Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability
DNA 7 Revised Papers from the 7th International Workshop on DNA-Based Computers: DNA Computing
In vitro selection of non-cross hybridizing oligonucleotides for computation
Natural Computing: an international journal
Development, evaluation and benchmarking of simulation software for biomolecule-based computing
Natural Computing: an international journal
Natural Computing: an international journal
Whole-genome prokaryotic phylogeny
Bioinformatics
Characterization of Non-crosshybridizing DNA Oligonucleotides Manufactured in vitro
Natural Computing: an international journal
Highly scalable algorithms for robust string barcoding
International Journal of Bioinformatics Research and Applications
Proceedings of the 13th international conference on DNA computing
DNA13'07 Proceedings of the 13th international conference on DNA computing
Hardware acceleration for thermodynamic constrained DNA code generation
DNA13'07 Proceedings of the 13th international conference on DNA computing
Sensitivity and capacity of microarray encodings
DNA'05 Proceedings of the 11th international conference on DNA Computing
In search of optimal codes for DNA computing
DNA'06 Proceedings of the 12th international conference on DNA Computing
“Reasoning” and “talking” DNA: can DNA understand english?
DNA'06 Proceedings of the 12th international conference on DNA Computing
Theory and applications of DNA codeword design
TPNC'12 Proceedings of the First international conference on Theory and Practice of Natural Computing
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The codeword design problem is an important problem in DNA computing and its applications. Several theoretical analyses as well as practical solutions for short oligonucleotides (up to 20-mers) have been generated recently. These solutions have, in turn, suggested new applications to DNA-based indexing and natural language processing, in addition to the obvious applications to the problems of reliability and scalability that generated them. Here we continue the exploration of this type of DNA-based indexing for biological applications and show that DNA noncrosshybridizing (nxh) sets can be successfully applied to infer ab initio phylogenetic trees by providing a way to measure distances among different genomes indexed by sets of short oligonucleotides selected so as to minimize crosshybridization. These phylogenies are solidly established and well accepted in biology. The new technique is much more effective in terms of signal-to-noise ratio, cost and time than current methods. Second, it is demonstrated that DNA indexing does provide novel and principled insights into the phylogenesis of organisms hitherto inaccessible by current methods, such as a prediction of the origin of the Salmonella plasmid 50 as being acquired horizontally, likely from some bacteria somewhat related to Yesinia. Finally, DNA indexing can be scaled up to newly available universal DNA chips readily available both in vitro and in silico. In particular, we show how a recently obtained such set of nxh 16-mers can be used as a universal coordinate system in DNA spaces to characterize very large groups (families, genera, and even phylla) of organisms on a uniform biomarker reference system, a veritable and comprehensive "Atlas of Life", as it is or as it could be on earth.