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Publication Metadata only Exhaustive greedy algorithm for optimizing intermediate result sizes of join queries(2009-11-10) Areerat Trongratsameethong; Jarernsri L. Mitrpanont; Mahidol University, if memory size is not big enough, secondary storage will be needed. This paper proposes the Exhaustive Greedy (EG) algorithm to optimize the intermediate result sizes of join queries. Exhaustive search and greedy algorithm are combined and modified... are comparable to the results estimated by the Exhaustive Search algorithm that is modified to update join graphs, we name it ESU algorithm. © 2009 IEEE.Publication Metadata only An omnibus permutation test on ensembles of two-locus analyses for the detection of purely epistatic multi-locus interactions(2009-12-01) Waranyu Wongseree; Anunchai Assawamakin; Theera Piroonratana; Saravudh Sinsomros; Chanin Limwongse; Nachol Chaiyaratana; King Mongkut's University of Technology North Bangkok; Mahidol Universityfor the epistasis detection. However, exhaustive multi-locus analysis requires prohibitively large computational efforts when problems involve large-scale or genome-wide data. Furthermore, there is no explicit proof that a combination of multiple two-locus analyses... can lead to the correct identification of multi-locus interactions. 2LOmb which performs an omnibus permutation test on ensembles of two-locus analyses is proposed. The algorithm consists of four main steps: two-locus analysis, a permutation testPublication Open Access FlexiChip package: an universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance.(2009-10-15) Steenkeste, Nicolas; Dillies, Marie-Agnès; Khim, Nimol; Sismeiro, Odile; Chy, Sophy; Lim, Pharath; Crameri, Andreas; Bouchier, Christiane; Mercereau-Puijalon, Odile; Beck, Hans-Peter; Mallika Imwong; มัลลิกา อิ่มวงศ์; Dondorp, Arjen M.; Socheat, Duong; Rogier, Christophe; Coppée, Jean- Yves; Ariey, Frédéric; Steenkeste, Nicolas; Mahidol University. Faculty of Tropical MedicineBACKGROUND: A number of molecular tools have been developed to monitor the emergence and spread of anti-malarial drug resistance to Plasmodium falciparum. One of the major obstacles to the wider implementation of these tools is the absence of practical methods enabling high throughput analysis. Here a new Zip-code array is described, called FlexiChip, linked to a dedicated software program, which largely overcomes this problem. METHODS: Previously published microarray probes detecting single-nucleotide polymorphisms (SNP) associated with parasite resistance to anti-malarial drugs (ResMalChip) were adapted for a universal microarray FlexiChip format. To evaluate the overall sensitivity of the FlexiChip package (microarray + software), the results of FlexiChip were compared to ResMalChip microarray, using the same extension probes and with the same PCR products. In both cases, sequence results were used as gold standard to calculate sensitivity and specificity. FlexiChip results obtained with a set of field isolates were then compared to those assessed in an independent reference laboratory. RESULTS: The FlexiChip package gave results identical to the ResMalChip results in 92.7% of samples (kappa coefficient 0.8491, with a standard error 0.021) and had a sensitivity of 95.88% and a specificity of 97.68% compared to the sequencing as the reference method. Moreover the method performed well compared to the results obtained in the reference laboratories, with 99.7% of identical results (kappa coefficient 0.9923, S.E. 0.0523). CONCLUSION: Microarrays could be employed to monitor P. falciparum drug resistance markers with greater cost effectiveness and the possibility for high throughput analysis. The FlexiChip package is a promising tool for use in poor resource settings of malaria endemic countries.