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Trevor Cickovski Portrait

Trevor Cickovski

Associate Director & Associate Teaching Professor

tcickovs@fiu.edu
(305) 348-8043
http://cis.fiu.edu/~tcickovs
CASE 344A
Mo & We 12:00 pm- 4:00 pm, Tu 12:00 pm-5:00 pm, Th 12:00 pm-2:00 pm
ORCID: 0000-0003-2724-6951

Biography

Dr. Trevor Cickovski received his Ph.D. from the University of Notre Dame in 2008. He holds Graduate Faculty status and specializes in teaching hardware and Unix coursework, and is IRB-certified and a member of the Bioinformatics Research Group (BioRG) at FIU. He also is a member of the ACM, IEEE, and the National Learning Assistant Alliance (LAA). Before coming to FIU Trevor was Discipline Coordinator of Computer Science at Eckerd College, instructing a variety of computer science and cross-disciplinary liberal arts courses. He has received three teaching excellence awards, from the FIU College of Engineering (2019), FIU Knight Foundation School of Computing and Information Sciences (2017), and from Notre Dame as a graduate instructor (2006). Trevor was named a Center for the Advancement of Teaching (CAT) fellow in 2019, participating in a University-wide effort to improve teaching evaluation and developing a website for CAT referenced in Panther180. He has received funding from Nvidia to bring GPU computing to the classroom. Trevor is passionate about health and explores roles played the microbiome in maintaining homeostasis. Microbiomes have enormous influence given their ubiquity and involvement in host metabolic reactions. He has explored connections with ADHD, A1AD, COPD, smoking, and red tides using multi-omics approaches that integrate DNA, RNA and metabolites through large-scale processing, GPUs, and network analyses. He has several peer-reviewed publications including JMM, LNBI, Bioinformatics, BMC, ICCABS, IWBBIO, and ACM TCBB. He has received funding from NIJ (epigenetics), and NSF (machine learning and Covid-19 vaccine discovery). Trevor is lead software developer of PluMA, facilitating natural progress by allowing construction of new ideas as plugins in a choice programming language. These can be uniformly tested alongside other plugins and committed to a centralized plugin pool. The PluMA plugin pool has grown from 70 to 225+ plugins from 2019 to 2020, and continues to grow.

Honors and Awards

  • Graduate Faculty Status (2020), FIU
  • Center for Advancement of Teaching (CAT) Fellow (2019), FIU
  • Faculty Teaching Award (2019), College of Engineering, FIU
  • 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
  • Software Engineering
  • GPU computing
  • Network Analysis
  • Hardware
  • Unix

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 (2018-2019) Instructor Hiring Committee, School of Computing and Information Sciences, FIU (2017-present) Undergraduate Program Committee, School of Computing and Information Sciences, FIU (2016-present, chair 2020-present) Discipline Coordinator, Department of Computer Science, Eckerd College (2012-2015) Reviewer, ACM, Springer, and Wiley

Professional Experience

  • Assistant Teaching Professor, 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. Cickovski, T. M., Mathee, K., Deoraj, A., Narasimhan, G., & Stollstorff, M. (2020). Gut Microbiome and Neuropsychiatric Disorders: Implications for Attention Deficit Disorder. Journal of Medical Microbiology, 69(1), 14–24.
  2. Cickovski, T. M., Manuel, A., Mathee, K., Campos, M., & Narasimhan, G. (2020). Effects of Various Alpha-1 Antitrypsin Supplement Dosages on the Lung Microbiome and Metabolome (Vol. Lecture Notes in Computer Science (LNCS), pp. 90–101). Presented at the IEEE 9th International Conference on Computational Advances in Bio and medical Sciences (ICCABS), Miami: Springer.
  3. Cickovski, T. M., Aguiar-Pulido, V., & Narasimhan, G. (2019). MATria: A Unified Centrality Algorithm. BMC Bioinformatics, 20(S1), 278.
  4. Sazal, M., Ruiz-Perez, D., Cickovski, T. M., & Narasimhan, G. (2018). Inferring Relationships in Microbiomes from Signed Bayesian Networks (Vol. 1, p. 1). Presented at the IEEE 8th International Conference on Computational Advances in Bio and medical Sciences (ICCABS), Las Vegas, NV: IEEE.
  5. Cickovski, T. M., & Narasimhan, G. (2018). Constructing Lightweight and Flexible Pipelines Using Plugin-based Microbiome Analysis (PluMA). Bioinformatics, 34(17), 2881–2888.
  6. Cickovski, T. M., Aguiar-Pulido, V., & Narasimhan, G. (2017). MATria, A Unified Centrality Algorithm (p. 278). Presented at the IEEE 7th International Conference on Computational Advances in Bio and medical Sciences (ICCABS), Orlando, FL:IEEE.
  7. Cickovski, T. M., Peake, E., Aguiar-Pulido, V., & Narasimhan, G. (2017). ATria: A Novel Centrality Algorithm Applied To Biological Networks. BMC Bioinformatics, 18(S8), 239–248.
  8. Cickovski, T., Aguiar-Pulido, V. . ., Huang, W., Mahmoud, S., & Narasimhan, G. (2016). Lightweight Microbiome Analysis Pipelines (pp. 225–227). Presented at the International Work Conference on Bioinformatics and Biomedical Engineering (IWBBIO16), Granada, Spain.
  9. Aguiar-Pulido, V., Huang, W., Suarez-Ulloa, V., Cickovski, T., Mathee, K., & Narasimhan, G. (2016). Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis. Evol Bioinform Online, 12(S1), 5–16.
  10. Cickovski, T., Peake, E., Aguiar-Pulido, V. . ., & Narasimhan, G. (2015). ATria: A Novel Centrality Algorithm Applied To Biological Networks. Presented at the IEEE 5th International Conference on Computational Advances in Bio and medical Sciences (ICCABS), Miami, FL: IEEE. http://doi.org/10.1109/ICCABS.2015.7344710
  11. Cickovski, T., Flor, T., Irving-Sachs, G. . ., Parda, J., Novikov, P., & Narasimhan, G. (2015). GPUDePiCT: A Parallel Implementation of a Clustering Algorithm for Computing Degenerate Primers on Graphics Processing Units. IEEE/ACMTCBB, 12(2), 445–454.
  12. Sweet, J. C., Nowling, R. J., Cickovski, T., Sweet, C. R., Pande, V. S., & Izaguirre, J. A. (2013). Long Timestep Molecular Dynamics on the Graphical Processing Unit. Journal of Chemical Theory and Computation, 9(8), 3267–3281.
  13. Vance, A., & Cickovski, T. M. (2012). A Case Study on Developing a Classroom Application Using Behavior-Driven Development. American Journal of Undergraduate Research, 11(3), 9–16.
  14. Margolin, G., Gregoretti, I. V., Cickovski, T. M., Li, C., Shi, W., Alber, M. S., & Goodson, H. V. (2012). The Mechanisms of Microtubule Catastrophe and Rescue: Implications from Analysis of a Dimer-Scale Computational Model. Mol Biol Cell, 23(4), 642–656.
  15. Cickovski, T., Chatterjee, S., Wenger, J., Sweet, C. R., & Izaguirre, J. A. (2010). MDLab: A Molecular Dynamics Simulation Prototyping Environment. Journal of Computational Chemistry, 31(7), 1345–1356.
  16. Cickovski, T., Aras, K., Swat, M., Merks, R. M., Glimm, T., Hentschel, H., … Izaguirre, J. A. (2007). From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development. Computing in Science and Engineering, 9(4), 50–60.
  17. Cickovski, T., Sweet, C., & Izaguirre, J. A. (2007). MDL, A Domain-Specific Language for Molecular Dynamics. Presented at the 40th Annual Simulation Symposium (ANSS’07), Norfolk, VA: IEEE.
  18. Cickovski, T. M., Huang, C., Chaturvedi, R., Glimm, T., Hentschel, H., Alber, M. S., … Izaguirre, J. A. (2005). A Framework for Three-Dimensional Simulation of Morphogenesis. IEEE/ACM TCBB, 2(4), 273–288.
  19. Izaguirre, J. A., Chaturvedi, R., Huang, C., Cickovski, T., Coffland, J., Thomas, G., … Glazier, J. A. (2004). CompuCell, A Multi-Model Framework for Simulation of Morphogenesis. Bioinformatics, 20(7), 1129.
  20. Matthey, T., Cickovski, T., Hampton, S., Ko, A., Ma, Q., Nyerges, M., … Izaguirre, J. A. (2004). ProtoMol, An Object-Oriented Framework for Prototyping Novel Algorithms for Molecular Dynamics. ACM TOMS, 30(3), 237–265.
  21. Chaturvedi, R., Izaguirre, J. A., Huang, C., Cickovski, T., Virtue, P., Thomas, G., … Glazier, J. A. ". (2003). Multi-Model Simulations of Chicken Limb Morphogenesis. Presented at the International Conference on Computational Science, Melbourne, Australia and St. Petersburg, Russia: Springer.