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ORCIDBMC 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 Jáuregui, 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, 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, Cheston 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 R. 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, Lianyi Han, H. L. Zhang, C. J. Zheng, B. Xie, Zhi Wei Cao, Yuzong 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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