Haluk resat



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HALUK RESAT

509-335-6579 (office) Washington State University

haluk.resat@wsu.edu School of Chemical Engineering & Bioengineering

Pullman, WA 99164-2710


Professional:

7/2013 - current Associate Professor

Washington State University

Gene and Linda Voiland School of

Chemical Engineering & Bioengineering

Pullman, Washington


1/2006 – 7/2013 Chief Scientist, Level V

8/2000 - 12/2005 Senior Research Scientist, Level IV

9/1999 - 7/2000 Visiting Faculty Fellow

Pacific Northwest National Laboratory

Computational Biology & Bioinformatics Group

Richland, Washington


8/2012 - current Battelle Faculty

Washington State University

School of Electrical Engineering & Computer Science

Pullman, Washington


7/1999 - 7/2000 Associate Professor

9/1996 - 6/1999 Assistant Professor

Koç University

Faculty of Science

Istanbul, Turkey
9/1994 - 8/1996 Postdoctoral research associate

Supervisor: J. Andrew McCammon

University of California at San Diego

Department of Chemistry and Biochemistry

San Diego, California
9/1992 - 8/1994 Postdoctoral research associate

Supervisor: Mihaly Mezei

Mount Sinai School of Medicine

Department of Physiology and Biophysics

New York, New York

Education:

1992 Ph. D. in Physics

Thesis advisor: Harold L. Friedman

Department of Chemistry

State University of New York at Stony Brook
1986 B. S. in Electrical Engineering

1986 B. S. in Physics (double major)

Bosphorus University, Istanbul, Turkey
Honors, Awards:

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).

Numerous PNNL outstanding performance awards.


Professional Activities:

Department representative (effectively the Department Head) to the Dean, Koc University (8/98 – 8/99).

Editorial Board: Frontiers in Systems Biology journal, Review Editor.

Membership:

American Society of Cell Biology;

Biophysical Society;

International Receptor Tyrosine Kinase Consortium (founding member);

International Society for Computational Biology;

Society for Industrial and Applied Mathematics.

Review Panelist for:

NSF/Computational Biology, 2004;

NIH/MABS Modeling and Analysis of Biological Systems, 2005.

NIH/MABS Modeling and Analysis of Biological Systems, 2006.

NIH/ARRA/BST-M Bioengineering Sciences and Technologies, 2009.

NIH/BST-H Bioengineering Sciences and Technologies, 2010.

NIH/MABS Modeling and Analysis of Biological Systems, 2011.

NIH/MIST Molecular and Integrative Signal Transduction, 2012.

NIH/MIST Molecular and Integrative Signal Transduction, 2013.

Scientific reviewer for:

Cell Systems Initiative, University of Washington;

Department of Pharmacology, University of California-San Diego;

DOE-SBIR/STTR program;

NSF Career Awards;

NSF/Molecular and Cellular Biosciences;

NSF-RUI Research at Undergraduate Institutions Program;

NSF University-Industry Fellowship Program;

Petroleum Research Fund/American Chemical Society;

PNNL Data Intensive Computing Initiative;

PNNL Environmental Biomarkers Initiative;

PNNL Biomolecular Systems Initiative;

PNNL Exascale Computing Initiative.

Reviewer for:

Bioinformatics; Biophysical Journal; BMC Bioinformatics; BMC Genomics; BMC Systems Biology; Bulletin for Mathematical Biology; Ecological Applications; European Journal of Biochemistry; FEBS Journal; FEBS Letters; In Silico Biology; Journal of American Chemical Society; Journal of Cellular Physiology; Journal of Chemical Physics; Journal of Chemical Theory and Computation; Journal of Computational Chemistry; Journal of Computer-Aided Molecular Design; Journal of Physical Chemistry; Molecular BioSystems; Molecular Medicine; Molecular Systems Biology; Nature Structural Biology; Pacific Symposium on Biocomputing; Physical Review E; Physical Review Letters; PLoS Computational Biology; PLoS ONE; Protein Science; Theoretical Biology and Medical Modeling.

Reviewed chapter for the book: Computational methods for understanding bacterial and archaeal genomes.


Organizational Experience:

Session chair: Generating models that predict, The 2005 Northwest Symposium for Systems Biology: Towards a Predictive Science, Richland, Washington, June 2005.

Organizer of the mini-symposium: “Biological Simulations: Model Development and Practical Applications”, SIAM Conference on the Life Sciences, Portland, Oregon, USA, July 2004.

Co-organizer of the mini-symposium: “Mathematical Modeling of Cellular Dynamics”, SIAM Conference on the Life Sciences, Portland, Oregon, USA, July 2004.

Organizer of the mini-symposium: “Simulation of Cellular Processes Using Spatially and Temporally Resolved Methods”, SIAM Workshop on Computational Models and Simulation for Intra-cellular Processes, Washington D.C., USA, October 2002.

Co-organizer of the “Chemical Physics III” meeting, Istanbul, Turkey, October 1998.

Organizer of the symposium: “Structure and dynamics in molecular systems: Existing problems and possible tools”, Istanbul, Turkey, April 1997.

Organizer of the regular weekly Science faculty seminars, Koç University (10/96-9/97).

Session chair: Bioinformatics III, International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, Las Vegas, June 2004.

Advisory board: “7th World Congress on Computational Mechanics (WCCM VII)” meeting, Los Angeles, California, 2006.


Mentorship:

Postdoctoral associates:

Linyong Mao (10/02-9/04), Iowa;

Harish Shankaran (11/03-6/06), PNNL;

Yi Zhang (12/05-9/09), UT-Memphis;

Chunhong Gong (9/09-9/12), PNNL.

Ph.D. thesis:

Mudita Singhal (thesis committee, Washington State University; 2007)

M.S. thesis:

Ozlem Unver (co-advisor, Middle East Technical University; 2/2000)

Students:

Bilgin Ersoy (Honor’s project, 1999, Koc University);

Oguz Sebik (Independent study project, 1998-99, Koc University);

Yusuf Sahin (Independent study project, 1998-99, Koc University);

Esen Onur (Independent study project, 1998-99, Koc University);

Chantell Perry (high school student, Summer 2003, PNNL);

Diane Hu (undergraduate student, Summer 2004, PNNL);

Peter Divalentin (undergraduate student, Summer 2004, PNNL);

Jeff Kilpatrick (CSGF intern, graduate student, Summer 2010, PNNL);

Yunbing Tan (graduate student, Summer 2011, PNNL);

Rebecca Sadowitz (undergraduate student, Summer 2012, PNNL).
Coursed taught:

Introductory Mathematics (various courses);

Introductory Physics (various courses);

Introductory Science;

Differential Equations;

Statistical Physics;

Advanced Statistical Mechanics.
Other:

Math Club mentor (Delta High school, Tri-Cities, WA);

Math is Cool coach (Lewis & Clark Elementary, Richland, WA)

Substitute instructor, various math courses (WSU Tri-Cities).



Grant Support:
Current:

Principal investigator: Modeling Cell Receptor Signaling Pathways. H. Resat. NIH/NIGMS (R01, 3/05-6/09, $290 K per year; competitive renewal, 7/09-6/13, $325 K per year).

Principal investigator: Multiscale Simulation of Microbial Carbon Transformation in Soils: Connecting Intra- and Inter-Aggregate Scales. H. Resat and T. Scheibe. Laboratory Directed Research and Development Program, Pacific Northwest National Laboratory (FY12-FY13, $225 K per year).
Pending:

Principal investigator: Cellular Communication between Epithelial Cells and Macrophages. H. Resat and B. Linggi. NIH/NIGMS (R01; $2,275,500 total for 5 years).

Principal investigator: Mechanistic Models of Carbon Cycling in Soils: Scaling up from Aggregates to Ecosystems. H. Resat (WSU) and Robert L. Sinsabaugh (U. New Mexico). DOE/TES ($870,000 total for 3 years). This proposal has been submitted through my joint appointment and will be administered by WSU if funded.

Completed:

Principal investigator: Computational Approaches and Framework for Microbial Cell Simulations. H. Resat (PI), J. Oliveira, H. Sofia, and H. Trease. DOE-ASCR/MICS (FY01-FY03, no-cost extension to FY04, $360 K per year/$1.08 M total).

Investigator: Exploratory Data Intensive Computing for Complex Biological Systems. T. P. Straatsma and N. Samatova (PIs). DOE-ASCR. Joint proposal with ORNL. Role: Task Lead (FY04-FY07; no cost extension FY08-10).

Principal investigator: Multiscale Models for Microbial Communities. H. Resat. Laboratory Directed Research and Development Program, Pacific Northwest National Laboratory (FY09-FY12, $240 K per year).

Principal investigator: Crosstalk Between Receptor Signaling Pathways. H. Resat. Laboratory Directed Research and Development Program, Pacific Northwest National Laboratory (FY05-FY07, $170 K to $215 K per year).

Principal investigator: Kinetic Simulations and Network Analysis: The EGF Receptor Signaling Network. H. Resat. Laboratory Directed Research and Development Program, Pacific Northwest National Laboratory (FY02-FY04, $395 K total).

Co-principal investigator: Development of Live and LC-NMR Microbial Metabolomics Methods for Systems Biology Studies. N. Isern (PI), B. Ahring, P. Majors, and H. Resat. Laboratory Directed Research and Development Program, Pacific Northwest National Laboratory (FY09-FY11).

Investigator: Modeling of Microbial Communities in Soil Aggregates. L.A. McCue (PI). Laboratory Directed Research and Development Program, Pacific Northwest National Laboratory (FY08-FY09, $155 K/year).

Investigator: Protein-Protein Interaction Network Prediction. M. Singhal (PI). Laboratory Directed Research and Development Program, Pacific Northwest National Laboratory (FY06-FY07, $125 K).

Co-principal investigator: Single Molecule Approach for Understanding EGF Receptor Interactions. S. Colson (PI), G. Orr, C.-S. Chen, and H. Resat. Laboratory Directed Research and Development Program, Pacific Northwest National Laboratory (FY02-FY03, $420 K total).

Co-principal investigator: Enabling the silicon cell: Development of models of cell-signaling pathways and networks. D. A. Dixon, J. S. Oliveira, J. H. Miller, and H. Resat. Laboratory Directed Research and Development Program, Pacific Northwest National Laboratory. $344,000 for the FY2000.

Investigator: Multicellular Models for Cell-Cell Communication. C. Oehmen (PI). Laboratory Directed Research and Development Program, Pacific Northwest National Laboratory (FY05, $100 K).

Investigator: Multiscale Modeling and Uncertainty Quantification for Bioremediation. K. Jarman (PI). Laboratory Directed Research and Development Program, Pacific Northwest National Laboratory (FY05-FY06, $170 K per year).

Co-principal investigator: Investigation of the antibiotic amphotericin B-lipid membrane interactions using computational chemistry methods. Joint proposal by M. Baginski and E. Borowski of Technical University of Gdansk, Poland, and H. Resat. Polish State Committee for Scientific Research. $33,800 for three years and 16,000 Cray T3E cpu hours, 1/1998-12/2000.

Principal investigator: Analysis of the solvation patterns at polymer surfaces. Joint proposal by H. Resat, I. Yilgor, and E. Yilgor from Koç University, and F. Fogolari of University of Udine, Italy. FIAT funds. $13,300 for one year, 1997.

Publications:
Journal articles/Book/Book chapters:
56. Model-based analysis of HER activation in cells co-expressing EGFR, HER and HER3, Harish Shankaran, Yi Zhang, Yunbing Tan, and Haluk Resat, PLoS Computational Biology (2013, in print).

55. Microbial dynamics in soil aggregates: Sensitivity to exo-enzyme production and kinetics under carbon-limited conditions, Haluk Resat, Fred J. Brockman, and Allan Konopka (submitted, 2013).



54. Flow partitioning in fully saturated soil aggregates, Xiaofan Yang, Marshall C. Richmond, Timothy D. Scheibe, William A. Perkins, and Haluk Resat (submitted, 2013).

53. Integrated experimental and model-based analysis reveals the spatial aspects of EGFR activation dynamics, Harish Shankaran, Yi Zhang, William B. Chrisler, Jonathan A. Ewald, H. Steven Wiley, and Haluk Resat, Molecular BioSystems 8:2868-2882 (2012). (PMC22952062, NIHMS414380) doi:10.1039/C2MB25190F. Cover article.

52. Modeling microbial dynamics in heterogeneous environments: Growth on soil carbon sources, Haluk Resat, Vanessa Bailey, Lee Ann McCue, and Allan Konopka, Microbial Ecology 63:883-897 (2012). doi:10.1007/s00248-011-9965-x.

51. An adaptive coarse graining method for signal transduction in three dimensions, Michelle N. Archuleta, Jason E. McDermott, Jeremy S. Edwards, and Haluk Resat, Fundamenta Informaticae 118:371-384 (2012). doi:10.3233/FI-2012-720. (Alan Turing special issue)

50. Spatial Aspects in Biological System Simulations, Haluk Resat, Michelle N. Costa, and Harish Shankaran, in Computer Methods, Part C, Methods in Enzymology book series, Editors: ML Johnson and L Brand, Academic Press/Elsevier (2011). (PMC3371646, NIHMS378297)

49. HER/ErbB receptor interactions and signaling patterns in human mammary epithelial cells, Yi Zhang, Lee Opresko, Harish Shankaran, William B. Chrisler, H. Steven Wiley, and Haluk Resat, BMC Cell Biology 10:68 (2009). doi:10.1186/1471-2121-10-78. (PMC2776588)

48. Rapid and sustained nuclear-cytoplasmic ERK oscillation induced by epidermal growth factor, Harish Shankaran, Danielle L. Ippolito, William B. Chrisler, Haluk Resat, Nikki Bollinger, Lee K. Opresko, and H. Steven Wiley, Molecular Systems Biology 5:332 (2009). (PMC2824491)

47. Kinetic modeling of biological systems, Haluk Resat, Linda Petzold, and Michel F. Pettigrew, in Computational Systems Biology, Methods in Molecular Biology book series, Editors: J. McDermott, R. Samudrala, R. Bumgarner, K. Montgomery, and R. Ireton, Humana Press (2009). (NIHMS198040, PMC2877599)

46. System theoretical investigation of HER mediated signaling, Yi Zhang, Harish Shankaran, Lee Opresko, and Haluk Resat, IET Systems Biology 2, 273-284 (2008). (NIHMS84956, PMC2707181)

45. Quantifying the effects of EGFR-HER2 co-expression on HER activation and trafficking, Harish Shankaran, Yi Zhang, Lee Opresko, and Haluk Resat, Biochemical and Biophysical Research Communications 371, 220-224 (2008). (NIHMS87980, PMC2864016)

44. A domain based approach to predict protein-protein interactions, Mudita Singhal and Haluk Resat, BMC Bioinformatics 8, 199 (2007).

43. Cell surface receptors for signal transduction and ligand transport: A design principles study, Harish Shankaran, Haluk Resat, and H. Steven Wiley, PLoS Computational Biology, 3 (6) e101 (2007). doi:10.1371/journal.pcbi.0030101. (PMC1885276)

42. Receptor downregulation and desensitization enhance the information processing ability of signalling receptors, Harish Shankaran, H. Steven Wiley, and Haluk Resat, BMC Systems Biology 1, 48 (2007). doi:10.1186/1752-0509-1-48. (PMC2228318)

41. A multinomial tau-leaping method for stochastic kinetic simulations, Michel F. Pettigrew and Haluk Resat, J. Chem. Phys. 126, 084101 (2007). Also listed in the Virtual Journal of Biological Physics Research, March 1 (2007).

40. Modeling the effects of HER/ErbBs 1-3 coexpression on receptor dimerization and biological response, Harish Shankaran, H. Steven Wiley, and Haluk Resat, Biophysical J. 90, 3993-4009 (2006). (PMC1459488)

39. Combining microarray and genomic data to predict DNA binding motifs, Linyong Mao, R. Chris Mackenzie, Jung H. Roh, Jesus M. Eraso, Samuel Kaplan, and Haluk Resat, Microbiology 151, 3197-3213 (2005). Highlighted in the Nature Reviews Microbiology as the selected Bioinformatics paper (Nov. 2005).

38. Modeling signal transduction networks: A comparison of two basic stochastic kinetic simulation algorithms, Michel F. Pettigrew and Haluk Resat, J. Chem. Phys. 123, 114707 (2005). Also listed in the Virtual Journal of Biological Physics Research, Oct. 1 (2005).

37. A model of cytokine shedding induced by low doses of gamma irradiation, John H. Miller, Fang Zheng, Shuangshuang Jin, Lee K. Opresko, H. Steven Wiley, and Haluk Resat, Radiation Research 163, 337-342 (2005).

36. Probabilistic representation of gene regulatory networks, Linyong Mao and Haluk Resat, Bioinformatics 20, 2258-2269 (2004).

35. An integrated model of EGF receptor trafficking and signal transduction, Haluk Resat, Jonathan A. Ewald, David A. Dixon, and H. Steven Wiley, Biophysical J. 85, 730-743 (2003).

34. Comparative Molecular Dynamics simulations of amphotericin B-cholesterol/ergosterol membrane channels, Maciej Baginski, Haluk Resat, and Edward Borowski, Biochem. Biophys. Acta - Biomembranes, 1567, 63-78 (2002).

33. Ion passage pathways and thermodynamics of amphotericin-B membrane channel, Haluk Resat and Maciej Baginski, Eur. Biophys. J. 31, 294-305 (2002).

32. Probability weighted dynamic Monte Carlo method for reaction kinetics simulations, Haluk Resat, H. Steven Wiley, and David A. Dixon, J. Phys. Chem. B 105, 11026-11034 (2001).

31. The arginine finger of RasGAP helps Gln61 align the nucleophilic water in GAP-stimulated hydrolysis of GTP, Haluk Resat, T. P. Straatsma, David A. Dixon, and John H. Miller, Proc. Natl. Aca. Sci. USA 98, 6033-6038 (2001).



30. Calculating the local chemical potential in crystal hydrates, Haluk Resat and Mihaly Mezei, Phys. Rev. E 62, 7077-7081 (2000).

29. Conformational properties of amphotericin-B amide derivatives – impact on selective toxicity, Haluk Resat, F. Aylin Sungur, Maciej Baginski, Edward Borowski, and Viktorya Aviyente, J. Computer-Aided Molecular Design 14, 689-703 (2000).

28. Correcting for solvent-solvent electrostatic cutoffs considerably improves the ion pair potential of mean force, Haluk Resat, J. Chem. Phys. 110, 6887-6889 (1999).

27. A computational study of the reactivity of diethenylnaphtalenes towards anionic polymerization, Ahu Akin, Safiye S. Erdem, Turgut Nugay, Viktorya Aviyente, and Haluk Resat, J. Chem. Soc. Perkin II 5-13 (1999).

26. Solvation studies of DMP323 and A76928 bound to HIV protease: Analysis of water sites using grand canonical Monte Carlo simulations, Tami J. Marrone, Haluk Resat, C. Nicholas Hodge, Chong-Hwan Chang, and J. Andrew McCammon, Protein Science 7, 573-579 (1998).

25. Correcting for electrostatic cutoffs in free energy simulations: Toward consistency between simulations with different cutoffs, Haluk Resat and J. Andrew McCammon, J. Chem. Phys. 108, 9617-9623 (1998).

24. Molecular properties of amphotericin B membrane channel - A molecular dynamics simulation, Maciej Baginski, Haluk Resat, and J. Andrew McCammon, Molecular Pharmacology 52, 560-570 (1997).

23. Enzyme-inhibitor association thermodynamics: Explicit and continuum solvent studies, Haluk Resat, Tami Marrone, and J. Andrew McCammon, Biophys. J. 72, 522-532 (1997). Cover article.

22. The sensitivity of conformational free energies of the alanine-dipeptide to atomic site charges, Haluk Resat, Peter Maye, and Mihaly Mezei, Biopolymers 41, 73-81 (1997).

21. Grand canonical ensemble Monte Carlo simulation of the dCpG/Proflavine crystal hydrate, Haluk Resat and Mihaly Mezei, Biophys. J. 71, 1179-1190 (1996). Cover article.

20. Use of the grand canonical ensemble in potential of mean force calculations, Haluk Resat, Mihaly Mezei, and J. Andrew McCammon, J. Phys. Chem. 100, 1426-1433 (1996).

19. Free energy simulations: Correcting for electrostatic cutoffs by use of the Poisson equation, Haluk Resat and J. Andrew McCammon, J. Chem. Phys. 104, 7645-7651 (1996).

18. Extracting fluid structures from neutron diffraction data, Haluk Resat, Enci Zhong, and Harold L. Friedman, Chem. Phys. Lett. 236, 1-7 (1995).

17. Grand canonical Monte Carlo simulation of water positions in crystal hydrates, Haluk Resat and Mihaly Mezei, J. Am. Chem. Soc. 116, 7451-7452 (1994).

16. A molecular theory of solvation dynamics, Fernando O. Raineri, Haluk Resat, Baw-Ching Perng, Fumio Hirata, and Harold L. Friedman, J. Chem. Phys. 100, 1477-1491 (1994).

15. Temperature dependence of ion solvation dynamics in liquid water, Haluk Resat, Fernando O. Raineri, Baw-Ching Perng, and Harold L. Friedman, in Hydrogen-bond networks, M.-C. Bellissent-Funel and J. Dore (eds.), pg. 247-250, Kluwer Academic Publishers, NATO-ARW series (1994).

14. Applications of a molecular theory of solvation dynamics, Harold L. Friedman, Baw-Ching Perng, Haluk Resat, and Fernando O. Raineri, J. of Phys.: Condensed Matter 6, A131-136 (1994).

13. Studies on free energy calculations. II. A theoretical approach to molecular solvation, Haluk Resat and Mihaly Mezei, J. Chem. Phys. 101, 6126-6140 (1994).

12. Studies on free energy calculations. I. Thermodynamic integration using a polynomial path, Haluk Resat and Mihaly Mezei, J. Chem. Phys. 99, 6052-6061 (1993).

11. Studies of the optical like high frequency dispersion in liquid water, Haluk Resat, Fernando O. Raineri, and Harold L. Friedman, J. Chem. Phys. 98, 7277-7280 (1993).

10. Smoluchowski-Vlasov equations, reference memory function approximation, and molecular models for transport and relaxation in fluids, Harold L. Friedman, Fernando O. Raineri, and Haluk Resat, in Molecular liquids: New perspectives in physics and chemistry, J. J. C. Teixeira-Dias (ed.), pg. 95-119, Kluwer Academic Publishers, NATO-ASI series (1992).

9. A dielectric theory of the optical-like high frequency mode in liquid water, Haluk Resat, Fernando O. Raineri, and Harold L. Friedman, J. Chem. Phys. 97, 2618-2625 (1992).

8. Static longitudinal dielectric function of model molecular fluids, Fernando O. Raineri, Haluk Resat, and Harold L. Friedman, J. Chem. Phys. 96, 3068-3084 (1992).

7. Static and dynamic dielectric properties of model polar molecular fluids, Ph.D. dissertation, State University of New York at Stony Brook (August 1992).

6. Investigation of interfacial roughness of In(x)Ga(1-x)As epitaxial layers on GaAs and InP substrates by soft X-ray reflectivity, A. Krol, H. Resat, C. J. Sher, S. Woronick, W. Ng, Y. H. Kao, T. L. Cole, A. K. Green, C. Lowe-Ma, T. W. Nee, and V. Rehn, J. Appl. Phys. 69, 949 (1991).

Proceedings (peer-reviewed):

5. Identifying DNA binding motifs by combining data from different sources, Linyong Mao and Haluk Resat, in Applications of Informatics and Cybernetics in Science and Engineering, vol. VII of Proceedings of the 8th World Multiconference on Systemics, Cybernetics, and Informatics (SCI2004), N. Callaos, K. Horimoto, J. Chen, and A. K. . Chan (eds.), pg. 172-176, IIIS Press, Orlando, Florida (2004).

4. Genome scale identification of regulons, Linyong Mao and Haluk Resat, in Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS), F. Valafar and H. Valafar (eds.), pg. 322-328, CSREA Press, Las Vegas (2004).

3. EGF receptor sorting in endosomal compartments, Haluk Resat, in Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, F. Valafar and H. Valafar (eds.), pg. 451-457, CSREA Press, Las Vegas (2004).

2. FRET measurements between small numbers of molecules identifies subtle changes in receptor interactions, Serdar Ozcelik, Galya Orr, Dehong Hu, Chii-Shiarng Chen, Haluk Resat, Greg S. Harms, Lee K. Opresko, H. Steven Wiley, and Steven D. Colson, Proceedings of the International Society of Optical Engineering, vol. 5323, pg. 119-127 (2004).

1. Cellular signal regulation by endocytic trafficking, Haluk Resat, John H. Miller, David A. Dixon, and H. Steven Wiley, in Currents in Computational Molecular Biology, N. El-Mabrouk, T. Lengauer, and D. Sankoff (eds.), pg. 79-80, Les Publications CRM, Montreal (2001).


Presentations (talks only, posters are not listed):

50. Systems level investigation of cellular dynamics, School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, March 2013.



49. HER/ErbB Signaling: A Model-Based Analysis, First Annual Winter Q-Bio Meeting, Waikiki, Hawaii, February 2013.

48. Computational Analysis of Cell Signaling Pathways, AIM workshop on Systems Approaches in Oncology Drug Discovery, Palo Alto, California, February 2012.

47. Challenges in Multiscale Modeling of Bacterial Dynamics, Pore Scale Workshop, Pacific Northwest National Laboratory, Richland, Washington, August 2011.

46. Modeling Cellular Dynamics, Washington State University, Department of Electrical Engineering and Computer Science, Pullman, Washington, June 2011.

45. Kinetic Simulations of Cell Signaling Processes, Advanced Bioinformatics Tools conference, University of Warsaw, Warsaw, Poland, May 2010 (opening keynote seminar).

44. Computational molecular biology: Multiple models or multiscale models, Dagstuhl Seminar on Formal Methods in Molecular Biology, Wadern, Germany, February 2009 (keynote seminar).

43. Role of HER2 and HER3 Overexpression on EGF Receptor Signaling, the 52nd Annual Meeting of the Biophysical Society, Long Beach, California, February 2008.

42. Modeling signal transduction in space and time, The 2005 Northwest Symposium for Systems Biology: Towards a Predictive Science, Richland, Washington, June 2005.

41. Biological network modeling, Systems Biology Fellowship Lecture Series, PNNL, Richland, Washington, April 2005.

40. Probabilistic representation of gene regulatory networks, Rocky’04 Rocky Mountain Regional Bioinformatics Conference, Aspen, Colorado, December 2004.

39. Role of the receptor-receptor interactions on the signaling by the HER receptor family, SIAM Conference on the Life Sciences, Portland, July 2004.

38. Probabilistic representation of gene regulatory networks, SIAM Conference on the Life Sciences, Portland, July 2004.

37. Genome scale identification of regulons, the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, Las Vegas, June 2004.

36. Biological network modeling, Computational Biology and Bioinformatics Noontime Lecture Series, PNNL, Richland, Washington, June 2004.



35. EGF receptor sorting in endosomal compartments, the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, Las Vegas, June 2004.

30. Network Analysis: An Overview, CSE590 Lecture Series, University of Washington, Department of Computer Science and Engineering, Seattle, Washington, January 2004.

29. Modeling of Cellular Receptor Signaling Pathways, 13th Balkan Biochemical Biophysical Days, Kusadasi, Turkey, October 2003.

28. Investigation of membrane receptor dynamics with confocal microscopy, 15th Annual Meeting of the Turkish Biophysical Society, Denizli, Turkey, October 2003.

27. EGF receptor sorting in endosomal compartments, Novasite Biotechnology Company, San Diego, California, April 2003.

26. EGF receptor sorting in endosomal compartments, University of California at San Diego, Biomolecular Simulations Group, Department of Chemistry and Biochemistry, San Diego, California, April 2003.

25. Kinetic Simulations of Receptor Signaling Pathways, SIAM Workshop on Computational Models and Simulation for Intra-cellular Processes, Washington D.C., USA, October 2002.

24. Amphotericin-B membrane channel, Ankara University, School of Pharmacy, Ankara, Turkey, June 2001.

23. GAP Stimulated Hydrolysis of GTP, Middle East Technical University, Biology Department, Ankara, Turkey, May 2001.

22. Amphotericin-B membrane channel: Structure and thermodynamics, Schering-Plough Corp., Kenilworth, New Jersey, July 2000.

21. Amphotericin-B membrane channel: Structure and thermodynamics, Cerep Inc., Redmond, Washington, June 2000.

20. Amphotericin-B membrane channel: Structure and thermodynamics, Molecular Research Institute, Mountain View, California, June 2000.

19. Amphotericin-B membrane channel: Structure and thermodynamics, Texas A & M University, Department of Chemistry, College Station, Texas, May 2000.

18. Amphotericin-B membrane channel: Structure and thermodynamics, University of Kansas, Department of Medicinal Chemistry, Lawrence, Kansas, May 2000.

17. Ion passage pathways and thermodynamics of Amphotericin B membrane channel, Bilkent University, Chemistry Department, March 1999.

16. Biomolecular Systems: Thermodynamic and Solvation Properties, Bosphorus University, Polymer Research Center, December 1998.

15. Amphotericin-B membrane channel: Ion passage pathways and thermodynamics, Chemical Physics III, Istanbul, Turkey, September 1998.

14. Amphotericin-B membrane channel: Cation passage pathways and thermodynamics, International Society of Quantum Biology and Pharmacology (ISQBP) President’s Meeting: Molecular Structure and Dynamics in Biology, Elba Island, Italy, September 1998.

13. Molecular properties of Amphotericin-B membrane channel, Middle East Technical University, Biology Department, April 1998.

12. Amphotericin B transmembrane channel, Bosphorus University, Chemistry Department, November 1997.

11. Molecular properties of Amphotericin-B membrane channel, Bosphorus University, Physics Department, Istanbul, Turkey; April 1997.

10. Confined spaces in biological systems, Symposium on the Structure and Dynamics in Molecular Systems: Existing Problems and Possible Tools, Istanbul, Turkey, April 1997.

9. Enzyme-inhibitor association thermodynamics: Explicit and continuum solvent studies, Biophysical Society Annual Meeting, New Orleans; March 1997.

8. Molecular simulation of biological systems, III. Dynamical Systems Meeting, Bolu, Turkey; December 1996.

7. Enzyme-inhibitor association thermodynamics, University of California at San Diego, Department of Pharmacology; March 1996.

6. Enzyme-inhibitor association thermodynamics, SUNY at Stony Brook, New York, Department of Chemistry; December 1995.

5. Molecular simulation studies of proteins and nucleic acids, Bosphorus University, Department of Physics, Istanbul, Turkey; November 1995.

4. Molecular simulation studies of proteins and nucleic acids, Koc University, Faculty of Arts and Sciences, Istanbul, Turkey; November 1995.

3. Molecular simulation studies of proteins and nucleic acids, Middle East Technical University, Department of Physics, Ankara, Turkey; November 1995.

2. Potential of mean force between trypsin and benzamidine; A grand canonical ensemble molecular simulation study, Western Biotech Conference, San Diego; October 1995.

1. Grand canonical Monte Carlo simulation studies of proteins, West Coast Theoretical Chemistry Conference, San Diego; March 1995.


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