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BACKGROUND The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements,(More)
Whole genome amplification by the multiple displacement amplification (MDA) method allows sequencing of genomes from single cells of bacteria that cannot be cultured. However, genome assembly is challenging because of highly non-uniform read coverage generated by MDA. We describe an improved assembly approach tailored for single cell Illumina sequences that(More)
UNLABELLED Recent interests, such as RNA interference and antisense RNA regulation, strongly motivate the problem of predicting whether two nucleic acid strands interact. MOTIVATION Regulatory non-coding RNAs (ncRNAs) such as microRNAs play an important role in gene regulation. Studies on both prokaryotic and eukaryotic cells show that such ncRNAs usually(More)
The "dark matter of life" describes microbes and even entire divisions of bacterial phyla that have evaded cultivation and have yet to be sequenced. We present a genome from the globally distributed but elusive candidate phylum TM6 and uncover its metabolic potential. TM6 was detected in a biofilm from a sink drain within a hospital restroom by analyzing(More)
In addition to the theoretical value of challenging optimal control problmes, recent progress in autonomous vehicles mandates further research in optimal motion planning for wheeled vehicles. Since current numerical optimal control techniques suffer from either the curse of dimensional-ity, e.g. the Hamilton-Jacobi-Bellman equation, or the curse of(More)
MOTIVATION Assemblies of next-generation sequencing (NGS) data, although accurate, still contain a substantial number of errors that need to be corrected after the assembly process. We develop SEQuel, a tool that corrects errors (i.e. insertions, deletions and substitution errors) in the assembled contigs. Fundamental to the algorithm behind SEQuel is the(More)
Advisor Date DEDICATION To my family. ii ACKNOWLEDGEMENTS I would like to sincerely thank my adviser, Professor Hamidreza Chitsaz, for his support, novel ideas and the opportunity he provided for me to conduct my research. His patience and encouragements inspired me during the course of my graduate studies. I would also like to thank my dissertation(More)
We present biRNA, a novel algorithm for prediction of binding sites between two RNAs based on minimization of binding free energy. Similar to RNAup approach [29], we assume the binding free energy is the sum of accessibility and the interaction free energies. Our algorithm maintains tractability and speed and also has two important advantages over previous(More)
MOTIVATION Identification of every single genome present in a microbial sample is an important and challenging task with crucial applications. It is challenging because there are typically millions of cells in a microbial sample, the vast majority of which elude cultivation. The most accurate method to date is exhaustive single-cell sequencing using(More)