Applications

Bioinformatics

Natural Selection, Inc. has unique expertise in the application of a diverse range of computational intelligence methods applied to bioinformatics problems. Natural Selection, Inc. has experience in the following areas:

Transcription factor binding site identification
Target discovery
Microarray analysis
Phylogenetics
Population dynamics
Sequence alignment

Transcription factor binding site identification

In collaboration with Eli Lilly & Company, Natural Selection, Inc. used evolutionary computation to find transcription factor binding sites in co-expressed genes. This software tool (known as BEAGLE) has been demonstrated to be useful even when the sequences of the transcription factor binding sites are not known in advance, leading to the discovery of entirely novel binding sites. The method was extended to work for the discovery of composite transcription factor binding sites.

RNA structure analysis

In collaboration with Isis Pharmaceuticals, Natural Selection, Inc. developed software to search for common RNA structures in human pathogens using an evolutionary algorithm. This approach demonstrated the opportunity to search tremendous spaces of possible RNA structures and rapidly identify RNA motifs shared by multiple organisms.

Microarray analysis

Natural Selection, Inc. has worked with several commercial customers for pattern recognition from microarray data leading to cancer diagnostics. Natural Selection's tools allow for simultaneous feature reduction and model optimization.

For additional information on Natural Selection, Inc.'s efforts in bioinformatics, please review our publications or
contact Dr. Gary Fogel, CEO at gfogel [at] natural-selection.com.