CV

Robert M Flight, PhD

Curriculum Vitae


Education
Research Interests
Professional Experience
Honors & Awards
Professional Affiliations
Professional Activities
Research Grants and Contracts
Research Publications and Presentations
  Refereed Journal Publications
  Conference Presentations
  Proceedings
  Meeting Abstract
  Invited Talks


Center for Regulatory & Environmental Analytical Metabolomics (CREAM)
Department of Chemistry
Rm 309, Chemistry Building
University of Louisville
2320 South Brook Street
Louisville, KY  40292

work: 502 509 1827
email: robert dot flight at louisville dot edu


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


Period Position Location
2013-PresentPostDoctoral ScholarUniversity of Louisville - CREAM
2010-2013PostDoctoral Research AssociateUniversity of Louisville - KBRIN
2009-2010Research AssistantDalhousie University
2004-2009Graduate Research / Teaching AssistantDalhousie University
2007 (08-12)Research Assistant1Institute of Marine Biosciences - National Research Council
2002-2004Graduate Research / Teaching AssistantUniversity of New Brunswick
1999-2002Teaching AssistantUniversity of New Brunswick

1. This work was performed as part of a MITACS internship awarded to RM Flight


Honors and Awards


Dalhousie UniversityKenneth T. Leffek Prize for best PhD thesis in the Department of Chemistry2009
University of New BrunswickFaculty of Science Dean's List2002
University of New BrunswickDepartment of Chemistry Analytical Chemistry Award2001
University of New BrunswickDr. Willard Miles Jenkins Scholarship1997


Professional Affiliations


International Society for Computational Biology
Canadian Society for Systems Biology


Professional Activities


  • Organizing committee for University of Louisville Bioinformatics Journal Club, 2010-Present
  • Organizing cross-training workshops for Bioinformatics PostDocs and staff at University of Louisville, 2011-Present
  • Dalhousie University CGSS Graduate Student Seminar Evaluation Committee, 2006-2007
  • Organizing committee member of the CIC-APICS Student Chemistry Conference, 2000


Research Grants and Contracts


AgencyTypeAmountPeriodTitle
MITACS2Internship$15000 (CDN)2007 (08-12)DNA Microarray Studies of the Effect of Diet on Halibut

2. Mathematics of Information Technology and Complex Systems (Canadian NCE). Industrial partner was the Institute of Marine Biosciences of the National Research Council at Halifax, NS.



Research Publications and Presentations


Refereed Journal Publications
Conference Presentations
Proceedings
Meeting Abstract
Invited Talks


Refereed Journal Publications

Google Scholar Citations Page

  1. B.J. Harrison, R.M. Flight, C. Gomes, G. Venkat, S.R. Ellis, U. Sankar, J.L. Twiss, E.C. Rouchka and 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", 2013, J Comp Neurol dx.doi.org/10.1002/cne.23398
  2. F. Mohammad, R.M. Flight, B.J. Harrison, J.C. Petruska, E.C. Rouchka, "AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities", BMC Bioinformatics, 13:229 doi:10.1186/1471-2105-13-229
  3. F. Mohammad, 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 doi:10.1109/BIBE.2011.49
  4. F. Mohammad, 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 doi:10.1109/BIBE.2011.9
  5. 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 doi:10.1016/j.chemolab.2010.04.003
  6. 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 doi:10.1016/j.aquaculture.2009.11.001
  7. 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 doi:10.1089/omi.2009.0096
  8. 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 doi:10.1016/j.atmosenv.2009.05.018
  9. 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 doi:10.1007/s10126-009-9211-4
  10. R.M. Flight and P.D. Wentzell, “Potential Bias in GO::TermFinder”, Briefings in Bioinformatics, 2009, 10(3):289-294 doi:10.1093/bib/bbn054
  11. 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 doi:10.1111/j.1095-8649.2008.01861.x
  12. 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 doi:10.1007/s00216-007-1617-0


Conference Presentations


(*=presenting author, §=poster)
  1. 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 Full Text
  2. §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
  3. 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
  4. §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
  5. 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
  6. 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
  7. §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
  8. §B. Wielens*, R.M. Flight, and P.D. Wentzell, “The Gene Machine — Software for Gene Expression Analysis”, Poster Presentation, Atlantic OMICS Symposium and Expo, Moncton, NB, Canada, August 19-20, 2008
  9. §J. Onochie*, R.M. Flight, and P.D. Wentzell, “Investigation of Gene Expression Profiles in Saccharomyces Cerevisiae Exiting Stationary Phase”, Poster Presentation, Atlantic OMICS Symposium and Expo, Moncton, NB, Canada, August 19-20, 2008
  10. 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
  11. §J. Boutillier*, R. Flight, and P. Wentzell, “Gridding Reproducibility in Spotted DNA Microarrays”, Atlantic OMICS Symposium and Expo, Moncton, NB, Canada, August 2007
  12. 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
  13. §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
  14. §R.M. Flight*, L.A. Calhoun, and G. Deslongchamps, “SPLASH Docking” 36th American Chemical Society Central Regional Meeting, Indianapolis, June 2-4, 2004
  15. 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


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 2012, 13(Suppl 12):A1 (not refereed) doi: 10.1186/1471-2105-13-S12-A1
  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) doi: 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)
    doi: 10.1186/1471-2105-11-S4-I1


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 2012, 13(Suppl 12):A4
    doi: 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)
    doi: 10.1186/1471-2105-12-S7-A16


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
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