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6th Atlantic Symposium on Computational Biology and Genome Informatics (CBG)
CBG-1: Computational Methods
Go-Chart, a toolkit for visualization of genes in the context of gene ontology with variable p-values D. Shah, M. Ma, G. Tromp
Linking multiple genes to human chromosomal locations to facilitate knowledge discovery T. Wang, M. Ma, P. Soteropoulos
Statistical identification of biclusters in gene expression data A. Chakraborty
Wavelet analysis on temporal expression profiles of malaria parasite H. Cai, S. Agaian, J. Gu, Y. Wang
Precise Gridding of Microarray Images by Detecting and Correcting Rotations in Subarrays Yu Wang, Frank Y. Shih, Marc Q. Ma
SNP auto-calling using support vector machines K. Zhang, M. Ma, H.-Y. Wang, Y. Wang, M. Baerjee, A. Karmaker, F. Shih, J. Wang, H. Li

CBG-2: Metabolic Networks
Exploring protein networks with a semantic similarity measure across gene ontology Z. Lubovac, J. Gamalielsson, B. Olsson, A. Lindlof
Efficient validation of metabolic pathway databases L. Felix, G. Valiente
Testing feasibility in metabolic pathways is as easy as matrix R. Nigam
A combined approach to the identification of transcription factor binding sites in prokaryote H.K. Dai, L. Zhao

CBG-3: Structure Alignment
Finding global similarities between proteins using vector algorithms S. Hamel
Randomized algorithms for three-dimensional protein structures alignment Y.-L. Lin, Y.-H. Lin, P.-S. Yu, H.-C. Chang
Aligning two RNA secondary structures with l-block Z. Wang, E.R.M. Tillier
Peak alignment using restricted edit distances V. Makinen
The similarity metric and the distance metric B. Ma, K. Zhang
ParaRNA: A parametric tool for aligning two RNA structures L. Wang, W. Feng, H. Zhao, K. Zhang, X. Liu

CBG-4: Genomic Data Analysis
Phylogenetic information integration: research issues and techniques K.G. Herbert, J.T.L. Wang
Combinatorial reconstruction of sibling relationships T.Y. Berger-Wolf, B. DasGupta, W. Chaovalitwongse, M.V. Ashley
Genomic data mining for species identification using principal component analysis S. Sen, S. Narasimhan, A. Konar, U.K. Chakraborty
Comparison of gene structure in microbial genomes G. Rao, D.K.Y. Chiu
PROFESS, a system to support extracting protein function information from literature Y. Kaneta, M. Numa, M. A. Munna, Y. Sakurai, T. Ohkawa

CBG-5: Pattern Analysis Methods
Local sequence alignment using parallel memory-efficient dynamic programming L. Pichl, M. Arai, K. Hanabusa, T. Hayashi
Finding double-stranded RNA structures in the 3’ untranslated eukaryotic mRNAs S.-Y. Le, J.V. . Maizel, Jr
Splice site prediction with linear kernel and Bayesian mapping Y. Zhang, C.-H. Chu, H. Zha, Y. Chen, X. Ji
Sequence-structure patterns: discovery and applications T. Milledge, S. Khuri, X. Wei, C. Yang, G. Zheng, G. Narasimhan
Determining thresholds for binding site sequence models using information theory C. Bi, P.K. Rogan

CBG-6: Pattern Search Methods
Exploring the space of consensus RNA secondary structure motifs using suffix arrays T. Nguyen, M. Turcotte
YUCCA: An efficient algorithm for small molecule docking V. Choi
Algorithms for searching RNA motifs in genomic sequences J. Liu, K. Zhang
A method for retrieving protein with a local structure similar to known interaction site using profile Y. Nonomura, K. Yoshino, T. Ohkawa
Identification of protein patterns in nucleic acid sequences and exploration of synonymous codons in tissue differentiation G. Anogianakis, E. Kapritsos, Ch. Makris, N. Mpaltas, K. Perdikuri, K. Themelis, A. Tsakalidis
Classifying SARS-CoV genomes based on their unique sequences P.-H. Liu, S.-L. Peng, C.Y. Tang, Y.-W. Tsay, J.T.L. Wang

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