Cemal Cagatay Bilgin

ccbilgin at lbl dot gov

PostDoctoral Fellow, Imaging and Informatics Group, Life Sciences Division Lawrence Berkeley National Lab Berkeley, CA, 94720.


I am a post-doctoral fellow in Life Science Division at Lawrence Berkeley National Laboratory working with Dr. Parvin. I received my PhD and MS degrees from the Computer Science department at RPI in 2011 and 2007 respectively under the supervision of Prof. Yener. Here is a link to my old website.

Research Interest

My research interests broadly include image analysis, computer aided tissue analysis and modeling, graph theory and machine learning.



  1. Cemal Cagatay Bilgin, Hang Chang, Bahram Parvin. "Integrated profiling of multicellular systems from 3D microscopy". Bioinformatics 2013.
  2. Bugra Caskurlu, Anish Gehani, Cemal Cagatay Bilgin, K Subramani. "Analytical Models for Intrusion Detection in Networks". Computer Networks 2013.
  3. Cemal Cagatay Bilgin, Shayoni Ray, William Daley, Banu Baydil, Bulent Yener, Melinda Larsen. "Multiscale Feature Analysis of Branching Morphogenesis". PLoS One, 2012.
  4. Cemal Cagatay Bilgin, Jens Rittscher, Bob Filkins, Ali Can. "Digitally Adjusting Chromogenic Dye Proportions in Pathology Images". Journal of Microscopy 2011.
  5. Cemal Cagatay Bilgin, Amanda Lund, Ali Can, George Plopper, Bulent Yener. "Modeling of 3D Stem-Cell Mediated Collagen Fibrillogenesis". PLoS ONE, 2010.
  6. Amanda Lund, Cemal Cagatay Bilgin, Mohammad Al Hasan, Lindsey McKeen, Jan Stegemann, Bulent Yener, Mohammad Zaki and George Plopper. "Quantification of Spatial Parameters in 3D Cellular Constructs Using Graph Theory". Journal of Biomedicine and Biotechnology, 2010.
  7. Cemal Cagatay Bilgin, Peter Bullough, George E. Plopper Bulent Yener. "ECM-Aware Cell-Graph Mining for Bone Tissue Modeling and Classification". Journal of Data Mining and Knowledge Discovery, 2010.
  8. Lindsey McKeen, Kira Henderson, Basak Oztan, Cemal Cagatay Bilgin, Bulent Yener, George Plopper. "Quantitative metric profiles capture three-dimensional temporo-spatial architecture to discriminate cellular functional states". BMC Medical Imaging, 2010.
  9. Mert Akdere, Cemal Cagatay Bilgin, Ozan Gerdaneri, Ibrahim Korpeoglu, Ozgur Ulusoy, Ugur Cetintemel. "A Comparison of Epidemic Algorithms in Wireless Sensor Networks", Elsevier Computer Communications, 2006.


  1. Ali Can, Cemal Cagatay Bilgin, Jens Rittscher, Bob Filkins. Methods and Systems for Digitally Enhancing an Image of a Stained Material.


  1. Cemal Cagatay Bilgin, Hang Chang, Bahram Parvin. "Segmentation and Morphometric Representation of Multicellular Systems from 3D Microscopy". IEEE ISBI , 2013, San Francisco, USA.
  2. Basak Oztan, Lindsey M. Polizzotti, Cemal Cagatay Bilgin, Kira M. Henderson, George E. Plopper, Bulent Yener. "Classification of Breast Cancer Grades through Quantitative Characterization of Ductal Structure Morphology in Three-Dimensional Cultures". ACM BCB , 2011, Chicago, USA.
  3. Cemal Cagatay Bilgin, Shayoni Ray, William Daley, Banu Baydil, Sharon Sequeira, Bulent Yener, Melinda Larsen. "Cell-Graph Modeling of Salivary Gland Morphology." IEEE ISBI , 2010, Rotterdam, Netherlands.
  4. Cemal Cagatay Bilgin, Cigdem Gunduz, Chandandeep Nagi, Bulent Yener. "Cell-Graph Mining for Breast Tissue Modelling and Classification". EMBS, France, 2007.
  5. Posters

  6. Cemal Cagatay Bilgin, Sun Kim, Hang Chang, Bahram Parvin. "Molecular basis of Morphogenesis in Multicellular Systems via High Content Screening". ASCB , 2012, San Francisco, USA.
  7. Y. Yui, R. Bainer, J. Lakins, S. Mumenthaler, P. Mallick, C.C. Bilgin, B. Parvin, V. Weaver. " Self-Assembling Peptide Gels Enable Comprehensive Phenotypic and Molecular Characterization of Cellular Responses to Extracellular Stiffness Cues in 3D". ASCB , 2012, San Francisco, USA.
  8. Cemal Cagatay Bilgin, Shayoni Ray, William Daley, Banu Baydil, Sharon Sequeira, Bulent Yener, Melinda Larsen. "Quantification of Changes in Salivary Gland Morphology Using Cell Graphs." AADR, Washington, USA, 2010.
  9. K. Henderson, Cemal Cagatay Bilgin, B. Yener, G. Plopper. "Signal Transduction Mediates the Remodeling of the Stem Cell Microenvironment (449 B396)." ASCB , 2009, San Diego, CA, USA.
  10. L. McKeen, Cemal Cagatay Bilgin, G. Plopper, B. Yener. "Investigation of Structure- Function Relationships of Breast Cancer's Metastatic Potential (2007 B386). " ASCB , 2009, San Diego, CA, USA.
  11. C. Aksay, A. Ayaz, O. Babur, C.C. Bilgin, A. Cetintas, et al "PATIKA: An Informatics Infrastructure for Cellular Networks. " ISMB , 2004, Glasgow, Scotland.