Deciphering life: One bit at a time

Robert M Flight's home on the web

Curriculam Vitae

Contact

Electronic

Mailing

Center for Environmental and Systems Biochemistry
Markey Cancer Center
CC434 Roach Building
800 Rose Street
University of Kentucky
Lexington, KY 40536-0093

Education

PhD, Chemistry, Dalhousie University, Halifax, NS, 2004-2009
Research Supervisor: Dr. P.D. Wentzell
Thesis Title: A workflow for the analysis of DNA microarray time-course data

MSc, Chemistry, University of New Brunswick, Fredericton, NB, 2002-2004
Research Supervisors: Dr. G. Deslongchamps & Dr. L.A. Calhoun
Thesis Title: Development and testing of SPLASH docking with acetylcholinesterase

BSc, Biology-Chemistry, University of New Brunswick, Fredericton, NB, 1997-2002

Research Interests

My primary research interests are in the areas where biology, chemistry, and computers intersect. This has ranged from using molecular docking tools to examine the interactions of ligands with an individual protein, applying and refining tools used in the analysis of serial DNA microarray data, to developing new methods of meta-analysis for high-throughput molecular biology experiments. All of these areas require an understanding of the basic chemistry involved, the biological systems, and an understanding of how the software / algorithms work. I believe that in order to analyze *omics data, there is a need to understand the data from a measurement perspective in order to develop effective methods of mining the data for useful information.

Professional Experience

  • 2014 - Present: Research Associate, Senior, University of Kentucky
  • 2013 - 2014: PostDoctoral Research Associate, University of Kentucky
  • 2010 - 2013: PostDoctoral Research Associate, University of Louisville
  • 2009 - 2010: Research Assistanct, University of Dalhousie
  • 2004 - 2009: Graduate Research / Teaching Assistant, Dalhousie University
  • 2007 (08 - 12): Research Assitant, Institute of Marine Biosciences – National Research Council
  • 2002 - 2004: Graduate Research / Teaching Assistant, University of New Brunswick
  • 1999-2002: Teaching Assistant, University of New Brunswick

Honors and Awards

  • Dalhousie University, Kenneth T. Leffek Prize for best PhD thesis in the Department of Chemistry, 2009
  • University of New Brunswick, Faculty of Science Dean’s List, 2002
  • University of New Brunswick, Department of Chemistry Analytical Chemistry Award, 2001
  • University of New Brunswick, Dr. Willard Miles Jenkins Scholarship, 1997

Professional Activities

  • Organizer for University of Kentucky Systems Biology and Omics Integration (SBOI) Journal Club and Seminar Series
  • Organizing committee for University of Louisville Bioinformatics Journal Club, 2010-2013
  • Organizing cross-training workshops for Bioinformatics PostDocs and staff at University of Louisville, 2011-2013
  • Dalhousie University CGSS Graduate Student Seminar Evaluation Committee, 2006-2007
  • Organizing committee member of the CIC-APICS Student Chemistry Conference, 2000

Publications and Presentations

J. Refereed Journal Publications

  1. N. Narasimharao, T. Al-jumaily, A. M. Eteleeb, R. M. Flight, S. Xiaorong, H. N. B. Moseley, E. C. Rouchka, Y. Fondufe-Mittendorf, Genome-wide profiling of PARP1 reveals an interplay with gene regulatory regions and DNA methylation, PLOS One, 2015 dx.doi.org/10.1371/journal.pone.0135410

  2. S. Yao, R.M. Flight, E.C. Rouchka, H.N.B. Moseley, A Less-Biased ANalysis of Metalloproteins Reveals Novel Zinc Coordination Geometries, Proteins, 2015, 83:1470-1487 dx.doi.org/10.1002/prot.24834

  3. R.M. Flight, B.J. Harrison, F. Mohammad, M.B. Bunge, L.D.F. Moon, J.C. Petruska, E.C. Rouchka, “categoryCompare, an Analytical Tool Based on Feature Annotation, Frontiers In Genetics, 2014, 5 dx.doi.org/10.3389/fgene.2014.00098

  4. B.J. Harrison, R.M. Flight, C. Gomes, G. Venkat, S.R. Ellis, U. Sankar, J.L. Twiss, E.C. Rouchka, J.C. Petruska "IB4‐binding sensory neurons in the adult rat express a novel 3' UTR‐extended isoform of CaMK4 that is associated with its localization to axons”, Journal of Comparative Neurology, 2013, 522 (2) dx.doi.org/10.1002/cne.23398

  5. W.J. Carreer, R.M. Flight, H.N.B. Moseley, “A Computational Framework for High-Throughput Isotopic Natural Abundance Correction of Omics-Level Ultra-High Resolution FT-MS Datasets”, Metabolites, 3(4), 853-866 dx.doi.org/10.3390/metabo3040853

  6. F. Mohammed, R.M. Flight, B. Harrison, J.C. Petruska, E.C. Rouchka, “AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities”, BMC Bioinformatics, 13:229 dx.doi.org/10.1186/1471-2105-13-229

  7. F. Mohammed, R.M. Flight, B. Harrison, J.C. Petruska, E.C. Rouchka, "Interval Trees for Detection of Overlapping Genetic Entities”, Proceedings of the 11th IEEE International Conference on Bioinformatics and Bioengineering, 2011: 278-281 dx.doi.org/10.1109/BIBE.2011.49

  8. F. Mohammed, R.M. Flight, B. Harrison, J.C. Petruska, E.C. Rouchka, “A Heuristic Algorithm for Detecting and Predicting Intercellular Interactions”, Proceedings of the 11th IEEE International Conference on Bioinformatics and Bioengineering, 2011:1-8 dx.doi.org/10.1109/BIBE.2011.9

  9. T.K. Karakach, R.M. Flight, S.E. Douglas, P.D. Wentzell, “An introduction to DNA microarrays for gene expression analysis”, Chemometrics and Intelligent Laboratory Systems, 2010, 104(1):28-52 dx.doi.org/10.1016/j.chemolab.2010.04.003

  10. H.M. Murray, S.P. Lall, R. Rajaselvam, L.A. Boutilier, B. Blanchard, R.M. Flight, S. Colombo, and S.E. Douglas, "A nutrigenomic analysis of intestinal response to partial soybean meal replacement in diets for juvenile Atlantic halibut, Hippoglossus hippoglossus, L.”, Aquaculture, 2010, 298(3-4):282-293 dx.doi.org/10.1016/j.aquaculture.2009.11.001

  11. R.M. Flight and P.D. Wentzell, “Preliminary Exploration of Time-Course DNA Microarray Data with Correlation Maps”, OMICS: A Journal of Integrative Biology, February 2010, 14(1):99-107 dx.doi.org/10.1089/omi.2009.0096

  12. R. Tauler, M. Viana, X. Querol, A. Alastuey, R.M. Flight, P.D. Wentzell, and P.K. Hopke, "Comparison of the results obtained by four receptor modeling methods in aerosol source apportionment studies”, Atmospheric Environment, 2009, 43(26):3989-3997 dx.doi.org/10.1016/j.atmosenv.2009.05.018

  13. H.M. Murray, S.P. Lall, R. Rajaselvam, L.A. Boutilier, R.M. Flight, B. Blanchard, S. Colombo, V. Mohindra, M. Yufera, and S.E. Douglas, “Effect of early introduction of microencapsulated diet to larval Atlantic Halibut, Hippoglossus hippoglossus, L. assessed by microarray analysis”, Marine Biotechnology, 2009 dx.doi.org/10.1007/s10126-009-9211-4

  14. R.M. Flight and P.D. Wentzell, “Potential Bias in GO::TermFinder”, Briefings in Bioinformatics, 2009, 10(3):289-294 dx.doi.org/10.1093/bib/bbn054

  15. S.E. Douglas, L.C. Knickle, J. Williams, R.M. Flight and M.E. Reith, “A First Generation Atlantic Halibut Hippoglossus hippoglossus (L.) Microarray: Application to Developmental Studies”, Journal of Fish Biology, 2008, 72(9):2391-2406 dx.doi.org/10.1111/j.1095-8649.2008.01861.x

  16. T.K. Karakach, R.M. Flight, and P.D. Wentzell, “Bootstrap Method for the Estimation of Measurement Uncertainty in Spotted Dual-Color DNA Microarrays”, Analytical and Bioanalytical Chemistry, 2007, 389:2125-2141 dx.doi.org/10.1007/s00216-007-1617-0

P. Conference Presentations (: indicates poster, and * indicates presenting author)

  1. T. Fahrenholz*, R. Higashi, H.N.B. Moseley, R.M. Flight, M. Bruno, R. Deshpande, Y. Yang, Y. Zhang, F. Mehmeti, A. Lane, T. Fan. “Using Exosome Lipid Profiles from Early Stage Lung Cancer Patients Before and After Surgery to Evaluate Response”, Resource Center for Stable Isotope-Resolved Metabolomics Metabolomics Symposium, Lexington, KY (2015).

  2. S. Yao, R.M. Flight, E.C. Rouchka, H.N.B. Moseley. A less biased analysis of metalloproteins reveals novel zinc coordination geometries, The Hitchhiker's Guide to the Protein Galaxy, West Lafayette, IN (2015)

  3. : R.M. Flight*, H.N.B. Moseley, Characterization and Visualization of Error in Omics Technologies, 2015 Markey Cancer Center Research Day, Lexington, KY, May 28 2015 link

  4. : R.M. Flight*, H.N.B. Moseley, categoryCompare v2.0: Easier, More Versatile Annotation-Based Meta-Analysis, 2015 Markey Cancer Center Research Day, Lexington, KY, May 28, 2015 link

  5. S. Yao, R.M. Flight, E.C. Rouchka, H.N.B. Moseley. A less biased analysis of metalloproteins reveals novel zinc coordination geometries, 14th Annual UT-KBRIN Bioinformatics Summit, Paris Landing, TN (2015)

  6. : A.M. Eteleeb*, R.M. Flight, B.J. Harrison, J.C. Petruska and E.C. Rouchka, “An Island-Based Approach for Differential Expression Analysis”, 2013 ACM ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, Washington D.C, USA, September 22-25, 2013

  7. R.M. Flight*, A. Eteleeb and E.C. Rouchka, “Affymetrix® Mismatch (MM) Probes: Useful After All”, 2012 ASE International Conference on BioMedical Computing, Washington, D.C., USA 14-16 December 2012

  8. : B.J. Harrison*, R.M. Flight*, A. Eteleeb, E.C. Rouchka and J.C. Petruska, “RNASeq profiling of UTR expression during neuronal plasticity”, 11th Annual UT-ORNL-KBRIN Bioinformatics Summit, Louisville, KY, March 30-April 1, 2012

  9. R.M. Flight*, B.J. Harrison, J.C. Petruska and E.C. Rouchka, “categoryCompare: High-throughput Data Meta-analysis using Gene Annotations”, 8th Annual Rocky Mountain Bioinformatics Conference, Snowmass, CO, December 9-11, 2010

  10. : R.M. Flight*, B.J. Harrison, J.C. Petruska and E.C. Rouchka, “categoryCompare: High-throughput Data Meta-analysis using Gene Annotations”, Research!Louisville, Louisville, KY, USA, October 11-15, 2010

  11. R.M. Flight*, T.K. Karakach and P.D. Wentzell, “Sequential Normalization of Time-Course DNA Microarray Data”, Atlantic Computational Life Sciences Challenges Workshop, Sackville, NB, Canada, November 14, 2009

  12. R.M. Flight*, T.K. Karakach and P.D. Wentzell, “Normalization Methods for Time-Course DNA Microarray Data”, Robert Cedergren Colloquium in Bioinformatics, Universite de Montreal, Montreal, QC, Canada, November 5-6, 2009

  13. : R.M. Flight* and P.D. Wentzell, “What's in a Workflow? Understanding Time Course DNA Microarray Data Using Multivariate Curve Resolution”, Atlantic OMICS Symposium and Expo, Moncton, NB, Canada, August 19-20, 2008

  14. : B. Wielens*, R.M. Flight, and P.D. Wentzell, “The Gene Machine — Software for Gene Expression Analysis”, Atlantic OMICS Symposium and Expo, Moncton, NB, Canada, August 19-20, 2008

  15. : J. Onochie*, R.M. Flight, and P.D. Wentzell, “Investigation of Gene Expression Profiles in Saccharomyces Cerevisiae Exiting Stationary Phase”, Atlantic OMICS Symposium and Expo, Moncton, NB, Canada, August 19-20, 2008

  16. P.D.Wentzell*, R.M. Flight, J. Boutillier, B. Wielens, and J. Onochie, "From Measurement to Knowledge: A Workflow for Multivariate Curve Resolution of DNA Microarray Time Course Data”, CAC 2008, 11th Conference on Chemometrics in Analytical Chemistry, Montpellier, France, June 30 - July 4, 2008

  17. : J. Boutillier*, R. Flight, and P. Wentzell, “Gridding Reproducibility in Spotted DNA Microarrays”, Atlantic OMICS Symposium and Expo, Moncton, NB, Canada, August 2007

  18. R.M. Flight* and P.D. Wentzell, “Deciphering the Transcription Patterns of a Malaria Parasite Using Multivariate Curve Resolution”, CAC 2006, 10th International Conference on Chemometrics in Analytical Chemistry, Aguas de Lindoia, Brazil, September 10-15, 2006

  19. : R.M. Flight* and P.D. Wentzell, “Deciphering the Transcription Patterns of a Malaria Parasite Using Multivariate Curve Resolution”, Atlantic Microarray Symposium and Exposition, Moncton, NB, August 24-25, 2006

  20. : R.M. Flight*, L.A. Calhoun, and G. Deslongchamps, “SPLASH Docking” 36th American Chemical Society Central Regional Meeting, Indianapolis, June 2-4, 2004

  21. R.M. Flight* and L.A. Calhoun, “Molecular Docking of Acetylcholine and Butyrylcholine to Acetylcholinesterase and Butyrylcholinesterase: Using Probe Fragments to Screen for the Correct Binding Orientation”, CIC-APICS Atlantic Student Chemistry Conference, Corner Brook, NF, May 2002

O. Proceedings

  1. E.C. Rouchka, R.M. Flight and H.N.B Moseley, “Proceedings of the Eleventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2012”, BMC Bioinformatics, 13(Suppl 12):A1 (not refereed)

  2. E.C. Rouchka, R.M. Flight and R Homayouni, “Proceedings of the tenth annual UT-ORNL-KBRIN Bioinformatics Summit 2011”, BMC Bioinformatics, 12(Suppl 7):A1 (not refereed) dx.doi.org/10.1186/1471-2105-12-S7-A1

  3. E.C. Rouchka, R.M. Flight and C Rinehart, “Proceedings of the ninth annual UT-ORNL-KBRIN Bioinformatics Summit 2010”, BMC Bioinformatics, 11(Suppl 4):I1 (not refereed) dx.doi.org/10.1186/1471-2105-11-S4-I1

M. Meeting Abstract

  1. B.J. Harrison, R.M. Flight, A. Eteleeb, E.C. Rouchka and J.C. Petruska, “RNASeq profiling of UTR expression during neuronal plasticity”, BMC Bioinformatics, 13(Suppl 12):A4 (not refereed) dx.doi.org/10.1186/1471-2105-13-S12-A4

  2. R.M. Flight, J.C. Petruska, B.J. Harrison and E.C. Rouchka, “categoryCompare: high-throughput data meta-analysis using gene annotations”, BMC Bioinformatics, 12(Suppl 7):A16 (not refereed) dx.doi.org/10.1186/1471-2105-12-S7-A16

I. Invited Talks

  1. R.M. Flight, “Bioinformatics in Neuroscience: New perspectives on high-throughput data analyses from effective interdisciplinary collaboration”, given at the University of Louisville Computer Science seminar series, October 14, 2011