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Journal Publications

1. Ramin Pashaie, “Fourier Decomposition Analysis of Anisotropic Inhomogeneous Dielectric Waveguide Structures,” IEEE Transaction on Microwave Theory and Techniques, Vol. 55, No. 8, pp. 1689-1696, Aug. 2007.
2. Ramin Pashaie, and Nabil H. Farhat, “Self-Organization in a Parametrically Coupled Logistic Map Network: A Model for Information Processing in the Visual Cortex,” IEEE Transaction on Neural Networks, Vol. 20, No. 4, pp. 597-608, April 2009.
3. Ramin Pashaie, and Nabil H. Farhat, “Dynamics of electron-trapping materials under blue light and near infrared exposure: an improved model,” Journal of the Optical Society of America B, Vol. 24, No. 8, pp. 1927-1941, Aug. 2007.
4. Ramin Pashaie, and Nabil H. Farhat, “An Analytical Model for the Dynamics of the Electron Trapping Materials with Applications in Nonlinear Optical Signal Processing,” Journal of the Optical Society of America B, Vol. 25, No. 1, pp. 15-21, Jan. 2008.
5. Ramin Pashaie, and Nabil H. Farhat, “Realization of Receptive Fields with Excitatory and inhibitory Responses in Equilibrium-State Luminescence of Electron Trapping Materials,” Optics Letters, Vol. 32, No. 11, pp. 1501-1503, June 2007.
6. Ramin Pashaie, and Nabil H. Farhat, “Optical Realization of Bio-inspired Spiking Neurons in Electron Trapping Material Thin Films,” Applied Optics, Vol. 46, No. 34, pp. 8411-8418, Dec. 2007.
7. Diester I, Kaufman MT, Mogri M, Pashaie Ramin, Goo W, Yizhar O, Ramakrishnan C, Deisseroth Karl, Shenoy KV, “An optogenetic toolbox designed for primates,” Nature Neuroscience, Vol. 14, No. 3, pp. 387-397, March 2011.
8. Ramin Pashaie, Ryan Falk, “Single Optical Fiber Probe for Fluorescence Detection and Optogenetic Stimulation,” IEEE Transaction Biomedical Engineering, Vol. 60, No. 2, p. 268-280, Feb. 2013.
9. Ramin Pashaie, Ryan Falk, “Spectral Analysis of Whisking Output via Optogenetic Modulation of Vibrissa Cortex in Rat,” Biomedical Optics Express, Vol. 4, No.1, pp. 122-133, Jan. 2013.
10. Ramin Pashaie, ” Associative Memory in a Volume Holographic Medium: A New Approach Based on Operator Theory,” Journal of Optics, Vol. 16, 075701, 2014.
11. Ramin Pashaie, “Distributed Light Delivery and Detection via Single Optical Fiber and Tilted Grating,” Journal of Modern Optics, Vol. 16, No. 6, 518-529, 2014.
12. Mehdi Azimipour, Ramin Pashaie, “Nonlinear Optical Signal Processing on Multiwavelength Sensitive Materials,” Optics Letters, Vol. 38, No. 2, pp. 4324-4326, Nov. 2013.
13. Ramin Pashaie, Polina Anikeeva, Jin Hyung Lee, Rohit Prakash, Ofer Yizhar, Matthias Prigge, Divya chander, Thomas Richner, Justin Williams, “Optogenetic Brain Interfaces,” IEEE Reviews in Biomedical Engineering, Vol. 7, pp. 3-30, 2014.
14. Thomas J Richner, Sanitta Thongpang, Sarah K Brodnick, Amelia A Schendel, Ryan W Falk, Lisa A Krugner-Higby, Ramin Pashaie, and Justin C Williams, “Optogenetic micro-electrocorticography for modulating and localizing cerebral cortex activity,” Journal of Neural Engineering, 11, 016010 (12pp), Jan. 2014.
15. Thomas J. Richner, Ryan Baumgartner, Sarah K. Brodnick, Kevin W. Eliceiri, Justin C. Williams, and Ramin Pashaie, ” Patterned optogenetic modulation of neurovascular and metabolic signals,” Nature – Journal of Cerebral Blood Flow and Metabolism, vol. 35, pp. 140-147, 2015.
16. Farid Atry, Seth Frye, Thomas J. Richner, Sarah K. Brodnick, Alana Soehartono, Justin Williams, Ramin Pashaie, “Monitoring Cerebral Hemodynamics Following Optogenetic Stimulation via Optical Coherence Tomography,” IEEE Transaction on Biomedical Engineering, vol. 62, no. 2, pp. 766-773, 2015.
17. Amelia A. Schendel, Michael W. Nonte, Corinne Vokoun, Thomas J. Richner, Sarah K. Brodnick, Farid Atry, Seth Frye, Paige Bostrom, Ramin Pashaie, Sanitta Thongpang, Kevin W. Eliceiri, and Justin C. Williams, “The effect of micro-ECoG substrate footprint on the meningeal tissue response,” Journal of Neural Engineering, Vol. 11, No. 4, Aug. 2014.
18. Amelia A. Schendel, Dong-Wook Park, Solomon Mikael, Thomas J. Richner, Sarah K. Brodnick, Farid Atry, Seth Frye, Ramin Pashaie, Sanitta Thongpang, Justin C. Williams and Zhenqiang Ma, “Carbon Layered Electrode Array (CLEAR) technology for neural imaging and optogenetic applications,” Nature Communications, vol. 5, no. 5258, pp. 1-11, 2014.
19. Mehdi Azimipour, Ryan Baumgartner, Yuming Liu, Steven Jacques, Kevin Eliceiri, Ramin Pashaie, “Extraction of Optical Properties and Prediction of Light Distribution in Rat Brain Tissue,” Journal of Biomedical Optics, Vol. 19, No. 7, 075001, July, 2014.
20. Ramin Pashaie, Ryan Baumgartner, Thomas Richner, Sarah Brodnick, Mehdi Azimipour, Kevin Eliceiri, Justin Williams “Closed-loop Optogenetic Brain Interface,” IEEE Transaction on Biomedical Engineering, Vol. 62, No. 10, pp. 2327-2337, Oct. 2015.
21. Mehdi Azimipour, Farid Atry, Ramin Pashaie, “Effect of Blood Vessels on Light Distribution in Optogenetic Stimulation of Cortex,” Vol. 40, Issue 10, pp-2173- 2176, Optics Letters, 2015.
22. Farid Atry, Ramin Pashaie, “Analysis of intermediary scan-lens and tube-lens mechanisms for optical coherence tomography,” Applied Optics, Vol. 55, No. 4, Feb. 2016.
23. Mehdi Azimipour, Farid Atry, Ramin Pashaie, “Calibration of Digital Optical Conjugation Setup Based on Orthonormal Rectangular Polynomials,” Accepted, Applied Optics, March 2016.
24. Christopher Pawela, Edgar DeYoe, Ramin Pashaie, “Intracranial Injection of an Optogenetics Viral Vector Followed by Optical Cannula Implantation for Neural Stimulation in Rat Brain Cortex,” Optogenetic Methods and Protocols, Springer Protocols, 2015.
25. Dong-Wook Park, Sarah Brodnick, Jared Ness, Farid Atry, Lisa Krugner-Higby, Amelia Sandberg, Solomon Mikael, Thomas Richner, Joseph Novello, Hyungsoo Kim, Dong-Hyun Baek, Jihye Bong, Cuong Nguyen, Seth Frye, Sanitta Thongpang, Kyle Swanson, Wendell Lake, Ramin Pashaie, Justin Williams, and Zhenqiang Ma, “Fabrication and utility of a transparent graphene neural electrode array for electrophysiology, in vivo imaging, and optogenetics,” Nature Protocol, Minor Revision Requested, March 2016.

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Conference Papers & Workshops

1. Ramin Pashaie, and Nabil Farhat, “Equilibrium-State Emission of Electron-Trapping Material Thin-Film for applications in Nonlinear-Dynamics,” Proc. Of SPIE, Vol. 6469, pp. 1-6, 2007.
2. Ramin Pashaie, and Nabil Farhat, “Optical realization of Bio-inspired spiking neurons in thin film,” paper ID code: JWD69, Presented in the 90th OSA annual meeting, Frontiers in optics, Rochester, NY, Oct. 2006.
3. Ramin Pashaie, and Nabil Farhat, “Optical Realization of the Retinal Ganglion Receptive Fields in Electron- Trapping Material Thin Films,” Proc. of the IEEE 32nd Annual Northeast Bioengineering Conference, pp. 1- 2, 2006.
4. Ramin Pashaie, and Nabil Farhat, “Optoelectronic Realization of Photonic Cortex,” Presented in the Annual Scientific Retreat, The Mahoney Institute of Neurological Sciences, University of Pennsylvania, April 18, 2007.
5. Ramin Pashaie, and Nabil H. Farhat, “An Analytical Model for the Dynamics of the Electron Trapping Materials with Applications in Nonlinear Optical Signal Processing,” Journal of the Optical Society of America B, Vol. 25, No. 1, pp. 15-21, Jan. 2008.
6. Ramin Pashaie, and Nabil Farhat, “Photonic Cortex,” Graduate Research Symposium, School of Engineering and Applied Sciences, University of Pennsylvania, 2006.
7. Ramin Pashaie, Murtaza Mogri, Karl Deisseroth, “A single fiber probe for optogenetics,” Annual Meeting, Society for Neuroscience, Oct. 2009.
8. Ryan Baumgartner, Ryan Falk, Ramin Pashaie, “Realization of an endoscope equipped with microprojection system for Optogenetics,” SPIE photonic West, Jan 2012.
9. Mohammad Habibi, Ramin Pashaie, ” A new approach for implementation of associative memory using volume holographic materials,” SPIE Photonic West, Jan 2012.
10. Ryan Falk, Mohammad Habibi, Ramin Pashaie, “Single Optical Fiber Probe for Optogenetics,” SPIE Photonic West Jan 2012.
11. Mohammad Habibi, Ramin Pashaie, “Distributed light delivery system (DLDS) for optogenetics,” SPIE Photonic West Jan 2012.
12. Ryan Falk, Ramin Pashaie, “Single optical fiber probe for optogenetics,” SFN 2012.
    Ramin Pashaie, Ryan Falk, Ryan Baumgartner, “Realization of an endoscope equipped with microprojection system for optogenetics,” SFN 2012.
13. Thomas Richner, Sarah Thongpang, Ryan Falk, Sarah Brodnick, Barry Van Veen, L. Krougner-higby, Ramin Pashaie, Justin Williams, “Cortical layer specific micro- electrocorticography potentials and gamma power evoked by optogenetic stimulation,” SFN 2012.
14. S. Thongpang, T Richner, S. Broadnick, R. Falk, A. Schendel, L. Krugner-Higby, Ramin Pashaie, Justin Williams, “Optogenetic Micro-Electrocortocography,” SFN 2012.
15. Thomas Richner, Ryan Baumgartner, Sarah Brodnik, Amelia Schendel, Kevin Eliceiri, Ramin Pashaie, Justin williams, “Closed-loop optogenetic spatial light modulation through real-time micro-electrocorticography feedback,” SFN 2013.
16. Mehdi Azimipour, Ryan Baumgartner, Yuming Liu, Amy L. Kaczmarowski, Steven L. Jacques, Kevin Eliceiri, Ramin Pashaie, ” Development of a simulation toolbox for predicting light distribution in rat brain tissue during optical stimulation,” SPIE Photonic West Feb. 2014.
17. Ryan Baumgartner, Thomas J. Richner, Sarah Brodnick, Justin Williams, Kevin W. Eliceiri, Ramin Pashaie, “Spatial light modulation and imaging system for investigation of neurometabolic and neurovascular coupling,” SPIE Photonic West Feb. 2014.
18. Seth Frye, Alana Soehartono, Farid Atry, Amy L. Kaczmarowski, Ramin Pashaie, “Monitoring of hemodynamic signals post optogenetic stimulation via optical coherence tomography,” SPIE Photonic West Feb. 2014.
19. Bora Novakovic, Ramin Pashaie, Adel Nasiri, “Neural Network Based Energy Storage Control for Wind Farms,” Power Electronics and Machines for Wind and Water Applications (PEMWA), IEEE Symposium, July 2014.
20. Farid Atry, Ramin Pashaie, “Design of a scan-lens and tube-lens for OCT applications,” SPIE Photonic West, paper 9697-104, 2016.
21. Mehdi Azimipour, Farid Atry, Ramin Pashaie, “Light pattern preservation in rodent’s cortical tissue during optogenetic neuro-stimulation,” SPIE Photonic West, paper 9706-35, 2016.
22. Mehdi Azimipour, Farid Atry, Ramin Pashaie, “Iterative calibration of a digital optical phase conjugation system,” SPIE Photonic West, paper 9717-58, 2016.