In Silico Science

Share Last Updated: June 28, 2012

Characterization of morphologic properties of glial neoplasms at the organ, tissue, cellular and sub-cellular scales using novel computer-based imaging algorithms may lead to a greater understanding of glioma types and their molecular foundations and clinical associations.  Using the TCGA image repository, we have developed methodologies, information models, tools, and analytic pipelines that make it feasible to systematically carry out large-scale comparative analyses of brain tumor histology and radiology by comparing imaging features with patient outcome and genomics, as presented in the following papers.


Conference and Journal Publications:

L. Cooper, D. Gutman, C. Chisolm, C. Appin, J. Kong, Y. Rong, T. Kurc, E. Van Meir, J. Saltz, C. Moreno, D. Brat. “The tumor microenvironment strongly impacts master transcriptional regulators and gene expression class of glioblastoma.” Am J Pathol., 180(5):2108-2119, May 2012. 

SM Cork, B Kaur, NS Devi, L Cooper, JH Saltz, EM Sandberg, S Kaluz, and EG Van Meir, “A proprotein convertase/MMP-14 proteolytic cascade releases a novel 40 kDa vasculostatin from tumor suppressor BAI1”, Oncogene, pp. 1-9, 2012.

Lee A.D. Cooper, Jung Kong, David A. Gutman, Fusheng Wang, Jingjing Gao, Christina Appin, Sharath Cholleti, Tony Pan, Ashish Sharma, Lisa Scarpace, Tom Mikkelsen, Tahsin Kurc, Carlos S. Moreno, Daniel J. Brat, Joel H. Saltz. "Integrated Morphologic Analysis for the Identification and Characterization of Disease Subtypes." Journal of the American Medical Informatics Association. Vol. 19, Issue 2. January 24, 2012.

Fusheng Wang, Tae W. Oh, Cristobal Vergara-Niedermayr, Tahsin Kurc, Joel Saltz, "Managing and Querying Whole Slide Images." In Proc. of SPIE Medical Imaging. San Diego, California, USA. Feb 4-9, 2012.

Fusheng Wang, Jun Kong, Lee Cooper, Tony Pan, Tahsin Kurc, Wenjin Chen, Ashish Sharma, Cristobal Niedermayr, Tae W. Oh, Daniel Brat, Alton B. Farris, David Foran, Joel Saltz, “A Data Model and Database for High-resolution Pathology Analytical Image Informatics,” Journal of Pathology Informatics, Vol. 2, Issue 1, pp. 32-40, 2011.

Lee A.D. Cooper, Alexis B. Carter, Alton B. Farris, Fusheng Wang, Jun Kong, David A. Gutman, Patrick Widener, Tony Pan, Sharath Cholleti, Ashish Sharma, Tahsin Kurc, Daniel J. Brat, Joel H. Saltz, "Digital Pathology: Data Intensive Frontier in Medical Imaging" to appear in IEEE Special Bicentennial Issue on Audiovisual Frontiers, 2012.

F. Wang, R. Lee, X. Zhang and J. Saltz, “Towards Building High Performance Medical Image Management System for Clinical Trials”, In Proc. of SPIE Medical Imaging, Orland, Florida, USA, Feb 12-17, 2011.

Lee Cooper, Jun Kong, David Gutman, Fusheng Wang, Sharath Cholleti, Tony Pan, Patrick Widener, Ashish Sharma, Tom Mikkelsen, Adam Flanders, Daniel Rubin, Erwin Van Meir, Tahsin Kurc, Carlos Moreno, Daniel Brat, Joel Saltz, “An Integrative Approach for In Silico Glioma Research”, IEEE Transactions on Biomedical Engineering, Vol. 57, No. 10, pp. 2617-2621, October 2010.

Cooper LA, Gutman DA, Long Q, Johnson BA, Cholleti SR, Kurc T, Saltz JH, Brat DJ, Moreno CS., “The proneural molecular signature is enriched in oligodendrogliomas and predicts improved survival among diffuse gliomas.“, PLoS One., 2010 Sep 3;5(9):e12548.

Jun Kong, Lee A.D. Cooper, Fusheng Wang, David A. Gutman, Jingjing Gao, Candace Chisolm, Ashish Sharma, Tony C. Pan, Erwin G. Van Meir, Tahsin M. Kurc, Carlos S. Moreno, Joel H. Saltz and Daniel J. Brat, “Integrative, Multi-modal Analysis of Glioblastoma Using TCGA Molecular Data, Pathology Images and Clinical Outcomes”, Special Issue of IEEE Transactions on Biomedical Engineering LETTERS on Multi-scale Modeling and Analysis for Computational Biology and Medicine, 2011.

Sharath Cholleti, Lee Cooper, Jun Kong, Candace Chisolm, Daniel Brat, Joel Saltz, “Region Classification of Brain Tumor Pathology Images,” International Conference on Tools with Artificial Intelligence, Boca Raton, FL, November, 2011.

Fusheng Wang, Jun Kong, Jingjing Gao, Cristobal Vergara-Niedermayr, David Adler, Lee Cooper, Weian Chen, Tahsin Kurc, Joel Saltz, “High Performance Analytical Pathology Imaging Database for Algorithm Evaluation”, Workshop on High Performance and Distributed Computing for Medical Imaging HP-MICCAI/MICCAI-DCI, Toronto, Canada, September, 2011.


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