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Publications

A. Publications By CVRG Team Members Citing CVRG Support - 2011:

  1. Steinert-Threlkeld, S., Ardekani, S., Shaw, M., Detwiler, L.,Kikinis, R., Winslow, R. L., Miller, M. I., Ratnanather, J. T. (2011). Ontological labels for automated location of left ventricular remodeling. J. Biomed. Inf., submitted.
  2. Ardekani, S., Jain, A., Jain, S., Abraham, T. P., Abraham, M. R., Zimmerman, S., Winslow, R. L., Miller, M. I., Younes, L. (2011) Matching sparse sets of cardiac image cross-sections using large deformation diffeomorphic metric mapping, 14th International Conferences on Medical Image Computing and Computer Assisted Intervention (MICCIA) 2011, in press.
  3. J. Kong, L. Cooper, F. Wang, D. Gutman, J. Gao, C. Chisolm, A. Sharma, T. Pan, E. Van Meir, T. Kurc, C. Moreno, J. Saltz and D. 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, in press, 2011.
  4. Steinert-Threlkeld, S., Ardekani, S., Mejinoz, J. L. V., Detwilerz, L. T., Brinkley, J. F., Halle, M., Kikinis, R., Winslow, R. L., Miller, M. I., Ratnanather, J. T. (2011). Ontological Labels for Automated Location of Left Ventricular Remodeling. Proc. IEEE Intern. Conf. Semantic Computing, September 21, Stanford University, in press.
  5. Pearson, G. D., Tennstedt, S., Winslow, R. L., Keller, M. A., Fernandez, A. T., (2011) The Pediatric Heart Network Portal – A Collaboration of Pediatric Heart Centers, Academia, Government and Industry to Improve Image Workflow for Pediatric Cardiac Multi-site Studies. Proc. AMIA 2011 Annual Symposium, Washington DC, Oct. 22-26.
  6. Quinn TA, Bollensdorff C, Bub G, Burton RAB, Earm YE, Fink M, Hunter PJ, Garny A, Granite S, Hannes T, Lord P, McCulloch AD, Mirams GR, Noble D, Rosenbaum DS, Trayanova NA, Ravens U, Wang K, Winslow RL, Kohl P (2011). Minimum information about a cardiac electrophysiology experiment (MICEE): Standardised reporting for model reproducibility, interoperability, and data sharing, Progress in Biophysics and Molecular Biology (2011), doi:10.1016/j.pbiomolbio.2011.07.001
  7. Winslow, R. L., Saltz, J., Foster, I., Carr, J. J., Ge, Y., Miller, M. I, Younes, L., Geman, D., Graniote, S., Kurc, T., Madduri, R., Ratnanather, T., Larkin, J., Ardekani, S., Brown, T., Kolasny, A., Reynolds, K., Shipway, M., Toerper, M. (2011) The CardioVascular Research Grid (CVRG) Project, Proceedings of the AMIA Summit on Translational Bioinformatics 2011, pgs. 77-81
  8. L. Cooper, A. Carter, A. Farris, F. Wang, J. Kong, D. Gutman, P. Widener, T. Pan, S. Cholleti, A. Sharma, T. Kurc, D. Brat, J. Saltz, "Digital Pathology: Data Intensive Frontier in Medical Imaging" to appear in IEEE Special Bicentennial Issue on Audiovisual Frontiers, 2012.
  9. F. Wang, J. Kong, L. Cooper, T. Pan, T. Kurc, W. Chen, A. Sharma, C. Niedermayr, T. Oh, D. Brat, A. Farris, D. Foran, J. 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.
  10. A. Mohan, T. Kurc, A. Post, J. Saltz, D. Blough, Detection of Conflicts and Inconsistencies in Taxonomy-based Authorization Policies, IEEE International Conference on Bioinformatics & Biomedicine (BIBM), November 2011.
  11. L. Cooper, J. Kong, F. Wang, D. Gutman, S. Cholleti, T. Kurc, C. Moreno, D. Brat, J. Saltz, “In Silico Analysis of Diffuse Gliomas Identifies Microenvironmental Influence on Key Transcription Factors and Morphological Signatures of Glioblastoma”, Pathology Informatics 2011, Pittsburgh, PA, September, 2011.
  12. F. Wang, J. Kong, J. Gao, C. Vergara-Niedermayr, D. Adler, L. Cooper, W. Chen, T. Kurc, J. 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.
  13. Foran, D.J., Yang, L., Chen, W., Hu, J., Goodell, L.A., Reiss, M., Wang, F., Kurc, T., Pan, T., Sharma, A. and Saltz, J.H., 2011. ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology, Journal of the American Medical Informatics Association. 18, 403-415.

B. Publications By CVRG Team Members Citing CVRG Support – 2010:

  1. Arrate, F., Ratnanather, J.T. and Younes, L., 2010. Diffeomorphic Active Contours, SIAM Journal on Imaging Sciences. 3, 176-198.
  2. Kumar, V.S., Kurc, T., Ratnakar, V., Kim, J., Mehta, G., Vahi, K., Nelson, Y.L., Sadayappan, P., Deelman, E., Gil, Y., Hall, M. and Saltz, J., 2010. Parameterized specification, configuration and execution of data-intensive scientific workflows, Cluster Computing. 13, 315-333.
  3. Wang, F., Pan, T., Sharma, A. and Saltz, J., 2010. Managing and Querying Image Annotation and Markup in XML., Proceedings of SPIE. 7628, 762805.
  4. Ardekani, S., Weiss, R.G., Lardo, A.C., George, R.T., Lima, J.A.C., Wu, K.C., Miller, M.I., Winslow, R.L. and Younes, L., 2009. Computational method for identifying and quantifying shape features of human left ventricular remodeling., Ann Biomed Eng. 37, 1043-1054.

C. Publications By CVRG Team Members Citing CVRG Support – 2009:

  1. Ardekani, S., Weiss, R.G., Lardo, A.C., Miller, M.I., Winslow, R.L. and Younes, L., 2009 Cardiac Motion Analysis in Ischemic and Non-Ischemic Cardiomyopathy Using Parallel Transport., Proceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging. 899.
  2. Kumar, V., Sadayappan, P., Mehta, G. and Vahi, K., 2009. An integrated framework for parameter-based optimization of scientific workflows, in: An integrated framework for parameter-based optimization of scientific workflows. City.
  3. Kumar, V.S., Sadayappan, P., Mehta, G., Vahi, K., Deelman, E., Ratnakar, V., Kim, J., Gil, Y., Hall, M., Kurc, T. and Saltz, J., 2009. An integrated framework for performance-based optimization of scientific workflows, in: An integrated framework for performance-based optimization of scientific workflows. ACM  Request Permissions, City.
  4. Narayanan S, Kurc T, Catalyurek U, Saltz J.(2009) Parallel Materialization of Large ABoxes. 24th Annual ACM Symposium on Applied Computing (SAC 2009), Proceedings of the 2009 ACM Symposium on Applied Computing. Honolulu. Hawaii, pgs 1257-1261
  5. Tahsin Kurc, Shannon Hastings, Vijay Kumar, Stephen Langella, Ashish Sharma, Tony Pan, Scott Oster, David Ervin, Justin Permar, Sivaramakrishnan Narayanan, Yolanda Gil, Ewa Deelman, Mary Hall, Joel Saltz (2009) HPC and Grid Computing for Integrative Biomedical Research, International Journal of High Performance Computing Applications, 23: 252. PMCID in process, NIHMSID #168239
  6. V. Kumar, T. Kurc, P. Sadayappan, G. Mehta, K. Vahi, E. Deelman, V. Ratnakar, J. Kim, Y. Gil, M. Hall, J. Saltz (2009) An Integrated Framework for Parameter-based Optimization of Scientific Workflows”, High Performance and Distributed Computing (HPDC 2009): Proceedings of the 18th ACM International Symposium on High Performance Distributed Computing, Munich, Germany, June 2009, pages 177-186. PMCID in process, NIHMSID #168242
  7. Kurc, T., Hastings, S., Kumar, V., Langella, S., Sharma, A., Pan, T., Oster, S., Ervin, D., Permar, J., Narayanan, S., Gil, Y., Deelman, E., Hall, M. and Saltz, J., 2009. HPC and Grid Computingfor Integrative Biomedical Research, The international Journal of High Performance Computing Applications. 23, 252.
  8. Granite, SJ and RL Winslow (2009), Utilizing NCBO Tools to Develop an Ontology: A new tool that leverages the NCBO BioPortal REST Services. (2009).Proceedings of the 11th International Protégé Conference - Amsterdam, Netherlands. June 23-26, 2009
  9. Ceritoglu, C., Oishi, K., Li, X., Chou, M.-C., Younes, L., Albert, M., Lyketsos, C., van Zijl, P.C.M., Miller, M.I. and Mori, S., 2009. Multi-contrast large deformation diffeomorphic metric mapping for diffusion tensor imaging., NeuroImage. 47, 618-627.
  10. Michael I. Miller, Anqi Qiu (2009), The emerging discipline of Computational Functional Anatomy, NeuroImage, Volume 45, Issue 1, Supplement 1, Mathematics in Brain Imaging, March 2009, Pages S16-S39. PMCID in process, NIHMSID 168261
  11. Younes, L., Arrate, F. and Miller, M.I., 2009. Evolutions equations in computational anatomy., NeuroImage. 45, S40-50.

D. Publications By CVRG Team Members Citing CVRG Support – 2008:

  1. Khanna, G., Catalyurek, U., Kurc, T., Kettimuthu, R., Sadayappan, P., Foster, I. and Saltz, J., 2008. Using overlays for efficient data transfer over shared wide-area networks, in: Editor (Ed.)^(Eds.), Book Using overlays for efficient data transfer over shared wide-area networks. IEEE Press, City.
  2. Ma, Michael I. Miller Alain Trouvé and Laurent Younes (2008) Bayesian template estimation in computational anatomy, Neuroimage 42(1): 252. PMC2602958  
  3. Saltz J, Oster S, Hastings S, Langella S, Ferreira R, Permar J, Sharma A, Ervin D, Pan T, Catalyurek U, Kurc T. (2008) Translational Research Design Templates, Grid Computing, and HPC. 22nd IEEE International Parallel & Distributed Processing Symposium (IPDPS'08), pgs.1-15
  4. Saltz, J., Kurc, T., Hastings, S., Langella, S., Oster, S., Ervin, D., Sharma, A., Pan, T., Gurcan, M., Permar, J., Ferreira, R., Payne, P., Catalyurek, U., Caserta, E., Leone, G., Ostrowski, M.C., Madduri, R., Foster, I., Madhavan, S., Buetow, K.H., Shanbhag, K. and Siegel, E., 2008. E-Science, caGrid, and Translational Biomedical Research, IEEE Computer. 41, 58-66.
  5. Langella S, Hastings S, Oster S, Pan T, Sharma A, Permar J, Ervin D, Cambazoglu BB, Kurc T, Saltz J. (2008) Sharing data and analytical resources securely in a biomedical research Grid environment. J Am Med Inform Assoc. 15(3): 363-373. PMC2409996
  6. Saltz, J., Oster, S., Hastings, S., Langella, S., Ferreira, R., Permar, J., Sharma, A., Ervin, D., Pan, T., Catalyurek, U. and Kurc, T., 2008. Translational Research Design Templates, Grid Computing, and HPC., International Parallel and Distributed Processing Symposium. IPDPS  2008, 1-15.
  7. Younes L, Qui A, Winslow RL, Miller MI. (2008) Transport of Relational Structures in Groups of Diffeomorphisms. J. Math. Imaging Vis. 32:41-56 PMC275669