Journal: BMC Bioinformatics

Volume 7, Issue S-5

0 -- 0Alan Christoffels, Richard Bartfai, Hamsa Srinivasan, Hans Komen, Laszlo Orban. Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome
0 -- 0Urmila Kulkarni-Kale, Shriram Bhosle, G. Sunitha Manjari, Manali Joshi, Sandeep Bansode, Ashok S. Kolaskar. Curation of viral genomes: challenges, applications and the way forward
0 -- 0H. 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
0 -- 0Josefine Sprenger, J. Lynn Fink, Rohan D. Teasdale. Evaluation and comparison of mammalian subcellular localization prediction methods
0 -- 0Anita Suresh, Chandra Verma. Modelling study of dimerization in mammalian defensins
0 -- 0Asif 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
0 -- 0Abdur R. Sikder, Albert Y. Zomaya. Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index
0 -- 0Sarita Ranjan, Ranjit Kumar Gundu, Akash Ranjan. MycoperonDB: a database of computationally identified operons and transcriptional units in Mycobacteria
0 -- 0Xiaomei Wu, Lei Zhu, Jie Guo, Cong Fu, Hongjun Zhou, Dong Dong, Zhenbo Li, Da-Yong Zhang, Kui Lin. SPIDer: ::::Saccharomyces ::::protein-protein interaction database
0 -- 0Joo 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
0 -- 0Manisha 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
0 -- 0Shoba Ranganathan, Martti Tammi, Michael Gribskov, Tin Wee Tan. Establishing bioinformatics research in the Asia Pacific
0 -- 0A. K. M. A. Baten, Bill C. H. Chang, Saman K. Halgamuge, Jason Li. Splice site identification using probabilistic parameters and SVM classification
0 -- 0Lawrence J. K. Wee, Tin Wee Tan, Shoba Ranganathan. SVM-based prediction of caspase substrate cleavage sites
0 -- 0Richard 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
0 -- 0Sourangshu Bhattacharya, Chiranjib Bhattacharyya, Nagasuma Chandra. Projections for fast protein structure retrieval
0 -- 0Rahul Thadani, Martti T. Tammi. MicroTar: predicting microRNA targets from RNA duplexes
0 -- 0Chung-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
0 -- 0Akihiko Konagaya. Trends in life science grid: from computing grid to knowledge grid
0 -- 0Shigeru Takasaki, Yoshihiro Kawamura, Akihiko Konagaya. Selecting effective siRNA sequences by using radial basis function network and decision tree learning
0 -- 0Sylvain Forêt, Miriam R. Kantorovitz, Conrad J. Burden. Asymptotic behaviour and optimal word size for exact and approximate word matches between random sequences
0 -- 0Suresh 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

Volume 7, Issue S-4

0 -- 0Linyong Mao, W. Jim Zheng. Combining comparative genomics with ::::de novo ::::motif discovery to identify human transcription factor DNA-binding motifs
0 -- 0Zhong-Hui Duan, Brent Hughes, Lothar Reichel, Dianne Perez, Ting Shi. The relationship between protein sequences and their gene ontology functions
0 -- 0Xiuzhen Huang, Jing Lai, Steven F. Jennings. Maximum common subgraph: some upper bound and lower bound results
0 -- 0Kang Ning, Hon Wai Leong. Towards a better solution to the shortest common supersequence problem: the deposition and reduction algorithm
0 -- 0Hang Chen, Fei Gu, Zhengge Huang. Improved Chou-Fasman method for protein secondary structure prediction
0 -- 0Guoqing 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
0 -- 0Susmita Datta, Somnath Datta. Evaluation of clustering algorithms for gene expression data
0 -- 0Kun Yang, Jianzhong Li, Hong Gao. The impact of sample imbalance on identifying differentially expressed genes
0 -- 0Xiao-Li Li, Yin-Chet Tan, See-Kiong Ng. Systematic gene function prediction from gene expression data by using a fuzzy nearest-cluster method
0 -- 0Kuan Yang, Youping Deng, Chaoyang Zhang, Mohamed Elasri. Identification of new members of hydrophobin family using primary structure analysis
0 -- 0Ying Wang, Wei Chen, Xu Li, Bing Cheng. Degenerated primer design to amplify the heavy chain variable region from immunoglobulin cDNA
0 -- 0Yixin Chen, Andrew Wan, Wei Liu. A fast parallel algorithm for finding the longest common sequence of multiple biosequences
0 -- 0Lily 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
0 -- 0Ling Qin, Yixin Chen, Yi Pan, Ling Chen. A novel approach to phylogenetic tree construction using stochastic optimization and clustering
0 -- 0Wei Shi, Wanlei Zhou. Frequency distribution of TATA Box and extension sequences on human promoters
0 -- 0Chaoyang Zhang, Peng Li, Arun Rajendran, Youping Deng, Dequan Chen. Parallelization of multicategory support vector machines (PMC-SVM) for classifying microarray data
0 -- 0Guoqing Lu, The V. Nguyen, Yuannan Xia, Michael Fromm. AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data
0 -- 0Maria Stepanova, Feng Lin, Valerie C.-L. Lin. ::::In silico ::::modelling of hormone response elements
0 -- 0Longde Yin, Chun-Hsi Huang, Jun Ni. Clustering of gene expression data: performance and similarity analysis
0 -- 0Yonghui Chen, Kevin D. Reilly, Alan P. Sprague, Zhijie Guan. SEQOPTICS: a protein sequence clustering system
0 -- 0Mehdi Pirooznia, Youping Deng. SVM Classifier - a comprehensive java interface for support vector machine classification of microarray data
0 -- 0Youping 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)
0 -- 0Qiangfeng Zhang, YuZhong Zhao, Guoliang Chen, Yun Xu. Estimate haplotype frequencies in pedigrees
0 -- 0Fang-Xiang Wu, W. J. Zhang, Anthony J. Kusalik. Determination of the minimum number of microarray experiments for discovery of gene expression patterns
0 -- 0Edward 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
0 -- 0Ryuzo Azuma, Tetsuji Kitagawa, Hiroshi Kobayashi, Akihiko Konagaya. Particle simulation approach for subcellular dynamics and interactions of biological molecules
0 -- 0Ling Qin, Yi Pan, Ling Chen, Yixin Chen. An improved ant colony algorithm with diversified solutions based on the immune strategy

Volume 7, Issue S-3

0 -- 0Sophia Ananiadou, Juliane Fluck. Proceedings of the Second International Symposium for Semantic Mining in Biomedicine
0 -- 0K. Bretonnel Cohen, Lawrence Hunter. A critical review of PASBio s argument structures for biomedical verbs
0 -- 0Fleur Mougin, Anita Burgun, Olivier Bodenreider. Mapping data elements to terminological resources for integrating biomedical data sources
0 -- 0Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko. Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches
0 -- 0Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess, Martin Romacker. An environment for relation mining over richly annotated corpora: the case of GENIA
0 -- 0Hong-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

Volume 7, Issue S-2

0 -- 0Lei 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
0 -- 0Raja Loganantharaj, Satish Cheepala, John Clifford. Metric for Measuring the Effectiveness of Clustering of DNA Microarray Expression
0 -- 0Tao 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
0 -- 0Tao 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
0 -- 0Andrey A. Ptitsyn, Sanjin Zvonic, Jeffrey M. Gimble. Permutation test for periodicity in short time series data
0 -- 0Hongmei 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
0 -- 0Stephen Winters-Hilt, Anil Yelundur, Charlie McChesney, Matthew Landry. Support Vector Machine Implementations for Classification & Clustering
0 -- 0Robert R. Delongchamp, Taewon Lee, Cruz Velasco. A method for computing the overall statistical significance of a treatment effect among a group of genes
0 -- 0Stephen Winters-Hilt. Hidden Markov Model Variants and their Application
0 -- 0Venkata Thodima, Mehdi Pirooznia, Youping Deng. RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers
0 -- 0Jonathan D. Wren. A scalable machine-learning approach to recognize chemical names within large text databases
0 -- 0Jonathan D. Wren, Yuriy Gusev, Andrey A. Ptitsyn, Stephen Winters-Hilt. Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society
0 -- 0Vijayaraj 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
0 -- 0Stephen 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
0 -- 0Raja Tanveer Iqbal, Matthew Landry, Stephen Winters-Hilt. DNA Molecule Classification Using Feature Primitives
0 -- 0Ronald L. Frank, Ajay Mane, Fikret Erçal. An Automated Method for Rapid Identification of Putative Gene Family Members in Plants
0 -- 0Alexander E. Kel, Nico Voss, Ruy Jauregui, Olga V. Kel-Margoulis, Edgar Wingender. Beyond microarrays: Finding key transcription factors controlling signal transduction pathways
0 -- 0Yuanyuan Ding, Dawn Wilkins. Improving the Performance of SVM-RFE to Select Genes in Microarray Data
0 -- 0Laila 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
0 -- 0Tao 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
0 -- 0Nan 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::::)
0 -- 0Tomasz 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
0 -- 0Stephen Winters-Hilt. Nanopore Detector based analysis of single-molecule conformational kinetics and binding interactions

Volume 7, Issue S-1

0 -- 0Michal Linial. The Secrets of a Functional Synapse - From a Computational and Experimental Viewpoint
0 -- 0Jason Weston, Rui Kuang, Christina S. Leslie, William Stafford Noble. Protein Ranking by Semi-Supervised Network Propagation
0 -- 0Adam 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
0 -- 0Gunnar Rätsch, Sören Sonnenburg, Christin Schäfer. Learning Interpretable SVMs for Biological Sequence Classification
0 -- 0Zizhen Yao, Walter L. Ruzzo. A Regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data
0 -- 0Sean O Rourke, Gal Chechik, Robin Friedman, Eleazar Eskin. Discrete profile comparison using information bottleneck
0 -- 0Asa Ben-Hur, William Stafford Noble. Choosing negative examples for the prediction of protein-protein interactions
0 -- 0Tsuyoshi Kato, Yukio Murata, Koh Miura, Kiyoshi Asai, Paul Horton, Koji Tsuda, Wataru Fujibuchi. Network-based de-noising improves prediction from microarray data
0 -- 0Anshul Kundaje, Manuel Middendorf, Mihir Shah, Chris Wiggins, Yoav Freund, Christina S. Leslie. A classification-based framework for predicting and analyzing gene regulatory response
0 -- 0Cornelis A. Albers, Martijn A. R. Leisink, Hilbert J. Kappen. The Cluster Variation Method for Efficient Linkage Analysis on Extended Pedigrees
0 -- 0Tomer Hertz, Chen Yanover. PepDist: A New Framework for Protein-Peptide Binding Prediction based on Learning Peptide Distance Functions