Staff information

Biography

Dr. Haluk Resat, Senior Research Scientist, has an interdisciplinary background integrating engineering with physical sciences and biology. He has authored more than 45 peer-reviewed publications. His current research interests include kinetic simulations of biological systems, biological network construction and verification, investigation of regulatory interactions in biological networks, use of systems approach to biological sciences, and development of multiscale methods to study biological processes.

Research Interests

• Biomolecular networks: Cell signaling and its regulation
• Role of physiological regulation on cellular behavior
• Microbial communities and their dynamical behavior
• Multiscale models for biological systems
• Hybrid simulation algorithms

Education and Credentials

• Postdoctoral research associate (9/94 - 8/96)
  Supervisor: J. Andrew McCammon
  Department of Chemistry and Biochemistry
  University of California at San Diego
• Postdoctoral research associate (9/92 - 8/94)
  Supervisor: Mihaly Mezei
  Department of Physiology and Biophysics
  Mount Sinai School of Medicine
• Ph. D. in Physics (8/92)
  Thesis advisor: Harold L. Friedman
  State University of New York at Stony Brook
  (new name: Stony Brook University)
• B. S. in Electrical Engineering (7/86)
  B. S. in Physics (7/86)
  Bosphorus University, Istanbul, Turkey

Affiliations and Professional Service

• American Society of Cell Biology
• Biophysical Society
• International Receptor Tyrosine Kinase Consortium
• International Society for Computational Biology
• Society for Industrial and Applied Mathematics

Awards and Recognitions

• Recipient of the 1998 Promising Young Scientist Award, National Scientific and Technological Research Institute of Turkey, (TUBITAK, equivalent of NSF in Turkey).
• Recipient of Fellowship for the Advancement of Science, National Scientific and Technological Research Institute of Turkey (1978-86).
• Various PNNL outstanding performance awards.

PNNL Publications

2012

• Resat H, VL Bailey, LA McCue, and A Konopka. 2012. "Modeling microbial dynamics in heterogeneous environments: Growth on soil carbon sources." Microbial Ecology 63(4):883-897.  doi:10.1007/s00248-011-9965-x
• Archuleta MN, JE McDermott, JS Edwards, and H Resat. 2012. "An Adaptive Coarse Graining Method for Signal Transduction in Three-Dimensions." FUNDAMENTA INFORMATICAE 118(4):371-384.  doi:10.3233/FI-2012-720
• Shankaran H, Y Zhang, WB Chrisler, JA Ewald, HS Wiley, and H Resat. 2012. "Integrated Experimental and Model-based Analysis Reveals the Spatial Aspects of EGFR Activation Dynamics." Molecular Biosystems 8(11):2868-2882.  doi:10.1039/C2MB25190F

2011

• Resat H, MN Costa, and H Shankaran. 2011. "Spatial Aspects in Biological System Simulations." Chapter 17 in Methods in Enzymology: Computer Methods, Part C, vol. 487, ed. M Johnson and L Brand, pp. 485-511.  Elsevier, Amsterdam, Netherlands. 
• Hess NJ, M Oostrom, MA Celia, M Hilpert, Q Kang, LJ Pyrak-Nolte, TD Scheibe, AM Tartakovsky, CJ Werth, D Wildenschild, C Zhang, SE Bialkowski, TA Ghezzehei, G Tang, F Doster, J Kumar, R Parashar, R Gerlach, H Yoon, GD Redden, T Zhang, H Huang, J Nogues, W Deng, H Resat, KA Rod, DR Baer, RT Kelly, W Um, G Wang, MC Richmond, DR Rector, ML Stewart, HB Jung, and C Plata. 2011. EMSL Pore Scale Modeling Challenge/Workshop. PNNL-21086, Pacific Northwest National Laboratory, Richland, WA. 

2009

• Resat H, L Petzold, and MF Pettigrew. 2009. "Kinetic Modeling of Biological Systems." Chapter 14 in Computational Systems Biology, vol. 541, pp. 311-336.  Humana Press, New York, NY. 
• Shankaran H, DL Ippolito, WB Chrisler, H Resat, N Bollinger, LK Opresko, and HS Wiley. 2009. "Rapid and Sustained Nuclear-Cytoplasmic ERK Oscillations Induced by Epidermal Growth Factor." Molecular Systems Biology 5:Article Number: 332.  doi:10.1038/msb.2009.90
• Zhang Y, LK Opresko, H Shankaran, WB Chrisler, HS Wiley, and H Resat. 2009. "HER/ErbB Receptor Interactions and Signaling Patterns in Human Mammary Epithelial Cells." BMC Cell Biology 10 :Article No. 78.  doi:10.1186/1471-2121-10-78

2008

• Shankaran H, Y Zhang, L Opresko, and H Resat. 2008. "Quantifying the effects of co-expressing EGFR and HER2 on HER activation and trafficking." Biochemical and Biophysical Research Communications 371(2):220-224.  doi:10.1016/j.bbrc.2008.04.043
• Zhang Y, H Shankaran, L Opresko, and H Resat. 2008. "System theoretical investigation of human epidermal growth factor receptor-mediated signalling." IET Systems Biology 2(5):273-284.  doi:10.1049/iet-syb:20080116

2007

• Pettigrew MF, and H Resat. 2007. "Multinomial Tau-Leaping Method for Stochastic Kinetic Simulations ." Journal of Chemical Physics 126(8):Art. No. 084101. 
• Samatova NF, A Gorin, E Uberbacher, TV Karpinets, BH Park, C Pan, TP Straatsma, WR Cannon, H Resat, RD Lins, and CS Oehmen. 2007. "Data driven computing for Biological Systems." SciDAC Review 5(Fall 2007):10-25. 
• Shankaran H, H Resat, and HS Wiley. 2007. "Cell surface receptors for signal transduction and ligand transport - a design principles study." PLoS Computational Biology 3(6):e101.  doi:10.1371/journal.pcbi.0030101
• Shankaran H, HS Wiley, and H Resat. 2007. "Receptor downregulation and desensitization enhance the information processing ability of signaling receptors." BMC Systems Biology 1:Art. No. 48. 
• Singhal M, and H Resat. 2007. "A Domain-Based Approach to Predict Protein-Protein Interactions ." BMC Bioinformatics 8:Art. No. 199.  doi:10.1186/1471-2105-8-199

2006

• Shankaran H, HS Wiley, and H Resat. 2006. "Modeling the effects of HER/ErbB1-3 co-expression on receptor dimerization and biological response." Biophysical Journal 90(11):3993-4009. 
• Shankaran H, HS Wiley, and H Resat. 2006. "Modeling the Effects of HER/ErbB1-3 Coexpression on Receptor Dimerization and Biological Response ." Biophysical Journal 90(11):3993-4009.  doi:10.1529/biophysj.105.080580

2005

• Mao L, RC Mackenzie, JH Roh, JM Eraso, S Kaplan, and H Resat. 2005. "Combining Microarray and Genomic Data to Predict DNA Binding Motifs." Microbiology 151(10):3197-3213.  doi:10.1099/mic.0.28167-0
• Miller JH, F Zheng, S Jin, L Opresko, HS Wiley, and H Resat. 2005. " A Model of cytokine shedding induced by low doses of gamma radiation." Radiation Research 163 (3):337-342. 
• Pettigrew MF, and H Resat. 2005. "Modeling Signal Transduction Networks: A comparison of two Stochastic Kinetic Simulation Algorithms." Journal of Chemical Physics 123(11):114707-1 - 114707-13.  doi:10.1063/1.2018641

2004

• Resat H. 2004. "EGF Receptor Sorting in Endosomal Compartments." In Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS '04, June 21-24, 2004, Las Vegas, USA, pp. 451-457.  CSREA Press, Bogart, GA. 
• Mao L, and H Resat. 2004. "Genome Scale Identification of Regulons ." In Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS '04, June 21-24, 2004, Las Vegas, USA, pp. 322-328.  CSREA Press, Bogart, GA. 
• Mao L, and H Resat. 2004. "Identifying DNA Binding Motifs by Combining Data from Different Sources ." In Eight World Multi-conference on Systemics, Cybernetics, and Informatics. July 18-21, 2004. Orlando, Florida. Applications of Informatics and Cybernetics in Science and Engineering, vol. VII, ed. Nagib Callaos; Katsuhisa Horimoto; Jake Chen; Amy Sze Chan, pp. 172-176.  International Institute of Informatics and Systemics, Orlando, FL. 
• Mao L, and H Resat. 2004. "Probabilistic Representation of Gene Regulatory Networks." Bioinformatics 20(14):2258-2269. 

2003

• Resat H, JA Ewald, DA Dixon, and HS Wiley. 2003. "An Integrated Model of Epidermal Growth Factor Receptor Trafficking and Signal Transduction ." Biophysical Journal 85(2):730-743. 

2001

• Resat H, HS Wiley, and DA Dixon. 2001. "Probability-Weighted Dynamic Monte Carlo Method for Reaction Kinetics Simulations ." Journal of Physical Chemistry B 105(44):11026-11034. 
• Resat H, HS Wiley, and DA Dixon. 2001. "Probability-Weighted Dynamic Monte Carlo Method for Reaction Kinetics Simulations." Journal of Physical Chemistry B 105(44):11026-11034. 
• Resat H, T Straatsma, DA Dixon, and JH Miller. 2001. "The Arginine Finger of RasGAP Helps Gln-61 Align the Nucleophilic Water in GAP-Stimulated Hydrolysis of GTP." Proceedings of the National Academy of Sciences of the United States of America 98(11):6033-6038.