Staff information

PNNL Publications

2024

• Oster M.R., I.D. Amburg, S. Chatterjee, D.A. Eisenberg, D.G. Thomas, F. Pan, and A.R. Ganguly. 2024. "A Tri-Level Optimization Model for Interdependent Infrastructure Network Resilience Against Compound Hazard Events." International Journal of Critical Infrastructure Protection 47, no. _:Art. No. 100723. PNNL-SA-191126. doi:10.1016/j.ijcip.2024.100723
• Overstreet R.E., D.G. Thomas, and J.R. Cort. 2024. "NCAP: Noncanonical Amino Acid Parameterization Software for CHARMM Potentials." Journal of Chemical Information and Modeling 64, no. 24:9424-9432. PNNL-SA-197394. doi:10.1021/acs.jcim.4c00986

2023

• Chatterjee S., D.G. Thomas, D.C. Fortin, K. Pazdernik, B.A. Wilson, and L. Newburn. 2023. "Dynamic Network Analysis of Nuclear Science Literature for Research Influence Assessment." ESARDA Bulletin 65. PNNL-SA-166748. doi:10.3011/ESARDA.IJNSNP.2023.3
• Gosline S., D. Kim, P. Pande, D.G. Thomas, L. Truong, P. Hoffman, and M. Barton, et al. 2023. "The Superfund Research Program Analytics Portal: linking environmental chemical exposure to biological phenotypes." Scientific Data 10. PNNL-SA-177557. doi:10.1038/s41597-023-02021-5
• Thomas D.G., Z.J. Weems, R.E. Overstreet, and B.A. Wilson. 2023. Inverse Reinforcement Learning based Bayesian Goal Inference Method for Early Nuclear Proliferation Detection. PNNL-34896. Richland, WA: Pacific Northwest National Laboratory. Inverse Reinforcement Learning based Bayesian Goal Inference Method for Early Nuclear Proliferation Detection

2022

• Phalak P., H. Bernstein, S.R. Lindemann, R.S. Renslow, D.G. Thomas, M.A. Henson, and H. Song. 2022. "Spatiotemporal Metabolic Network Models Reveal Complex Autotroph-Heterotroph Biofilm Interactions Governed by Photon Incidences." In IFAC-PapersOnLine, Part of special issue 13th IFAC Symposium on Dynamics and Control of Process Systems, including Biosystems, DYCOPS 2022, 55, 112-118. PNNL-SA-173653. doi:10.1016/j.ifacol.2022.07.430

2021

• Jones R.D., D.C. Fortin, S. Chatterjee, D.G. Thomas, and L. Newburn. 2021. "User Role Identification in Software Vulnerability Discussions over Social Networks." In IEEE International Conference on Intelligence and Security Informatics (ISI 2021), November 2-3, 2021, VIrtual, Online, 1-3. Piscataway, New Jersey:IEEE. PNNL-SA-166021. doi:10.1109/ISI53945.2021.9624857
• Joshi R., A.D. McNaughton, D.G. Thomas, C. Henry, S. Canon, L. McCue, and N. Kumar. 2021. "Quantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical Reactions." ACS Omega 6, no. 14:9948-9959. PNNL-SA-157024. doi:10.1021/acsomega.1c00997
• Mansouri K., A. Karmaus, J. Fitzpatrick, G. Patlewicz, P. Pradeep, D. Alberga, and N. Alepee, et al. 2021. "CATMoS: Collaborative Acute Toxicity Modeling Suite." Environmental Health Perspectives 129, no. 4:047013. PNNL-SA-159448. doi:10.1289/EHP8495
• Nielson F.F., S.M. Colby, D.G. Thomas, R.S. Renslow, and T.O. Metz. 2021. "Exploring the impacts of conformer selection methods on ion mobility collision cross section predictions." Analytical Chemistry 93, no. 8:3830-3838. PNNL-SA-157174. doi:10.1021/acs.analchem.0c04341

2020

• Meng Q., S. Moinuddin, S. Kim, D.L. Bedgar, M.A. Costa, D.G. Thomas, and R.P. Young, et al. 2020. "Pterocarpan synthase (PTS) structures suggest a common quinone methide-stabilizing function in dirigent proteins and proteins with dirigent-like domains." Journal of Biological Chemistry 295, no. 33:11584-11601. PNNL-SA-150677. doi:10.1074/jbc.RA120.012444
• Zhang T., M.J. Gaffrey, D.G. Thomas, T.J. Weber, B.M. Hess, K.K. Weitz, and P.D. Piehowski, et al. 2020. "A proteome-wide assessment of the oxidative stress paradigm for metal and metal-oxide nanomaterials in human macrophages." NanoImpact 17. PNNL-SA-147217. doi:10.1016/j.impact.2019.100194
• Zhang T., M.J. Gaffrey, M.E. Monroe, D.G. Thomas, K.K. Weitz, P.D. Piehowski, and V.A. Petyuk, et al. 2020. "Block design with common reference samples enables robust large-scale label-free quantitative proteome profiling." Journal of Proteome Research 19, no. 7:2863-2872. PNNL-SA-151164. doi:10.1021/acs.jproteome.0c00310

2019

• Arthur-Durett K.M., T.E. Carroll, D.G. Thomas, and N.J. Multari. 2019. "Towards Automated Cyber Mission Modelling." Journal of Information Warfare 18, no. 4 (Special Edition):70-84. PNNL-SA-145247.
• Colby S.M., D.G. Thomas, J. Nunez, D.J. Baxter, K.R. Glaesemann, J.M. Brown, and M.A. Pirrung, et al. 2019. "ISiCLE: A Quantum Chemistry Pipeline for Establishing in Silico Collision Cross Section Libraries." Analytical Chemistry 91, no. 7:4346-4356. PNNL-SA-138476. doi:10.1021/acs.analchem.8b04567
• Garcellano R.C., S. Moinuddin, R.P. Young, M.E. Bowden, M. Zhou, R.S. Renslow, and Y. Yesiltepe, et al. 2019. "Isolation of Tryptanthrin and Reassessment of Evidence for its Isobaric Isostere Wrightiadione in Plants of the Wrightia Genus." Journal of Natural Products 82, no. 3:440-448. PNNL-SA-135279. doi:10.1021/acs.jnatprod.8b00567
• Hess B.M., D.G. Thomas, T.J. Weber, J.R. Hutchison, T.M. Straub, C.J. Bruckner-Lea, and J.D. Powell, et al. 2019. "An integrated experimental-computational approach for predicting virulence in New Zealand white rabbits and humans following inhalation exposure to Bacillus anthracis spores." PLoS Pathogens 14, no. 7:e0219160. PNNL-SA-140673. doi:10.1371/journal.pone.0219160
• Nunez J., S.M. Colby, D.G. Thomas, M. Tfaily, N. Tolic, E. Ulrich, and J.R. Sobus, et al. 2019. "Evaluation of In Silico Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples." Journal of Chemical Information and Modeling 59, no. 9:4052-4060. PNNL-SA-148332. doi:10.1021/acs.jcim.9b00444
• Thomas D.G., H. Shankaran, L. Truong, R. Tanguay, and K.M. Waters. 2019. "Time-dependent behavioral data from embryonic zebrafish reveals novel signatures of chemical toxicity using point of departure analysis." Computational Toxicology 9. PNNL-SA-124559. doi:10.1016/j.comtox.2018.11.001
• Thrall B.D., V.K. Kodali, S.J. Skerret, S.J. Skerret, D.G. Thomas, C. Frevert, and J.G. Pounds, et al. 2019. "Modulation of susceptibility to lung bacterial infection by engineered nanomaterials: In vitro and in vivo correspondence based on macrophage phagocytic function." NanoImpact 14. PNNL-SA-128523. doi:10.1016/j.impact.2019.100155

2018

• Cheluvappa R., D.G. Thomas, and S. Selvendran. 2018. "The role of specific chemokines in the amelioration of colitis by appendicitis and appendectomy." Biomolecules 8, no. 3:Article Number 59. PNNL-SA-135758. doi:10.3390/biom8030059
• Karcher S., E.L. Willighagen, J. Rumble, F. Ehrhart, C.T. Evelo, M. Fritts, and S. Gaheen, et al. 2018. "Integration among databases and data sets to support productive nanotechnolgoy: Challenges and Recommendations." NanoImpact 9. PNNL-SA-118813. doi:10.1016/j.impact.2017.11.002
• Karcher S., E.L. Willighagen, J. Rumble, F. Ehrhart, C.T. Evelo, M. Fritts, and S. Gaheen, et al. 2018. "Integration among databases and data sets to support productive nanotechnology: challenges and recommendations." NanoImpact 9. PNNL-SA-128856. doi:10.1016/j.impact.2017.11.002
• Nobela O., R.S. Renslow, D.G. Thomas, S.M. Colby, S. Sitha, P.B. Njobeh, and L. Du Preez, et al. 2018. "Efficient discrimination of natural stereoisomers of chicoric acid, an HIV-1 integrase inhibitor." Journal of Photochemistry and Photobiology B: Biology 189. PNNL-SA-137796. doi:10.1016/j.jphotobiol.2018.10.025
• Smith J.N., D.G. Thomas, H.D. Jolley, V.K. Kodali, M.H. Littke, P. Munusamy, and D.R. Baer, et al. 2018. "All that is Silver is not Toxic: Silver Ion and Particle Kinetics Reveals the Role of Silver Ion Aging and Dosimetry on the Toxicity of Silver Nanoparticles." Particle and Fibre Toxicology 15. PNNL-SA-135829. doi:10.1186/s12989-018-0283-z
• Thomas D.G., J.N. Smith, B.D. Thrall, D.R. Baer, H.D. Jolley, P. Munusamy, and V.K. Kodali, et al. 2018. "ISD3: A Particokinetic Model for Predicting the Combined Effects of Particle Sedimentation, Diffusion and Dissolution on Cellular Dosimetry for In Vitro Systems." Particle and Fibre Toxicology 15. PNNL-SA-125563. doi:10.1186/s12989-018-0243-7
• Yang X., H. Lei, P. Gao, D.G. Thomas, D.L. Mobley, and N.A. Baker. 2018. "Atomic radius and charge parameter uncertainty in biomolecular solvation energy calculations." Journal of Chemical Theory and Computation 14, no. 2:759-767. PNNL-SA-126404. doi:10.1021/acs.jctc.7b00905
• Yesiltepe Y., J. Nunez, S.M. Colby, D.G. Thomas, M.I. Borkum, P.N. Reardon, and N.M. Washton, et al. 2018. "An automated framework for NMR chemical shift calculations of small organic molecules." Journal of Cheminformatics 10. PNNL-SA-137588. doi:10.1186/s13321-018-0305-8

2017

• Carroll T.E., S. Chikkagoudar, K.M. Arthur-Durett, and D.G. Thomas. 2017. "Automating Network Node Behavior Characterization by Mining Communication Patterns." In IEEE International Symposium on Technologies for Homeland Security (HST 2017), April 25-26, 2017, Waltham, MA, 1-7. Piscataway, New Jersey:IEEE. PNNL-SA-122293. doi:10.1109/THS.2017.7943510
• Chikkagoudar S., S. Chatterjee, D.G. Thomas, T.E. Carroll, and G. Muller. 2017. "Machine Learning." In Research Methods for Cyber Security, edited by TW Edgar and DO Manz. 153-173. Cambridge, Massachusetts:Syngress. PNNL-SA-122747. doi:10.1016/B978-0-12-805349-2.00006-6
• Ma J., C.P. Casey, X. Zheng, Y.M. Ibrahim, C.S. Wilkins, R.S. Renslow, and D.G. Thomas, et al. 2017. "PIXiE: An Algorithm for Automated Ion Mobility Arrival Time Extraction and Collision Cross Section Calculation using Global Data Association." Bioinformatics 33, no. 17:2715-2722. PNNL-SA-122828. doi:10.1093/bioinformatics/btx305
• Metz T.O., E.M. Baker, E.L. Schymanski, R.S. Renslow, D.G. Thomas, T.J. Causon, and I.K. Webb, et al. 2017. "Integrating Ion Mobility Spectrometry into Mass Spectrometry-based Exposome Measurements: What Can It Add and How Far Can It Go?." Bioanalysis 9, no. 1:81-98. PNNL-SA-121158. doi:10.4155/bio-2016-0244
• Smith J.N., K.J. Tyrrell, J.R. Hansen, D.G. Thomas, T.A. Murphree, A.K. Shukla, and T. Luders, et al. 2017. "Plasma Protein Turnover Rates in Rats Using Stable Isotope Labeling, Global Proteomics, and Activity-Based Protein Profiling." Analytical Chemistry 89, no. 24:13559-13566. PNNL-SA-129561. doi:10.1021/acs.analchem.7b03984
• Song H., D.G. Thomas, J.C. Stegen, M. Li, C. Liu, X. Song, and X. Chen, et al. 2017. "Regulation-structured dynamic metabolic model provides a potential mechanism for delayed enzyme response in denitrification process." Frontiers in Microbiology 8. PNNL-SA-129317. doi:10.3389/fmicb.2017.01866
• Zheng X., R.S. Renslow, M.M. Makola, I.K. Webb, L. Deng, D.G. Thomas, and N. Govind, et al. 2017. "Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry." The Journal of Physical Chemistry Letters 8, no. 7:1381-1388. PNNL-SA-123119. doi:10.1021/acs.jpclett.6b03015

2016

• Sushko M.L., D.G. Thomas, S. Pabit, L. Pollack, A. Onufriev, and N.A. Baker. 2016. "The role of correlation and solvation in ion interactions with B-DNA." Biophysical Journal 110, no. 2:315-326. PNNL-SA-110226. doi:10.1016/j.bpj.2015.12.011
• Zhang X., M.V. Romm, X. Zheng, E.M. Zink, Y. Kim, K.E. Burnum-Johnson, and D.J. Orton, et al. 2016. "SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in bio?uids." Clinical Mass Spectrometry 2. PNNL-SA-117436. doi:10.1016/j.clinms.2016.11.002

2015

• Harper B., D.G. Thomas, S. Chikkagoudar, N.A. Baker, K. Tang, A. Heredia-Langner, and R.D. Lins, et al. 2015. "Comparative hazard analysis and toxicological modeling of diverse nanomaterials using the embryonic zebrafish (EZ) metric of toxicity." Journal of Nanoparticle Research 17, no. 6:Article No. 250. PNNL-SA-101181. doi:10.1007/s11051-015-3051-0

2014

• Medasani B., Z. Ovanesyan, D.G. Thomas, M.L. Sushko, and M. Marucho. 2014. "Ionic Asymmetry and Solvent Excluded Volume Effects on Spherical Electric Double Layers: A Density Functional Approach." Journal of Chemical Physics 140, no. 20:Article No. 204510. PNNL-SA-101131. doi:10.1063/1.4876002
• Pham C., D.G. Thomas, J. Beiser, L. Mitchell, J. Huang, A. Senpan, and G. Hu, et al. 2014. "Application of a hemolysis assay for analysis of complement activation by perfluorocarbon nanoparticles." Nanomedicine: Nanotechnology, Biology and Medicine 10, no. 3:651-660. PNWD-SA-10120. doi:10.1016/j.nano.2013.10.012
• Thomas D.G., S. Chikkagoudar, A. Heredia-Langner, M.F. Tardiff, Z. Xu, D. Hourcade, and C. Pham, et al. 2014. "Physicochemical signatures of nanoparticle-dependent complement activation." Computational Science and Discovery 7, no. 1:Article No. 015003. PNNL-SA-99801. doi:10.1088/1749-4699/7/1/015003
• Thomas D.G., S.I. Jaramillo Riveri, D.J. Baxter, and W.R. Cannon. 2014. "Comparison of Optimal Thermodynamic Models of the Tricarboxylic Acid Cycle from Heterotrophs, Cyanobacteria, and Green Sulfur Bacteria." Journal of Physical Chemistry B 118, no. 51:14745-14760. PNNL-SA-100020. doi:10.1021/jp5075913

2013

• Joslyn C.A., E.A. Hogan, P.R. Paulson, E.S. Peterson, E.G. Stephan, and D.G. Thomas. 2013. "Order Theoretical Semantic Recommendation." In Proceedings of the 2nd International Workshop on Ordering and Reasoning (OrdRing 2013), October 22, 2013, Sydney, Australia, edited by I Celino, et al, 1059, 9-20. Karlsruhe:Semantic Web Science Association. PNNL-SA-97159.
• Thomas D.G., J. Chun, Z. Chen, G. Wei, and N.A. Baker. 2013. "Parameterization of a Geometric Flow Implicit Solvation Model." Journal of Computational Chemistry 34, no. 8:687-695. PNWD-SA-9830. doi:10.1002/jcc.23181
• Thomas D.G., S. Gaheen, S. Harper, M. Fritts, F. Klaessig, E. Hahn-Dantona, and D. Paik, et al. 2013. "ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format." BMC Bioinformatics 13. PNWD-SA-9668. doi:10.1186/1472-6750-13-2

2012

• Chen Z., S. Zhao, J. Chun, D.G. Thomas, N.A. Baker, P.W. Bates, and G. Wei. 2012. "Variational approach for nonpolar solvation analysis." Journal of Chemical Physics 137, no. 8:Article No. 084101. PNWD-SA-9814. doi:10.1063/1.4745084
• Ren P., J. Chun, D.G. Thomas, M. Schnieders, M. Marucho, J. Zhang, and N.A. Baker. 2012. "Biomolecular electrostatics and solvation: a computational perspective." Quarterly Reviews of Biophysics 45, no. 4:427-491. PNNL-SA-84152. doi:10.1017/S003358351200011X
• Thomas D.G., S. Chikkagoudar, A.R. Chappell, and N.A. Baker. 2012. "Annotating the structure and components of a nanoparticle formulation using computable string expressions." In IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2012): October 4-7, 2012, Philadelphia, PA, 889-894. Piscataway, New Jersey:IEEE. PNWD-SA-9974. doi:10.1109/BIBMW.2012.6470259

2011

• Thomas D.G., F. Klaessig, S. Harper, M. Fritts, M.D. Hoover, S. Gaheen, and T. Stokes, et al. 2011. "Informatics and Standards for Nanomedicine Technology." Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology 3, no. 5:511-532. PNWD-SA-9296. doi:10.1002/wnan.152