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Biological Sciences Staff information

Dennis Thomas

Computational Biology
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-18
Richland, WA 99352

PNNL Publications


  • Chikkagoudar S, S Chatterjee, DG Thomas, TE Carroll, and G Muller. 2017. "Machine Learning." Chapter 6 in Research Methods for Cyber Security, ed. TW Edgar and DO Manz, pp. 153-173.  Syngress, CAMBRIDGE, MA.  doi:10.1016/B978-0-12-805349-2.00006-6
  • Ma J, CP Casey, X Zheng, YM Ibrahim, CS Wilkins, RS Renslow, DG Thomas, SH Payne, ME Monroe, RD Smith, JG Teeguarden, EM Baker, and TO Metz. 2017. "PIXiE: An Algorithm for Automated Ion Mobility Arrival Time Extraction and Collision Cross Section Calculation using Global Data Association." Bioinformatics 33(17):27152722.  doi:10.1093/bioinformatics/btx305
  • Metz TO, EM Baker, EL Schymanski, RS Renslow, DG Thomas, TJ Causon, IK Webb, S Hann, RD Smith, and JG Teeguarden. 2017. "Integrating Ion Mobility Spectrometry into Mass Spectrometry-based Exposome Measurements: What Can It Add and How Far Can It Go?" Bioanalysis 9(1):81-98.  doi:10.4155/bio-2016-0244
  • Smith JN, KJ Tyrrell, JR Hansen, DG Thomas, TA Murphree, AK Shukla, T Luders, JM Madden, Y Li, AT Wright, and PD Piehowski. 2017. "Plasma Protein Turnover Rates in Rats Using Stable Isotope Labeling, Global Proteomics, and Activity-Based Protein Profiling." Analytical Chemistry 89(24):13559-13566.  doi:10.1021/acs.analchem.7b03984
  • Song HS, DG Thomas, JC Stegen, M Li, C Liu, X Song, X Chen, JK Fredrickson, JM Zachara, and TD Scheibe. 2017. "Regulation-structured dynamic metabolic model provides a potential mechanism for delayed enzyme response in denitrification process." Frontiers in Microbiology 8:1866.  doi:10.3389/fmicb.2017.01866
  • Zheng X, RS Renslow, MM Makola, IK Webb, L Deng, DG Thomas, N Govind, YM Ibrahim, MM Kabanda, IA Dubery, HM Heyman, RD Smith, NE Madala, and EM Baker. 2017. "Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry." The Journal of Physical Chemistry Letters 8(7):1381-1388.  doi:10.1021/acs.jpclett.6b03015


  • Sushko ML, DG Thomas, S Pabit, L Pollack, A Onufriev, and NA Baker. 2016. "The role of correlation and solvation in ion interactions with B-DNA." Biophysical Journal 110(2):315-326.  doi:10.1016/j.bpj.2015.12.011
  • Zhang X, MV Romm, X Zheng, EM Zink, YM Kim, KE Burnum-Johnson, DJ Orton, A Apffel, YM Ibrahim, ME Monroe, RJ Moore, JN Smith, J Ma, RS Renslow, DG Thomas, A Blackwell, G Swinford, J Sausen, RT Kurulugama Lekamlage, N Eno, E Darland, G Stafford, JC Fjeldsted, TO Metz, JG Teeguarden, RD Smith, and ES Baker. 2016. "SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in bio?uids." Clinical Mass Spectrometry 2:1-10.  doi:10.1016/j.clinms.2016.11.002


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


  • Medasani B, Z Ovanesyan, DG Thomas, ML 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(20):Article No. 204510.  doi:10.1063/1.4876002
  • Pham C, DG Thomas, J Beiser, L Mitchell, J Huang, A Senpan, G Hu, M Gordon, NA Baker, D Pan, GM Lanza, and D Hourcade. 2014. "Application of a hemolysis assay for analysis of complement activation by perfluorocarbon nanoparticles." Nanomedicine: Nanotechnology, Biology and Medicine 10(3):651-660.  doi:10.1016/j.nano.2013.10.012
  • Thomas DG, S Chikkagoudar, A Heredia-Langner, MF Tardiff, Z Xu, D Hourcade, C Pham, GM Lanza, KQ Weinberger, and NA Baker. 2014. "Physicochemical signatures of nanoparticle-dependent complement activation." Computational Science and Discovery 7(1):Article No. 015003.  doi:10.1088/1749-4699/7/1/015003
  • Thomas DG, SI Jaramillo Riveri, DJ Baxter, and WR 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(51):14745-14760.  doi:10.1021/jp5075913


  • Joslyn CA, EA Hogan, PR Paulson, ES Peterson, EG Stephan, and DG Thomas. 2013. "Order Theoretical Semantic Recommendation." In Proceedings of the 2nd International Workshop on Ordering and Reasoning (OrdRing 2013), October 22, 2013, Sydney, Australia, vol. 1059, ed. I Celino, et al, pp. 9-20.  Semantic Web Science Association, Karlsruhe, Germany. 
  • Thomas DG, J Chun, Z Chen, G Wei, and NA Baker. 2013. "Parameterization of a Geometric Flow Implicit Solvation Model." Journal of Computational Chemistry 34(8):687-695.  doi:10.1002/jcc.23181
  • Thomas DG, S Gaheen, S Harper, M Fritts, F Klaessig, E Hahn-Dantona, D Paik, S Pan, G Stafford, E Freund, J Klemm, and NA Baker. 2013. "ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format." BMC Bioinformatics 13:Article No. 2.  doi:10.1186/1472-6750-13-2


  • Chen Z, S Zhao, J Chun, DG Thomas, NA Baker, PW Bates, and G Wei. 2012. "Variational approach for nonpolar solvation analysis." Journal of Chemical Physics 137(8):Article No. 084101.  doi:10.1063/1.4745084
  • Ren P, J Chun, DG Thomas, M Schnieders, M Marucho, J Zhang, and NA Baker. 2012. "Biomolecular electrostatics and solvation: a computational perspective." Quarterly Reviews of Biophysics 45(4):427-491.  doi:10.1017/S003358351200011X
  • Thomas DG, S Chikkagoudar, AR Chappell, and NA 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, pp. 889-894.  IEEE, Piscataway, NJ.  doi:10.1109/BIBMW.2012.6470259


  • Thomas DG, F Klaessig, S Harper, M Fritts, MD Hoover, S Gaheen, T Stokes, R Reznik-Zellen, E Freund, J Klemm, D Paik, and NA Baker. 2011. "Informatics and Standards for Nanomedicine Technology." Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology 3(5):511-532.  doi:10.1002/wnan.152

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