BMC Bioinformatics, Volume 7 - Supplements

Volume 7, Number S-1, 2006

• 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

• 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.
  
• 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

• 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, W. J. 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.