Marisa Torres has been a bioinformatics software developer at LLNL since 2002. She designs, implements, and integrates data in relational databases, provides software engineering support for DNA signature discovery, and responds to internal and external customer requests for signature analysis. She has provided signature development and bioinformatics analysis for the Environmental Protection Agency and the National Bio-Forensics Analysis Center
She studied Molecular and Cell Biology and Computer Science at University of California, Berkeley. In 2000, she designed DNA signatures that were promoted for use in the BASIS program. This highlights the first achievement of computationally derived signatures prior to LLNL’s automated whole-genome signature generation system. She was a key software developer of the BASIS signature screening database in preparation for the 2002 Winter Olympic Games.
A year later, Marisa led the design and implementation of infrastructure for determining the amount of genomic sequencing necessary for developing high-quality diagnostic and forensic DNA and protein signatures. The NIGSCC (National Interagency Genomics Sciences Coordinating Committee) used the LLNL report to guide US pathogen and near-neighbor sequencing decisions from 2004–2006.
In 2005, Marisa was the technical team lead and principal systems architect of the software and database infrastructure for protein-based detection. Over the past few years Marisa has taken the lead on signature erosion checking, which during the most recent DHS proposal cycle was recognized as important for continued reliable detection of pathogens. To Marisa’s credit, LLNL was sought out to perform signature erosion work in support of currently fielded assays. She supports public health and biosecurity customers combining her versatile skill set of software engineering and biology background.
Quickly Identifying Viable Pathogens from the Environment (2010).
Lawrence Livermore Microbial Detection Array (LLMDA) (2010).
Time-Critical Technology Identifies Deadly Bloodborne Pathogens (2010).
Swine Flu Genes Show Virus May Be Weak (2009).
On the Trail of Rogue Genetically Modified Pathogens (2008).
New molecular clock from LLNL and CDC indicates smallpox evolved earlier than believed (2007).
Characterizing Virulent Pathogens - Multiplexed assays and proteomics research are helping the nation counter potential biothreats (2007).
Diagnosing Flu Fast - A new Livermore tool can quickly tell which patients have influenza or another respiratory virus (2006).
Protecting the Nation's Livestock - A Livermore developed assay rapidly detects foot-and-mouth disease and look-alike livestock diseases (2006).
Landmark Work on SARS Signatures (2006).
Finding genetic fingerprints of disease-causing microbes (2006).
On the Front Lines of Biodefense - A Livermore team is developing DNA-based signatures to quickly and accurately identify pathogens (2004).
BASIS Counters Airborne Bioterrorism (2003).
Although Challenges Remain 'Unprecedented' Progress Made in Countering Biological, Chemical Terrorism (2003).
Lawrence Livermore Research Team Finds Unique DNA Signatures to Improve Anthrax Detection (2002).
Advances Developed to Detect Bioterrorist Agents Could Find Use In Protecting Food Supplies (2002).
Lab DNA signature tools used to detect naturally occurring food pathogens (2002).
Lab work speeds plague detection (2001).
Uncovering Bioterrorism - DNA-based signatures are needed to quickly and accurately identify biological warfare agents and their makers (2000)
Gardner, S. N., M. W. Lam, C. Torres, T. R. Slezak, T S. Brettin, R A. Walters (2010), ‘Genomic SNP and Indel Analysis of 12 Bacterial Biothreat and Foodborne Pathogens’, in preparation.
Torres, C. L., E. A. Vitalis, B. Baker, S. N. Gardner, M. W. Lam, J. Dzenitis (2010), ‘LAVA: An Open-Source Approach to Designing LAMP (Loop-Mediated Isothermal Amplification) DNA Signatures’, BMC Bioinformatics, submitted.
Slezak T., S. Gardner, J. Allen, E. Vitalis, M. Torres, C. Torres, C. Jaing (2010), ‘Design of Genomic Signatures for Pathogen Identification and Characterization’, Microbial Forensics, Second Edition, 493-508.
Zemla, A., C. E. Zhou, J. Smith, M. Lam, B. Kirkpatrick, M. Wagner, T. Slezak, and B. V. Geisbrecht (2007), ‘STRALCP: Structure Alignment-based Clustering of Proteins’, Nucleic Acids Research, doi:10.1093/nar/gkm1049.
Zhou, C. E., J. Smith, M. Lam, A. Zemla, M. D. Dyer, and T. Slezak (2007), ‘MvirDB – A microbial database of protein toxins, virulence factors, and antibiotic resistance genes for bio-defence applications’, Nucleic Acids Research, 35:D391-D394.
Zhou, C. E., M. Lam, J. Smith, A. Zemla, M. D. Dyer, T. Kuczmarski, and T. Slezak (2006), ‘MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization, BMC Bioinformatics, 7:459.
Zhou, C. E., A. Zemla, D. Roe, M. Young, M. Lam, J. S. Schoeniger, and R. Balhorn (2005), ‘Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin’, Bioinformatics, 21(14):3089-3096.
Gardner, S. N., M. W. Lam, T. Kuczmarski, J. R. Smith, C. L. Torres, and T. R. Slezak (2005), ‘Draft versus finished sequence data for DNA and protein diagnostic signature development’, Nucleic Acids Research, 33(18):5838-5850.
Gardner, S. N., T. Kuczmarski, C. E. Zhou, M. Lam, and T. Slezak (2005), ‘System to assess genome sequencing needs for viral protein diagnostics and therapeutics’, Journal of Clinical Microbiology, 43:1807-1817.
Gardner, S. N., M. Lam, N. Mulakken, C. Torres, J. Smith, and T. Slezak (2004), ‘Sequencing needs for viral diagnostics’, Journal of Clinical Microbiology, 42:5472–5476.
Slezak, T., T. Kuczmarski, L. Ott, C. Torres, D. Medeiros, J. Smith, B. Truitt, N. Mulakken, M. Lam, E. Vitalis, A. Zemla, C. E. Zhou, and S. N. Gardner (2003), ‘Comparative genomics tools applied to bioterrorism defense’, Briefings in Bioinformatics, 4(2):133-149.