore, James C. Fuscoe, Tao Chen: Microarray analysis distinguishes differential gene expression patterns from large and small colony Thymidine kinase mutants of L5178Y mouse lymphoma cells.
• 
  Andrey A. Ptitsyn, Sanjin Zvonic, Jeffrey M. Gimble: Permutation test for periodicity in short time series data.
• 
  Robert R. Delongchamp, Taewon Lee, Cruz Velasco: A method for computing the overall statistical significance of a treatment effect among a group of genes.
• 
  Yuanyuan Ding, Dawn Wilkins: Improving the Performance of SVM-RFE to Select Genes in Microarray Data.
• 
  Alexander E. Kel, Nico Voss, Ruy Jauregui, Olga V. Kel-Margoulis, Edgar Wingender: Beyond microarrays: Finding key transcription factors controlling signal transduction pathways.
• 
  Stephen Winters-Hilt: Hidden Markov Model Variants and their Application.
• 
  Raja Tanveer Iqbal, Matthew Landry, Stephen Winters-Hilt: DNA Molecule Classification Using Feature Primitives.
• 
  Nan Mei, Lei Guo, Lu Zhang, Leming M. Shi, Yongming Andrew Sun, Chris Fung, Carrie L. Moland, Stacey L. Dial, James C. Fuscoe, Tao Chen: Analysis of gene expression changes in relation to toxicity and tumorigenesis in the livers of Big Blue transgenic rats fed comfrey (Symphytum officinale).
• 
  Tao Han, Cathy D. Melvin, Leming M. Shi, William S. Branham, Carrie L. Moland, P. Scott Pine, Karol L. Thompson, James C. Fuscoe: Improvement in the Reproducibility and Accuracy of DNA Microarray Quantification by Optimizing Hybridization Conditions.
• 
  Lei Guo, Hong Fang, Jim Collins, Xiao-hui Fan, Stacey L. Dial, Alex Wong, Kshama Mehta, Ernice Blann, Leming M. Shi, Weida Tong, Yvonne P. Dragan: Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor alpha agonists.
• 
  Ronald L. Frank, Ajay Mane, Fikret Erçal: An Automated Method for Rapid Identification of Putative Gene Family Members in Plants.
• 
  Tao Chen, Lei Guo, Lu Zhang, Leming M. Shi, Hong Fang, Yongming Sun, James C. Fuscoe, Nan Mei: Gene Expression Profiles Distinguish the Carcinogenic Effects of Aristolochic Acid in Target (Kidney) and Non-target (Liver) Tissues in Rats.
• 
  Stephen Winters-Hilt: Nanopore Detector based analysis of single-molecule conformational kinetics and binding interactions.
• 
  Stephen Winters-Hilt, Matthew Landry, Mark Akeson, Maria Tanase, Iftekhar Amin, Amy Coombs, Eric Morales, John Millet, Carl Baribault, Srikanth Sendamangalam: Cheminformatics methods for novel nanopore analysis of HIV DNA termini.
• 
  Hongmei Sun, Hong Fang, Tao Chen, Roger Perkins, Weida Tong: GOFFA: Gene Ontology For Functional Analysis - A FDA Gene Ontology Tool for Analysis of Genomic and Proteomic Data.

Volume 7, Number S-3, 2006

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  Sophia Ananiadou, Juliane Fluck: Proceedings of the Second International Symposium for Semantic Mining in Biomedicine.
• 
  Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko: Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches.
• 
  Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess, Martin Romacker: An environment for relation mining over richly annotated corpora: the case of GENIA.
• 
  Hong-Woo Chun, Yoshimasa Tsuruoka, Jin-Dong Kim, Rie Shiba, Naoki Nagata, Teruyoshi Hishiki, Jun'ichi Tsujii: Automatic recognition of topic-classified relations between prostate cancer and genes using MEDLINE abstracts.
• 
  K. Bretonnel Cohen, Lawrence Hunter: A critical review of PASBio's argument structures for biomedical verbs.
• 
  Fleur Mougin, Anita Burgun, Olivier Bodenreider: Mapping data elements to terminological resources for integrating biomedical data sources.

Volume 7, Number S-4, 2006

• 
  Youping Deng, Jun Ni, Chaoyang Zhang: Development of computations in bioscience and bioinformatics and its application: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB06).
• 
  Wei Shi, Wanlei Zhou: Frequency distribution of TATA Box and extension sequences on human promoters.
• 
  Ling Qin, Yi Pan, Ling Chen, Yixin Chen: An improved ant colony algorithm with diversified solutions based on the immune strategy.
• 
  Yixin Chen, Andrew Wan, Wei Liu: A fast parallel algorithm for finding the longest common sequence of multiple biosequences.
• 
  Qiangfeng Zhang, YuZhong Zhao, Guoliang Chen, Yun Xu: Estimate haplotype frequencies in pedigrees.
• 
  Xiuzhen Huang, Jing Lai, Steven F. Jennings: Maximum common subgraph: some upper bound and lower bound results.
• 
  Lily R. Liang, Shiyong Lu, Xuena Wang, Yi Lu, Vinay Mandal, Dorrelyn Patacsil, Deepak Kumar: FM-test: a fuzzy-set-theory-based approach to differential gene expression data analysis.
• 
  Kun Yang, Jianzhong Li, Hong Gao: The impact of sample imbalance on identifying differentially expressed genes.
• 
  Ying Wang, Wei Chen, Xu Li, Bing Cheng: Degenerated primer design to amplify the heavy chain variable region from immunoglobulin cDNA.
• 
  Yonghui Chen, Kevin D. Reilly, Alan P. Sprague, Zhijie Guan: SEQOPTICS: a protein sequence clustering system.
• 
  Zhong-Hui Duan, Brent Hughes, Lothar Reichel, Dianne Perez, Ting Shi: The relationship between protein sequences and their gene ontology functions.
• 
  Kang Ning, Hon Wai Leong: Towards a better solution to the shortest common supersequence problem: the deposition and reduction algorithm.
• 
  Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik: Determination of the minimum number of microarray experiments for discovery of gene expression patterns.
• 
  Hang Chen, Fei Gu, Zhengge Huang: Improved Chou-Fasman method for protein secondary structure prediction.
• 
  Chaoyang Zhang, Peng Li, Arun Rajendran, Youping Deng, Dequan Chen: Parallelization of multicategory support vector machines (PMC-SVM) for classifying microarray data.
• 
  Kuan Yang, Youping Deng, Chaoyang Zhang, Mohamed O. Elasri: Identification of new members of hydrophobin family using primary structure analysis.
• 
  Susmita Datta, Somnath Datta: Evaluation of clustering algorithms for gene expression data.
• 
  Guoqing Lu, Liying Jiang, Resa M. K. Helikar, Thaine W. Rowley, Luwen Zhang, Xianfeng Chen, Etsuko N. Moriyama: GenomeBlast: a web tool for small genome comparison.
• 
  Longde Yin, Chun-Hsi Huang, Jun Ni: Clustering of gene expression data: performance and similarity analysis.
• 
  Ryuzo Azuma, Tetsuji Kitagawa, Hiroshi Kobayashi, Akihiko Konagaya: Particle simulation approach for subcellular dynamics and interactions of biological molecules.
• 
  Linyong Mao, W. Jim Zheng: Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.
• 
  Edward J. Perkins, Wenjun Bao, Xin Guan, Choo-Yaw Ang, Russell D. Wolfinger, Tzu-Ming Chu, Sharon A. Meyer, Laura S. Inouye: Comparison of transcriptional responses in liver tissue and primary hepatocyte cell cultures after exposure to hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine.
• 
  Xiaoli Li, Yin-Chet Tan, See-Kiong Ng: Systematic gene function prediction from gene expression data by using a fuzzy nearest-cluster method.
• 
  Ling Qin, Yixin Chen, Yi Pan, Ling Chen: A novel approach to phylogenetic tree construction using stochastic optimization and clustering.
• 
  Mehdi Pirooznia, Youping Deng: SVM Classifier - a comprehensive java interface for support vector machine classification of microarray data.
• 
  Guoqing Lu, The V. Nguyen, Yuannan Xia, Michael Fromm: AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data.
• 
  Maria Stepanova, Feng Lin, Valerie C.-L. Lin: In silico modelling of hormone response elements.

Volume 7, Number S-5, 2006

• 
  Shoba Ranganathan, Martti Tammi, Michael Gribskov, Tin Wee Tan: Establishing bioinformatics research in the Asia Pacific.
• 
  Alan Christoffels, Richard Bartfai, Hamsa Srinivasan, Hans Komen, Laszlo Orban: Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome.
• 
  Josefine Sprenger, J. Lynn Fink, Rohan D. Teasdale: Evaluation and comparison of mammalian subcellular localization prediction methods.
• 
  Asif M. Khan, A. T. Heiny, Kenneth X. Lee, Kellathur N. Srinivasan, Tin Wee Tan, J. Thomas August, Vladimir Brusic: Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus.
• 
  Sourangshu Bhattacharya, Chiranjib Bhattacharyya, Nagasuma Chandra: Projections for fast protein structure retrieval.
• 
  Abdur R. Sikder, Albert Y. Zomaya: Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index.
• 
  Joo Chuan Tong, Tin Wee Tan, Animesh A. Sinha, Shoba Ranganathan: Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6- associated Pemphigus vulgaris.
• 
  Manisha Brahmachary, Christian Schönbach, Liang Yang, Enli Huang, Sin Lam Tan, Rajesh Chowdhary, S. P. T. Krishnan, Chin-Yo Lin, David A. Hume, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Vladimir B. Bajic: Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes.
• 
  Sarita Ranjan, Ranjit Kumar Gundu, Akash Ranjan: MycoperonDB: a database of computationally identified operons and transcriptional units in Mycobacteria.
• 
  Akihiko Konagaya: Trends in life science grid: from computing grid to knowledge grid.
• 
  Richard Tzong-Han Tsai, Cheng-Lung Sung, Hong-Jie Dai, Hsieh-Chuan Hung, Ting-Yi Sung, Wen-Lian Hsu: NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition.
• 
  Urmila Kulkarni-Kale, Shriram Bhosle, G. Sunitha Manjari, Manali Joshi, Sandeep Bansode, Ashok S. Kolaskar: Curation of viral genomes: challenges, applications and the way forward.
• 
  H. H. Lin, L. Y. Han, H. L. Zhang, C. J. Zheng, B. Xie, Zhi Wei Cao, Yu Zong Chen: Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach.
• 
  Lawrence J. K. Wee, Tin Wee Tan, Shoba Ranganathan: SVM-based prediction of caspase substrate cleavage sites.
• 
  A. K. M. A. Baten, Bill C. H. Chang, Saman K. Halgamuge, Jason Li: Splice site identification using probabilistic parameters and SVM classification.
• 
  Xiaomei Wu, Lei Zhu, Jie Guo, Cong Fu, Hongjun Zhou, Dong Dong, Zhenbo Li, Da-Yong Zhang, Kui Lin: SPIDer: Saccharomyces protein-protein interaction database.
• 
  Anita Suresh, Chandra Verma: Modelling study of dimerization in mammalian defensins.
• 
  Chung-Yen Lin, Shu-Hwa Chen, Chi-Shiang Cho, Chia-Ling Chen, Fan-Kai Lin, Chieh Hua Lin, Pao-Yang Chen, Chen-Zen Lo, Chao A. Hsiung: Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology.
• 
  Suresh Mathivanan, Balamurugan Periaswamy, T. K. B. Gandhi, Kumaran Kandasamy, Shubha Suresh, Riaz Mohmood, Y. L. Ramachandra, Akhilesh Pandey: An evaluation of human protein-protein interaction data in the public domain.
• 
  Rahul Thadani, Martti T. Tammi: MicroTar: predicting microRNA targets from RNA duplexes.
• 
  Sylvain Forêt, Miriam R. Kantorovitz, Conrad J. Burden: Asymptotic behaviour and optimal word size for exact and approximate word matches between random sequences.
• 
  Shigeru Takasaki, Yoshihiro Kawamura, Akihiko Konagaya: Selecting effective siRNA sequences by using radial basis function network and decision tree learning.

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