Genomics & Systems Biology


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.

microRNA and RNASeq Analysis


Under SBIR funding by the National Science Foundation, Natural Selection, Inc. developed evolved classifiers to predict the locations of microRNA genes in genomic DNA. These predictions led to many novel microRNA sequences that were later confirmed by experimental analysis and deep sequencing. A portion of this data was licensed for commercial sale by Invitrogen (now ThermoFisher) for sale on the NCode™ Multi-species miRNA Microarray. This microarray has been used by researchers world-wide for the investigation of small RNA expression in various tissues, leading to a better understanding of cellular development. Have us help you understand your RNASeq data.

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.

Drug Discovery


Through a collaboration with Southwestern College under funding from the U.S. Army, Natural Selection, Inc. helped develop a novel approach for high-throughput small molecule screening that makes use of computational intelligence methods to literally evolve drugs in silico and screen drugs against protein targets. This process rapidly accelerates the search for new drug compounds over standard laboratory techniques and has been evaluated for its use in anti-malarial drug discovery.

Clinical Drug Development & Patient Segmentation


With our partner Theragence, Inc., we are helping in the identification of the right drug at the right time for the right patient, leading to companion diagnostics based on genomic, demographic, and other information.



Through a collaboration with BioInfoExperts and UC San Francisco under funding from the National Institutes of Health, Natural Selection, Inc. helped co-develop classifiers to predict viral tropism as well as classifiers for late-stage pathogenic effects of HIV infection including risk of dementia and lymphoma. The team continues to explore the biology of HIV-related dynamics, signatures, and structures associated with the development of AIDS-related pathogenicity.

Personalized Medicine


Tinnitus affects millions worldwide with spontaneous ringing in the ears. Under funding from the National Science Foundation, NSI has patented a novel pre-clinical approach called Serenity™ to personalize tinnitus "masks" using interactive evolutionary computation. Each user has the opportunity to customize the masks that help alleviate their particular tinnitus. Given each person is different, this tool allows people to personalize the sounds that work best for them in helping to alleviate their tinnitus.