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 on the Faculty

Before coming to FIU, Trevor served on the Faculty at Eckerd College and was Discipline Coordinator of Computer Science from 2012 to 2015. At Eckerd he instructed a wide range of computer science courses at the undergraduate level plus some cross-disciplinary courses in the liberal arts. As a graduate instructor at Notre Dame, Trevor received the Kaneb Award for Excellence in Teaching.Trevor’s research interests include high-performance

Trevor’s research interests include high-performance GPU computing and its application to bioinformatics. He was a Visiting Scholar at Stanford University in 2012 for his work with molecular dynamics, which includes publications in the Journal of Chemical Theory and Computation, Molecular Biology of the Cell, and the Journal of Computational Chemistry. He is currently studying connections between social network theory and the microbiome, and also methods for bringing GPU computing to the classroom. His previous institution, Eckerd College, was awarded as a GPU Education Center by NVIDIA in 2013.

Honors and Awards

  • Tenure and Promotion to Associate Professor (2014), Eckerd College
  • OpenMM Visiting Scholars Program (2012), Stanford University
  • Kaneb Award for Excellence in Teaching (2006), University of Notre Dame Department of Computer Science and Engineering
  • Upsilon Pi Epsilon (2004), Computer Science Honor Society
  • Tau Beta Pi (2001), Engineering Honor Society

Research and Educational Interests

Post-secondary Education, Microbiome, GPU Computing, Social Networks, Computational Biology/Bioinformatics, Molecular Dynamics, Domain-specific Languages, Software Engineering

Background Education

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

Professional Activities

Discipline Coordinator, Department of Computer Science, Eckerd College (2012-2015)
Reviewer, Journal of Computational Chemistry (2015)
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)
Senior Thesis Committees (Galen Irving-Sachs, 2015; Austin Vance, 2012, chair; RJ Nowling, 2010)
Eckerd Faculty Observer to Board of Trustees (Buildings and Grounds, 2011-2012)
Harvard Medical School/Center for Human Genetic Research Selection Committee (2009-2015)
Eckerd Writing Portfolio Reviewer (2010-2016)

Professional Experience

  • Visiting Professor of Computer Science (2015-2016), Florida International University
  • Associate Professor of Computer Science (2014-2016), Assistant Professor (2008-2014), Eckerd College
  • Research Assistant (2001-2008), University of Notre Dame
  • Graduate Instructor (2007), University of Notre Dame

Selected Publications

  • T. Cickovski, V. Aguiar-Pulido, W. Huang, S. Mahmoud and G. Narasimhan. Lightweight Microbiome Analysis Pipelines. Proceedings of International Work Conference on Bioinformatics and Biomedical Engineering (IWBBIO16), Granada, Spain, April 2016.
  • V. Aguiar-Pulido, W. Huang, V. Ulloa-Suarez, T. Cickovski, K. Mathee and G. Narasimhan. Metagenomics, Metatranscriptomics and Metabolomics Approaches for Microbiome Analysis. Evolutionary Biology S(1):5-16, 2016.
  • 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 Graphics Processing Unit. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(2):445-454, 2015.
  • 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 ‘15), Miami, FL, Oct. 2015.
  • J. 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.
  • 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.
  • G. Margolin, I.V. Gregoretti, T. Cickovski, C. Li, W. Shi, M.S. Alber and H.G. 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.
  • T. Cickovski, S. Chatterjee, J. Wenger, C. Sweet and J.A. Izaguirre. MDLab: A Molecular Dynamics Simulation Prototyping Environment. Journal of Computational Chemistry 31(7):1345-1356, 2010.
  • 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 Multi-Cellular Development. Computing in Science and Engineering 9(4):50-60, 2007.
  • T. Cickovski, C. Sweet and J.A. Izaguirre. MDL, A Domain-Specific Language for Molecular Dynamics. Proceedings of IEEE 40th Annual Simulation Symposium, Norfolk, VA, March 2007.
  • T. Cickovski, C. Huang, R. Chaturvedi, T. Glimm, H.G.E. Hentschel, M.S. Alber, J.A. Glazier, S.A. Newman and J.A. Izaguirre. A Framework for Three-Dimensional Simulation of Morphogenesis. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2(4):273-288, 2005.
  • J.A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffland, G. Thomas, G. Forgacs, M.S. Alber, H.G.E. Hentschel, S.A. Newman and J.A.Glazier. CompuCell, A Multi-Model Framework for Simulation of Morphogenesis. Bioinformatics 20(7):1129-1137, 2004.
  • T. Matthey, T. Cickovski, S. Hampton, A. Ko, Q. Ma, M. Nyerges, T. Raeder, T. Slabach and J.A. Izaguirre. ProtoMol, An Object-Oriented Framework for Prototyping Novel Algorithms for Molecular Dynamics. ACM Transactions on Mathematical Software 20(3):237-265, 2004.
  • R. Chaturvedi, J.A. Izaguirre, C. Huang, T. Cickovski, P. Virtue, G. Thomas, G. Forgacs, M.S.Alber, H.G.E. Hentschel, S.A. Newman and J.A.Glazier. Multi-model Simulations of Chicken Limb Morphogenesis. In ICCS 2003, International Conference, Melboune, Australia and St. Petersburg, Russia. Lecture Notes Comput. Sci. 2659, pages 39-49, Springer-Verlag, 2003.