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DR. TREVOR M. CICKOVSKI (CV (Updated Jun 2017))

FACULTY AND RESEARCH ASSOCIATE
FLORIDA INTERNATIONAL UNIVERSITY (site)
SCHOOL OF COMPUTING AND INFORMATION SCIENCES (site)

You may contact me at:
               
       Panthers


FLORIDA INTERNATIONAL UNIVERSITY
SCHOOL OF COMPUTING AND INFORMATION SCIENCES - ECS280D
11200 SW 8th Street
MIAMI, FL 33199

OFFICE PHONE: (305) 348-8043
E-MAIL: tcickovs@fiu.edu

Papers

1. Constructing Lightweight and Flexible Pipelines Using Plugin-Based Microbiome Analysis (PluMA). T. Cickovski and G. Narasimhan. Submitted to Bioinformatics, 2017.
2. MATria: A Unified Centrality Algorithm. T. Cickovski, V. Aguiar-Pulido, and G. Narasimhan. To appear in Proceedings of IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2017), Orlando, FL, Oct 2017.
3. ATria: A Novel Centrality Algorithm Applied to Biological Networks. T. Cickovski, E. Peake, V. Aguiar-Pulido and G. Narasimhan. BMC Bioinformatics 18(S8):239-248, 2017.
4. Lightweight Microbiome Analysis Pipelines. T. Cickovski, V. Aguiar-Pulido, W. Huang, S. Mahmoud, and G. Narasimhan. In Proceedings of International Work Conference on Bioinformatics and Biomedical Engineering (IWBBIO16), Granada, Spain, April 2016.
5. Metageonmics, Metatranscriptomics and Metabolomics Approaches for Microbiome Analysis. V. Aguiar-Pulido, W. Huang, V. Ulloa-Suarez, T. Cickovski, K. Mathee and G. Narasimhan. Evolutionary Biology 12(1):5-16, 2016.
6. ATria: A Novel Centrality Algorithm Applied to Biological Networks. T. Cickovski, E. Peake, V. Aguiar-Pulido and G. Narasimhan. Proceedings of 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2015, short abstract), Miami, FL, 2015.
7. GPUDePiCt: A Parallel Implementation of a Clustering Algorithm for Computing Degenerate Primers on the Graphics Processing Unit. T. Cickovski, T. Flor, G. Irving-Sachs, P. Novikov, J. Parda and G. Narasimhan. ACM TCBB 12(2):445-454, 2015.
8. Long Timestep Molecular Dynamics on the Graphics Processing Unit. J. C. Sweet, R. J. Nowling, T. Cickovski, C. R. Sweet, V. S. Pande and J. A. Izaguirre, Journal of Chemical Theory and Computation 9(8) 3267-3281, 2013.
9. A Case Study on Developing a Classroom Web Application Using Behavior-Driven Development. A. Vance and T. Cickovski, American Journal of Undergraduate Research 11(3):9-16, 2012.
10. The Mechanisms of Microtubule Catastrophe and Rescue: Implications From Analysis of a Dimer-Scale Computational Model G. Margolin, I. V. Gregoretti, T. Cickovski, C. Li, W. Shi, M. S. Alber and H. V. Goodson, M. Biol. Cell, 23(4):642-656, 2012.
11. MDLab: A Molecular Dynamics Simulation Prototyping Environment T. Cickovski, S. Chatterjee, J. Wenger, C. R. Sweet and J. A. Izaguirre, J. Comput. Chem.,31(7):1345-1356, 2010.
12. From Genes To Organisms Via The Cell: A Problem Solving Environment For Multicellular Development  T. Cickovski, K. Aras, M. Swat, R. M. H. Merks, T. Glimm, H. G. E. Hentschel, M. S. Alber, J. A. Glazier, S. A. Newman and J. A. Izaguirre, CISE,  9(4):50-60, 2007.
13. MDL, A Domain-Specific Language For Molecular Dynamics  T. Cickovski, C. Sweet and J. A. Izaguirre, Proceedings of IEEE 40th ANSS, Norfolk, VA, March 2007.
14
. A Framework for Three-Dimensional Simulation of Morphogenesis  T. Cickovski, C. Huang, R. Chaturvedi, T. Glimm, H. G. E. Hentschel, M. S. Alber, J. A. Glazier, S. A. Newman, J. A. Izaguirre.  ACM TCBB 2(4):273-288, 2005.
15. CompuCell, A Multi-Model Framework For Simulations Of Morphogenesis  J. A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffland, G. Thomas, G. Forgacs, M. S. Alber, S. A. Newman, J. A. Glazier :  Bioinformatics 20(7):1129-1137, 2004.

16. ProtoMol, An Object-Oriented Framework For Prototyping Novel Algorithms For Molecular Dynamics  T. Matthey, T. Cickovski, S. Hampton, A. Ko, Q. Ma, M. Nyerges, T. Raeder, T. Slabach, J. A. Izaguirre :  ACM TOMS, 20(3):237-265, 2004.

17. Multi-Model Simulations of Chicken Limb Morphogenesis  R. Chaturvedi, J. A. Izaguirre, C. Huang, T. Cickovski, P. Virtue, G. Thomas, G. Forgacs, M. S. Alber, S. A. Newman, and J. A. Glazier : Springer Verlag LNCS 2659, ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Part II, pp 39-49, 2003.
Courses
CDA 3103 - Fundamentals of Computer Systems
CDA 4101 - Structured Computer Organization


Awards and Honors
2001 - Inducted into Tau Beta Pi
2002 - Arthur J. Schmitt Graduate Student Fellowship
2004 - Inducted into Upsilon Pi Epsilon
2006 - Kaneb Award for Excellence in Teaching, Notre Dame
2012 - OpenMM Visiting Scholars Program, Stanford University
2014 - Tenure and Promotion to Associate Professor, Eckerd College



Highest Degree Earned
Ph.D. University of Notre Dame, Computer Science and Engineering, 2008



Research Software
PluMA A flexible and lightweight software pipeline for microbiome analysis
GPUDePiCt  A GPU-based degenerate primer construction tool
MDLab  A molecular dynamics simulation prototyping environment
CompuCell3D
A 3D multi-model software framework for morphogenesis
ProtoMol
An extensible framework for simulations of molecular dynamics



Conference Presentations

1. Midwest Numerical Analysis Day (presentation), May 2003 
2. Biocomplexity IV (poster), May 2003
3. Biocomplexity VI (poster), May 2004

4. SIAM (presentation), February 2005, SESSION CHAIR  
5. Biocomplexity VIII (poster), October 2005
6. Midwest Molecular Dynamics Workshop (discussion), November 2005
7. Midwest Society for Programming Languages and Systems Meeting (presentation), April 2006   PPT
8. ALife X, (poster and tutorial), June 2006
9. Helpful Hints for TAs in CSE (panelist), August 2006
10. Society for Advancement of Native Americans and Chicanos in Science (recruiter), October 2006
11. IEEE 40th Annual Simulation Symposium, March 2007
12. IMA Classical and Quantum Approaches in Molecular Modeling (presentation), July 2007
13. CompuCell3D Workshop (instructor), August 2007
14. Inaugural Florida Undergraduate Research Symposium (poster), March 2011
15. FURC '12 (poster), March 2012
16. FURC '14 (poster), February 2014
17. GPU Technology Conference (GPUTech '14) (presentation), March 2014
18. FURC '15 (poster), February 2015
19. ICCABS 2015 (presentation), October 2015
20. IWBBIO 2016 (presentation), April 2016
Technical Reports

1. Design Patterns For Generic Object-Oriented Scientific Software  T. Cickovski, T. Matthey and J. A. Izaguirre, Notre Dame TR 2004-29, November 2004.

2.
Empirical Analysis of Design Patterns in Scientific Application  K. Aras, T. Cickovski and J. A. Izaguirre, Notre Dame Technical Report 2005-08, May 2005.
3. Simulation of Chicken Limb Growth With Irregular Domain Shape  K. Aras, T. Cickovski, D. Cieslak, C. Huang and J. A. Izaguirre, Notre Dame Technical Report 2005-09, July 2005.
4. Interactive Molecular Dynamics  D. Brandtner, T. Cickovski and J. A. Izaguirre, Notre Dame Technical Report 2005-11, July 2005.
5. Molecular Dynamics Language (MDL)  C. B. B. Yau, T. Cickovski and J. A. Izaguirre, Notre Dame Technical Report 2005-13, August 2005.
6. Prototype to Release: Software Engineering for Scientific Software.  Biomedical Computation Review, R. J. Nowling and T. Cickovski, Stanford University, September 2012.
7. CUDA Tutorial,  T.Cickovski,  Eckerd College, August 2016.


In memory of Remo DiGirolamo, my high school classmate. 
You will not be forgotten.