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Bowden ME, Alvine KJ, Fulton JL, Lemmon JP, Lu X, Webb-Robertson BJ, et al. X-ray absorption measurements on nickel cathode of sodium-beta alumina batteries: Fe–Ni–Cl chemical associations. Journal of Power Sources. 2014 Feb;247:517–526.

Amidan BG, Orton DJ, LaMarche BL, Monroe ME, Moore RJ, Venzin AM, et al. Signatures for Mass Spectrometry Data Quality. J Proteome Res. 2014 Mar;

Freedman VL, Chen X, Finsterle S, Freshley MD, Gorton I, Gosink LJ, et al. A high-performance workflow system for subsurface simulation. Environmental Modelling & Software. 2014 May;55:176–189.

Thomas DG, Chikkagoudar S, Heredia-Langner A, Tardiff MF, Xu Z, Hourcade DE, et al. Physicochemical signatures of nanoparticle-dependent complement activation. Computational Science & Discovery. 2014 Jan;7(1):015003+.

Webb-Robertson BJ, Kim YM, Zink EM, Hallaian KA, Zhang Q, Madupu R, et al. A statistical analysis of the effects of urease pre-treatment on the measurement of the urinary metabolome by gas chromatography–mass spectrometry. 2014;p. 1–12.

Gosink LJ, Hogan EA, Pulsipher TC, Baker NA. Bayesian model aggregation for ensemble-based estimates of protein pKa values. Proteins. 2014 Mar;82(3):354–363.

Baker NA, Klemm JD, Harper SL, Gaheen S, Heiskanen M, Rocca-Serra P, et al. Standardizing data. Nat Nano. 2013 Feb;8(2):73–74.

Webb-Robertson BJ, Corley C, McCue LA, Wahl K, Kreuzer H. Fusion of laboratory and textual data for investigative bioforensics. Forensic Science International. 2013 Mar;226(1-3):118–124.

Dillard SE, Henry MJ, Bohn S, Gosink LJ. Coherent image layout using an adaptive visual vocabulary. vol. 8661; 2013. p. 86610Q–86610Q–14.

Tchitchek N, Eisfeld A, Go JT, Josset L, Gralinski L, Becavin C, et al. Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice. BMC Systems Biology. 2013;7(1):69+.

Olsen BN, Bielska AA, Lee T, Daily MD, Covey DF, Schlesinger PH, et al. The Structural Basis of Cholesterol Accessibility in Membranes. Biophysical Journal. 2013 Oct;105(8):1838–1847.

Taylor RC, Webb Robertson BJM, Markillie LM, Serres MH, Linggi BE, Aldrich JT, et al. Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria. Integr Biol. 2013;5(11):1393–1406.

Webb-Robertson BJ, Matzke M, Metz T, McDermott J, Walker H, Rodland K, et al. Sequential projection pursuit principal component analysis – dealing with missing data associated with new -omics technologies. BioTechniques. 2013 Mar;54(3):165–168.

Wiedner SD, Ansong C, Webb-Robertson BJ, Pederson LM, Fortuin S, Hofstad BA, et al. Disparate Proteome Responses of Pathogenic and Nonpathogenic Aspergilli to Human Serum Measured by Activity-Based Protein Profiling (ABPP). Molecular & Cellular Proteomics. 2013 Jul;12(7):1791–1805.

Tilton SC, Karin NJ, Webb-Robertson BJM, Waters KM, Mikheev V, Lee KM, et al. Impaired Transcriptional Response of the Murine Heart to Cigarette Smoke in the Setting of High Fat Diet and Obesity. Chem Res Toxicol. 2013 Jun;26(7):1034–1042.

Bramer LM, Hornbuckle BK, Caragea PC. How Many Measurements of Soil Moisture within the Footprint of a Ground-Based Microwave Radiometer Are Required to Account for Meter-Scale Spatial Variability? Vadose Zone Journal. 2013;12(3):0+.

Piepel GF. Comment: Spurious Correlation and Other Observations on Experimental Design for Engineering Dimensional Analysis. Technometrics. 2013 Aug;55(3):286–289.

Hafen R, Gibson TD, van Dam KK, Critchlow T. Large-scale Exploratory Analysis, Cleaning, and Modeling for Event Detection in Real-world Power Systems Data. In: Proceedings of the 3rd International Workshop on High Performance Computing, Networking and Analytics for the Power Grid. HiPCNA-PG ’13. New York, NY, USA: ACM; 2013.

Gralinski LE, Bankhead A, Jeng S, Menachery VD, Proll S, Belisle SE, et al. Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury. mBio. 2013 Aug;4(4):e00271–13+.

Gastelum ZN, White AM, Whitney PD, Gosink LJ, Sego LH. The lifecycle of Bayesian network models developed for Multi-Source Signature assessment of Nuclear Programs. In: Intelligence and Security Informatics (ISI), 2013 IEEE International Conference on. IEEE; 2013. p. 339–345.

Livnat Y, Jurrus E, Gundlapalli AV, Gestland P. The CommonGround visual paradigm for biosurveillance. In: Intelligence and Security Informatics (ISI), 2013 IEEE International Conference on. IEEE; 2013. p. 352–357.

Baker NA, Barr JL, Bonheyo GT, Joslyn CA, Krishnaswami K, Oxley ME, et al. Research towards a systematic signature discovery process. In: Intelligence and Security Informatics (ISI), 2013 IEEE International Conference on. IEEE; 2013. p. 301–308.

Sego LH, Holmes AE, Gosink LJ, Webb-Robertson BJM, Kreuzer HW, Anderson RM, et al. Assessing the quality of bioforensic signatures. In: Intelligence and Security Informatics (ISI), 2013 IEEE International Conference on. IEEE; 2013. p. 346–351.

Venzin AM, Oxley ME, Beagley N. An investigation into label fusion on sparse data. In: Intelligence and Security Informatics (ISI), 2013 IEEE International Conference on. IEEE; 2013. p. 309–314.

Harris MD, Datar M, Whitaker RT, Jurrus ER, Peters CL, Anderson AE. Statistical shape modeling of cam femoroacetabular impingement. J Orthop Res. 2013 Oct;31(10):1620–1626.

Gosink L, Bensema K, Pulsipher T, Obermaier H, Henry M, Childs H, et al. Characterizing and Visualizing Predictive Uncertainty in Numerical Ensembles Through Bayesian Model Averaging. Visualization and Computer Graphics, IEEE Transactions on. 2013 Dec;19(12):2703–2712.

Daily MD, Chun J, Heredia-Langner A, Wei G, Baker NA. Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies. The Journal of Chemical Physics. 2013 Nov;139(20):204108+.

Mosites E, Carpenter LR, McElroy K, Lancaster MJ, Ngo TH, McQuiston J, et al. Knowledge, Attitudes, and Practices Regarding Rocky Mountain Spotted Fever among Healthcare Providers, Tennessee, 2009. The American Journal of Tropical Medicine and Hygiene. 2013 Jan;88(1):162–166.

Stephan CN, Amidan B, Trease H, Guyomarc’h P, Pulsipher T, Byrd JE. Morphometric Comparison of Clavicle Outlines from 3D Bone Scans and 2D Chest Radiographs: A Shortlisting Tool to Assist Radiographic Identification of Human Skeletons. J Forensic Sci. 2013 Nov;p. n/a.

Wang J, Webb-Robertson BJM, Matzke MM, Varnum SM, Brown JN, Riensche RM, et al. A Semiautomated Framework for Integrating Expert Knowledge into Disease Marker Identification. Disease Markers. 2013;35:513–523.

Maciejewski R, Pattath A, Ko S, Hafen R, Cleveland WS, Ebert DS. Automated Box-Cox Transformations for Improved Visual Encoding. Visualization and Computer Graphics, IEEE Transactions on. 2013 Jan;19(1):130–140.

Lu N, Diao R, Hafen RP, Samaan N, Makarov YV. A comparison of forecast error generators for modeling wind and load uncertainty. In: Power and Energy Society General Meeting (PES), 2013 IEEE. IEEE; 2013. p. 1–5.

Tilton SC, Waters KM, Karin NJ, Webb-Robertson BJM, Zangar RC, Lee KM, et al. Diet-induced obesity reprograms the inflammatory response of the murine lung to inhaled endotoxin. Toxicology and Applied Pharmacology. 2013 Mar;267(2):137–148.

Vlachopoulou M, Gosink L, Pulsipher TC, Ferryman T, Zhou N, Tong J. An ensemble approach for forecasting net interchange schedule. In: Power and Energy Society General Meeting (PES), 2013 IEEE. IEEE; 2013. p. 1–5.

Nobles MA, Sego LH, Cooley SK, Gosink LJ, Anderson RM, Hays SE, et al. A decision-theoretic approach to evaluate radiation detection algorithms. In: Technologies for Homeland Security (HST), 2013 IEEE International Conference on. IEEE; 2013. p. 683–686.

Jurrus E, Watanabe S, Giuly RJ, Paiva AR, Ellisman MH, Jorgensen EM, et al. Semi-automated neuron boundary detection and nonbranching process segmentation in electron microscopy images. Neuroinformatics. 2013 Jan;11(1):5–29.

Watkins DM, Sego LH, Holmes AE, Webb-Robertson BJM, White AM, Wunschel DS, et al. Assessing performance and tradeoffs of bioforensic signature systems. In: Technologies for Homeland Security (HST), 2013 IEEE International Conference on. IEEE; 2013. p. 304–309.

Piepel G, Özler C, Şehirlioğlu A. Optimum tolerance design using component-amount and mixture-amount experiments. 2013;68(9-12):2359–2369.

Hathaway J, Walsh S, Sego L, Pulsipher B. Cross-combined composite sampling designs for identification of elevated regions. Environmental and Ecological Statistics. 2013 Jun;20(1):69–90.

Rodriguez DC, Anderson E, Anderson KK, Campbell LW, Fast JE, Jarman K, et al. Measurement and analysis of gamma-rays emitted from spent nuclear fuel above 3MeV. Applied Radiation and Isotopes. 2013 Dec;82:181–187.

Sims AC, Tilton SC, Menachery VD, Gralinski LE, Schäfer A, Matzke MM, et al. Release of Severe Acute Respiratory Syndrome Coronavirus Nuclear Import Block Enhances Host Transcription in Human Lung Cells. Journal of Virology. 2013 Apr;87(7):3885–3902.

Jones KB, Datar M, Ravichandran S, Jin H, Jurrus E, Whitaker R, et al. Toward an understanding of the short bone phenotype associated with multiple osteochondromas. J Orthop Res. 2013 Apr;31(4):651–657.

Kulisek JA, Anderson KK, Casella AM, Gesh CJ, Warren GA. Assaying Used Nuclear Fuel Assemblies Using Lead Slowing-Down Spectroscopy and Singular Value Decomposition. Nuclear Science, IEEE Transactions on. 2013 Apr;60(2):539–544.

Macdonald D, Clements SL, Patrick SW, Perkins C, Muller G, Lancaster MJ, et al. Cyber/physical security vulnerability assessment integration. In: Innovative Smart Grid Technologies (ISGT), 2013 IEEE PES. IEEE; 2013. p. 1–6.

Pham CTN, Thomas DG, Beiser J, Mitchell LM, Huang JL, Senpan A, et al. Application of a hemolysis assay for analysis of complement activation by perfluorocarbon nanoparticles. Nanomedicine: Nanotechnology, Biology and Medicine. 2013 Nov;

Matzke MM, Brown JN, Gritsenko MA, Metz TO, Pounds JG, Rodland KD, et al. A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments. Proteomics. 2013 Feb;13(3-4):493–503.

Hafen R, Gosink L, McDermott J, Rodland K, Dam KK, Cleveland WS. Trelliscope: A system for detailed visualization in the deep analysis of large complex data. In: 2013 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV). IEEE; 2013. p. 105–112.

Thomas DG, Chun J, Chen Z, Wei G, Baker NA. Parameterization of a geometric flow implicit solvation model. Journal of Computational Chemistry. 2013 Mar;34(8):687–695.


Dasgupta A, Kosara R, Gosink L. Meta parallel coordinates for visualizing features in large, high-dimensional, time-varying data. In: Large Data Analysis and Visualization (LDAV), 2012 IEEE Symposium on. IEEE; 2012. p. 85–89.

Ferryman TA, Amidan BG. Investigation of Phase Angle Differences Using Statistical Analysis of Real World State Estimator Data. In: System Science (HICSS), 2012 45th Hawaii International Conference on. IEEE; 2012. p. 2062–2071.

Olsen BN, Schlesinger PH, Ory DS, Baker NA. Side-chain oxysterols: From cells to membranes to molecules. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2012 Feb;1818(2):330–336.

Corley CD, Lancaster MJ, Brigantic RT, Chung JS, Walters RA, Arthur RR, et al. Assessing the Continuum of Event-Based Biosurveillance Through an Operational Lens. Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science. 2012 Mar;10(1):131–141.

Maojo V, Fritts M, Martin-Sanchez F, De la Iglesia D, Cachau R, Garcia-Remesal M, et al. Nanoinformatics: developing new computing applications for nanomedicine. Computing. 2012 Mar;94(6):521–539.

Peterson E, McCue LA, Rutledge AS, Jensen J, Walker H, Kobold M, et al. VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data. BMC Genomics. 2012 Apr;13(1):131+.

Hogrebe L, Paiva ARC, Jurrus E, Christensen C, Bridge M, Dai L, et al. Serial section registration of axonal confocal microscopy datasets for long-range neural circuit reconstruction. Journal of Neuroscience Methods. 2012 Jun;207(2):200–210.

Lee SJ, Schlesinger PH, Wickline SA, Lanza GM, Baker NA. Simulation of fusion-mediated nanoemulsion interactions with model lipid bilayers. Soft Matter. 2012;8(26):7024–7035.

Hunt RD, Silva GWCM, Lindemer TB, Anderson KK, Collins JL. Preparation of uranium fuel kernels with silicon carbide nanoparticles using the internal gelation process. Journal of Nuclear Materials. 2012 Aug;427(1-3):245–248.

Webb-Robertson BJM, Bailey VL, Fansler SJ, Wilkins MJ, Hess NJ. Spectral signatures for the classification of microbial species using Raman spectra. Analytical and Bioanalytical Chemistry. 2012;404(2):563–572.

Piepel G, Pasquini B, Cooley S, Heredia-Langner A, Orlandini S, Furlanetto S. Mixture-process variable approach to optimize a microemulsion electrokinetic chromatography method for the quality control of a nutraceutical based on coenzyme Q10. Talanta. 2012 Aug;97:73–82.

Hafen R, Henry M. Speech information retrieval: a review. Multimedia Systems. 2012 Jul;18(6):499–518.

Webb-Robertson BJ, Kreuzer H, Hart G, Ehleringer J, West J, Gill G, et al. Bayesian Integration of Isotope Ratio for Geographic Sourcing of Castor Beans. Journal of Biomedicine and Biotechnology. 2012;2012:1–8.

Chen Z, Zhao S, Chun J, Thomas DG, Baker NA, Bates PW, et al. Variational approach for nonpolar solvation analysis. The Journal of Chemical Physics. 2012 Aug;137(8):084101+.

McDermott JE, Wang J, Mitchell H, Webb-Robertson BJ, Hafen R, Ramey J, et al. Challenges in biomarker discovery: combining expert insights with statistical analysis of complex omics data. Expert Opin Med Diagn. 2012 Aug;7(1):37–51.

Harvey SD, Jarman KH, Moran JJ, Sorensen CM, Wright BW. Characterization of diesel fuel by chemical separation combined with capillary gas chromatography (GC) isotope ratio mass spectrometry (IRMS). Talanta. 2012 Sep;99:262–269.

Konecny R, Baker NA, McCammon JA. iAPBS: a programming interface to the adaptive Poisson–Boltzmann solver. Computational Science & Discovery. 2012 Jan;5(1):015005+.

Ren P, Chun J, Thomas DG, Schnieders MJ, Marucho M, Zhang J, et al. Biomolecular electrostatics and solvation: a computational perspective. Quarterly Reviews of Biophysics. 2012 Nov;45:427–491.

Thomas DG, Chikkagoudar S, Chappell AR, Baker NA. Annotating the structure and components of a nanoparticle formulation using computable string expressions. In: Bioinformatics and Biomedicine Workshops (BIBMW), 2012 IEEE International Conference on. IEEE; 2012. p. 889–894.

Fraga CG, Sego LH, Hoggard JC, Acosta GA, Viglino EA, Wahl JH, et al. Preliminary effects of real-world factors on the recovery and exploitation of forensic impurity profiles of a nerve-agent simulant from office media. Journal of Chromatography A. 2012 Dec;1270:269–282.

Diao R, Samaan N, Makarov Y, Hafen R, Ma J. Planning for variable generation integration through balancing authorities consolidation. In: Power and Energy Society General Meeting, 2012 IEEE. IEEE; 2012. p. 1–8.

Snee RD, Piepel GF. Assessing Component Effects in Formulation Systems. Quality Engineering. 2012 Dec;25(1):46–53.

Piepel GF, Amidan BG, Hu R. Laboratory studies on surface sampling of Bacillus anthracis contamination: summary, gaps and recommendations. J Appl Microbiol. 2012 Dec;113(6):1287–1304.

Liu T, Jurrus E, Seyedhosseini M, Ellisman M, Tasdizen T. Watershed merge tree classification for electron microscopy image segmentation. In: Pattern Recognition (ICPR), 2012 21st International Conference on. IEEE; 2012. p. 133–137.

Diamond DL, Krasnoselsky AL, Burnum KE, Monroe ME, Webb-Robertson BJ, McDermott JE, et al. Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus–mediated liver disease posttransplantation. Hepatology. 2012 Jul;56(1):28–38.

Jacob F, Gray J, Wynne A, Liu Y, Baker N. Domain-specific Languages for Composing Signature Discovery Workflows. In: Proceedings of the 2012 Workshop on Domain-specific Modeling. DSM ’12. New York, NY, USA: ACM; 2012. p. 61–64.

Corley CD, Lancaster MJ, Brigantic RT, Kunkel B, Muller G, McKenzie T. Outside the Continental United States International Travel and Contagion Impact Quick Look Tool. In: Proceedings of the First ACM SIGSPATIAL International Workshop on Use of GIS in Public Health. HealthGIS ’12. New York, NY, USA: ACM; 2012. p. 81–86.

Varnum SM, Springer DL, Chaffee ME, Lien KA, Webb-Robertson BJM, Waters KM, et al. The Effects of Low-Dose Irradiation on Inflammatory Response Proteins in a 3D Reconstituted Human Skin Tissue Model. Radiation Research. 2012 Oct;178(6):591–599.

Ma J, Lu S, Hafen RP, Etingov PV, Makarov YV, Chadliev V. The impact of solar photovoltaic generation on balancing requirements in the southern Nevada system. In: Transmission and Distribution Conference and Exposition (T&D), 2012 IEEE PES. IEEE; 2012. p. 1–9.

Sego LH, Márquez A, Rawson A, Cader T, Fox K, Gustafson WI, et al. Implementing the Data Center Energy Productivity Metric. J Emerg Technol Comput Syst. 2012 Nov;8(4).

Varnum SM, Webb-Robertson BJM, Pounds JG, Moore RJ, Smith RD, Frevert CW, et al. Proteomic Analysis of Bronchoalveolar Lavage Fluid Proteins from Mice Infected with Francisella tularensis ssp. novicida. J Proteome Res. 2012 Jun;11(7):3690–3703.

Rowlandson TL, Hornbuckle BK, Bramer LM, Patton JC, Logsdon SD. Comparisons of Evening and Morning SMOS Passes Over the Midwest United States. Geoscience and Remote Sensing, IEEE Transactions on. 2012 May;50(5):1544–1555.

Yang F, Waters KM, Webb-Robertson BJ, Sowa MB, von Neubeck C, Aldrich JT, et al. Quantitative phosphoproteomics identifies filaggrin and other targets of ionizing radiation in a human skin model. Experimental Dermatology. 2012 May;21(5):352–357.

Strom DJ, Joyce KE, MacLellan JA, Watson DJ, Lynch TP, Antonio CL, et al. Disaggregating measurement uncertainty from population variability and Bayesian treatment of uncensored results. Radiation Protection Dosimetry. 2012 Apr;149(3):251–267.

Bruillard P, Rowell E. Modular categories, integrality and Egyptian fractions. Proceedings of the American Mathematical Society. 2012;140(4):1141–1150.

Krauter PA, Piepel GF, Boucher R, Tezak M, Amidan BG, Einfeld W. False-Negative Rate and Recovery Efficiency Performance of a Validated Sponge Wipe Sampling Method. Applied and Environmental Microbiology. 2012 Feb;78(3):846–854.


Webb-Robertson BJM, Matzke MM, Jacobs JM, Pounds JG, Waters KM. A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors. Proteomics. 2011 Dec;11(24):4736–4741.

Nackos AN, Truong TV, Pulsipher TC, Kimball JA, Tolley HD, Robison RA, et al. One-step conversion of dipicolinic acid to its dimethyl ester using monomethyl sulfate salts for GC-MS detection of bacterial endospores. Anal Methods. 2011;3(2):245–258.

Olsen BN, Schlesinger PH, Ory DS, Baker NA. 25-Hydroxycholesterol Increases the Availability of Cholesterol in Phospholipid Membranes. Biophysical Journal. 2011 Feb;100(4):948–956.

Chen Z, Baker N, Wei GW. Differential geometry based solvation model II: Lagrangian formulation. Journal of mathematical biology. 2011 Dec;63(6):1139–1200.

Unni S, Huang Y, Hanson RM, Tobias M, Krishnan S, Li WW, et al. Web servers and services for electrostatics calculations with APBS and PDB2PQR. J Comput Chem. 2011 May;32(7):1488–1491.

Furlanetto S, Cirri M, Piepel G, Mennini N, Mura P. Mixture experiment methods in the development and optimization of microemulsion formulations. Journal of Pharmaceutical and Biomedical Analysis. 2011 Jun;55(4):610–617.

Gosink LJ, Garth C, Anderson JC, Bethel EW, Joy KI. An Application of Multivariate Statistical Analysis for Query-Driven Visualization. Visualization and Computer Graphics, IEEE Transactions on. 2011 Mar;17(3):264–275.

Maciejewski R, Hafen R, Rudolph S, Larew SG, Mitchell MA, Cleveland WS, et al. Forecasting Hotspots - A Predictive Analytics Approach. Visualization and Computer Graphics, IEEE Transactions on. 2011 Apr;17(4):440–453.

Malviya A, Fink GA, Sego L, Endicott-Popovsky B. Situational Awareness as a Measure of Performance in Cyber Security Collaborative Work. In: Information Technology: New Generations (ITNG), 2011 Eighth International Conference on. IEEE; 2011. p. 937–942.

Jarman KD, Scherrer C, Smith LE, Chilton LK, Anderson KK, Ressler JJ, et al. Indirect estimation of radioactivity in containerized cargo. Radiation Measurements. 2011 Jan;46(1):10–20.

Webb-Robertson BJ, Bunn AL, Bailey VL. Phospholipid fatty acid biomarkers in a freshwater periphyton community exposed to uranium: discovery by non-linear statistical learning. Journal of Environmental Radioactivity. 2011 Jan;102(1):64–71.

Anderson K, Huang Z, Li Y, Du P, Diao R, Lee B. Sensitivity analysis of the Kalman Filter and its applications in power systems. In: Innovative Smart Grid Technologies (ISGT), 2011 IEEE PES. IEEE; 2011. p. 1–6.

Du P, Huang Z, Diao R, Lee B, Anderson KK. Application of Kalman filter to improve model integrity for securing electricity delivery. In: Power Systems Conference and Exposition (PSCE), 2011 IEEE/PES. IEEE; 2011. p. 1–7.

Hossain KSMT, Kellogg CB, Friedman AM, Bradley MJ, Baker N, Ramakrishnan N. Using Physicochemical Properties of Amino Acids to Induce Graphical Models of Residue Couplings. In: Proceedings of the Tenth International Workshop on Data Mining in Bioinformatics. BIOKDD ’11. New York, NY, USA: ACM; 2011.

Jin H, Webb-Robertson BJ, Peterson ES, Tan R, Bigelow DJ, Scholand MB, et al. Smoking, COPD, and 3-Nitrotyrosine Levels of Plasma Proteins. Environmental Health Perspectives. 2011 Jun;119(9):1314–1320.

Sun Y, Du P, Huang Z, Kalsi K, Diao R, Anderson KK, et al. PMU placement for dynamic state tracking of power systems. In: North American Power Symposium (NAPS), 2011. IEEE; 2011. p. 1–7.

Du P, Huang Z, Sun Y, Diao R, Kalsi K, Anderson KK, et al. Distributed dynamic state estimation with extended Kalman filter. In: North American Power Symposium (NAPS), 2011. IEEE; 2011. p. 1–6.

Hogrebe L, Paiva ARC, Jurrus E, Christensen C, Bridge M, Korenberg JR, et al. Trace driven registration of neuron confocal microscopy stacks. In: Biomedical Imaging: From Nano to Macro, 2011 IEEE International Symposium on. IEEE; 2011. p. 1345–1348.

Hornbuckle BK, Rowlandson TL, Patton JC, Bramer LM. How is the angular signature of SMOS brightness temperature different in the morning and evening? In: Geoscience and Remote Sensing Symposium (IGARSS), 2011 IEEE International. IEEE; 2011. p. 3125–3128.

Kunkel BM, Su YF, Tonkyn RG, Stephan EG, Joly AG, Birnbaum JC, et al. Raman database considerations for near-infrared systems. vol. 8189; 2011. p. 818905–818905–9.

Amidan BG, Ferryman TA. Typical Patterns, Atypical Events, and Uncertainty in Complex Systems. In: ASME 2011 Pressure Vessels and Piping Conference: Volume 6, Parts A and B. ASME; 2011. p. 997–1004.

Heasler PG, Sanborn SE, Doctor SR, Anderson MT. The Treatment of ISI Uncertainty in Extremely Low Probability of Rupture. In: ASME 2011 Pressure Vessels and Piping Conference: Volume 6, Parts A and B. ASME; 2011. p. 1061–1067.

Seyedhosseini M, Kumar R, Jurrus E, Giuly R, Ellisman M, Pfister H, et al. Detection of Neuron Membranes in Electron Microscopy Images Using Multi-scale Context and Radon-Like Features. In: Fichtinger G, Martel A, Peters T, editors. Medical Image Computing and Computer-Assisted Intervention – MICCAI 2011. vol. 6891 of Lecture Notes in Computer Science. Springer Berlin Heidelberg; 2011. p. 670–677.

Best DM, Hafen RP, Olsen BK, Pike WA. Atypical behavior identification in large-scale network traffic. In: Large Data Analysis and Visualization (LDAV), 2011 IEEE Symposium on. IEEE; 2011. p. 15–22.

Varnum SM, Webb-Robertson BJM, Hessol NA, Smith RD, Zangar RC. Plasma Biomarkers for Detecting Hodgkin’s Lymphoma in HIV Patients. PLoS ONE. 2011 Dec;6(12):e29263+.

Kalsi K, Sun Y, Huang Z, Du P, Diao R, Anderson KK, et al. Calibrating multi-machine power system parameters with the extended Kalman filter. In: Power and Energy Society General Meeting, 2011 IEEE. IEEE; 2011. p. 1–8.

Makarov YV, Lu S, Samaan N, Huang Z, Subbarao K, Etingov PV, et al. Integration of uncertainty information into power system operations. In: Power and Energy Society General Meeting, 2011 IEEE. IEEE; 2011. p. 1–13.

Zhang H, Burnum KE, Luna ML, Petritis BO, Kim JS, Qian WJ, et al. Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size. Proteomics. 2011 Dec;11(23):4569–4577.

Thomas DG, Pappu RV, Baker NA. NanoParticle Ontology for cancer nanotechnology research. Journal of Biomedical Informatics. 2011 Feb;44(1):59–74.

Lee SJ, Schlesinger PH, Wickline SA, Lanza GM, Baker NA. Interaction of Melittin Peptides with Perfluorocarbon Nanoemulsion Particles. J Phys Chem B. 2011 Nov;115(51):15271–15279.

Matzke MM, Waters KM, Metz TO, Jacobs JM, Sims AC, Baric RS, et al. Improved quality control processing of peptide-centric LC-MS proteomics data. Bioinformatics. 2011 Oct;27(20):2866–2872.

Alexov E, Mehler EL, Baker N, Baptista, Huang Y, Milletti F, et al. Progress in the prediction of pKa values in proteins. Proteins. 2011 Dec;79(12):3260–3275.

Thomas DG, Klaessig F, Harper SL, Fritts M, Hoover MD, Gaheen S, et al. Informatics and standards for nanomedicine technology. WIREs Nanomed Nanobiotechnol. 2011 Sep;3(5):511–532.

Walsh S, Anderson K, Hathaway J, Pulsipher B. A Bayesian approach to monitoring and assessing unexploded ordnance remediation progress from munitions testing ranges. Stochastic Environmental Research and Risk Assessment. 2011 May;25(6):805–814.

Carstensen T, Farrell D, Huang Y, Baker NA, Nielsen JE. On the development of protein pKa calculation algorithms. Proteins. 2011 Dec;79(12):3287–3298.

Maciejewski R, Livengood P, Rudolph S, Collins TF, Ebert DS, Brigantic RT, et al. A pandemic influenza modeling and visualization tool. Journal of Visual Languages & Computing. 2011 Aug;22(4):268–278.

Teeguarden JG, Webb-Robertson BJ, Waters KM, Murray AR, Kisin ER, Varnum SM, et al. Comparative Proteomics and Pulmonary Toxicity of Instilled Single-Walled Carbon Nanotubes, Crocidolite Asbestos, and Ultrafine Carbon Black in Mice. Toxicological Sciences. 2011 Mar;120(1):123–135.


Burr T, Suzuki M, Howell J, Longo CE, Hamada MS. Signal estimation and change detection in tank data for nuclear safeguards. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 2011 Jun;640(1):200–212.

Jacob RE, Amidan BG, Soelberg J, Minard KR. In vivo MRI of altered proton signal intensity and T2 relaxation in a bleomycin model of pulmonary inflammation and fibrosis. J Magn Reson Imaging. 2010 May;31(5):1091–1099.

Beagley N, Stratton KG, Webb-Robertson BJM. VIBE 2.0: Visual Integration for Bayesian Evaluation. Bioinformatics. 2010 Jan;26(2):280–282.

Maciejewski R, Rudolph S, Hafen R, Abusalah A, Yakout M, Ouzzani M, et al. A Visual Analytics Approach to Understanding Spatiotemporal Hotspots. Visualization and Computer Graphics, IEEE Transactions on. 2010 Mar;16(2):205–220.

Robertson BJW, Ratuiste K, Oehmen C. Physicochemical property distributions for accurate and rapid pairwise protein homology detection. BMC Bioinformatics. 2010 Mar;11(1):145+.

Jurrus E, Paiva AR, Watanabe S, Anderson JR, Jones BW, Whitaker RT, et al. Detection of neuron membranes in electron microscopy images using a serial neural network architecture. Medical image analysis. 2010 Dec;14(6):770–783.

Webb-Robertson BJM, Cannon WR, Oehmen CS, Shah AR, Gurumoorthi V, Lipton MS, et al. A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics. Bioinformatics. 2010 Jul;26(13):1677–1683.

Chen Z, Baker NA, Wei GW. Differential geometry based solvation model I: Eulerian formulation. Journal of Computational Physics. 2010 Nov;229(22):8231–8258.

Lee SJ, Olsen B, Schlesinger PH, Baker NA. Characterization of Perfluorooctylbromide-Based Nanoemulsion Particles Using Atomistic Molecular Dynamics Simulations. J Phys Chem B. 2010 Jul;114(31):10086–10096.

Anderson KK, Tardiff MF, Chilton LK. Predicting the Detectability of Thin Gaseous Plumes in Hyperspectral Images Using Basis Vectors. Sensors. 2010 Sep;10(9):8652–8662.

Callenberg KM, Choudhary OP, de Forest GL, Gohara DW, Baker NA, Grabe M. APBSmem: A Graphical Interface for Electrostatic Calculations at the Membrane. PLoS ONE. 2010 Sep;5(9):e12722+.

McClay JL, Adkins DE, Isern NG, O’Connell TM, Wooten JB, Zedler BK, et al. 1H Nuclear Magnetic Resonance Metabolomics Analysis Identifies Novel Urinary Biomarkers for Lung Function. J Proteome Res. 2010 Apr;9(6):3083–3090.

Yurkovetsky Z, Skates S, Lomakin A, Nolen B, Pulsipher T, Modugno F, et al. Development of a Multimarker Assay for Early Detection of Ovarian Cancer. Journal of Clinical Oncology. 2010 May;28(13):2159–2166.

Ferryman TA, Amidan BG. Statistical Analysis of Abnormal Electric Power Grid Behavior. In: System Sciences (HICSS), 2010 43rd Hawaii International Conference on. IEEE; 2010. p. 1–8.

Du P, Huang Z, Diao R, Lee B, Anderson KK. PMU Placement for enhancing dynamic observability of a power grid. In: Innovative Technologies for an Efficient and Reliable Electricity Supply (CITRES), 2010 IEEE Conference on. IEEE; 2010. p. 15–21.

Amidan BG, Piepel GF, Heredia-Langner A, Meyer PA, Wells BE, Fort JA, et al. A Statistical Intelligence (STI) Approach to Discovering Spurious Correlation in a Physical Model and Resolving the Problem With an Example of Designing a Pulse Jet Mixing System at Hanford. In: ASME 2010 Pressure Vessels and Piping Conference: Volume 6, Parts A and B. ASME; 2010. p. 1167–1178.

Paiva ARC, Jurrus E, Tasdizen T. Using Sequential Context for Image Analysis. In: Pattern Recognition (ICPR), 2010 20th International Conference on. IEEE; 2010. p. 2800–2803.

Webb-Robertson BJM, McCue LA, Waters KM, Matzke MM, Jacobs JM, Metz TO, et al. Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-Based Proteomics Data. J Proteome Res. 2010 Sep;9(11):5748–5756.

Smith LE, Anderson KK, Ressler JJ, Shaver MW. Time-Spectral Analysis Methods for Spent Fuel Assay Using Lead Slowing-Down Spectroscopy. Nuclear Science, IEEE Transactions on. 2010 Aug;57(4):2230–2238.

Daly DS, Anderson KK, Seurynck-Servoss SL, Gonzalez RM, White AM, Zangar RC. An Internal Calibration Method for Protein-Array Studies. Statistical Applications in Genetics and Molecular Biology. 2010 Jan;9(1).

Wahl KL, Colburn HA, Wunschel DS, Petersen CE, Jarman KH, Valentine NB. Residual Agar Determination in Bacterial Spores by Electrospray Ionization Mass Spectrometry. Anal Chem. 2010 Jan;82(4):1200–1206.


Chen AA, Marucho M, Baker NA, Pappu RV. Simulations of RNA interactions with monovalent ions. Methods in enzymology. 2009;469:411–432.

Forrester JB, Valentine NB, Su YF, Johnson TJ. Chemometric analysis of multiple species of Bacillus bacterial endospores using infrared spectroscopy: Discrimination to the strain level. Analytica Chimica Acta. 2009 Sep;651(1):24–30.

Wunschel D, Webb-Robertson BJ, Frevert CW, Skerrett S, Beagley N, Willse A, et al. Differentiation of Gram-Negative Bacterial Aerosol Exposure Using Detected Markers in Bronchial-Alveolar Lavage Fluid. PLoS ONE. 2009 Sep;4(9):e7047+.

Webb-Robertson BJJ, McCue LAA, Beagley N, McDermott JE, Wunschel DS, Varnum SM, et al. A Bayesian integration model of high-throughput proteomics and metabolomics data for improved early detection of microbial infections. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing. 2009;p. 451–463.

Lombardo N, Knudson C, Ozanich R, Rutz F, Singh S, Tardiff M, et al. A next-generation countermeasure architecture to prevent explosives attacks at large public events. In: Technologies for Homeland Security, 2009. HST ’09. IEEE Conference on. IEEE; 2009. p. 256–262.

Venkataraju KU, Paiva ARC, Jurrus E, Tasdizen T. Automatic markup of neural cell membranes using boosted decision stumps. In: Biomedical Imaging: From Nano to Macro, 2009. ISBI ’09. IEEE International Symposium on. IEEE; 2009. p. 1039–1042.

Anderson JR, Jones BW, Yang JH, Shaw MV, Watt CB, Koshevoy P, et al. Ultrastructural mapping of neural circuitry: A computational framework. In: Biomedical Imaging: From Nano to Macro, 2009. ISBI ’09. IEEE International Symposium on. IEEE; 2009. p. 1135–1137.

Thomas DG, Pappu RV, Baker NA. Ontologies for cancer nanotechnology research. In: Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE. vol. 2009. IEEE; 2009. p. 4158–4161.

Becker M, Bruillard P, Downes S. Chiral supergravity. Journal of High Energy Physics. 2009 Oct;2009(10):004+.

Piepel GF, Landmesser SM. Mixture Experiment Alternatives to the Slack Variable Approach. Quality Engineering. 2009 Jun;21(3):262–276.

Bravar U, Woolf RS, Bruillard PJ, Fluckiger EO, Legere JS, MacKinnon AL, et al. Calibration of the Fast Neutron Imaging Telescope (FNIT) Prototype Detector. Nuclear Science, IEEE Transactions on. 2009 Oct;56(5):2947–2954.

Doucette P, Kovalerchuk B, Kovalerchuk M, Brigantic R. An evaluation methodology for vector data updating. vol. 7334; 2009. p. 73341F–73341F–9.

Johnson TJ, Williams SD, Valentine NB, Su YF, Kreuzer-Martin HW, Wahl K, et al. Infrared signatures of Bacillus bacteria: clear IR distinctions between sporulated and vegetative cells with chemical assignments. vol. 7304; 2009. p. 730407–730407–11.

Jones DM, Ferris KF, Webb-Robertson BJM, Muellerleile JT, Hyatt RW. Generic materials property data storage and retrieval for the semiconducting materials knowledge base. vol. 7449; 2009. p. 74491R–74491R–10.

Ferris KF, Webb-Robertson BJM, Jones DM. Semiconducting material property relationships: trends and their impact on design of radiation detection materials. vol. 7449; 2009. p. 74491H–74491H–8.

Brigantic RT, Muller GA, Taylor AE, Papatyi AF. Gaming to Predict Human Responses to Mass Casualty Events: An Approach for Quick Look Tools for Pandemic Influenza. In: Computational Science and Engineering, 2009. CSE ’09. International Conference on. vol. 4. IEEE; 2009. p. 1194–1198.


Baker N, Bashford D, Case D. Implicit Solvent Electrostatics in Biomolecular Simulation. In: Leimkuhler B, Chipot C, Elber R, Laaksonen A, Mark A, Schlick T, et al., editors. New Algorithms for Macro Molecular Simulation. vol. 49 of Lecture Notes in Computational Science and Engineering. Berlin/Heidelberg: Springer Berlin Heidelberg; 2006. p. 263–295.

Swanson JMJ, Wagoner JA, Baker NA, McCammon JA. Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies:? Lessons Learned with Atom-Centered Dielectric Functions. J Chem Theory Comput. 2006 Nov;3(1):170–183.


Baker NA, McCammon JA. Electrostatic Interactions. 2005;p. 427–440.

Baker NA. Biomolecular Applications of Poisson–Boltzmann Methods. 2005 Apr;21:349–379.


Vitalis A, Baker NA, McCammon JA. ISIM: A Program for Grand Canonical Monte Carlo Simulations of the Ionic Environment of Biomolecules. Molecular Simulation. 2004;30(1):45–61.


Baker NA, Sept D, Holst MJ, McCammon JA. The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers. IBM Journal of Research and Development. 2001 May;45(3.4):427–438.


Baker N, Holst M, Wang F. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems. Journal of Computational Chemistry. 2000 Nov;21(15):1343–1352.;2-k

Holst M, Baker N, Wang F. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples. Journal of Computational Chemistry. 2000 Nov;21(15):1319–1342.;2-8

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