Articles

DA Gutman, J Cobb, D Somanna, Y Park, F Wang, T Kurc, JH Saltz, DJ Brat, LAD Cooper, "Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data," Journal of the American Medical Informatics Association JAMIA, In Press [pubmed]

WC Rutledge, J Kong, J Gao, DA Gutman, LAD Cooper, C Apping, Y Park, L Scarpace, T Mikkelsen, ML Cohen, KD Aldape, RE McLendon, NL Lehman, CR Miller, MJ Schniederjan, CW Brennan, CS Moreno, JH Saltz, DJ Brat, "Tumor-infiltrating lymphocytes in glioblastoma are associated with specific genomic alterations and related to transcriptional class", Clinical Cancer Research, In Press [pubmed]

DA Gutman, LAD Cooper, SN Hwang, CA Holder, J Gao, TD Aurora, WD Dunn Jr, L Scarpace, T Mikkelsen, R Jain, M Wintermark, M Jilwan, P Raghavan, E Huang, RJ Clifford, P Mongkolwat, V Kleper, J Freymann, J Kirby, PO Zinn, CS Moreno, C Jaffe, R Colen, DL Rubin, JH Saltz, A Flanders, DJ Brat, "MR imaging predictors of molecular profile and survival: multi-institutional study of the TCGA glioblastoma data set", Radiology, 267(2), pp. 560-9, May 2013 [pubmed]

LAD Cooper, DA Gutman, C Chisolm, C Appin, J Kong, Y Rong, T Kurc, EG Van Meir, JH Saltz, CS Moreno, DJ Brat, "The Tumor Microenvironment Strongly Impacts Master Transcriptional Regulators and Gene Expression Class of Glioblastoma," The American Journal of Pathology, 180(5), pp. 2108-2129, May 2012 [pubmed]

LAD Cooper, AB Carter, AB Farris, F Wang, J Kong, DA Gutman, P Widener, TC Pan, SR Cholleti, A Sharma, T Kurc, DJ Brat, JH Saltz, "Digital Pathology: Data-Intensive Frontier in Medical Imaging," Proceedings of the IEEE, 100(4), pp. 991-1003, April 2012 [ieee]

LAD Cooper, J Kong, DA Gutman, F Wang, J Gao, C Appin, S Cholleti, T Pan, A Sharma, L Scarpace, T Mikkelsen, T Kurc, CS Moreno, DJ Brat, JH Saltz, "Integrated morphologic analysis for the identifcation and characterization of disease subtypes," Journal of the American Medical Informatics Association JAMIA, 19(2), pp. 317-323, March-April 2012 [pubmed]

SM Cork, B Kaur, NS Devi, LAD Cooper, JH Saltz, EM Sandberg, S Kaluz, EG Van Meir, "A proprotein convertase/MMP-14 proteolytic cascade releases a novel 40kDa vasculostatin from tumor suppressor BAI1," Oncogene, 31(50), pp. 5144-5152, February 2012 [pubmed]

LAD Cooper, DA Gutman, Q Long, BA Johnson, SR Cholleti, T Kurc, JH Saltz, DJ Brat, CS Moreno, "The Proneural Molecular Signature is Enriched in Oligodendrogliomas and Predicts Im- proved Survival among Diffuse Gliomas," PLoS ONE, 5(9), e12548. doi:10.1371/journal.pone.0012548, September 2010 [pubmed]

LAD Cooper, J Kong, DA Gutman, F Wang, SR Cholleti, T Pan, P Widener, A Sharma, T Mikkelsen, A Flanders, D Rubin, E Van Meir, T Kurc, C Moreno, DJ Brat, JH Saltz, "An Integrative Approach for In Silico Glioma Research," IEEE Transactions on Biomedical Engineering Letters, 57(10), pp.2617-21, October 2010 [pubmed]

K Mosaliganti, LAD Cooper, R Sharp, R Machiraju, G Leone, K Huang, JH Saltz, "Reconstruction of cellular biological structures from optical microscopy data," IEEE Transactions on Visualization and Computer Graphics, 14(4), pp.863-76, August 2008 [pubmed]

A Ruiz, M Ujaldon, LAD Cooper, K Huang, Non-rigid Registration for Large Set of Microscopic Images on Graphics Processors, Journal of Signal Processing Systems, 55(1), pp.229-50, 2009 [link]

LAD Cooper, O Sertel, J Kong, G Lozanski, K Huang, M Gurcan, "Feature-Based Registration of Histopathology Images with Different Stains: An Application for Computerized Follicular Lymphoma Prognosis," Computer Programs and Methods in Biomedicine, 96(3), pp.182-92, May 2009 [pubmed]

Proceedings

LAD Cooper, J Kong, F Wang, T Kurc, CS Moreno, DJ Brat, JH Saltz, Morhpological Signatures and Genomic Correlates in Glioblastoma, The 8th IEEE International Symposium on Biomedical Imaging, Chicago, IL, March 2011 [pubmed]

J Kong, LAD Cooper, F Wang, C Chisolm, CS Moreno, T Kurc, P Widener, DJ Brat, JH Saltz, A Comprehensive Framework for Classiffcation of Nuclei in Digital Microscopy Imaging: An Application to Diffuse Gliomas, The 8th IEEE International Symposium on Biomedical Imaging, Chicago, IL, March 2011 [pubmed]

LAD Cooper, JH Saltz, U Catalyurek, K Huang, Acceleration of Two Point Correlation Function Calculation for Pathology Image Segmentation, First International Conference on Healthcare Informatics, Imaging and Systems Biology (HISB), pp. 174-81, San Jose, CA, July 2011 [ieee]

LAD Cooper, JH Saltz, R Machiraju, K Huang, Two-Point Correlation as a Feature for Histology Images: Feature Space Structure and Correlation Updating, Mathematical Methods in Bioimage Analysis Workshop, 23rd IEEE Conference on Computer Vision and Pattern Recognition, pp.79-86, San Francisco, CA, June 2010 [ieee]

J Kong, LAD Cooper, A Sharma, T Kurc, DJ Brat, JH Saltz, Texture Based Image Recognition in Microscopy Images of Diffuse Gliomas with Multi-class Gentle Boosting Mechanism, The 35th International Conference on Acoustics, Speech, and Signal Processing (ICASSP), pp.457-60, Dallas, TX, March 2010 [ieee]

Abstracts

LAD Cooper, R Yacoub, DA Gutman, FWang, CS Moreno, DJ Brat, RM Bostick, JH Saltz, Quantitative imaging of protein expression using multiplex quantum dot immunohistochemistry, AACR 103rd Annual Meeting, March 31-April 4, 2012, Chicago, IL. [AACR]

LAD Cooper, CS Moreno, C Chisolm, C Appin, DA Gutman, J Kong, T Kurc, JH Saltz, DJ Brat, Integrated Analysis of Necrosis, Angiogenesis, and Gene Expression in Glioblastomas, American Association for Cancer Research (ACR-NCI) Conference on Systems Biology: Confronting the Complexity of Cancer, February 27-March 2, 2011, San Diego, CA.

CS Moreno, LAD Cooper, DA Gutman, C Chisolm, J Kong, SR Cholleti, T Kurc, JH Saltz, DJ Brat, MicroRNA Networks Associated with Necrosis in Glioblastomas, American Association for Cancer Research (ACR-NCI) Conference on Systems Biology: Confronting the Complexity of Cancer, February 27-March 2, 2011, San Diego, CA.

DJ Brat, DA Gutman, LAD Cooper, J Kong, C Chisolm, EG Van Meir, JH Saltz, CS Moreno, High Levels of Necrosis in Glioblastoma Samples are Associated with the Mesenchymal Gene Ex- pression Family and Characterized by Enhanced Expression of Master Transcriptional Regulators of the Mesenchymal Transition, The United States and Canadian Academy of Pathology 100th Annual Meeting, February 26-March 4, 2011, San Antonio, TX.

J Kong, LAD Cooper, C Chisolm, F Wang, CS Moreno, T Kurc, DJ Brat, JH Saltz, Computer- Based Classification of Nuclei in Gliomas, The United States and Canadian Academy of Pathology 100th Annual Meeting, February 26-March 4, 2011, San Antonio, TX.

LAD Cooper, J Kong, DA Gutman, F Wang, SR Cholleti, T Pan, P Widener, A Sharma, T Mikkelsen, A Flanders, D Rubin, EG Van Meir, T Kurc, CS Moreno, DJ Brat, JH Saltz, Integrative Analysis of Image and Molecular Data for Study of Brain Tumors, The NCI-NCRI Informatics Initiative Joint Conference: Biomedical Informatics without Borders: Implementing Interoperability, June 21-22, 2010, Bethesda, MD.

CS Moreno, LAD Cooper, SR Cholleti, D Gutman, T Kurc, DJ Brat, and JH Saltz, The TCGA proneural subtype predicts improved clinical outcome for low-grade oligodendrogliomas, AACR 101st Annual Meeting, April 17-21, 2010, Washington, DC.

CS Moreno, LAD Cooper, SR Cholleti, DJ Brat, T Kurc, JH Saltz, Gene expression analysis of low-grade gliomas that progress to GBM for predictive clustering and prognostic significance, The 7th Biennial Georgia Tech and Oak Ridge National Lab International Conference on Bioinformatics held on November 12-14, 2009, Atlanta, GA.

Book Chapters

LAD Cooper, K Huang, M Ujaldon, A Ruiz, Scalable Image Registration and 3D Reconstruction at Microscopic Resolution, Chapter 8 in High-Throughput Image Reconstruction and Analysis, Editors A. Ravishankar Rao, G.A. Cecchi, Artech House, 2009

K Huang, KR Mosaliganti, LAD Cooper, R Machiraju, G Leone, JH Saltz, Quantitative Phe- notyping Using Microscopic Images, Chapter 15 in Microscopic Image Analysis for Life Science Applications, Editors J. Rittscher, R. Machiraju, S. Wong, Artech House, 2008