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Urska Cvek, ScD, MBA

Name: Dr. Urska Cvek

Title: Professor

Start Year at LSUS: 2004

Credentials: UMass Lowell ScD (2004) and MBA (1997)

Department: Computer Science Department

School: Mathematics and Sciences

College: Arts and Sciences

Office Location: Technology Center 215

Office Phone: 318-795-4266

Email: urska.cvek@lsus.edu

Teaching Assignments:

Formal Teaching - Undergraduate
CSC 115 Computer Literacy
CSC 135 Object Oriented Programming I
CSC 145 Object Oriented Programming II
CSC 242 Computer Architecture and Organization
CSC 345 Data Structures
CSC 346 Analysis of Algorithms
CSC 405 Programming Languages
CSC 466 Introduction to Bioinformatics
CSC 468 Introduction to Data Mining and Knowledge Discovery
CSC 490 An Introduction to Microbial Community Sequencing and Analysis (site coordinator)

Formal Teaching-Graduate
CSC 605 Programming Languages
CSC 666 Introduction to Bioinformatics
CSC 668 Introduction to Data Mining and Knowledge Discovery
CSC 690 An Introduction to Microbial Community Sequencing and Analysis (site coordinator)
BIOS690 An Introduction to Microbial Community Sequencing and Analysis (site coordinator)
CST 711 Informatics
CST 790 Introduction to Human-Computer Interaction

Research Interests:

I have always been interested in data presentation in insightful and novel ways. The focus of my research is informatics, data mining and information visualization and I have been involved in independent, collaborative and multidisciplinary research and teaching over the past 20 years. I work with multivariate and multidimensional complex data sets, their management, analysis, and data integration as well as algorithmic technique development. I have been initiating, planning and developing research projects with collaborators in multidisciplinary teams that have resulted in grant-funded proposals and publications and include supervision of undergraduate and graduate students in the Laboratory for Advanced Biomedical Informatics (LABi) that I co-direct.

Selected Publications:

Refereed Journals and Refereed Proceedings Since 2013

Pharmacoproteomics Profile in Response to Acamprosate Treatment of an Alcoholism Animal Model. C.E. Germany, A.N. Reker, D.J. Hinton, A. Oliveros, X. Shen, L.G. Andres-Beck, K.M. Wininger, M. Trutschl, U. Cvek, D.-S. Choi, and H.W. Nam. Proteomics, 1700417. doi:10.1002/pmic.201700417.

Two Year Follow-up of Crohn's patients substituted to Certolizumab anti-TNFa therapy: SAVANT 2. A. Motlis, M. Boktor, P. Jordan, U. Cvek, M. Trutschl, J.S. Alexander. Pathophysiology; 2017 Aug 9. pii: S0928-4680(17)30051-2. doi: 10.1016/j.pathophys.2017.07.004.

Substitution with AlternatiVe Anti-TNFa Therapy (SaVANT) - Outcomes of a Crohn's Disease Cohort Undergoing Substitution Therapy with Certolizumab. M. Boktor, A. Motlis, A. Aravantagi, A. Sheth, P. Jordan, J. Morris, K. Manas, U. Cvek, M. Trutschl, J.S. Alexander. Inflammatory Bowel Diseases (LWW Journal) 2016 Jun; 22(6):1353-61. doi: 10.1097/MIB.0000000000000765.

Gastric cancer in women: A regional health-center seven year retrospective study. K. Suryawala, D. Soliman, M. Mutyala, S. Nageeb, M. Boktor, A. Seth, A. Aravantagi, A. Sheth, J. Morris, P. Jordan, K. Manas, U. Cvek, M. Trutschl, F. Becker, and J.S. Alexander. World Journal of Gastroenterology: WJG. 2015; 21(25): 7805-7813, doi:10.3748/wjg.v21.i25.7805.

Blood circulating microparticle species in relapsing-remitting and secondary progressive multiple sclerosis. J.S. Alexander, R. Chervenak, B. Weinstock-Guttman, I. Tsunoda, M. Ramanathan, N. Martinez, S. Omura, F. Sato, G.V. Chaitanya, A. Minagar, J. McGee, M.H. Jennings, C. Monceaux, F. Becker, U. Cvek, M. Trutschl, R. Zivadinov. A case-control, cross sectional study with conventional MRI and advanced iron content imaging outcomes. J. Neurological Sciences (2015), 355(1): 84-89.

Both MC1 and MC3 Receptors Provide Protection From Cerebral Ischemia-Reperfusion-Induced Neutrophil Recruitment. P.M. Holloway, P.F. Durrenberger, M. Trutschl, U. Cvek, D. Cooper, A.W. Orr, M. Perretti, S.J. Getting, F. N.E. Gavins. Arteriosclerosis Thrombosis and Vascular Biolology, June 25, 2015, doi:10.1161/ATVBAHA.115.305348.

MotifMutator: A Combinatoric Tool for Modeling Binding-Site Preferences, P.C.S.R. Kilgore, U. Cvek, M. Trutschl, B. Praslicka, C. Gissendanner. 7th Int. Conf. on Bioinformatics and Computational Biology (BICoB), March 2015.

Detection and Employment of Biological Sequence Motifs. M. Trutschl, P.C.S.R., Kilgore, R. Scott, C.E. Birdwell, U. Cvek. Big Data Analytics in Bioinformatics and Healthcare. B. Wang, R. Li, and W. Perrizo (Editors). IGI Global, 2015.

Computational Multivariate Analysis for Phase-Specific Biomarker Identification in Novel in Vivo and in Vitro Viral Myocarditis Models Induced by Cardiovirus. F. Shafiei, S. Omura, E. Kawai E, F. Sato, N.E. Martinez, V. Fernando, L. Morris, J.S. Alexander, U. Cvek, M. Trutschl, I. Tsunoda. J Am Coll Cardiol. 2014;63(12_S):. doi:10.1016/S0735-1097(14)60971-2.

Bioinformatics Multivariate Analysis Determined a Set of Phase-Specific Biomarker Candidates in a Novel Mouse Model for Viral Myocarditis. S. Omura, E. Kawai, F. Sato, N.E. Martinez, G.V. Chaitanya, P.A. Rollyson, U.Cvek, M. Trutschl, J.S. Alexander, I. Tsunoda. Circulation: Cardiovascular Genetics (2014) 7: 444-454.

Genome-wide DNA methylation as an epigenetic consequence of Epstein-Barr virus infection of immortalized keratinocytes. C.E. Birdwell, K.J. Queen, P. Kilgore, P. Rollyson, M. Trutschl, U. Cvek, R.S. Scott. Journal of virology (2014): JVI-00972.

Scalable Genome-Wide Discovery and Presentation of Motifs. M. Trutschl, P. Kilgore, U. Cvek, R. Scott. 6th Int. Conf. on Bioinformatics and Computational Biology (BICoB), March 2014.

Panoramic Interaction with Interval Data Based on the Slider Metaphor. P. Kilgore, M. Trutschl, U. Cvek. 7th Int. Conf. on Advances in Computer-Human Interaction, March 2014.

Self-organization in parallel coordinates. M. Trutschl, P.C.S.R. Kilgore, U. Cvek. 23rd International Conference on Artificial Neural Networks, Sofia, Bulgaria, September 2013.

Parallel execution of self-organized visualization. P.C.S.R. Kilgore, M. Trutschl, U. Cvek. Proc. of Modeling, Identification and Control - Advances in Computer Science Conference, DOI: 10.2316/P.2013.801-009, 2013.

Epstein-Barr virus induced epigenetic alterations following transient infection. K.J. Queen, M. Shi, F. Zhang, U. Cvek, R.S. Scott. Int. J. Cancer, May 1, 2013; 132(9):2076-86, doi: 10.1002/ijc.27893.

Exploration of Gene Expression Data Via Constrained Clustering, P. Kilgore, M. Trutschl, U. Cvek, R. Rhoads. 5th Int. Conf. on Bioinformatics and Computational Biology (BICoB), March 2013.

Book Chapters

Detection and Employment of Biological Sequence Motifs. M. Trutschl, P.C. Kilgore, R.S. Scott, C.E. Birdwell, U. Cvek. In B. Wang, R. Li, & W. Perrizo (Eds.) Big Data Analytics in Bioinformatics and Healthcare (pp. 86-116). Hershey, PA: Medical Information Science Reference. doi:10.4018/978-1-4666-6611-5.ch005 (2015).

Multidimensional Visualization of Microarray Data (Chapter). U. Cvek, M. Trutschl. Microarray Image and Data Analysis: Theory and Practice, Cat/ISBN: K20311/9781466586826, Edited by L. Rueda, CRC Press, March 2014.

Neural-network enhanced visualization of high-dimensional data. U. Cvek, M. Trutschl, J.L. Clifford. In: Self-Organizing Maps. ISBM 978-953-7619, 2009.

Personal Bio:

Urska Cvek, ScD, MBA is a computer scientist specializing in the design and application of data analytics and information visualization techniques. With more than twenty years of experience she brings unique multidisicplinary expertise and insight and has taken leadership roles in several large-scale projects. She is currently Professor of Computer Science and Lisa Burke Endowed Bioinformatics Professor at LSU Shreveport where she co-directs the Laboratory for Advanced Biomedical Informatics. She helped build bioinformatics skills and expertise in Shreveport/Bossier City and north Louisiana. She is Clinical Assistant Professor in the Department of Medicine at LSU Health Sciences Center Shreveport and Feist-Weiller Cancer Center. Dr. Cvek is on the Bioinformatics Core faculty of the Center of Molecular and Tumor Virology at LSU Health Sciences Center in Shreveport and Associate Director of the Bioinformatics, Biostatistics and Computational Biocomputing Core of the Louisiana Biomedical Research Network.

Prior to joining LSU Shreveport she co-founded Anvil, Inc., a visualization company, and worked as research assistant at the Institute for Visualization and Perception Research and Center for Family, Work and Community at UML. She co-founded the Laboratory for Advanced Biomedical Informatics at LSU Shreveport and was named its co-Director in 2007.

US Patent Title: Universal visualization platform
US Patent No. 7,734,607 issued June 8, 2010

The present invention provides methods and apparatus, including computer program products, for a universal visualization platform. As described herein, in one aspect, the invention includes a framework system for connecting a plurality of tools. The system includes a plug-in mechanism configured to dynamically load the plurality of tools, a data pool having storage space configured to store data sets associated with the plurality of tools, a linking mechanism configured to establish communications links between the loaded plurality of tools to enable coordinated operation of the loaded plurality of tools, a session component configured to record the process history of the operations of the loaded plurality of tool and the system states corresponding to the process history of the operations and an annotation module configured to associate user-provided data corresponding to one or more of the stored data sets.