Esin ÖZTÜRK IŞIK

Rank & Status: 

Assistant Professor

Director of Computational Imaging Laboratory

Biography: 

Esin Öztürk Işık has been conducting research in the field of magnetic resonance imaging (MRI). The main aim of her projects has been developing novel molecular magnetic resonance imaging techniques to allow for a better understanding of underlying biochemistry of diseases in order to improve patient health. The technical projects at her laboratory has focused on designing new algorithms for molecular MR imaging data acquisition, post-processing and quantitation, as well as biostatistical analysis. Her laboratory has also worked on developing computational methods based on machine learning for MR image analysis for understanding disease mechanisms. Another focus of technical projects has been developing novel quantitative molecular MR imaging methodologies for fast and accurate data acquisition and processing. She has worked on translating all the projects developed at her laboratory into the clinics in collaboration with the clinical investigators for the benefit of the patients. The projects she has proposed have focused on brain tumors, prostate cancer, and breast cancer, with the overarching goal of studying metabolism in various human systems.

Education: 
Ph.D. University of California at Berkeley and University of California at San Francisco. Joint Graduate Program in Bioengineering (August 2002–March 2007)
M.S. University of Alabama at Birmingham. Biomedical Engineering (September 1999-December 2001)
B.S. Middle East Technical University, Ankara, Turkey. Computer Engineering (September 1995-June 1999)

 

Experience: 

 

Research Positions

 

(September 2014-present) Assistant Professor. Biomedical Engineering Institute, Boğaziçi University.

•   Has worked on multimodality MR imaging of Parkinson disease at 3T.

•   Has worked on MR spectral editing methods for hepatic encephalopaty at 3T.

•   Instructor for the following classes:

•   BM641 “Magnetic Resonance Imaging”

•   BM590 “Magnetic Resonance Spectroscopic Imaging”

•   BM506 “Introduction to Biostatistical Methods for Research”

•   BM596 “Magnetic Resonance Image Reconstruction”

 

(December 2009-September 2014) Assistant Professor. Biomedical Engineering, Yeditepe University.

•Has worked on compressed sensing accelerated phosphorus MR spectroscopic imaging of brain tumors at 3T.

•Has worked on machine learning algorithms for classification of disease characteristics.

•Has developed T1 measurement and data acquisition methodologies for phosphorus MR spectroscopic imaging of the healthy human brain and brain tumors at 3T.

•Has worked on accurate data analysis methods for functional MRI data using FSL and SPM.

•Has developed fast T2 measurement and display techniques for human articular cartilage

•Has conducted research on simulation of brain metabolites using GAMMA MRS simulation package.

•Instructor for the following classes:

•BME 421 “Medical Imaging”

•BME 423  “ Biometry for Analytical Reasoning and Modeling”

•BME 444  “Magnetic Resonance Imaging”

•BME 412 “Magnetic Resonance Spectroscopic Imaging”

•BME 492 “ Engineering Thesis Project”

•BTEC 526 “Applications of Biostatistics for Research”

•EE 669 “Advanced Methods In Signal Processing: Medical Image Reconstruction”

 

(September 2009-September 2014) Part-time Instructor. Biomedical Engineering Institute, Bogazici University.

•Has taught BM599 “ Introduction to Biostatistics for Research” every Fall semester between 2009 and 2012, and in Spring 2014.

•Taught BM688 “Advanced MRI’ in Spring 2010

 

(March 2007-February 2009) Postdoctoral Fellow. Margaret Hart Surbeck Laboratory of Advanced Imaging, University of California at San Francisco.

•Implemented B1 mapping and transmit gain optimization for accurate spectroscopic imaging of human brain at 7T ultra high field MR systems.

•Implemented elliptical SENSE for high spatial resolution imaging of brain tumors at 7T MR systems.  

•Implemented lactate edited MR spectroscopic imaging of brain tumors based on elliptical SENSE at 3T imaging systems.

 

(August 2002-March 2007) Graduate Research Assistant. Margaret Hart Surbeck Laboratory of Advanced Imaging, University of California at San Francisco.

•Implemented fast data acquisition and reconstruction using conventional and elliptical SENSE and GRAPPA for imaging of brain tumors.  

•Implemented software to reduce the aliasing lipid peaks in MR spectra using parallel imaging techniques to increase the accuracy of spectral quantitation of brain tumors.

•Analyzed MR diffusion weighted, perfusion weighted and spectroscopic imaging to understand the anatomical and metabolic characteristics of Grade 3 and Grade 4 brain tumors.

•Studied the longitudinal effects of external beam radiation therapy in brain tumors utilizing MR diffusion weighted, perfusion weighted and spectroscopic imaging.

•Compared data reconstruction strategies in time domain and frequency domain for more accurate MR spectral quantitation of the prostate cancers.

 

(January 2002- August 2002) Junior Specialist. Department of Radiology, University of California at San Francisco.

•Acquired, processed and interpreted MR imaging and spectroscopic imaging data of brain tumor patients acquired on 1.5T GE Signa clinical scanner.

 

(September 1999 – December 2001) Graduate Research Assistant, Biomedical Engineering Department, University of Alabama at Birmingham

•Implemented and assessed the effects of regularization methods on MRI reconstruction problems.

•Implemented image reconstruction algorithms for a new fast single shot MRI technique in C and MATLAB.

•Implemented macros to integrate a reconstruction routine written in C into the ParaVision package of the Bruker MR systems.

 

 

Teaching

 

2003: Course assistant at University of California at San Francisco for UCSF/UC Berkeley Bioengineering 241, “Magnetic Resonance Spectroscopy”. Organized and led discussion sessions. Prepared and maintained the course website. (http://www.mrsc.ucsf.edu/~esin/Bioe241.html)

2003: Lecturer and course assistant at University of California at San Francisco for ‘Parallel Imaging Group Meeting’. Presented various prominent papers of the parallel imaging field.  Prepared and maintained the course website. (http://www.mrsc.ucsf.edu/~esin/Pimg.html)

2005: Lecturer and course assistant at University of California at San Francisco for UCSF/UC Berkeley Bioengineering 297, “Parallel Imaging Seminar”. Organized and led discussion sessions. Prepared and maintained the course website.  (http://www.mrsc.ucsf.edu/~esin/pimgseminar2005.htm)

2005: Lecturer at University of California at San Francisco for UCSF/UC Berkeley Bioengineering 297, “MR Pulse Sequences”.

2009 – 2012, 2014: Instructor at the Biomedical Engineering Institute of Bogazici University for BM 599, “Introduction to Biostatistical Methods for Research”

2010: Instructor at the Biomedical Engineering Institute of Bogazici University for BM 688, “Advanced MRI”

2010: Instructor at the Faculty of Engineering of Yeditepe University for ES106, “Technical Report Writing and Presentation Skills”

2010 - 2012: Instructor at the Biomedical Engineering department of Yeditepe University for BME 423, “Biometry for Analytical Reasoning and Modeling”

2010-2013: Instructor at the Biomedical Engineering Department of Yeditepe University for BME444, “Magnetic Resonance Imaging”

2010 - 2014: Instructor at the Biomedical Engineering department of Yeditepe University for BME 421, “Medical Imaging”

2010 - 2014: Instructor at the Biomedical Engineering Department of Yeditepe University for BME412, “Magnetic Resonance Spectroscopic Imaging”

2010 - 2014: Instructor and advisor at the Biomedical Engineering department of Yeditepe University for BME 492, “Engineering Project”

2011-2013: Instructor at the graduate level Biotechnology program of the Science Institute of Yeditepe University for BTEC 526, “Applications of Biostatistics for Research”

2013: Instructor at the graduate level Electrical and Electronics Engineering program of the Science Institute of Yeditepe University for EE669, “Advanced Methods In Signal Processing: Medical Image Reconstruction”

2015: Instructor at the Biomedical Engineering Institute of Bogazici University for BM 590, “Magnetic Resonance Spectroscopic Imaging”

2015: Instructor at the Biomedical Engineering Institute of Bogazici University for BM 506, “Introduction to Biostatistical Methods for Research”

2015-2016: Instructor at the Biomedical Engineering Institute of Bogazici University for BM 596, “Magnetic Resonance Image Reconstruction”

2015-2016: Instructor at the Biomedical Engineering Institute of Bogazici University for BM 641, “Magnetic Resonance Imaging Principles”

 

 

Reviewing Services

• The Scientific and Technological Research Council of Turkey (TUBITAK) (grant proposal review panelist)

• Magnetic Resonance in Medicine

• Journal of Magnetic Resonance Imaging

• Computer Methods an Programs in Biomedicine

• International Society of Magnetic Resonance in Medicine (ISMRM) Conference (2014)

• European Society of Magnetic Resonance in Medicine and Biology (ESMRMB)  Conference (2013)

• Electrical, Electronics and Computer Engineering Symposium (ELECO) (2010,2011,2012,2014)

• Biomedical Engineering Meeting (BIYOMUT) (2010, 2011, 2012, 2014)

• IEEE Signal Processing and Communication Applications Congress (SIU) (2012,2013, 2014)

• British Journal of Medicine and Medical Research (2013)

 

 

Guest Editorial Services

• Turkish Journal of Biology

• Turkish Journal of Electrical Engineering and Computer Sciences

 

Administrative Services

ERASMUS coordinator of the Biomedical Engineering Institute of Bogazici University (2014-present)

Summer internship coordinator of the Biomedical Engineering Institute of Bogazici University (2014-present)

• ERASMUS coordinator of the Biomedical Engineering department of Yeditepe University (2010-2014)

• MUDEK coordinator of the Biomedical Engineering department of Yeditepe University (2011-2014)

• Double major and minor program coordinator of the Biomedical Engineering department of Yeditepe University (2010-2014)

• Academic advisor at the Biomedical Engineering department of Yeditepe University (2010-2014)

 

Public Services

Board Member, Human Research and Ethics Committee, Yeditepe University (2012-2014)

 

Other Work Experience

 

Ada Engineering Inc., Ankara, Turkey, 1998

Engineering Summer Intern

•Participated in an automation project called KOBINET developed on Delphi platform.

•Specified user requirements, designed, and programmed company web pages using CGI Expert.

•Formed data exchange pathways between Microsoft SQL Server database and web pages.

•Integrated the CGI scripts into the Delphi program.

 

Turkish Air Force, Department of Automated Information Systems Ankara, Turkey, 1997

Engineering Summer Intern

•Participated in the automation of Air Museum in Istanbul project.

•Learned Delphi and UNIX.

•Organized Air Museum's database.

 

Skills

 

Pulse Programming: EPIC (GE, attended an in-house seminar series on EPIC programming held at UCSF), Paradise (Philips, attended Gyrotools Pulse Programming course on 13-17 September 2010 at ETH, Zurich)

 

Programming Languages: Delphi, UML, ANSI C, C++, GLUT, OpenGL, HTML, SQL, Assembly Language, Pascal, ML, Lisp, Prolog

 

Application Packages: MATLAB, ParaVision, Rational Rose, Front Page

 

Medical Imaging Systems: Experience with 1.5, 3, and 7 Tesla human MRI systems (GE), 3 Tesla human MRI system (Philips Achieva) and 4.1 Tesla Bruker MRI system

Research Areas: 

Magnetic resonance imaging; Magnetic resonance spectroscopic imaging; Parallel imaging; Arterial spin labeling; Diffusion tensor imaging; Functional magnetic resonance imaging; Biostatistics

 

Awards: 

•Bogazici University Academic Encouragement Award, 2014

•TUBITAK EU Project Submission Encouragement Award, 2010

•Educational Stipend Award, ISMRM conferences, 2004-2006

•High Field Workshop Trainee Award, 2007

•Educational Stipend Award, UC Systemwide Bioengineering Symposium, 2003-2006

•UCSF Graduate Division Earle C. Anthony Travel Award, University of California, SanFrancisco, 2006

•UCB Graduate Division Conference Travel Grant, University of California, Berkeley, 2006

Research Projects: 

‘Fast Phosphorus Magnetic Resonance Spectroscopic Imaging using Compressed Sensing for

Imaging Brain Tumors’. TUBITAK 3501 National Young Researchers Career Development

Program (CAREER), 2012-2014

 

‘Phosphorus MR Spectroscopic Imaging of Brain Tumors at 3T (31P_SPECTRA_3T)’.

Marie Curie International Reintegration Grant (IRG), 2010- 2014

 

‘Determination of Multimodality Magnetic Resonance Imaging Based Biomarkers for Mild Cognitive

Impairment in Parkinson Disease’, TUBITAK 1001 Research Projects, 2015- 2018

Publications: 

Ozturk-Isik E, Cha S, Chang SM, Berger MS, Nelson SJ. Lipid Unaliasing for MR Spectroscopic Imaging of Gliomas at 3T Utilizing Sensitivity Encoding (SENSE).  Magnetic Resonance in Medicine. 2006 May;55(5):1164-9.

Pels P, Ozturk-Isik E, Swanson M, Vanhamme L, Kurhanewicz J, Nelson SJ, Van Huffel S. Quantification of Prostate MRSI Data by Model-Based Time Domain Fitting and Frequency Domain Analysis. NMR in Biomedicine. 2006 Apr;19(2):88-97

Li  Y, Osorio J, Ozturk-Isik E, Chen A, Xu D, Crane J, VigneronDB, Nelson SJ. Considerations in applying 3-D PRESS H-1 brain MRSI with an eight-channel phased-array coil at 3T. Magnetic Resonance Imaging. 2006 Dec;24(10):1295-302.

Chen AP, Cunningham CH, Ozturk-Isik E, Xu D, Hurd RE, Kelly DAC, Pauly JM, Kurhanewicz J, Nelson SJ, Vigneron DB. High Speed 3T MR Spectroscopic Imaging of Prostate with Flyback Echo Planar Encoding. Journal of Magnetic Resonance Imaging. 2007 Jun;25(6):1288-92.

Osorio J, Ozturk-Isik E, Cha S, Chang SM, Berger MS, Nelson SJ. 3D 1H MRSI of Brain Tumors at 3.0 Tesla using an Eight-Channel Phased-Array Head Coil. Journal of Magnetic Resonance Imaging. 2007 Jul;26(1):23-30.

Ozturk E, Banerjee S, Majumdar S, Nelson SJ. Partially parallel MR spectroscopic imaging of gliomas at 3T. Proceedings of the IEEE EMBS Annual International Conference. 2006;1:493-6.

Banerjee S, Ozturk-Isik E, Nelson SJ, Majumdar S. Fast magnetic resonance spectroscopic imaging at 3 Tesla using autocalibrating parallel technique. Proceedings of the IEEE EMBS Annual International Conference. 2006;1:1866-9.

Ozturk-Isik E, Chen AP, Crane JC, Han ET, Xu D, Vigneron DB, Chang SM, Nelson SJ. 3D Sensitivity Encoded Ellipsoidal MR Spectroscopic Imaging of Gliomas at 3T. Magn Reson Imaging. 2009 Nov;27(9):1249-57.

Zierhut ML, Ozturk-Isik E , Chen AP, Vigneron DB, Nelson SJ. 1H Spectroscopic Imaging of Human Brainat 3T: Comparison of Fast 3D-MRSI Techniques. J Magn Reson Imaging. 2009 Sep;30(3):473-80.

 Banerjee S, Ozturk-Isik E, Nelson SJ, Majumdar S. Elliptical MRSI with GRAPPA for imaging brain tumors at 3 Tesla. Magn Reson Imaging. 2009 Dec;27(10):1319-25. 

Park I, Chen AP, Zierhut ML, Ozturk-Isik E, Vigneron DB, Nelson SJ. Implementation of 3 T Lactate-Edited 3D (1)H MR Spectroscopic Imaging with Flyback Echo-Planar Readout for Gliomas Patients. Ann Biomed Eng. 2011 Jan;39(1):193-204. Epub 2010 Jul 23.

Tropp J, Lupo JM, Chen A, Calderon P, McCunee D, Grafendorfer T, Ozturk-Isik E, Larson PEZ, Hu S, Yeng YF, Robbe F, Bokb R, Schulteh R, Xu D, Hurd R, Vigneron D, Nelson SJ. Multi-Channel Metabolic Imaging, with SENSE reconstruction, of Hyperpolarized [1-13C] Pyruvate in a Live Rat at 3.0 tesla on a Clinical MR Scanner. Journal of Magnetic Resonance. 2011 Jan;208(1):171-7.

Ozturk-Isik E, Pirzkall A, Lamborn K, Cha S, Chang SM, Nelson SJ. Spatial Characteristics of Newly Diagnosed Grade 3 Glioma Assessed by Magnetic Resonance Metabolic and Diffusion Tensor Imaging. Translational Oncology. 2012 Feb; 5(1):10-18.

Askin NC, Atis B, Ozturk-Isik E. Accelerated Phosphorus Magnetic Resonance Spectroscopic ImagingUsing Compressed Sensing. Proceedings of the IEEE EMBS Annual International Conference. 2012;1: 1106-9.

Li Y, Xu D, Ozturk-Isik E, Lupo JM, Chen AP, Vigneron DB, Nelson SJ. T1 and T2 Metabolite Relaxation Times in Normal Brain at 3T and 7T. Journal of Molecular Imaging Dynamics. 2012.S1:002.

Çıtak Er F, Firat Z, Kovanlikaya I, Ture U, Ozturk-Isik E.Multivariate Discriminant Analysis of Multiparametric Brain MRI to Differentiate High Grade and Low Grade Gliomas - A Computer-Aided Diagnosis Development Study. Proceedings of the IEEE BIBE Annual International Conference. 2013 Nov; 2013:1-5. doi: 10.1109/BIBE.2013.6701649.

Çıtak Er F, Vural M, Acar O, Esen T, Onay A, Ozturk-Isik E.Preliminary Results on Estimation of Final Gleason Score Using Discriminant Analysis on Preoperative Clinical Parameters and Multiparametric MRI Findings in Prostate Cancer. Proceedings of the International Conference on Applied Informatics for Health and Life Sciences. 2013:1.

Citak Er F, Hatay GH, Okeer E, Yildirim, M, Hakyemez B, Ozturk-Isik E. Classification of Phosphorus Magnetic Resonance Spectroscopic Imaging of Brain Tumors Using Support Vector Machine and Logistic Regression at 3T. Conf Proc IEEE Eng Med Biol Soc. 2014 Aug;2014:2392-5. doi: 10.1109/EMBC.2014.6944103.

 Cebeci H, Aydin O, Ozturk-Isik E, Gumus C, Inecikli F, Bekar A, Kocaeli H, Hakyemez B. Assesment of perfusion in glial tumors with arterial spin labeling; comparison with dynamic susceptibility contrast method. Eur J Radiol. 2014 Oct;83(10):1914-9. 

 Citak Er F, Vural M, Acar O, Esen T, Onay A, Ozturk-Isik E. Final Gleason Score Prediction Using Discriminant Analysis and Support Vector Machine Based on Preoperative Multiparametric MR Imaging of Prostate Cancer at 3T. Biomed Res Int. 2014;2014:690787. doi: 10.1155/2014/690787. Epub 2014 Dec 2.

Acar Ö, Ozturk-Isik E, Mut T, Sağlıcan Y, Onay A, Vural M, Musaoğlu A, Esen T. Comparison of the trifecta outcomes of robotic and open nephron-sparing surgeries performed in the robotic era of a single institution. Springerplus. 2015; 4:472. doi: 10.1186/s40064-015-1274-2. eCollection 2015.

Phone Number: 

+90 216 516 3463

E-Mail: 
esin.ozturk@boun.edu.tr
Courses: 

BM 506, “Introduction to Biostatistical Methods for Research”

BM 596, “Magnetic Resonance Image Reconstruction”

BM 590, “Magnetic Resonance Spectroscopic Imaging”

BM 641, “Magnetic Resonance Imaging Principles”