Development, evaluation and benchmarking of simulation software for biomolecule-based computing
Natural Computing: an international journal
Natural Computing: an international journal
Characterization of Non-crosshybridizing DNA Oligonucleotides Manufactured in vitro
Natural Computing: an international journal
DNA Chips for Species Identification and Biological Phylogenies
DNA Computing and Molecular Programming
Sensitivity and capacity of microarray encodings
DNA'05 Proceedings of the 11th international conference on DNA Computing
“Reasoning” and “talking” DNA: can DNA understand english?
DNA'06 Proceedings of the 12th international conference on DNA Computing
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We continue the exploration of DNA-based indexing 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 comprehensive "Atlas of Life", as it is or as it could be on earth. We provide a second confirmation that DNA noncrosshybridizing (nxh) sets can be successfully applied to infer ab-initio phylogenetic trees by providing a method to measure distances among entire genomes indexed by sets of short oligonucleotides selected so as to minimize crosshybridization. These phylogenies are solidly established and well accepted in bacterial biology, albeit done by analyses of relatively small segments of highly conserved rybozomic DNA. Second, it is further demonstrated that DNA indexing does provide novel and principled genome-wide predictions 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. We conclude with some discussion about the scalability and potential of this method to develop a comprehensive tree of life based on genome-wide methods.