Mustafa Mir

Posted on March 27, 2011 by admin

If you have any questions please contact me at: mmir2 at illinois dot edu

I am currently a Ph.D. candidate at the University of Illinois at Urbana-Champaign and am seeking a post-doctoral research position in a highly interdisciplinary environment to design new instrumentation and analysis tools to study fundamental problems in the areas of biophysics and bioengineering. My graduate research has focused on using novel optical and analytical methods to answer pressing biological questions and has had major impact in the areas of blood screening, cell growth measurements, measuring sub-cellular structure and analyzing organization in developing neural cultures. I have presented my work through a variety of peer-reviewed journals and at various conferences and technical forums and have received two departmental awards in recognition of this work. In addition I have mentored several successful students and volunteered my time to serve in several student leadership roles including organizing a successful seminar series. In the future I hope to continue and expand on my interdisciplinary research with collaborators in the areas of neuroscience, cell biology, microelectomechanical systems and theoretical biology.

RESEARCH EXPEREINCE_____________________________________________________                        

GRADUATE RESEARCH ASSISTANT      

Quantitative Light Imaging Laboratory, Beckman Institute for Advanced Science and Technology Advisor: Gabriel Popescu, University of Illinois, February 2008 – Present

  • Characterized fundamental properties of neural network formation.
  • Studied the effects of commonly used treatments on breast cancer growth at the single cell level.
  • Measured single cell, cycle dependent, mass growth with femtogram accuracy.
  • Studied metabolic response of E. coli and measured 3-D sub-cellular structure in a label-free manner.
  • Characterized differentiation process of neuronal progenitor cells to neurons.
  • Developed a micro-absorption spectroscopy technique that operates in conjunction with Spatial Light Interference microscopy to measure the hemoglobin concentration of single red blood cells.
  • Established quantitative phase imaging as a clinical blood screening tool including the first clinical verification, the development of a low cost and high throughput instrument utilizing commercial CD-ROM technology and a micro-absorption spectroscopy technique that operates measures the hemoglobin concentration of single cells.
  • Supervised the research of five undergraduate students.
  • Independently started three collaborations.
  • Participated in writing grant applications to NIH, NSF, Keck Foundation and Gates Foundation.

RESEARCH ASSISTANT

Nanobiooptics Laboratory, Beckman Institute for Advanced Science and Technology, Advisor: Gregory Timp

University of Illinois, September 2006 – January 2008

  • Developed a micro manufacturing technique, using optical tweezers, in conjunction with acoustic optical deflectors and spatial light modulators to manipulate micron scale particles and living cells into large arrays, held in place using synthetic hydrogel matrices.
  • Maintained bacterial cell cultures along with general maintenance and upkeep of all lab equipment.

AWARDS & HONORS_______________________________________________                _          

  • Ernest A. Reid Fellowship Award in Electrical Engineering, 2012.
  • Yuen T. Lo Outstanding Graduate Research Award in area of Electromagnetics, 2012.
  • Selected to represent Illinois Students at NSF site visit for EBICS STC, MIT, January 26th, 2012.
  • Publication of the week, Cell Observatory, University of Leiden, August 8th, 2011.
  • Best Poster Award, Bioengineering @ Illinois Day Graduate Student Poster Competition, 2011.
  • Honorable Mention, 1st International Symposium on Nanomedicine, Karachi, Pakistan, 2010.
  • Image of the Week, Beckman Institute, Imaging Technology Group, 2008.
  • Margaret Sanders Foundation, International Schools Scholarship, 2004.

PROFESSIONAL MEMBERSHIP______________________________________________      __                  

  • International Society for Optics and Photonics (SPIE),
  • Optical Society of America (OSA)

REFEREE FOR PEER REVIEWED JOURNALS_________________________________      _      

I have reviewed 10 papers over the last year.

  • Optics Express
  • Biomedical Optics Express
  • Journal of Biomedical Optics
  • IEEE Photonics Journal
  • Optics and Lasers in Engineering

TEACHING EXPERIENCE______           ___________________________                  

  • Lecturer at Biophotonics summer school, gave a one hour lecture on live cell imaging applications quantitative phase imaging, May 2012
  • Teachers Assistant for ECE 445 Senior Design Lab, managing several teams of senior undergraduate electrical engineering teams as they work on a wide range of challenging projects, Spring 2012
  • Lab instructor for Nanobiophotonics summer school, taught a lab session on interferometry and coherence to a professionally diverse group of graduate students, May 2011
  • Open House exhibit leader, setup an exhibit to teach K-12 students about the basics of the nature of light, inteferometry and phase imaging, March 201

MENTORING EXPERIENCE______           ___________________________                 

Supervised undergraduates on various projects, guiding them through experiments, data analysis and writing and evaluating scientific papers.

  • Physics Sophomore, Ryan Tapping on neuron image analysis, 2012
  • ECE Sophomore, Mike Xiang on stem cell differentiation analysis, 2012
  • ECE Senior Anwen Jiang on cancer cell growth, 2010
  • BioE Senior Shamira Sridharan on S2 cell growth, 2010 (1 1st author
  • High School Graduate, Kirill Lagoutchev on image segmentation and analysis, 2010

LEADERSHIP AND SERVICE_____________________________________                             

  • Member NSF-STC EBICS Student Leadership Council, provides guidance regarding student programs and activities within the EBICS STC.
  • Co-founder and organizer of iOptics, a weekly seminar series on optics and photonics, 2009-2011
  • President of Engineers Without Borders, UIUC Chapter. Oversaw 10 projects, 4 committees and headed a 12 member board who managed all chapter activities, 2007
  • Communications Officer, Engineers Without Borders, UIUC Chapter, published weekly electronic newsletter distributed to 900 people, archived and distributed documents and minutes, setup discussion forums on current issues in global development, 2005-2006
  • Project Leader, Maharashtra Electrification Project, Engineers Without Borders. Team designed inverters and charge controllers for pedal powered generators and photovoltaic panels installed in a village in India, 2004-2006

PRESS              ________________________________________________                         

•      “Stealthy Microscopy Method Visualizes E. coli Sub-cellular Structure in 3-D”, Beckman Institute News, June 28, 2012 (Published on over 2000 other sites as of September 2012)

•      “Microscopy technology sees sub-cellular in 3D”, Futurity.org, June 29, 2012 (Posted on over 100,000 other sites as of September 2012)

•      “Biomedical optics research breakthrough by Urban-Champaign scientists”, Biotechnology Calendar Inc., November 2, 2011

•           “Optically Measuring Single Cell Mass, Imaging & Microscopy, November 22, 2011

•      “Beckman researchers report on biomedical imaging advances, Beckman Institute News, November 1, 2011

•      “Spatial Light Interference Microscopy”, Imaging and Microscopy, August 29, 2011

•           “Publication of the week”, University of Leiden, Cell Observatory, August 8, 2011

•      “Optics used to track single cell’s growth”, Futurity.org, August 16, 2011(Posted on over 100,000 other sites as of September 2012)

•      “New imaging method sheds light on cell growth”, Univ. of Illinois News Bureau, August 25, 2011 (Published on over 100,000 other sites as of September 2012).

•      “Microscopy mixes it up”, Advanced Imaging Magazine, June10, 2011

•           “Imagining Life Through the Eyes of Technology”, Beckman Institute News, March 17, 2010

•           “The Cell Whisperers”, Beckman Institute News, January 4, 2010

TALKS / PRESENTATIONS__________  _____________________________________________                

  1. M. Mir , A. Majumder,  S. Sridharan, R. Wang, Z. Shen, C. Liu, S. Prasanth, M. Gillette, S. Stice and G. Popescu, “Label Free quantification of cellular behavior”, NSF-STC: Emergent Behaviors of Integrated Cellular Systems, 2nd Annual Retreat, Urbana, IL, USA, June 24-27, 2012
  2. C. Liu, M. Mir , G. Popescu and M. Gillette “Characterizing the development of neuron clusters”, NSF-STC: Emergent Behaviors of Integrated Cellular Systems, 2nd Annual Retreat, Urbana, IL, USA, June 24-27, 2012
  3. M. Mir, “Quantitative phase imaging: live cell applications”, 4th Biophotonics Summer School, Urbana, IL, USA, May 28th, 2012 (invited).
  4. M. Mir, “Imaging cellular systems using quantitative light microscopy”, EBICS STC NSF Site Visit, Cambridge, MA, USA, January 26, 2012
  5. M. Mir, “Imaging cellular systems using quantitative light microscopy”, EBICS Multi-Institutional Trainee Research Symposium, Online, November 14, 2011.
  6. M. Mir , Z. Wang, Z. Shen, M. Bednarz, I. Golding, S. Prasanth and G. Popescu, “Quantitative Phase Microscopy for Cell Dry Mass Measurements”, NSF-STC: Emergent Behaviors of Integrated Cellular Systems, 1st Annual Retreat, Atlanta, GA, USA, June 26-28, 2011 (Invited).

PUBLICATIONS____________________________________________________________            

As of September 2012 my papers have been cited a total of 169 times, h-index=7, i-10 index=6.

BOOK CHAPTERS

  1. M. Mir, B. Bhaduri, R. Wang, R. Zhu and G. Popescu, “Quantitative Phase Imaging”, Progress in Optics, Chennai: B.V.; (2012), pp. 133-217. (invited)

JOURNAL PUBLICATIONS

  1. M. Mir, A. Bergamaschi, B.S. Katzenellenbogen and G. Popescu, “Effects of estrogen, ICI and tomaxifen on breast cancer growth at the single cell level”, (to be submitted)
  2. M. Mir, A. Majumder, M. Xiang, R. Wang, S. C. Liu, M. U. Gillette, S. Stice and G. Popescu, “Emergent properties of a forming neural network”, Proc. Natl. Acad. Sci., (under review)
  3. R. Wang, T. W. Kim, M. Mir, K. and G. Popescu, “Optical measurement of nanoscale fluctuations in droplets”, Appl. Opt., (under review)
  4. M. Mir, M. Bednarz, D. Babacan, I. Golding and G. Popescu, “Three Dimensional Deconvolution Spatial Light Interference Microscopy for studying Subcellular Structure in E. coli ”, PLoS ONE, 7 (6), e38916 (2012)
  5. B. Bhaduri, H. Pham, M. Mir, and G. Popescu, “Diffraction Phase Microscopy with White Light”, Opt. Lett., 37 (6), (2012): 1094-1096 (In top downloads, March, 2012)
  6. M. Mir, K. Tangella and G. Popescu, “Blood Testing at the Single Cell Level using Quantitative Phase and Amplitude Microscopy”, Biomed. Opt. Exp., 2 (12), (2011): 3259-3266. (In top downloads, November, 2011)
  7. S. Sridharan, M. Mir, and G. Popescu, “Simultaneous Optical Measurements of Cell Motility and Growth”, Biomed. Opt. Exp., 2 (10), (2011): 285-2820
  8. J. Lim, H. Ding, M. Mir, R. Zhu, K. Tangella and G. Popescu, “Born Approximation Model Light Scattering by Red Blood Cells”, Biomed. Opt. Exp., 2 (10), (2011): 2784-2791
  9. M. Mir, Z. Wang, Z. Shen, M. Bednarz, R. Bashir, I. Golding and G. Popescu , “Optical Measurement of Cell Cycle Dependent Growth”, Proc. Nat. Acad. Sci., 108 (32), (2011): 13124-13129
  10. R. Wang, H. Ding, M. Mir, K. Tangella and G. Popescu, “Effective 3D Viscoelasticity of Red Blood Cells Measured by Diffraction Phase Microscopy”, J. Biomed. Opt., 2 (3), (2011): 485-490
  11. Z. Wang, L. Millet, M. Mir, H. Ding, S. Unarunotai, J. Rogers, M. Gillette, and G. Popescu, “Spatial Light Interference Microscopy”, Optics Express, 19 (2), (2011): 1016-1026
  12. M. Mir, H. Ding, Z. Wang, J. Reedy, K. Tangella and G. Popescu, “Blood Screening using Diffraction Phase Cytometry”, J. Biomed. Opt, 15 (2), (2010): 027016
  13. M. Mir, Z. Wang, K. Tangella and G. Popescu, “Diffraction Phase Cytometry: Blood on a CD-ROM”, Optics Express, 17 (4), (2009): 2579-2585
  14. U. Mirsaidov, J. Scrimgeour, W. Timp, K. Beck, M. Mir, P. Matsudaira and G. Timp, “Live Cell Lithography: Using Optical Tweezers to Create Synthetic Tissue”, Lab Chip, 8 (12), (2008): 2174-2181
  15. U. Mirsaidov, W. Timp, K. Timp, M. Mir, P. Matsudaira and G. Timp, “Optimal Optical Trap for Bacterial Viability”, Phys. Rev. E, 78 (2), (2008): 021910

CONFERENCES

  1. M. Mir, K. Tangella, and G. Popescu, “Measurement of single erythrocyte morphology and hemoglobin concentration”, Imaging at Illinois: The Next Generation, Urbana, IL, USA, June 1st, 2012
  2. M. Mir, S. D. Babacan, M. Bednarz, M. Do, I. Golding and G. Popescu “Imaging sub-cellular structures using three-dimensional sparse deconvolution SLIM”, OSA Topical Meeting of Biomedical Optics (BIOMED), Miami, FL, USA, April 30, 2012
  3. M. Mir , K. Tangella, and G. Popescu, “Simultaneous quantitative phase and Soret band absorption microscopy for comprehensive blood screening”, Engineering Conferences International, Advances in Optics for Biotechnology, Medicine and Surgery XII,  Naples, FL, USA, June 5-8, 2011
  4. M. Mir, K. Tangella, and G. Popescu, “Measurement of single erythrocyte oxygenation state, morphology and hemoglobin concentration”, College of American Pathologists Conference, Grapevine, TX, USA, September 11-14, 2011
  5. Z. Wang, D. Marks, S. Carney, M. Mir and G. Popescu, “Tomographic Reconstruction by Quantitative Phase Imaging with Broadband Fields”, OSA Optics and Photonics Congress, Monterey, CA, USA, April 4-6, 2011
  6. M. Mir , Z. Wang, M. Bednarz and G. Popescu, “Multiscale Optical Measurements of Bacterial Growth”, Photonic West, San Jose, CA, USA, January 21-27, 2011
  7. M. Mir , H. Ding, K. Tangella and G. Popescu, “Comprehensive blood screening using quantitative phase imaging”, Photonic West, San Jose, CA, USA, January 21-27, 2011
  8. M. Mir , H. Ding, K. Tangella and G. Popescu, “Blood Screening Using Diffraction Phase Cytometry”, 1st International Symposium on Nanomedicine, Karachi, Pakistan, December 20-22, 2010
  9. M. Mir, Z. Wang, S. Sridharan, A. Jiang, Z. Shen, M. Bednarz, B. Blehm, E. Chaney, X. Liang, S. Boppart, I. Golding, P. Selvin, S. Prasanth, and G. Popescu, “Quantitative optical measurements of cell dry mass as a tool for studying cell growth”, Annual Meeting of Strategic Initiative on Imaging, Urbana, IL, USA, October 14-15, 2010
  10. M. Mir , H. Ding, K. Tangella and G. Popescu, “Blood Screening Using Diffraction Phase Cytometry”, OSA Topical Meeting of Biomedical Optics (BIOMED), Miami, FL, USA, April 11-14, 2010
  11. M. Mir,  R. Wang, H. Ding, K. Tangella and G. Popescu, “Morphology and Dynamics of Red Blood Cells”, Annual Meeting of Strategic Initiative on Imaging, Urbana, IL, USA, October 1-2, 2009