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Fundamental and Computational Sciences Directorate

Staff information


Amanda White

Artif Intell & Mathem Modeling
Data Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: K7-20
Richland, WA 99352

PNNL Publications


  • Degnan D.J., L.M. Bramer, A.M. White, M. Zhou, A. Bilbao Pena, and L. McCue. 2021. "PSpecteR: a user-friendly and interactive application for visualizing top-down and bottom-up proteomics data in R." Journal of Proteome Research 20, no. 4:2014-2020. PNNL-SA-157638. doi:10.1021/acs.jproteome.0c00857


  • Bramer L.M., A.M. White, K.G. Stratton, A.M. Thompson, D.M. Claborne, K.S. Hofmockel, and L. McCue. 2020. "ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data." PLoS Computational Biology 16, no. 3:Article No. e1007654. PNNL-SA-152118. doi:10.1371/journal.pcbi.1007654


  • Bramer L.M., K.G. Stratton, A.M. White, A.A. Bleeker, M.A. Kobold, K.M. Waters, and T.O. Metz, et al. 2019. "P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data." Journal of Proteome Research 18, no. 3:1426-1432. PNNL-SA-140572. doi:10.1021/acs.jproteome.8b00840


  • Webb-Robertson B.M., L.M. Bramer, J.L. Jensen, M.A. Kobold, K.G. Stratton, A.M. White, and K.D. Rodland. 2017. "P-MartCancer-Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets." Cancer Research 77, no. 21:e47-e50. PNNL-SA-123730. doi:10.1158/0008-5472.CAN-17-0335
  • Zalesny M.D., P.D. Whitney, A.M. White, T.R. Plasse, and M.T. Grundy. 2017. "A Conceptual Model to Identify Intent to Use Chemical-Biological Weapons." Journal of Strategic Security 10, no. 3:54-86. PNNL-SA-129050. doi:10.5038/1944-0472.10.3.1612


  • White A.M., Z.N. Gastelum, and P.D. 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, 229-236. Deerfield, Illinois:Institute of Nuclear Materials Management. PNNL-SA-102659.


  • Gastelum Z.N., A.M. White, P.D. Whitney, L.J. Gosink, and L.H. 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, edited by K Glass, et al, 339-345. Piscataway, New Jersey:IEEE. PNNL-SA-94497. doi:10.1109/ISI.2013.6578855
  • Gastelum Z.N., P.D. Whitney, and A.M. 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. Deerfield, Illinois:Institute for Nuclear Materials Management. PNNL-SA-96554.
  • Watkins D.M., L.H. Sego, A.E. Holmes, B.M. Webb-Robertson, A.M. White, D.S. Wunschel, and H.W. Kreuzer, et al. 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, 304-309. Piscataway, New Jersey:IEEE. PNNL-SA-96498. doi:10.1109/THS.2013.6699019


  • Choo J., S.J. Bohn, G.C. Nakamura, A.M. 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, 177-188. Philadelphia, Pennsylvania:SIAM. PNNL-SA-85324.
  • Janik T., A.M. White, N.H. Pawley, K.L. Myers, and C.S. Oehmen. 2012. Annotated Bibliography for the MATADOR Project. PNNL-21448. Richland, WA: Pacific Northwest National Laboratory. Annotated Bibliography for the MATADOR Project
  • Shrestha S., C. Su, A.M. White, J.B. Manzano Franco, A. Marquez, and J.T. 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. New York, New York:Association for Computing Machinery. PNNL-SA-91114.


  • Coles G.A., A.J. Brothers, P.D. Whitney, A.C. Dalton, J. Olson, A.M. White, and S.K. Cooley, et al. 2011. Utility of Social Modeling in Assessment of a State’s Propensity for Nuclear Proliferation. PNNL-20492. Richland, WA: Pacific Northwest National Laboratory. Utility of Social Modeling in Assessment of a State’s Propensity for Nuclear Proliferation
  • Sanfilippo A.P., R.S. Butner, A.J. Cowell, A.C. Dalton, J.N. Haack, S.J. Kreyling, and R.M. Riensche, et al. 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, edited by J Salerno, SJ Yang, D Nau and SK Chai, 6589, 374-381. Heidelberg:Springer-Verlag. PNNL-SA-76558. doi:10.1007/978-3-642-19656-0_51
  • White A.M., D.S. Daly, and R.C. Zangar. 2011. "Analysis of High-Throughput ELISA Microarray Data." In Bioinformatics for Comparative Proteomics, Methods in Molecular Biology, edited by CH Wu and C Chen. 191-211. New York, New York:Humana Press. PNNL-SA-69834.
  • Whitney P.D., A.M. White, S.J. Walsh, A.C. Dalton, and A.J. 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, edited by J Salerno, SJ Yang, D Nau and SK Chai, 6589, 227-235. Heidelberg:Springer-Verlag. PNNL-SA-76187. doi:10.1007/978-3-642-19656-0_33


  • Daly D.S., K.K. Anderson, S.L. Seurynck-Servoss, R.M. Gonzalez, A.M. White, and R.C. Zangar. 2010. "An internal calibration method for protein-array studies." Statistical Applications in Genetics and Molecular Biology 9, no. 1:Article Number: 14. PNNL-SA-67909.
  • Walsh S.J., A.C. Dalton, P.D. Whitney, and A.M. White. 2010. "Parameterizing Bayesian network Representations of Social-Behavioral Models by Expert Elicitation." In IEEE International Conference on Intelligence and Security Informatics (ISI 2010), 227-232. Piscataway, New Jersey:Institute of Electrical and Electronics Engineers, Inc,. PNNL-SA-72080. doi:10.1109/ISI.2010.5484730


  • Chappell A.R., A. Bladek, C.A. Joslyn, E.J. Marshall, L.R. McGrath, P.R. Paulson, and S.E. Stolberg, et al. 2009. "Supporting the Analytic Knowledge Manager: Formal Methods for Ontology Display and Management." In ONTOLOGY FOR THE INTELLIGENCE COMMUNITY: OIC 2009. Fairfax, Virginia:Center of Excellence in Command, Control, Communications, Computing and Intelligence (C4I). PNWD-SA-8710.
  • Joslyn C.A., P.R. Paulson, and A.M. 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, edited by P Shvaiko, et al, 551. Aachen:CEUR Workshop Proceedings. PNWD-SA-8703.
  • Joslyn C.A., R.L. Baddeley, J. Blake, C. Bult, M. Dolan, R.M. Riensche, and K.D. Rodland, et al. 2009. "Automated Annotation-Based Bio-Ontology Alignment with Structural Validation." In International Conference on Biomedical Ontology (ICBO), July 24-26, 2009, Buffalo, New York, edited by B Smith. Buffalo, New York:University of Buffalo. PNWD-SA-8546.
  • Taylor R.C., M. Singhal, D.S. Daly, J.M. Gilmore, W.R. Cannon, K.O. Domico, and A.M. White, et al. 2009. "An analysis pipeline for the inference of protein-protein interaction networks." International Journal of Data Mining and Bioinformatics 3, no. 4) (Sp. Iss. SI:409-430. PNNL-SA-59756. doi:10.1504/IJDMB.2009.029204
  • White A.M., J.L. Collett, S.L. Seurynck-Servoss, D.S. Daly, and R.C. Zangar. 2009. "ELISA-BASE: An Integrated Bioinformatics Tool for Analyzing and Tracking ELISA Microarray Data." Bioinformatics 25, no. 12:1566-1567. PNNL-SA-63806.


  • Daly D.S., K.K. Anderson, A.M. White, R.M. Gonzalez, S.M. Varnum, and R.C. Zangar. 2008. "Predicting protein concentrations with ELISA microarray assays, monotonic splines and Monte Carlo simulation." Statistical Applications in Genetics and Molecular Biology 7, no. 1:Article 21. PNNL-SA-53347.
  • Gilmore J.M., D.L. Auberry, J.L. Sharp, A.M. White, K.K. Anderson, and D.S. Daly. 2008. "A Bayesian Estimator of Protein-Protein Association Probabilities." Bioinformatics 24, no. 13:1554-1555. PNNL-SA-57281. doi:10.1093/bioinformatics/btn238


  • Posse C., A.M. 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, 111-116. Piscataway, New Jersey:Institute of Electrical and Electronics Engineers. PNNL-SA-57857. doi:10.1109/THS.2007.370030
  • Seurynck-Servoss S.L., A.M. White, C.L. Baird, K.D. Rodland, and R.C. Zangar. 2007. "Evaluation of Surface Chemistries for Antibody Microarrays." Analytical Biochemistry 371, no. 1:105-115. PNNL-SA-55339.
  • Sharp J.L., K.K. Anderson, G.B. Hurst, D.S. Daly, D.A. Pelletier, W.R. Cannon, and D.L. Auberry, et al. 2007. "Statistically Inferring Protein-Protein Asociations with Affinity Isolation LC-MS/MS Assays." Journal of Proteome Research 6, no. 9:3788-3795. PNNL-SA-57329. doi:10.1021/pr0701106
  • Taylor R.C., M. Singhal, D.S. Daly, K.O. Domico, A.M. White, D.L. Auberry, and K.J. Auberry, et al. 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), 587-593. Washington Dc:IEEE Computer Society. PNNL-SA-55941. doi:10.1109/ICMLA.2007.63


  • Chandler D.P., O. Alferov, B. Chernov, D.S. Daly, J. Golova, A.N. Perov, and M. Protic, et al. 2006. "Diagnostic Oligonucleotide Microarray Fingerprinting of Bacillus Isolates." Journal of Clinical Microbiology 44, no. 1:244-250. PNNL-SA-45391. doi:10.1128/JCM.44.1.244-250.2066
  • Sanfilippo A.P., S.C. Tratz, M.L. Gregory, A.R. Chappell, P.D. Whitney, C. Posse, and P.R. Paulson, et al. 2006. "Automating Ontological Annotation with WordNet." In Proceedings of the Third International Global WordNet Conference (GWC-06), Jan. 22-26, South Jeju Island, Korea, edited by Petr Sojka, Key-Sun Choi, Christiane Fellbaum & Piek Vossen, 85-93. Brno:Masaryk University. PNNL-SA-47525. Automating Ontological Annotation with WordNet
  • Sanfilippo A.P., S.C. Tratz, M.L. Gregory, A.R. Chappell, P.D. Whitney, C. Posse, and P.R. Paulson, et al. 2006. "Ontological Annotation with WordNet." In SemAnnot 2005, 5th International Workshop on Knowledge Markup and Semantic Annotation, 7th November 2005, Galway, Ireland, edited by Siegfried Handschuh, Thierry Declerck, & Marja-Riitta Koivun, 185, 27-36. Aachen:Sun SITE Central Europe Workshop Proceedings ( PNNL-SA-54089. Ontological Annotation with WordNet
  • White A.M., D.S. Daly, S.M. Varnum, K.K. Anderson, N. Bollinger, and R.C. Zangar. 2006. "ProMAT: protein microarray analysis tool." Bioinformatics 22, no. 10:1278-1279. PNNL-SA-47930. doi:10.1093/bioinformatics/btl093
  • Zangar R.C., D.S. Daly, and A.M. White. 2006. "ELISA microarray technology as a high-throughput system for cancer biomarker validation." Expert Review of Proteomics 3, no. 1:37-44. PNNL-SA-47022. doi:10.1586/14789450.3.1.37


  • Daly D.S., A.M. White, S.M. Varnum, K.K. Anderson, and R.C. Zangar. 2005. "Evaluating concentration estimation errors in ELISA microarray experiments." BMC Bioinformatics 6. PNNL-SA-42198. doi:10.1186/1471-2105-6-17.
  • White A.M., D.S. Daly, A.R. Willse, M. Protic, and D.P. Chandler. 2005. "Automated Microarray Image Analysis Toolbox for MATLAB." Bioinformatics 21, no. 17:3578-3579. PNWD-SA-6685. doi:doi:10.1093/bioinformatics/bti576
  • Willse A.R., D.P. Chandler, A.M. White, M. Protic, D.S. Daly, and S.C. Wunschel. 2005. "Comparing Bacterial DNA Microarray Fingerprints." Statistical Applications in Genetics and Molecular Biology 4, no. 1:Article 19 (38 pages). PNNL-SA-45381.


  • Visher J., S. Wandzura, and A.M. White. 2004. "Stable, high-order discretization for evolution of the wave equation in 1+1 dimensions." Journal of Computational Physics 194, no. 2:395-408. PNNL-SA-41283.

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