Publications

The following publications have been authored by CVRG team members and are citing CVRG support:

2014:

  1. Bo Liu, Ravi K Madduri, Borja Sotomayor, Kyle Chard, Lukasz Lacinski, Utpal J Dave, Jianqiang Li, Chunchen Liu, Ian T Foster (2014) Cloud-based  Bioinformatics  Workflow  Platform  for  Large-scale  Next-generation  Sequencing  Analyses, J Biomed Inform. Jan 22. pii: S1532-0464(14)00007-0. doi: 10.1016/j.jbi.2014.01.005. [Epub ahead of print]

2013:

  1. Maheshwari K., Rodriguez A., Kelly D., Madduri R., Wozniak J. M., Wilde M., and Foster I. (2013) Extending the Galaxy portal with parallel and distributed execution capability. 4th International Workshop on Data-Intensive Computing in the Clouds (DataCloud at SC13)  |  Denver, Colorado  |  IEEE/ACM
  2. Madduri, Ravi K; Dave, Paul; Sulakhe, Dinanath; Lacinski, Lukasz; Liu, Bo; Foster, Ian T; (2013) Experiences in building a next-generation sequencing analysis service using galaxy, globus online and Amazon web services: Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery, 34, ACM
  3. Dinanath Sulakhe, Alex Rodriguez, Nick Prozorovsky, Nilesh Kavthekar, Amol Parikh, Lukasz Lacinski, Ravi Madduri, Utpal Dave, Ian Foster; Distributed tools deployment and management in multiple Galaxy workflow instances in Globus Genomics WORKS 2013 Workshop, Super Computing 2013
  4. Ketan Maheshwari, Alex Rodriguez, David Kelly, Ravi Madduri, Justin Wozniak, Michael Wilde and Ian Foster; (2013) Enabling Multi-task computation on Galaxy-based Gateways using Swift Science Gateways IEEE Workshop, Indianapolis
  5. Dinanath Sulakhe, Stephen Granite, Ravi K Madduri, Ian T Foster, Raimond Winslow; Integration of Globus Online with RSNA Clinical Trial Processor (CTP) for High-throughput Image Data Transfer: RSNA 2013
  6. Post AR, Kurc T, Cholleti S, Gao J, Lin X, Bornstein W, Cantrell D, Levine D, Hohmann S, Saltz JH. The Analytic Information Warehouse (AIW): a Platform for Analytics using Electronic Health Record Data. J Biomed Inform 2013;46(3):410-24
  7. Post AR, Kurc T, Rathod H, Agravat S, Mansour M, Torian W, Saltz JH. Semantic ETL into i2b2 with Eureka! AMIA Summits Transl Sci Proc 2013;203-207
  8. Brown J, Ahamad M, Ahmed M, Blough D, Kurc T, Post A, Saltz J. Redactable and Auditable Data Access for Bioinformatics Research. AMIA Summits Transl Sci Proc 2013;21-5
  9. Strauss, G. G., Mewton, N., Verrier, R., Nearing, B. D., Marchlinski, F. E., Killian, T., Moxley, J., Tereshcenko, L. G., Wu, K. C., Winslow, R. L., Cox, C., Spooner, P. M., and Lima, J. A. C. (2013) Screening entire health system ECG databases to identify patients with arrhythmogenic substrate at increased risk of death. Circ. Arrhythmia Electrophysiol. DOI: 10.1161/CIRCEP.113.000411
  10. Post AR, Kurc T, Willard R, Rathod H, Mansour M, Pai A, Torian W, Agravat S, Sturm S, Saltz JH. Temporal Abstraction-based Clinical Phenotyping with Eureka!. AMIA Annu Symp Proc 2013;1160-1169.

2012:

  1. Liu, Bo; Sotomayor, Borja; Madduri, Ravi; Chard, Kyle; Foster, Ian; Deploying Bioinformatics Workflows on Clouds with Galaxy and Globus Provision: High Performance Computing, Networking, Storage and Analysis (SCC), 2012 SC Companion:",1087-1095,2012,IEEE
  2. Ardekani, S., Jain. S., Corona-Villalobos, C. P., Abraham, T., Abraham, M. R., Simmerman, S., Wu, K. C., Winslow, R. L., Miller, M. I., and Younes, L. (2012) Shape Analysis of Hypertrophic and Hypertensive Cardiomyopathies Using MRI based 3D surface models of Left Ventricular Geometry, Mag. Res. Med., submitted
  3. Cholleti S, Post A, Gao J, Lin X, Bornstein W, Cantrell D, Saltz J. (2012) Leveraging derived data elements in data analytic models for understanding and predicting hospital readmissions. AMIA AnnuSymp Proc, pg 103-111.
  4. Kim M, Cobb J, Harrold MJ, Kurc T, Orso A, Saltz J, Post A, Malhotra K, Navathe S. (2012) Efficient regression testing of ontology-driven systems. ISSTA 2012 Proceedings of the 2012 International Symposium on Software Testing and Analysis,  July 15-20, Minneapolis, MN pg. 320 - 330.
  5. Vadakkumpadan, F., Trayanova, N., Younes, L., Wu, K. C. (2012) Left ventricular shape analysis for predicting sudden cardiac death risk, 34th Annual Conference of the IEEE-EMBS, San Diego, CA Aug 28 – Sept 1, pgs., 4067-4070
  6. 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, (2012) "Digital Pathology: Data Intensive Frontier in Medical Imaging" to appear in Proceedings of the IEEE, Apr.,2012;100(4):991-1003

2011:

  1. Saltz, J., 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., 2012 Jun;45(3):522-7. 
  2. B. Allen, J. Bresnahan, L. Childers, I. Foster, G. Kandaswamy, R. Kettimuthu, J.Kordas, M. Link, S. Martin, K. Pickett, and S. Tuecke (2011) Globus online: Radical simplification of data movement via SaaS, Preprint ANL/MCS-P1905-0611
  3. 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, pgs. 572, September 21, Stanford University.
  4. 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.
  5. 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): Standardized Reporting for Model Reproducibility, Interoperability, and Data Sharing. Prog. Biophys. Molec. Biol. 107(1), 4-10., 
  6. 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
  7. 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.
  8. 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, Lecture Notes in Computer Science, 2012, Volume 7085, Statistical Atlases and Computational Models of the Heart. Imaging and Modelling Challenges, Pages 234-243.
  9. 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”, IEEE Trans Biomed Eng. 2011 Dec;58(12):3469-74. doi: 10.1109/TBME.2011.2169256.
  10. 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.
  11. 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), Nov. 2011.
  12. 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.
  13. 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.

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. L. Cooper, J. Kong, D. Gutman, F. Wang, S. Cholleti, T. Pan, P. Widener, A. Sharma, T. Mikkelsen, A. Flanders, D. Rubin, E. V. Meir, T. Kurc, C. Moreno, D. Brat, J. Saltz. An Integrative Approach for In Silico Glioma Research. IEEE Transactions on Biomedical Engineering Letters, 2010 Oct;57(10):2617-21.

2009:

  1. 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.
  2. 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.
  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: Proc Int Symp High Perform Distrib Comput.177-186.
  4. Kumar, V.S., Kurc, T., Saltz, J., Abdullah, G., Kohn, S. R., Matarazzo, C. (2009) Architectural Implications for Spatial Object Association Algorithms. Int Symp Parallel & Distributed Processing 2009, pgs. 1-12. PMCID in process, NIHMSID # 436247
  5. 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
  6. 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, Int J High Perform Comput Appl. 2009 August 1; 23(3): 252. PMCID #PMC2811341, NIHMSID #16823.
  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.
  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, Mar. 2009, Pages S16-S39. PMID #19103297 PMCID #PMC2839904, NIHMSID 168261
  11. 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
  12. Younes, L., Arrate, F. and Miller, M.I., 2009. Evolutions equations in computational anatomy., NeuroImage. 45, S40-50.

2008:

  1. Teodoro, G., Tavares, T., Ferreira, R., Kurc, T., Meira, W., Guedes, D., Pan, T., Saltz, J. (2008) A run-time system for efficient execution of scientific workflows on distributed environments. Int. J. Parallel Program. 36(2): 250-266. PMCC3348585
  2. 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. International Conference for High Performance Computing, Networking, Storage and Analysis, 2008. SC 2008. IEEE Press. 
  3. Ma, Michael I. Miller Alain Trouvé and Laurent Younes (2008) Bayesian template estimation in computational anatomy, Neuroimage 42(1): 252. PMC2602958  
  4. 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
  5. 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 (Long Beach Calif). 2008 November; 41(11): 58–66
  6. 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
  7. 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.
  8. 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

Other Publications Citing R24 HL085343:

  1. Patel, R.S., Sun, Y. V., Hrtiala, J., Veledar, E., Su, S., Sher, S., Liu, Y. X., Rahman, A., Patel, R., Rab, S.T., Vaccarino, V., Zafari, A. M., Samady, H., Tang, W. H., Allayee, H., Hazen, S. L., Quyyumi, A. A. (2012) Association of a Genetic Risk Score with Prevalent and Incident Myocardial Infarction in Subjects Undergoing Coronary Angiography. Circ Cardiovasc Genet. 5(4): 441-449 PMID 22767652