Boston University

Optical Characterization and Nanophotonics Laboratory

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[Books & Chapters][Journal Articles][Conference Papers][Theses]

Emre Ozkumur

Research Associate
Doctor of Philosophy
Boston University
ENG - College of Engineering

Projects

Interferometric Reflectance Imaging Sensor

Books & Chapters

1.) M. S. Ünlü, E. Ozkumur, D. A. Bergstein, A. Yalcin, M. F. Ruane, and B. B. Goldberg, "Applications of Optical Resonance to Biological Sensing and Imaging: II. Resonant Cavity Biosensors," Biophotonics, Biological and Medical Physics, Biomedical Engineering Series, 2008

Journal Articles

12.) S. Ahn, C. Huang, E. Ozkumur, X. Zhang, J. Chinnala, A. Yalcin, S. Bandyopadhyay, S. Russek, M. S. Ünlü, C. DeLisi, and R. Irani, "TATA binding proteins can recognize nontraditional DNA sequences," Biophysical Journal, Vol. 103, October 2012, pp. 1510-1517

11.) G. G. Daaboul, R. S. Vedula, S. Ahn, C. A. Lopez, A. Reddington, E. Ozkumur, and M. S. Ünlü, "LED-based Interferometric Reflectance Imaging Sensor for quantitative dynamic monitoring of biomolecular interactions," Biosensors and Bioelectronics, Vol. 26, January 2011, pp. 2221-2227

10.) C. A. Lopez, G. G. Daaboul, R. S. Vedula, E. Ozkumur, D. A. Bergstein, T. W. Geisbert, H. Fawcett, B. B. Goldberg, J. H. Connor, and M. S. Ünlü, "Label-free multiplexed virus detection using spectral reflectance imaging," Biosensors and Bioelectronics, 2011

9.) R. S. Vedula, G. G. Daaboul, A. Reddington, E. Ozkumur, D. A. Bergstein, and M. S. Ünlü, "Self-Referencing Substrates for Optical Interferometric Biosensors," Journal of Modern Optics, Vol. 57, No. 16, 20 September 2010, pp. 1564–1569

8.) E. Ozkumur, C. A. Lopez, A. Yalcin, J. H. Connor, M. Chiari, and M. S. Ünlü, "Spectral Reflectance Imaging for a Multiplexed, High-Throughput, Label-Free, and Dynamic Biosensing Platform," IEEE Journal of Selected Topics in Quantum Electronics, Vol. 16, No. 3, May/June 2010, pp. 635-46

7.) E. Ozkumur, S. Ahn, A. Yalcin, C. A. Lopez, E. Cevik, R. Irani, C. DeLisi, M. Chiari, and M. S. Ünlü, "Label-free microarray imaging for direct detection of DNA hybridization and single-nucleotide mismatches," Biosensors and Bioelectronics, Vol. 25, No. 7, 15 March 2010, pp. 1789-1795

6.) C. Joo, E. Ozkumur, M. S. Ünlü, and J. F. de Boer, "Spectral-domain optical coherence phase microscopy for label-free multiplexed protein microarray assay," Biosensors and Bioelectronics, Vol. 25, No. 2, 15 October 2009, pp. 275-281

5.) E. Ozkumur, A. Yalcin, M. Cretich, C. A. Lopez, D. A. Bergstein, B. B. Goldberg, M. Chiari, and M. S. Ünlü, "Quantification of DNA and protein adsorption by optical phase shift ," Biosensors and Bioelectronics, Vol. 25, September 2009, pp. 167-172

4.) A. Yalcin, F. Damin, E. Ozkumur, G. di Carlo, B. B. Goldberg, M. Chiari, and M. S. Ünlü, "Direct Observation of Conformation of a Polymeric Coating with Implications in Microarray Applications," Analytical Chemistry, Vol. 81, 2009, pp. 625-630

3.) E. Ozkumur, J. Needham, D. A. Bergstein, R. Gonzalez, M. Cabodi, J. Gershoni, B. B. Goldberg, and M. S. Ünlü, "Label-free and dynamic detection of biomolecular interactions for high-throughput microarray applications," Proceedings of the National Academy of Science, Vol. 105, 10 June 2008, pp. 7988-7992

2.) J. R. Dupuis, J. Needham, E. Ozkumur, D. A. Bergstein, B. B. Goldberg, J. R. Engel, D. L. Carlson, and M. S. Ünlü, "Hyperspectral Fourier transform spectrometer for reflection spectroscopy and spectral self-interference fluorescence microscopy," Applied Optics, Vol. 47, 20 March 2008, pp. 1223-1234

1.) D. A. Bergstein, E. Ozkumur, A. C. Wu, A. Yalcin, J. Needham, R. Irani, J. Gershoni, B. B. Goldberg, C. DeLisi, M. F. Ruane, and M. S. Ünlü, "Resonant Cavity Imaging: A Means Toward High-Throughput Label-Free Protein Detection," IEEE Journal of Selected Topics in Quantum Electronics, Vol. 14, No. 1, January/February 2008

Conference Papers

16.) R. Irani, E. Ozkumur, S. Ahn, A. Yalcin, M. S. Ünlü, and C. DeLisi, "Label-free, high-throughput DNA-protein interaction studies: Re-evaluating Eukaryotic Transcription.," Pittcon 2010, 4th March 2010

15.) G. G. Daaboul, R. S. Vedula, A. Reddington, E. Ozkumur, C. A. Lopez, J. H. Connor, H. Fawcett, and M. S. Ünlü, "LED-based spectral reflectance imaging biosensor for label-free high-throughput multi-analyte and single-pathogen detection ," SPIE Photonics West 2010 - BIOS, January/February 2010

14.) M. S. Ünlü, E. Ozkumur, C. A. Lopez, A. Yalcin, M. Chiari, S. Ahn, G. G. Daaboul, A. Reddington, M. R. Monroe, R. S. Vedula, and J. H. Connor, "Spectral reflectance imaging for a multiplexed, high-throughput, label-free, and dynamic biosensing platform: protein, DNA and virus detection," SPIE Photonics West 2010 - BIOS, No. Paper 7553-17 , 23-28 January 2010

13.) E. Ozkumur, A. Yalcin, M. Cretich, F. Damin, C. A. Lopez, D. A. Bergstein, B. B. Goldberg, M. Chiari, and M. S. Ünlü, "Optical Phase to Biological Mass Conversion for Label-free Interferometric Sensing Methods," Proceedings of IEEE Photonics Society 2009 Annual Meeting, October 2009

12.) E. Ozkumur, A. Yalcin, S. Ahn, B. B. Goldberg, M. Chiari, and M. S. Ünlü, "Spectral Reflectance Imaging Biosensor for high-throughput and label-free detection of biomolecular interactions," Proceedings of IEEE Photonics Society 2009 Annual Meeting, October 2009

11.) E. Ozkumur, A. Yalcin, M. Cretich, M. S. Ünlü, and M. Chiari, "Label-free, dynamic and quantitative measurement of biomolecular interactions," 23rd International Symposium on MicroScale Bioseparations (MSB) 2009, February 2009

10.) A. Yalcin, F. Damin, E. Ozkumur, G. di Carlo, L. Sola, M. S. Ünlü, and M. Chiari, "Nanoscale Determination of a Polymeric Coating for Microarray Applications," 23rd International Symposium on MicroScale Bioseparations (MSB) 2009, February 2009

9.) E. Ozkumur, A. Yalcin, F. Damin, B. B. Goldberg, M. Chiari, and M. S. Ünlü, "Label-free and dynamic measurement of biomolecular interactions for high-throughput diagnostics," Photonics West 2009 - BIOS, January 2009

8.) A. Yalcin, E. Ozkumur, B. B. Goldberg, and M. S. Ünlü, "High lateral resolution spectral self-interference fluorescence microscopy using annular apertures," Photonics West 2009 - BIOS, January 2009

7.) A. Yalcin, F. Damin, E. Ozkumur, G. di Carlo, B. B. Goldberg, M. Chiari, and M. S. Ünlü, "Nanoscale Determination of Conformation of a Polymeric Coating on Layered Surfaces," AVS 55th International Symposium and Exhibition, October 2008

6.) E. Ozkumur, J. Needham, D. A. Bergstein, B. B. Goldberg, and M. S. Ünlü, "Label-free real-time microarray imaging using spectral reflectivity information," Photonics West 2008 - BIOS, January 2008

5.) M. S. Ünlü, E. Ozkumur, J. Needham, D. A. Bergstein, B. B. Goldberg, A. Yalcin, P. S. Spuhler, R. Irani, and C. DeLisi, "Applications of Optical Resonance to Biological Imaging and Label-free Protein Microarrays (invited paper)," EMBC08, Vancouver, Canada, August 20-24, 2008, 2008

4.) E. Ozkumur, J. Needham, D. A. Bergstein, M. F. Ruane, B. B. Goldberg, and M. S. Ünlü, "Label-free and high-throughput screening of biomolecular interactions," Proceedings of CLEO/QELS 2008, 2008

3.) A. Yalcin, F. Damin, E. Ozkumur, G. di Carlo, B. B. Goldberg, M. S. Ünlü, and M. Chiari, "Characterization of A Polymeric Coating for Microarray Applications using Spectral Self-Interference Fluorescence Microscopy," Photonics West 2008 - BIOS, 2008

2.) A. Yalcin, F. Damin, E. Ozkumur, G. di Carlo, B. B. Goldberg, M. Chiari, and M. S. Ünlü, "Characterization of Swelling of A Polymeric Coating for DNA Microarray Applications Using Spectral Self-Interference Fluorescence Microscopy," Proceedings of IEEE Lasers and Electro-Optics Society 2007 Annual Meeting, October 2007

1.) E. Ozkumur, J. Needham, D. A. Bergstein, A. C. Wu, M. F. Ruane, B. B. Goldberg, and M. S. Ünlü, "Label-free microarray imaging using spectral reflectance information," 2007 BMES Annual Fall Meeting, September 2007

Theses

1.) E. Ozkumur, "Optical Interference Based Microarray Imaging for Label-Free Multi-Analyte Detection ," Ph.D. Dissertation, May 2009

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