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Fundamental and Computational Sciences Directorate

Staff information


Don Daly

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

Education and Credentials

  • Ph.D., Statistics, Montana State University
  • M.S., Statistics, Montana State University
  • B.S., Mathematics, Montana College of Mineral Science and Technology

PNNL Publications


  • Scott MJ, DS Daly, MI Hejazi, GP Kyle, L Liu, HC McJeon, A Mundra, PL Patel, JS Rice, and N Voisin. 2016. "Sensitivity of Future U.S. Water Shortages to Socioeconomic and Climate Drivers: A Case Study in Georgia Using an Integrated Human-Earth System Modeling Framework." Climatic Change 136(2):233-246.  doi:10.1007/s10584-016-1602-8


  • Scott MJ, DS Daly, JE Hathaway, CS Lansing, Y Liu, HC McJeon, RH Moss, PL Patel, MJ Peterson, JS Rice, and Y Zhou. 2015. "Calculating Impacts of Energy Standards on Energy Demand in U.S. Buildings with Uncertainty in an Integrated Assessment Model." Energy 90(Part 2):1682-1694.  doi:10.1016/


  • Jin H, TS Hallstrand, DS Daly, MM Matzke, P Nair, DJ Bigelow, JG Pounds, and RC Zangar. 2014. "A Halotyrosine Antibody that Detects Increased Protein Modifications in Asthma Patients." Journal of Immunological Methods 403(1-2):17-25. 
  • Scott MJ, DS Daly, JE Hathaway, CS Lansing, Y Liu, HC McJeon, RH Moss, PL Patel, MJ Peterson, JS Rice, and Y Zhou. 2014. Calculating Impacts of Energy Standards on Energy Demand in U.S. Buildings under Uncertainty with an Integrated Assessment Model: Technical Background DataPNNL-23918, Pacific Northwest National Laboratory, Richland, WA. 
  • Scott MJ, DS Daly, Y Zhou, JS Rice, PL Patel, HC McJeon, GP Kyle, SH Kim, J Eom, and LE Clarke. 2014. "Evaluating sub-national building-energy efficiency policy options under uncertainty: Efficient sensitivity testing of alternative climate, technolgical, and socioeconomic futures in a regional intergrated-assessment model. ." Energy Economics 43(2014):22-33.  doi:10.1016/j.eneco.2014.01.012
  • Wood TW, BD Reid, C Toomey, K Krishnaswami, KA Burns, LO Casazza, DS Daly, and LL Duckworth. 2014. "The Future of Nuclear Archeology: Reducing Legacy Risks of Weapons Fissile Material." Science and Global Security 22(1):4-26.  doi:10.1080/08929882.2014.874217


  • Bell EB, EJ Marshall, RE Hull, AK Fligg, AP Sanfilippo, DS Daly, and DW Engel. 2012. "Classifying Scientific Performance on a Metric-by-Metric Basis." In Proceedings of the Twenty-Fifth International Florida Artificial Intelligence Research Society (FLAIRS) Conference, May 23-25, 2012, Marco Island, Florida, ed. GM Youndblood and PM McCarthy, pp. 400-403.  AAAI Press, Palo Alto, CA. 


  • 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. 
  • Gonzales RM, DS Daly, R Tan, JR Marks, and RC Zangar. 2011. "Plasma Biomarker Profiles Differ Depending on Breast Cancer Subtype but RANTES is Consistently Increased." Cancer Epidemiology, Biomarkers and Prevention 20(7):1543-1551.  doi:10.1158/1055-9965.EPI-10-1248
  • Thompson SE, PD Whitney, MR Weimar, TW Wood, DS Daly, AJ Brothers, AP Sanfilippo, D Cook, and L Holder. 2011. Model and Analytic Processes for Export License AssessmentsPNNL-18189, Pacific Northwest National Laboratory, Richland, WA. 


  • 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. 
  • Weimar MR, DS Daly, and TW Wood. 2010. "Using Economic Input/Output Tables to Predict a Country’s Nuclear Status." In Proceedings of the 51st Annual Meeting of the Institute of Nuclear Materials Management, July 11-15, 2010, Baltimore, Maryland.  INMM, Deerfield, IL. 
  • Wood TW, PG Heasler, and DS Daly. 2010. "ALGORITHMS FOR OPTIMIZATION OF SYSYTEM PERFORMANCE IN LAYERED DETECTION SYSTEMS UNDER DETECTOR COORELATION ." In Proceedings of the 51st Annual Meeting of the Institute of Nuclear Materials Management, July 11-15, 2010, Baltimore, Maryland.  INMM, Deerfield, IL. 


  • Chilton MC, SJ Walsh, and DS Daly. 2009. "Prediction Metrics for Chemical Detection in Long-Wave Infrared Hyperspectral Imagery." Journal of Undergraduate Research IX:48-52. 
  • 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. 
  • Sharp JL, JJ Borkowski, DA Schmoyer, DS Daly, SO Purvine, WR Cannon, and GB Hurst. 2009. "Statistically Appraising Process Quality of Affinity Isolation Experiments ." Computational Statistics & Data Analysis 53(5):1720-1726 (special issue). 
  • Springer DL, JH Miller, SL Spinelli, L Pasa-Tolic, SO Purvine, DS Daly, RC Zangar, S Jin, N Blumberg, CW Francis, MB Taubman, AE Casey, SD Wittlin, and RP Phipps. 2009. "Platelet Proteome Changes Associated with Diabetes and During Platelet Storage for Transfusion." Journal of Proteome Research 8(5):2261-2272. 
  • 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. 
  • Zangar RC, DS Daly, A White, S Servoss, R Tan, and JR Collett. 2009. "ProMAT Calibrator: A Tool for Reducing Experimental Bias in Antibody Microarrays." Journal of Proteome Research 8(8):3937-3943. 


  • 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. 
  • Daly DS, KK Anderson, EA Panisko, SO Purvine, R Fang, ME Monroe, and SE Baker. 2008. "A mixed-effects Statistical Model for Comparative LC-MS Proteomics Studies." Journal of Proteome Research 7(3):1209-1217.  doi:10.1021/pr070441i
  • Jin S, DS Daly, DL Springer, and JH Miller. 2008. "The effects of shared peptides on protein quantitation in label-free proteomics by LC/MS/MS ." Journal of Proteome Research 7(1):164-169.  doi:10.1021/pr0704175
  • Miller JH, A Suleiman, DS Daly, DL Springer, SL Spinelli, N Blumberg, and RP Phipps. 2008. "Extracting Biological Meaning From Global Proteomic Data on Circulating-Blood Platelets: Effects of Diabetes and Storage Time." In Proceedings of 2008 IEEE International Conference on Bioinformatics and Biomedicine, pp. 132-135.  IEEE Computer Society, Los Alamitos, CA.  doi:10.1109/BIBMW.2008.4686226
  • Monroe ME, JL Shaw, DS Daly, JN Adkins, and RD Smith. 2008. "MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features." Computational Biology and Chemistry 32(3):215-217.  doi:10.1016/j.compbiolchem.2008.02.006
  • Pelletier DA, GB Hurst, LJ Foote, PK Lankford, CK McKeown, TYS Lu, DD Schmoyer, MB Shah, WJ Hervey IV, WH McDonald, BS Hooker, WR Cannon, DS Daly, JM Gilmore, HS Wiley, DL Auberry, Y Wang, F Larimer, SJ Kennel, MJ Doktycz, J Morrell-Falvey, ET Owens, and MV Buchanan. 2008. "A general system for studying protein-protein interactions in gram-negative bacteria." Journal of Proteome Research 7(8):3319-3328.  doi:10.1021/pr8001832


  • Sharp JL, KK Anderson, DS Daly, DL Auberry, JJ Borkowski, and WR Cannon. 2007. "Inferring Protein Associations Using Protein Pulldown Assays." In 2006 Joint Statistical Meetings: Statistics for an Uncertain World: Meeting Global Challenges, August 6-10, Seattle, WA, p. 5 pages.  American Statistical Association, Alexandria, VA. 
  • 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
  • Anderson KK, ME Monroe, and DS Daly. 2006. "Estimating Probabilities of Peptide Database Identifications to LC-FTICR-MS Observations." Proteome Science 4(1):1-11.  doi:10.1186/1477-5956-4-1
  • 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
  • Good MS, CF Wend, LJ Bond, JS Mclean, PD Panetta, S Ahmed, SL Crawford, and DS Daly. 2006. "An Estimate of Biofilm Properties using an Acoustic Microscope." IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control 53(9):1637-1648. 
  • 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


  • Norbeck AD, ME Monroe, JN Adkins, KK Anderson, DS Daly, and RD Smith. 2005. "The utility of accurate mass and LC elution time information in the analysis of complex proteomes." Journal of the American Society for Mass Spectrometry 16(8):1239-1249. 
  • 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). 


  • Anderson KK, ME Monroe, and DS Daly. 2004. "Estimating Probabilities of Peptide Assignments to LC-FTICR-MS Observations." In Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'04), ed. Faramarz Valafar and Homayoun Valafar, pp. 151-156.  CSREA Press, Las Vegas, NV. 
  • Bamberger JA, DS Daly, RS Brown, JA Vucelick, DK Tano, KK Anderson, and AA Diaz. 2004. "Using Radiofrequency Tags to Assess Mixing in Fluids." In Proceedings of the 16th World Conference on Nondestructive Testing (WCNDT 2004), August 30 - September 2, 2004, Montreal, Canada.  Canadian Institute for Non-Destructive Evaluation, Hamilton, ON, Canada. 
  • Willse AR, TM Straub, SC Wunschel, JA Small, DR Call, DS Daly, and DP Chandler. 2004. "Quantitative Oligonucleotide Microarray Fingerprinting of Salmonella enterica isolates." Nucleic Acids Research 32(5):1848-1856. 


  • Jarman KH, DS Daly, KK Anderson, and KL Wahl. 2003. "A new approach to automated peak detection." Chemometrics and Intelligent Laboratory Systems 69(1-2):61-76. 
  • Chandler DP, GJ Newton, JA Small, and DS Daly. 2003. "Sequence versus Structure for the Direct Detection of 16S rRNA on Planar Oligonucleotide Microarrays." Applied and Environmental Microbiology 69(5):2950-2958. 
  • Whitney PD, D Cox, DS Daly, HP Foote, DL McQuerry, and JM Sloughter. 2003. "Toward the Routine Analysis of Diverse Data Types." Journal of Computational and Graphical Statistics 12(4):915-926. 


  • Daly DS, RA Wind, PD Majors, KK Anderson, GR Holtom, and EJ Ackerman. 2002. "An Integrated Confocal and Magnetic Resonance Microscope for Observing Living Cells." In 2002 IEEE International Symposium on Biomedical Imaging Macro to Nano, pp. 801-804.  IEEE, New York, NY. 
  • Kingsley MT, TM Straub, DR Call, DS Daly, SC Wunschel, and DP Chandler. 2002. "Fingerprinting Closely Related Xanthomonas Pathovars with Random Nonamer Oligonucleotide Microarrays." Applied and Environmental Microbiology 68(12):6361-6370. 
  • Petrie GM, PG Heasler, EM Perry, SE Thompson, and DS Daly. 2002. "Inverse Kriging to Enhance Spatial Resolution of Imagery." In Algorithms and Systems for Optical Information Processing, Proceedings-SPIE, vol. 4789, pp. 55-63.  SPIE , Bellingham. 
  • Straub TM, DS Daly, SC Wunschel, PA Rochelle, R Deleon, and DP Chandler. 2002. "Genotyping Cryptosporidium parvum with an hsp70 Single- Nucleotide Polymorphism Microarray." Applied and Environmental Microbiology 68(4):1817-1826. 
  • Wind RA, PD Majors, KR Minard, EJ Ackerman, DS Daly, GR Holtom, BD Thrall, and TJ Weber. 2002. "Combined Confocal and Magnetic Resonance Microscopy." Applied Magnetic Resonance 22(2):145-158. 


  • Wind RA, KR Minard, GR Holtom, PD Majors, EJ Ackerman, SD Colson, D Cory, DS Daly, PD Ellis, NF Metting, CI Parkinson, JM Price, and XW Tang. 2000. "An Integrated Confocal and Magnetic Resonance Microscope for Cellular Research." Journal of Magnetic Resonance 147(2):371-377. 


  • Jarman KH, DS Daly, CE Petersen, AJ Saenz, NB Valentine, and KL Wahl. 1999. "Extracting and Visualizing Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectral Fingerprints." Rapid Communications in Mass Spectrometry 13(15):1586-1594. 


  • Johnson RL, DS Daly, and GE Johnson. 1998. "Combining Hydroacoustics, Flow Models to Study Fish Behavior." Hydro Review XVII(7):40-56. 

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