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Fundamental and Computational Sciences Directorate

Staff information


Amanda White

Pacific Northwest National Laboratory
PO Box 999
MSIN: K7-90
Richland, WA 99352

PNNL Publications


  • Webb-Robertson BJM, LM Bramer, JL Jensen, MA Kobold, KG Stratton, AM White, and KD Rodland. 2017. "P-MartCancer-Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets." Cancer Research 77(21):e47-e50.  doi:10.1158/0008-5472.CAN-17-0335


  • White AM, ZN Gastelum, and PD Whitney. 2014. "Developing a Validation Methodology for Expert-Informed Bayesian Network Models Supporting Nuclear Nonproliferation Analysis." In Proceedings of the Information Analysis Technologies, Techniques and Methods for Safeguards, Nonproliferation and Arms Control Verification Workshop, May 12-14, 2014, Portland, Oregon, pp. 229-236.  Institute of Nuclear Materials Management, Deerfield, IL. 


  • Gastelum ZN, AM White, PD Whitney, LJ Gosink, and LH Sego. 2013. "The Lifecycle of Bayesian Network Models Developed for Multi-Source Signature Assessment of Nuclear Programs." In IEEE International Conference on Intelligence and Security Informatics (ISI 2013), June 4-7, 2013, Seattle, Washington, ed. K Glass, et al, pp. 339-345.  IEEE, Piscataway, NJ.  doi:10.1109/ISI.2013.6578855
  • Gastelum ZN, PD Whitney, and AM White. 2013. "Bayesian Model Development for Analysis of Open Source Information to Support the Assessment of Nuclear Programs." In Proceedings of the 54th Annual Meeting of the Institute of Nuclear Materials Management (INMM 2013) , July 20-24, 2013, Atlanta, Georgia.  Institute for Nuclear Materials Management, Deerfield, IL. 
  • Watkins DM, LH Sego, AE Holmes, BJM Webb-Robertson, AM White, DS Wunschel, HW Kreuzer, CD Corley, and MF Tardiff. 2013. "Assessing Performance and Tradeoffs of Bioforensic Signature Systems." In IEEE International Conference on Technologies for Homeland Security (HST 2013), November 12-14, 2013, Waltham, Massachusetts, pp. 304-309.  IEEE, Piscataway, NJ.  doi:10.1109/THS.2013.6699019


  • Choo J, SJ Bohn, GC Nakamura, AM White, and H Park. 2012. "Heterogeneous Data Fusion via Space Alignment Using Nonmetric Multidimensional Scaling." In 2012 SIAM International Conference on Data Mining, April 26-28, 2012, Anaheim, California, pp. 177-188.  SIAM, Philadelphia, PA. 
  • Janik T, AM White, NH Pawley, KL Myers, and CS Oehmen. 2012. Annotated Bibliography for the MATADOR ProjectPNNL-21448, Pacific Northwest National Laboratory, Richland, WA. 
  • Shrestha S, CY Su, AM White, JB Manzano Franco, A Marquez, and JT Feo. 2012. "MODA A Framework for Memory Centric Performance Characterization." In Workshop on High-performance Infrastructure for Scalable Tools (WHIST), June 29, 2012, Venice, Italy.  Association for Computing Machinery, New York, NY. 


  • White AM, DS Daly, and RC Zangar. 2011. "Analysis of High-Throughput ELISA Microarray Data." In Bioinformatics for Comparative Proteomics, Methods in Molecular Biology, vol. 694, ed. CH Wu and C Chen, pp. 191-211.  Humana Press, New York, NY. 
  • Coles GA, AJ Brothers, PD Whitney, AC Dalton, J Olson, AM White, SK Cooley, PM Youchak, and SV Stafford. 2011. Utility of Social Modeling in Assessment of a State’s Propensity for Nuclear ProliferationPNNL-20492, Pacific Northwest National Laboratory, Richland, WA. 
  • Sanfilippo AP, RS Butner, AJ Cowell, AC Dalton, JN Haack, SJ Kreyling, RM Riensche, AM White, and PD Whitney. 2011. "Technosocial Predictive Analytics for Illicit Nuclear Trafficking." In SBP'11: Proceedings of the 4th International Conference on Social Computing, Behavioral-Cultural Modeling and Prediction, March 29-31, 2011, College Park, MD. Lecture Notes in Computer Science, vol. 6589, ed. J Salerno, SJ Yang, D Nau and SK Chai, pp. 374-381.  Springer-Verlag, Heidelberg, Germany.  doi:10.1007/978-3-642-19656-0_51
  • Whitney PD, AM White, SJ Walsh, AC Dalton, and AJ Brothers. 2011. "Bayesian Networks for Social Modeling." In SBP 2011: Proceedings of the 4th International Conference on Social Computing, Behavioral-Cultural Modeling, and Prediction, March 29-31, 2011, College Park, MD: Lecture Notes in Computer Science, vol. 6589, ed. J Salerno, SJ Yang, D Nau and SK Chai, pp. 227-235.  Springer-Verlag, Heidelberg , Germany.  doi:10.1007/978-3-642-19656-0_33


  • Daly DS, KK Anderson, SL Seurynck-Servoss, RM Gonzalez, AM White, and RC Zangar. 2010. "An internal calibration method for protein-array studies ." Statistical Applications in Genetics and Molecular Biology 9(1):Article Number: 14. 
  • Walsh SJ, AC Dalton, PD Whitney, and AM White. 2010. "Parameterizing Bayesian network Representations of Social-Behavioral Models by Expert Elicitation ." In IEEE International Conference on Intelligence and Security Informatics (ISI 2010), pp. 227-232.  Institute of Electrical and Electronics Engineers, Inc,, Piscataway, NJ.  doi:10.1109/ISI.2010.5484730


  • White AM, JL Collett, SL Seurynck-Servoss, DS Daly, and RC Zangar. 2009. "ELISA-BASE: An Integrated Bioinformatics Tool for Analyzing and Tracking ELISA Microarray Data." Bioinformatics 25(12):1566-1567. 
  • Chappell AR, A Bladek, CA Joslyn, EJ Marshall, LR McGrath, PR Paulson, SE Stolberg, and AM White. 2009. "Supporting the Analytic Knowledge Manager: Formal Methods for Ontology Display and Management." In ONTOLOGY FOR THE INTELLIGENCE COMMUNITY: OIC 2009 .  Center of Excellence in Command, Control, Communications, Computing and Intelligence (C4I), Fairfax, VA. 
  • Joslyn CA, PR Paulson, and AM White. 2009. "Measuring the Structural Preservation of Semantic Hierarchy Alignments." In The Fourth International Workshop on Ontology Matching (OM-2009), October 25, 2009, Chantilly, Virginia, vol. 551, ed. P Shvaiko, et al.  CEUR Workshop Proceedings, Aachen, Germany. 
  • Joslyn CA, RL Baddeley, J Blake, C Bult, M Dolan, RM Riensche, KD Rodland, AP Sanfilippo, and AM White. 2009. "Automated Annotation-Based Bio-Ontology Alignment with Structural Validation." In International Conference on Biomedical Ontology (ICBO), July 24-26, 2009, Buffalo, New York, ed. B Smith.  University of Buffalo, Buffalo, NY. 
  • Taylor RC, M Singhal, DS Daly, JM Gilmore, WR Cannon, KO Domico, AM White, DL Auberry, KJ Auberry, BS Hooker, GB Hurst, JE McDermott, WH McDonald, DA Pelletier, DA Schmoyer, and HS Wiley. 2009. "An analysis pipeline for the inference of protein-protein interaction networks." International Journal of Data Mining and Bioinformatics 3(4) (Sp. Iss. SI):409-430. 


  • Gilmore JM, DL Auberry, JL Sharp, AM White, KK Anderson, and DS Daly. 2008. "A Bayesian Estimator of Protein-Protein Association Probabilities ." Bioinformatics 24(13):1554-1555.  doi:10.1093/bioinformatics/btn238
  • Daly DS, KK Anderson, AM White, RM Gonzalez, SM Varnum, and RC Zangar. 2008. "Predicting protein concentrations with ELISA microarray assays, monotonic splines and Monte Carlo simulation." Statistical Applications in Genetics and Molecular Biology 7(1):Article 21. 


  • Posse C, AM White, and N Beagley. 2007. "Human-Centered Fusion Framework." In 2007 IEEE Conference on Technologies for Homeland Security: Enhancing Critical Infrastructure Dependability, May 16-17, 2007, Woburn, MA, pp. 111-116.  Institute of Electrical and Electronics Engineers, Piscataway, NJ.  doi:10.1109/THS.2007.370030
  • Seurynck-Servoss SL, AM White, CL Baird, KD Rodland, and RC Zangar. 2007. "Evaluation of Surface Chemistries for Antibody Microarrays." Analytical Biochemistry 371(1):105-115. 
  • Sharp JL, KK Anderson, GB Hurst, DS Daly, DA Pelletier, WR Cannon, DL Auberry, DD Schmoyer, WH McDonald, AM White, BS Hooker, KD Victry, MV Buchanan, V Kery, and HS Wiley. 2007. "Statistically Inferring Protein-Protein Asociations with Affinity Isolation LC-MS/MS Assays." Journal of Proteome Research 6(9):3788-3795.  doi:10.1021/pr0701106
  • Taylor RC, M Singhal, DS Daly, KO Domico, AM White, DL Auberry, KJ Auberry, BS Hooker, GB Hurst, JE McDermott, WH McDonald, DA Pelletier, DD Schmoyer, and WR Cannon. 2007. "SEBINI-CABIN: An Analysis Pipeline for Biological Network Inference, with a Case Study in Protein-Protein Interaction Network Reconstruction ." In Sixth International Conference on Machine Learning and Applications, (ICMLA 2007) , pp. 587-593.  IEEE Computer Society, Washington DC.  doi:10.1109/ICMLA.2007.63


  • White AM, DS Daly, SM Varnum, KK Anderson, N Bollinger, and RC Zangar. 2006. "ProMAT: protein microarray analysis tool ." Bioinformatics 22(10):1278-1279.  doi:10.1093/bioinformatics/btl093
  • Chandler DP, O Alferov, B Chernov, DS Daly, J Golova, AN Perov, M Protic, R Robison, M Shipma, AM White, and AR Willse. 2006. "Diagnostic Oligonucleotide Microarray Fingerprinting of Bacillus Isolates." Journal of Clinical Microbiology 44(1):244-250.  doi:10.1128/JCM.44.1.244-250.2066
  • Sanfilippo AP, SC Tratz, ML Gregory, AR Chappell, PD Whitney, C Posse, PR Paulson, B Baddeley, RE Hohimer, and AM White. 2006. "Ontological Annotation with WordNet." In SemAnnot 2005, 5th International Workshop on Knowledge Markup and Semantic Annotation, 7th November 2005, Galway, Ireland, vol. 185, ed. Siegfried Handschuh, Thierry Declerck, & Marja-Riitta Koivun, pp. 27-36.  Sun SITE Central Europe Workshop Proceedings (, Aachen, Germany. 
  • Sanfilippo AP, SC Tratz, ML Gregory, AR Chappell, PD Whitney, C Posse, PR Paulson, BL Baddeley, RE Hohimer, and AM White. 2006. "Automating Ontological Annotation with WordNet." In Proceedings of the Third International Global WordNet Conference (GWC-06), Jan. 22-26, South Jeju Island, Korea, ed. Petr Sojka, Key-Sun Choi, Christiane Fellbaum & Piek Vossen, pp. 85-93.  Masaryk University, Brno, Czech Republic. 
  • Zangar RC, DS Daly, and AM White. 2006. "ELISA microarray technology as a high-throughput system for cancer biomarker validation ." Expert Review of Proteomics 3(1):37-44.  doi:10.1586/14789450.3.1.37


  • White AM, DS Daly, AR Willse, M Protic, and DP Chandler. 2005. "Automated Microarray Image Analysis Toolbox for MATLAB." Bioinformatics 21(17):3578-3579.  doi:doi:10.1093/bioinformatics/bti576
  • Daly DS, AM White, SM Varnum, KK Anderson, and RC Zangar. 2005. "Evaluating concentration estimation errors in ELISA microarray experiments." BMC Bioinformatics 6:17.  doi:10.1186/1471-2105-6-17.
  • Willse AR, DP Chandler, AM White, M Protic, DS Daly, and SC Wunschel. 2005. "Comparing Bacterial DNA Microarray Fingerprints." Statistical Applications in Genetics and Molecular Biology 4(1):Article 19 (38 pages). 


  • Visher J, S Wandzura, and AM White. 2004. "Stable, high-order discretization for evolution of the wave equation in 1+1 dimensions ." Journal of Computational Physics 194(2):395-408. 

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