Articles
Volume 10 Supplement 1
Selected papers from the Seventh Asia-Pacific Bioinformatics Conference (APBC 2009)
Research
The Seventh Asia Pacific Bioinformatics Conference (APBC 2009)
Beijing, China
13-16 January 2009
Edited by Michael Q Zhang, Michael S Waterman and Xuegong Zhang
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Introduction
The Seventh Asia Pacific Bioinformatics Conference (APBC2009) Michael Q Zhang, Michael S Waterman, Xuegong Zhang BMC Bioinformatics 2009, 10(Suppl 1):S1 (30 January 2009) |
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Research
Genome aliquoting with double cut and join Robert Warren, David Sankoff BMC Bioinformatics 2009, 10(Suppl 1):S2 (30 January 2009) |
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Pathogenic GX Yu BMC Bioinformatics 2009, 10(Suppl 1):S3 (30 January 2009) |
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SE: an algorithm for deriving sequence alignment from a pair of superimposed structures Chin-Hsien Tai, James J Vincent, Changhoon Kim, Byungkook Lee BMC Bioinformatics 2009, 10(Suppl 1):S4 (30 January 2009) |
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ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets Guan Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty, Dong Xu BMC Bioinformatics 2009, 10(Suppl 1):S5 (30 January 2009) |
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Maximum independent sets of commuting and noninterfering inversions Krister M Swenson, Yokuki To, Jijun Tang, Bernard ME Moret BMC Bioinformatics 2009, 10(Suppl 1):S6 (30 January 2009) |
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Inversion-based genomic signatures Krister M Swenson, Bernard ME Moret BMC Bioinformatics 2009, 10(Suppl 1):S7 (30 January 2009) |
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Triplet supertree heuristics for the tree of life Harris T Lin, J Gordon Burleigh, Oliver Eulenstein BMC Bioinformatics 2009, 10(Suppl 1):S8 (30 January 2009) |
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Sorting by reversals, block interchanges, tandem duplications, and deletions Martin Bader BMC Bioinformatics 2009, 10(Suppl 1):S9 (30 January 2009) |
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Improved algorithms for approximate string matching (extended abstract) Dimitris Papamichail, Georgios Papamichail BMC Bioinformatics 2009, 10(Suppl 1):S10 (30 January 2009) |
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Simultaneous phylogeny reconstruction and multiple sequence alignment Feng Yue, Jian Shi, Jijun Tang BMC Bioinformatics 2009, 10(Suppl 1):S11 (30 January 2009) |
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Methods for comparative metagenomics Daniel H Huson, Daniel C Richter, Suparna Mitra, Alexander F Auch, Stephan C Schuster BMC Bioinformatics 2009, 10(Suppl 1):S12 (30 January 2009) |
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DNA motif alignment by evolving a population of Markov chains Chengpeng Bi BMC Bioinformatics 2009, 10(Suppl 1):S13 (30 January 2009) |
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Parallel short sequence assembly of transcriptomes Benjamin G Jackson, Patrick S Schnable, Srinivas Aluru BMC Bioinformatics 2009, 10(Suppl 1):S14 (30 January 2009) |
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Finding optimal threshold for correction error reads in DNA assembling Francis YL Chin, Henry CM Leung, Wei-Lin Li, Siu-Ming Yiu BMC Bioinformatics 2009, 10(Suppl 1):S15 (30 January 2009) |
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Crystallizing short-read assemblies around seeds Mohammad Hossain, Navid Azimi, Steven Skiena BMC Bioinformatics 2009, 10(Suppl 1):S16 (30 January 2009) |
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Short read DNA fragment anchoring algorithm Wendi Wang, Peiheng Zhang, Xinchun Liu BMC Bioinformatics 2009, 10(Suppl 1):S17 (30 January 2009) |
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REMAS: a new regression model to identify alternative splicing events from exon array data Hao Zheng, Xingyi Hang, Ji Zhu, Minping Qian, Wubin Qu, Chenggang Zhang, Minghua Deng BMC Bioinformatics 2009, 10(Suppl 1):S18 (30 January 2009) |
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A voting approach to identify a small number of highly predictive genes using multiple classifiers Md Rafiul Hassan, M Maruf Hossain, James Bailey, Geoff Macintyre, Joshua WK Ho, Kotagiri Ramamohanarao BMC Bioinformatics 2009, 10(Suppl 1):S19 (30 January 2009) |
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Knowledge driven decomposition of tumor expression profiles Martin H van Vliet, Lodewyk FA Wessels, Marcel JT Reinders BMC Bioinformatics 2009, 10(Suppl 1):S20 (30 January 2009) |
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Network-based support vector machine for classification of microarray samples Yanni Zhu, Xiaotong Shen, Wei Pan BMC Bioinformatics 2009, 10(Suppl 1):S21 (30 January 2009) |
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Using random forest for reliable classification and cost-sensitive learning for medical diagnosis Fan Yang, Hua-zhen Wang, Hong Mi, Cheng-de Lin, Wei-wen Cai BMC Bioinformatics 2009, 10(Suppl 1):S22 (30 January 2009) |
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A statistical framework for integrating two microarray data sets in differential expression analysis Yinglei Lai, Sarah E Eckenrode, Jin-Xiong She BMC Bioinformatics 2009, 10(Suppl 1):S23 (30 January 2009) |
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Reija Autio, Sami Kilpinen, Matti Saarela, Olli Kallioniemi, Sampsa Hautaniemi, Jaakko Astola BMC Bioinformatics 2009, 10(Suppl 1):S24 (30 January 2009) |
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Integrative disease classification based on cross-platform microarray data Chun-Chi Liu, Jianjun Hu, Mrinal Kalakrishnan, Haiyan Huang, Xianghong Zhou BMC Bioinformatics 2009, 10(Suppl 1):S25 (30 January 2009) |
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Principal component tests: applied to temporal gene expression data Wensheng Zhang, Hong-Bin Fang, Jiuzhou Song BMC Bioinformatics 2009, 10(Suppl 1):S26 (30 January 2009) |
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Biclustering of gene expression data using reactive greedy randomized adaptive search procedure Smitha Dharan, Achuthsankar S Nair BMC Bioinformatics 2009, 10(Suppl 1):S27 (30 January 2009) |
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Identification of histone modifications in biomedical text for supporting epigenomic research Corinna Kolářik, Roman Klinger, Martin Hofmann-Apitius BMC Bioinformatics 2009, 10(Suppl 1):S28 (30 January 2009) |
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Searching for bidirectional promoters in Quan Wang, Lin Wan, Dayong Li, Lihuang Zhu, Minping Qian, Minghua Deng BMC Bioinformatics 2009, 10(Suppl 1):S29 (30 January 2009) |
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ModuleDigger: an itemset mining framework for the detection of Hong Sun, Tijl De Bie, Valerie Storms, Qiang Fu, Thomas Dhollander, Karen Lemmens, Annemieke Verstuyf, Bart De Moor, Kathleen Marchal BMC Bioinformatics 2009, 10(Suppl 1):S30 (30 January 2009) |
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Transcriptional interaction-assisted identification of dynamic nucleosome positioning Zhiming Dai, Xianhua Dai, Qian Xiang, Jihua Feng, Yangyang Deng, Jiang Wang, Caisheng He BMC Bioinformatics 2009, 10(Suppl 1):S31 (30 January 2009) |
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Predicting microRNA targets in time-series microarray experiments via functional data analysis Brian J Parker, Jiayu Wen BMC Bioinformatics 2009, 10(Suppl 1):S32 (30 January 2009) |
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A structural interpretation of the effect of GC-content on efficiency of RNA interference Chi Chan, C Steven Carmack, Dang D Long, Anil Maliyekkel, Yu Shao, Igor B Roninson, Ye Ding BMC Bioinformatics 2009, 10(Suppl 1):S33 (30 January 2009) |
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Je-Gun Joung, Zhangjun Fei BMC Bioinformatics 2009, 10(Suppl 1):S34 (30 January 2009) |
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HHMMiR: efficient Sabah Kadri, Veronica Hinman, Panayiotis V Benos BMC Bioinformatics 2009, 10(Suppl 1):S35 (30 January 2009) |
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Computational prediction of novel non-coding RNAs in Dandan Song, Yang Yang, Bin Yu, Binglian Zheng, Zhidong Deng, Bao-Liang Lu, Xuemei Chen, Tao Jiang BMC Bioinformatics 2009, 10(Suppl 1):S36 (30 January 2009) |
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Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA Fei Xia, Yong Dou, Xingming Zhou, Xuejun Yang, Jiaqing Xu, Yang Zhang BMC Bioinformatics 2009, 10(Suppl 1):S37 (30 January 2009) |
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Prediction of RNA secondary structure with pseudoknots using integer programming Unyanee Poolsap, Yuki Kato, Tatsuya Akutsu BMC Bioinformatics 2009, 10(Suppl 1):S38 (30 January 2009) |
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Sequence-structure relations of pseudoknot RNA Fenix WD Huang, Linda YM Li, Christian M Reidys BMC Bioinformatics 2009, 10(Suppl 1):S39 (30 January 2009) |
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Weitao Sun, Jing He BMC Bioinformatics 2009, 10(Suppl 1):S40 (30 January 2009) |
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Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses Jhang-Wei Huang, Chwan-Chuen King, Jinn-Moon Yang BMC Bioinformatics 2009, 10(Suppl 1):S41 (30 January 2009) |
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Predicting disordered regions in proteins using the profiles of amino acid indices Pengfei Han, Xiuzhen Zhang, Zhi-Ping Feng BMC Bioinformatics 2009, 10(Suppl 1):S42 (30 January 2009) |
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Thai Tung, Doheon Lee BMC Bioinformatics 2009, 10(Suppl 1):S43 (30 January 2009) |
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Studying the unfolding process of protein G and protein L under physical property space Liling Zhao, Jihua Wang, Xianghua Dou, Zanxia Cao BMC Bioinformatics 2009, 10(Suppl 1):S44 (30 January 2009) |
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Prediction of amyloid fibril-forming segments based on a support vector machine Jian Tian, Ningfeng Wu, Jun Guo, Yunliu Fan BMC Bioinformatics 2009, 10(Suppl 1):S45 (30 January 2009) |
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Yi Jia, Jun Huan, Vincent Buhr, Jintao Zhang, Leonidas N Carayannopoulos BMC Bioinformatics 2009, 10(Suppl 1):S46 (30 January 2009) |
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Semi-supervised protein subcellular localization Qian Xu, Derek Hu, Hong Xue, Weichuan Yu, Qiang Yang BMC Bioinformatics 2009, 10(Suppl 1):S47 (30 January 2009) |
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Krongsakda Phakthanakanok, Khanok Ratanakhanokchai, Khin Kyu, Pornthep Sompornpisut, Aaron Watts, Surapong Pinitglang BMC Bioinformatics 2009, 10(Suppl 1):S48 (30 January 2009) |
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Quality assessment of tandem mass spectra using support vector machine (SVM) An-Min Zou, Fang-Xiang Wu, Jia-Rui Ding, Guy G Poirier BMC Bioinformatics 2009, 10(Suppl 1):S49 (30 January 2009) |
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Yan Fu, Wei Jia, Zhuang Lu, Haipeng Wang, Zuofei Yuan, Hao Chi, You Li, Liyun Xiu, Wenping Wang, Chao Liu, Leheng Wang, Ruixiang Sun, Wen Gao, Xiaohong Qian, Si-Min He BMC Bioinformatics 2009, 10(Suppl 1):S50 (30 January 2009) |
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Analysis of mass spectrometry data using sub-spectra Wouter Meuleman, Judith YMN Engwegen, Marie-Christine W Gast, Lodewyk FA Wessels, Marcel JT Reinders BMC Bioinformatics 2009, 10(Suppl 1):S51 (30 January 2009) |
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Mutual information estimation reveals global associations between stimuli and biological processes Taiji Suzuki, Masashi Sugiyama, Takafumi Kanamori, Jun Sese BMC Bioinformatics 2009, 10(Suppl 1):S52 (30 January 2009) |
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Hong-Hee Won, Inho Park, Eunjung Lee, Jong-Won Kim, Doheon Lee BMC Bioinformatics 2009, 10(Suppl 1):S53 (30 January 2009) |
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Dongxiao Zhu BMC Bioinformatics 2009, 10(Suppl 1):S54 (30 January 2009) |
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Extract interaction detection methods from the biological literature Hongning Wang, Minlie Huang, Xiaoyan Zhu BMC Bioinformatics 2009, 10(Suppl 1):S55 (30 January 2009) |
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Human gene expression sensitivity according to large scale meta-analysis Pei Hao, Siyuan Zheng, Jie Ping, Kang Tu, Christian Gieger, Rui Wang-Sattler, Yang Zhong, Yixue Li BMC Bioinformatics 2009, 10(Suppl 1):S56 (30 January 2009) |
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Jisu Kim, De-Shuang Huang, Kyungsook Han BMC Bioinformatics 2009, 10(Suppl 1):S57 (30 January 2009) |
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Analysis on relationship between extreme pathways and correlated reaction sets Yanping Xi, Yi-Ping Chen, Ming Cao, Weirong Wang, Fei Wang BMC Bioinformatics 2009, 10(Suppl 1):S58 (30 January 2009) |
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A new graph-based method for pairwise global network alignment Gunnar W Klau BMC Bioinformatics 2009, 10(Suppl 1):S59 (30 January 2009) |
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Kelvin X Zhang, BF Francis Ouellette BMC Bioinformatics 2009, 10(Suppl 1):S60 (30 January 2009) |
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On optimal comparability editing with applications to molecular diagnostics Sebastian Böcker, Sebastian Briesemeister, Gunnar W Klau BMC Bioinformatics 2009, 10(Suppl 1):S61 (30 January 2009) |
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Zixiang Xu, Xiao Sun, Shihai Yu BMC Bioinformatics 2009, 10(Suppl 1):S62 (30 January 2009) |
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An unsupervised partition method based on association delineated revised mutual information Jing Chen, Guangcheng Xi BMC Bioinformatics 2009, 10(Suppl 1):S63 (30 January 2009) |
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Tomasz Gambin, Krzysztof Walczak BMC Bioinformatics 2009, 10(Suppl 1):S64 (30 January 2009) |
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A random forest approach to the detection of epistatic interactions in case-control studies Rui Jiang, Wanwan Tang, Xuebing Wu, Wenhui Fu BMC Bioinformatics 2009, 10(Suppl 1):S65 (30 January 2009) |
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Jan Freudenberg, Mingyi Wang, Yaning Yang, Wentian Li BMC Bioinformatics 2009, 10(Suppl 1):S66 (30 January 2009) |
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Copy-number-variation and copy-number-alteration region detection by cumulative plots Wentian Li, Annette Lee, Peter K Gregersen BMC Bioinformatics 2009, 10(Suppl 1):S67 (30 January 2009) |
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Identifying disease associations via genome-wide association studies Wenhui Huang, Pengyuan Wang, Zhen Liu, Liqing Zhang BMC Bioinformatics 2009, 10(Suppl 1):S68 (30 January 2009) |
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Erdahl T Teber, Jason Y Liu, Sara Ballouz, Diane Fatkin, Merridee A Wouters BMC Bioinformatics 2009, 10(Suppl 1):S69 (30 January 2009) |
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Advanced analysis and visualization of gene copy number and expression data Reija Autio, Matti Saarela, Anna-Kaarina Järvinen, Sampsa Hautaniemi, Jaakko Astola BMC Bioinformatics 2009, 10(Suppl 1):S70 (30 January 2009) |
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CGTS: a site-clustering graph based tagSNP selection algorithm in genotype data Jun Wang, Mao-zu Guo, Chun-yu Wang BMC Bioinformatics 2009, 10(Suppl 1):S71 (30 January 2009) |
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Minimizing recombinations in consensus networks for phylogeographic studies Laxmi Parida, Asif Javed, Marta Melé, Francesc Calafell, Jaume Bertranpetit, Genographic Consortium BMC Bioinformatics 2009, 10(Suppl 1):S72 (30 January 2009) |
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PCA-based population structure inference with generic clustering algorithms Chih Lee, Ali Abdool, Chun-Hsi Huang BMC Bioinformatics 2009, 10(Suppl 1):S73 (30 January 2009) |
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A fast algorithm for genome-wide haplotype pattern mining Søren Besenbacher, Christian NS Pedersen, Thomas Mailund BMC Bioinformatics 2009, 10(Suppl 1):S74 (30 January 2009) |
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Detecting disease-associated genotype patterns Quan Long, Qingrun Zhang, Jurg Ott BMC Bioinformatics 2009, 10(Suppl 1):S75 (30 January 2009) |
