Jason D. Gans
Technical Staff Member
Los Alamos National Laboratory
Bioscience Division
 Phone: (505) 667-3770
Fax: (505) 665-2564
Email: jgans@lanl.gov
My 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.
  1. Gans, J.D., M. Wolinsky (2008) Improved assay dependent searching of nucleic acid sequence databases. Nucleic Acids Research, Vol 36, No. 12, e74
  2. Gans, J.D., M. Wolinsky (2007) Genomorama: Genome visualization and analysis. BMC Bioinformatics 8:204
  3. Gans, J., M. Wolinsky, J. Dunbar. (2006) Response to comment by Volkov et al. on "Computational improvements reveal great bacterial diversity and high metal toxicity in soil". Science. 313:917; www.sciencemag.org/cgi/content/full/313/5789/918b
  4. Gans, J., M. Wolinsky, J. Dunbar. (2006) Response to comment by Bunge et al. on "Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science. 313:917; www.sciencemag.org/cgi/content/full/313/5789/918d
  5. Gans, J., M. Wolinsky and J. Dunbar. (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science. 309(5739):1387-1390.
  6. Pawley, N.H., J.D. Gans, and R. Michalczyk. (2005) APART: Automated Pre-processing for NMR With Reduced Tedium. Bioinformatics. 21(5):680-682.
  7. Pawley, N.H., J.D. Gans, and L.K. Nicholson. (2002) Factors Determining the Reliable Description of Global Tumbling Parameters in solution NMR. Journal of Biomolecular NMR. 24:215-229.
  8. Gans, J. and D. Shalloway. (2001) Qmol: A program for molecular visualization on Windows based PCs. Journal of Molecular Graphics and Modeling. v.19:557-559.
  9. Gans, J. and D. Shalloway. (2000) Shadow mass and the relationship between velocity and momentum in symplectic numerical integration. Physical Review E. v.61:4587.
Available Software
ThermonucleotideBLAST
program logo
A program for searching nucleic acid-based assays against sequence databases. Current version is 1.05.
 ProSig
A program for designing nucleic acid-based pathogen detection assays. Current version is 1.0.
 SeqStrap
A program for "extrapolating" partial or fragmentary nucleic acid sequences prior to assay design. Current version is 1.0.
Genomorama
Program screen shot
A program for visualizing, editing and analyzing genomes. Current version is 1.54.
 QMol
Program screen shot
A program for visualizing protein stuructures on Windows-based computers. No longer actively developed.
 PrestoPlot
Program screen shot
A program for plotting 2D data on Windows-based computers. No longer actively developed.