Trevor Cickovski Portrait

Trevor Cickovski

Instructor
Biography

Dr. Trevor Cickovski received his Ph.D. from the University of Notre Dame in 2008. He currently works at Florida International University as an Instructor primarily of hardware courses, and also a member of the Bioinformatics Research Group (BioRG).

Before coming to FIU Trevor served as Discipline Coordinator of Computer Science at Eckerd College from 2012 to 2015, where he instructed a variety of computer science undergraduate courses plus some cross-disciplinary courses in the liberal arts. He has received two teaching excellence awards, one from the SCIS department at FIU in 2017 and the other from the University of Notre Dame as a graduate instructor in 2006. Trevor has received funding and resources from NVIDIA for bringing GPU computing to the classroom at both FIU and Eckerd, which he continues to pursue in his Structured Computer Organization course.

Trevor is passionate about health and his research with the BioRG explores the roles of the microbiome in maintaining stability of host organisms and environments. His team has explored connections between the microbiome and ADHD, Alpha-1 Antitrypsin Deficiency, COPD, smoking, and red tides by taking a multi-omics approach that integrates DNA, RNA and metabolites using large-scale data processing, GPU computing and network analysis. He has several peer-reviewed publications with the BioRG including Bioinformatics, BMC, ICCABS, Evolutionary Biology, IWBBIO, and ACM TCBB.

Trevor is also lead developer of the software PluMA (http://biorg.cis.fiu.edu/pluma), which includes a community accessible plugin pool where users can contribute extensions to PluMA in the programming language of their choice and then integrate with other users’ plugins, with a goal of facilitating natural development of microbiome analysis by providing the opportunity for communal exchange of ideas and algorithms. PluMA currently has over seventy plugins in several different languages, and continues to grow.

Honors and Awards
  • Teaching Excellence Award (2017), School of Computing and Information Sciences, FIU
  • Tenure and Promotion to Associate Professor (2014), Eckerd College
  • OpenMM Visiting Scholars Program (2012), Stanford University
  • Kaneb Award for Excellence in Teaching (2006), Department of Computer Science and Engineering, University of Notre Dame
  • Upsilon Pi Epsilon (2004), Computer Science Honor Society
  • Tau Beta Pi (2001), Engineering Honor Society
Research and Educational Interests
  • Microbiome
  • GPU Computing
  • Network Analysis
  • Social Networks
  • Parallelism
  • Software Engineering
Background Education

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

Professional Activities

Annual Awards Committee, School of Computing and Information Sciences, FIU (2018-present)

Instructor Hiring Committee, School of Computing and Information Sciences, FIU (2017-present)

Undergraduate Program Committee, School of Computing and Information Sciences, FIU (2016-present)

Discipline Coordinator, Department of Computer Science, Eckerd College (2012-2015)

Reviewer, BioDirect (2017-present)

Reviewer, Chemistry: A European Journal (2017-present)

Reviewer, Journal of Computational Chemistry (2015-present)

Eckerd Intercollegiate Athletics Committee (2014-2015)

Eckerd Graduate Fellowship Advisor (2013-2014)

Eckerd Admissions and Scholarships Committee (2011-2013, chair 2012-2013)

Eckerd Computer Policy Group (2009-2011, chair 2010-2011)

Harvard Medical School/Center for Human Genetic Research Selection Committee (2009-2015)

Professional Experience
  • Instructor, School of Computing and Information Sciences, FIU (2016-present)
  • Research Associate, Bioinformatics Research Group, FIU (2015-present)
  • Visiting Professor, School of Computing and Information Sciences, FIU (2015-2016)
  • Associate Professor, Computer Science, Eckerd College (2014-2016)
  • Assistant Professor, Computer Science, Eckerd College (2008-2014)
  • Research Assistant, Department of Computer Science and Engineering, University of Notre Dame (2001-2008)
  • Graduate Instructor, Department of Computer Science and Engineering, University of Notre Dame (2007)
Selected Publications
  1. T. Cickovski, V. Aguiar-Pulido, and G. Narasimhan. MATria: A Unified Centrality Algorithm. To appear in BMC Bioinformatics, 2018.
  2. T. Cickovski and G. Narasimhan. Constructing Lightweight and Flexible Pipelines Using Plugin-Based Microbiome Analysis (PluMA). To Appear in Bioinformatics, 2018.
  3. T. Cickovski, V. Aguiar-Pulido, and G. Narasimhan. MATria: A Unified Centrality Algorithm. In Proceedings of IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2017), Orlando, FL, Oct 2017.
  4. T. Cickovski, E. Peake, V. Aguiar-Pulido and G. Narasimhan. ATria: A Novel Centrality Algorithm Applied to Biological Networks. BMC Bioinformatics 18(S8):239-248, 2017.
  5. T. Cickovski, V. Aguiar-Pulido, W. Huang, S. Mahmoud, and G. Narasimhan. Lightweight Microbiome Analysis Pipelines. In Proceedings of International Work Conference on Bioinformatics and Biomedical Engineering (IWBBIO16), Granada, Spain, April 2016.
  6. V. Aguiar-Pulido, W. Huang, V. Ulloa-Suarez, T. Cickovski, K. Mathee and G. Narasimhan. Metageonmics, Metatranscriptomics and Metabolomics Approaches for Microbiome Analysis. Evolutionary Biology 12(1):5-16, 2016.
  7. T. Cickovski, E. Peake, V. Aguiar-Pulido and G. Narasimhan. ATria: A Novel Centrality Algorithm Applied to Biological Networks. Proceedings of 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2015, short abstract), Miami, FL, 2015.
  8. T. Cickovski, T. Flor, G. Irving-Sachs, P. Novikov, J. Parda and G. Narasimhan. GPUDePiCt: A Parallel Implementation of a Clustering Algorithm for Computing Degenerate Primers on the Graphics Processing Unit. ACM TCBB 12(2):445-454, 2015.
  9. J. C. Sweet, R. J. Nowling, T. Cickovski, C. R. Sweet, V. S. Pande and J. A. Izaguirre. Long Timestep Molecular Dynamics on the Graphics Processing Unit. Journal of Chemical Theory and Computation 9(8) 3267-3281, 2013.
  10. A. Vance and T. Cickovski. A Case Study on Developing a Classroom Web Application Using Behavior-Driven Development. American Journal of Undergraduate Research 11(3):9-16, 2012.
  11. G. Margolin, I. V. Gregoretti, T. Cickovski, C. Li, W. Shi, M. S. Alber and H. V. Goodson. The Mechanisms of Microtubule Catastrophe and Rescue: Implications From Analysis of a Dimer-Scale Computational Model. M. Biol. Cell, 23(4):642-656, 2012.
  12. T. Cickovski, S. Chatterjee, J. Wenger, C. R. Sweet and J. A. Izaguirre. MDLab: A Molecular Dynamics Simulation Prototyping Environment. J. Comput. Chem.,31(7):1345-1356, 2010.
  13. 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. From Genes To Organisms Via The Cell: A Problem Solving Environment For Multicellular Development. CISE, 9(4):50-60, 2007.
  14. T. Cickovski, C. Sweet and J. A. Izaguirre. MDL, A Domain-Specific Language For Molecular Dynamics. Proceedings of IEEE 40th ANSS, Norfolk, VA, March 2007.
  15. T. Cickovski, C. Huang, R. Chaturvedi, T. Glimm, H. G. E. Hentschel, M. S. Alber, J. A. Glazier, S. A. Newman, J. A. Izaguirre. A Framework for Three-Dimensional Simulation of Morphogenesis ACM TCBB 2(4):273-288, 2005.
  16. J. A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffland, G. Thomas, G. Forgacs, M. S. Alber, S. A. Newman, J. A. Glazier. CompuCell, A Multi-Model Framework For Simulations Of Morphogenesis. Bioinformatics 20(7):1129-1137, 2004.
  17. T. Matthey, T. Cickovski, S. Hampton, A. Ko, Q. Ma, M. Nyerges, T. Raeder, T. Slabach, J. A. Izaguirre. ProtoMol, An Object-Oriented Framework For Prototyping Novel Algorithms For Molecular Dynamics. ACM TOMS, 20(3):237-265, 2004.
  18. 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. Multi-Model Simulations of Chicken Limb Morphogenesis. Springer Verlag LNCS 2659, ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Part II, pp 39-49, 2003.