Accelerated bioinformatics algorithms have played an important role in high throughput
genomics, and DeCypher systems have been widely published as an
enabling technology for genomic discovery in over 180 peer-reviewed scientific research articles, including the selected milestones below: In 1997, the annotation of the first complete sequence of the
E. coli K12 genome used DeCypher Smith-Waterman to determine the function of new translated sequences. In 2002, the rice genome, the first completely sequenced crop, was annotated using DeCypher FrameSearch "to detect and guide the correction of
frameshifts caused by
indels." In 2004, a high throughput genomic approach to the study of
horizontal gene transfer in plant-parasitic nematodes was conducted using DeCypher Tera-BLAST, Timelogic's implementation of the
BLAST algorithm. In 2007,
HMM profiling of
metagenomics sequences generated by the
Sorcerer II Global Ocean Sampling Expedition (GOS) were performed using DeCypherHMM to discover 1700 new
protein families and matches to 6000 sequences previously categorized in scientific literature as
ORFans. Dr.
Craig Venter credited TimeLogic in his biography, noting that the DeCypher system performed "an order of magnitude or two more than had been achieved before. The final computation took two weeks but would have run for well more than a century on a standard computer." Also in 2007, a physical map of the soybean pathogen
Fusarium virguliforme was developed using
exonic fragments identified with DeCypher GeneDetective. In 2011, a global assessment of the genomic variation in cattle was conducted using DeCypher Tera-BLAST "to accurately detect chromosomal positions of the
SNP sites." ==Products==