|Jason D. Gans||
Technical Staff Member
Los Alamos National Laboratory
|Phone: (505) 667-3770
Fax: (505) 665-2564
research is focused on the computational design of biochemical assays
for pathogen detection. I have developed efficient, parallel
(cluster-based) computer codes to (a) design nucleic acid-based
detection assays (ProSig), (b) search
assays against large numbers of pathogen genomes
(ThermonucleotideBLAST), and (c) visualize genome annotations
(Genomorama). Applications of these codes include designing and
screening detection assays for biothreat
reduction, disease surveillance, forensics and clinical diagnosis.
For DNA-based detection assays (e.g. PCR), the physics and biology of the detection assay are used to define a similarity metric for sequence searches. For example, when designing a hybridization probe to bind a set of target genomes (while not binding to any potential background or near-neighbor genomes), either predicted DNA melting temperature or free energy change is used to identify specific probes.
Other scientific interests include high performance computing, pathogen biology, metagenomics, microbial diversity, optimization techniques and data visualization.
A program for searching nucleic acid-based assays against sequence databases. Current version is 1.05.
A program for designing nucleic acid-based pathogen detection assays. Current version is 1.1.
A program for "extrapolating" partial or fragmentary nucleic acid sequences prior to assay design. Current version is 1.0.
A program for visualizing, editing and analyzing genomes. Current version is 1.54.
A program for visualizing protein structures on Windows-based computers. No longer actively developed.
A program for plotting 2D data on Windows-based computers. No longer actively developed.