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Elena Peterson

Elena Peterson

Scientific Data Management
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-32
Richland, WA 99352
509/372-4573

Biography

Elena joined Pacific Northwest National Laboratory in 1990 as a scientist in the Software Engineering group. Her professional experience at the Lab ranges from general software engineering research to the development of problem-solving environments, collaborative environments, scientific data managment and most recently in bioinformatics and national security. She has written software for a wide variety of scientific domains including environmental clean-up, computational chemistry, physics, and bioinformatics, and cyber security.

Currently, she is leading 2 large NIH software development projects in the areas of environmental toxicology and proteogenomics. She is also a key developer of new methods to apply bioinformatic algorithms to cyber security issues.

Recently she completed work on the Data Intensive Computing for Complex Biological Systems project where she developed tools and data management techniques for supporting high-throughput computational chemistry simulations.

Research Interests

  • Scientific Data Management and Integration
  • Application architectures
  • Scientific application development

Education and Credentials

  • B.S., Computer and Information Science, University of Oregon, 1989

Affiliations and Professional Service

  • Institute for Electrical and Electronics Engineers and IEEE computer Society member
  • Association for Computing Machinery member

Awards and Recognitions

  • 2006 HPC Analytics Challenge Final 3, Supercomputing 2006
  • Software Creator Award, Pacific Northwest National Laboratory
  • Key Contributor Award, Pacific Northwest National Laboratory
  • 1996 Software Creator Award for the development of Spatial Paradigm for Information REtrieval (SPIRE)
  • 1996 Software Creator Award for the development of ReOpt™
  • 1996 Software Creator Award for the development of Remedial Action Assessment System (RAAS)
  • 1993 Top Five Finalist for PNNL Laboratory Directors Award (RAAS)
  • 1993 Nominated for R&D 100 award (RAAS)
  • 1993 Software Creator Award (RAAS)
  • 1992 Nominated for R&D Award (ReOpt™)
  • 1992 Software Creator Award (ReOpt™)

PNNL Publications

2013

  • Oehmen CS, DS Curtis, AR Phillips, and ES Peterson. 2013. "Novel Visual and Analytical Methods in Repurposing Legacy Scientific Code - A Case Study." In Proceedings of the The 2013 International Conference on Software Engineering Research and Practice (SERP 2013), July 22-25, 2013, Las Vegas, Nevada, ed. HR Arabnia, et al, pp. 455-461.  CSREA Press, Athens, GA. 
  • Peterson ES, DS Curtis, AR Phillips, JR Teuton, and CS Oehmen. 2013. "A Generalized Bio-inspired Method for Discovering Sequence-based Signatures." In IEEE International Conference on Intelligence and Security Informatics (ISI 2013), June 4-7, 2013, Seattle, Washington, ed. K Glass, et al, pp. 330-332.  IEEE, Piscataway, NJ.  doi:10.1109/ISI.2013.6578853

2012

  • Hobbie KA, ES Peterson, M Barton, KM Waters, and KA Anderson. 2012. "Integration of Data Systems and Technology Improves Research and Collaboration for a Superfund Research Center." JALA. Journal of the Association for Laboratory Automation 17(4):275-83. 
  • Oehmen CS, ES Peterson, and JR Teuton. 2012. "Evolutionary Drift Models for Moving Target Defense." In CSIIRW '12: Proceedings of the 8th Annual Cyber Security and Information Intelligence Research Workshop, October 30-November 2, 2012, Oak RIdge, Tennessee.  ACM, New York, NY. 
  • Peterson ES, LA McCue, AC Rutledge, JL Jensen, J Walker, MA Kobold, SR Webb, SH Payne, C Ansong, JN Adkins, WR Cannon, and BJM Webb-Robertson. 2012. "VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms Through Integration of Proteomic and Transcriptomic Data." BMC Genomics 13(1):Article No. 131.  doi:10.1186/1471-2164-13-131
  • Tilton SC, T Tal, SM Scroggins, J Franzosa, ES Peterson, R Tanguay, and KM Waters. 2012. "Bioinformatics Resource Manager v2.3: An Integrated Software Environment for Systems Biology with microRNA and Cross-species Analysis Tools." BMC Bioinformatics 13:Article No. 311.  doi:10.1186/1471-2105-13-311

2011

  • McDermott JE, AL Corrigan, ES Peterson, CS Oehmen, G Niemann, E Cambronne, D Sharp, JN Adkins, R Samudrala, and F Heffron. 2011. "Computational prediction of type III and IV secreted effectors in Gram-negative bacteria ." Infection and Immunity 79(1):23-32.  doi:10.1128/IAI.00537-10
  • Jin H, BJM Webb-Robertson, ES Peterson, R Tan, DJ Bigelow, MB Scholand, JR Hoidal, JG Pounds, and RC Zangar. 2011. "Smoking, COPD and 3-Nitrotyrosine Levels of Plasma Proteins." Environmental Health Perspectives 119(9):1314-1320.  doi:10.1289/ehp.1103745

2010

  • Oehmen CS, ES Peterson, and ST Dowson. 2010. "An Organic Model for Detecting Cyber Events." In Proceedings of the Sixth Annual Workshop on Cyber Security and Information Intelligence Research, p. Article No. 66.  Association for Computing Machinery, New York, NY.  doi:10.1145/1852666.1852740

2008

  • Curtis DS, ES Peterson, and CS Oehmen. 2008. "A Secure Web Application Providing Public Access to High-Performance Data Intensive Scientific Resources - ScalaBLAST Web Application." In 4th Annual International Conference on Web Information Systems and Technologies, ed. J. Cordeiro, J. Filipe and S. Hammoudi, pp. 244-251.  Springer, Berlin, Germany. 
  • Peterson ES, EG Stephan, AL Corrigan, RD Lins, TA Soares, RE Scarberry, SJ Rose, LK Williams, C Lai, TJ Critchlow, and TP Straatsma. 2008. "Northwest Trajectory Analysis Capability: A Platform for Enhancing Computational Biophysics Analysis." In Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008, pp. 558-562.  CSREA Press, Bogart, GA. 

2007

  • Webb-Robertson BJM, ES Peterson, M Singhal, KR Klicker, CS Oehmen, JN Adkins, and SL Havre. 2007. "PQuad - A visual analysis platform for proteomic data exploration of microbial organism." Bioinformatics 23(13):1705-1707.  doi:10.1093/bioinformatics/btm132

2006

  • Kiebel GR, KJ Auberry, N Jaitly, D Clark, ME Monroe, ES Peterson, N Tolic, GA Anderson, and RD Smith. 2006. "PRISM: A Data Management System for High-Throughput Proteomics ." Proteomics 6(6):1783-1790.  doi:10.1002/pmic.200500500

2001

  • Myers JD, ES Mendoza, and BL Hoopes. 2001. "A Collaborative Electronic Laboratory Notebook." In Proceedings of the IASTED International Conference, Internet and Multimedia Systems and Applications, August 13-16, 2001, Honolulu, Hawaii, USA, ed. MH Hamza, pp. 334-338.  IASTED/Acta Press, Anaheim, CA. 

1998

  • Mendoza ES, WT Valdez, WM Harris, PW Auman, EF Gage, and JD Myers. 1998. "EMSL's Electronic Laboratory Notebook, Proceedings of the WebNet 98 World Conference." In WebNet '98 World Conference on the WWW and Internet and Intranet, Orlando, Florida, November 1-12, 1998, ed. H Maurer and RG Olson.  Association for Advancement of Computing in Education , Charlottsville, VA. 

Selected Publications

2008

  • Curtis DS, ES Peterson, and CS Oehmen.  2008.  "A Secure Web Application Providing Public Access to High-Performance Data Intensive Scientific Resources."  In 4th Annual International Conference on Web Information Systems and Technologies.  Springer, Berlin, Germany. 
  • Curtis DS, ES Peterson, and CS Oehmen.  2008.  "ScalaBLAST Web Application."  Presented by Darren Curtis at WEBIST 2008, http://www.webist.org, Funchal, Madeira on May 4, 2008.  PNNL-SA-60214.

2007

  • Oehmen CS, JE McDermott, and ES Peterson.  2007.  "Systems Approach to Understanding Molecular Mechanisms in the Light-Dark Cycle of Cyanothece sp. 51142."  Presented by Chris Oehmen, Jason Mcdermott at EMSL MBGC Advisory Committee Review, Richland, WA on August 21, 2007.  PNNL-SA-56739. 
  • Stephan EG, KL Schuchardt, TD Gibson, ES Peterson, BT Didier, and JM Chase.  2007.  "A Data Virtualization Architecture."  Presented by Eric Stephan; Karen Schuchardt at DICI Mid-Year Review at PNNL, Richland, WA on March 6, 2007. PNNL-SA-54031. 
  • Webb-Robertson BJM, ES Peterson, M Singhal, KR Klicker, CS Oehmen, JN Adkins, and SL Havre.  2007.  "PQuad - A visual analysis platform for proteomic data exploration of microbial organism."  Bioinformatics 23(13):1705-1707.  doi:10.1093/bioinformatics/btm132

2006

  • Kiebel GR, KJ Auberry, N Jaitly, D Clark, ME Monroe, ES Peterson, N Tolic, GA Anderson, and RD Smith.  2006.  "PRISM: A Data Management System for High-Throughput Proteomics ."  Proteomics 6(6):1783-1790.  doi:10.1002/pmic.200500500
  • Oehmen CS, LA McCue, JN Adkins, KM Waters, T Carlson, WR Cannon, BJM Webb-Robertson, DJ Baxter, ES Peterson, M Singhal, A Shah, and KR Klicker.  2006.  "High-Throughput Visual Analytics for Biological Sciences: Turning Data into Knowledge ."  Presented by Christopher Oehmen (Invited Speaker) at Supercomputing 2006, Tampa, FL on November 14, 2006.  PNNL-SA-52705. 
  • Oehmen CS, LA McCue, JN Adkins, KM Waters, TS Carlson, WR Cannon, BJM Webb-Robertson, DJ Baxter, ES Peterson, M Singhal, A Shah, and KR Klicker.  2006.  "High-throughput visual analytics for biological sciences: turning data into knowledge."  Journal of Supercomputing.  doi:http://doi.acm.org/10.1145/1188455.1188769

2002

  • Bair RA, JD Myers, and ES Mendoza.  2002. "National Collaboratories Middleware Projects."  Presented by Raymond A Bair (Invited Speaker) at SciDAC PI Meeting - Computing for Science, Reston, VA on January 15, 2002.  PNNL-SA-36045. 

2001

  • Mendoza ES.  2001.  "Examining the Electronic Laboratory Notebook Software from PNNL."  Presented by Elena S Mendoza (Invited Speaker) at Laboratory Notebooks - Paper and Electronic, Washington, DC on May 10, 2001.  PNNL-SA-37306. 
  • Myers JD, ES Mendoza, A Geist, and J Schwidder.  2001.  "Scientific Annotation Middleware (SAM)."  Presented by James D. Myers (Invited Speaker) at SciDAC Conference, Reston, VA on September 25, 2001.  PNNL-SA-35845. 
  • Myers JD, ES Mendoza, and BL Hoopes.  2001.  "A Collaborative Electronic Laboratory Notebook."  In Proceedings of the IASTED International Conference, Internet and Multimedia Systems and Applications, August 13-16, 2001, Honolulu, Hawaii, USA, ed. MH Hamza, pp. 334-338.  IASTED/Acta Press, Anaheim, CA. 

2000

  • Hoopes BL, ES Mendoza, and JD Myers.  2000.  "PNNL Electronic Laboratory Notebook."  Presented by James D. Myers (Invited Speaker) at CSCW Conference, Philadelphia, PA on December 4, 2000.  PNNL-SA-34827. 
  • Mendoza ES, and JD Myers.  2000.  "Web-based Electronic Laboratory Notebook Developed by Battelle Pacific Northwest Laboratories ."  Presented by Elena S Mendoza and James D Myers (Invited Speaker) at 219th American Chemical Society (ACS) National Meeting , San Francisco, CA on March 26, 2000.  PNNL-SA-37305. 

1998

  • Mendoza ES, WT Valdez, WM Harris, PW Auman, EF Gage, and JD Myers.  1998.  "EMSL's Electronic Laboratory Notebook, Proceedings of the WebNet 98 World Conference."  In WebNet '98 World Conference on the WWW and Internet and Intranet, Orlando, Florida, November 1-12, 1998, ed. H Maurer and RG Olson.  Association for Advancement of Computing in Education, Charlottsville, VA. 

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