Michael E. Sparks January 2009

"What shortens the life-span of the existing truth is the volume of hypotheses offered to replace it;
the more the hypotheses, the shorter the time span of the truth."

--Robert M. Pirsig, Zen and the Art of Motorcycle Maintenance

Contact:

Email: mespar1@iastate.edu

Education:

• Ph.D. in Bioinformatics and Computational Biology; Iowa State University; Ames, Iowa, U.S.A.; December 2007.
  • Co-Advisors:
    • Volker Brendel, Ph.D.
    • Jonathan F. Wendel, Ph.D.
  • Committee:
    • Karin S. Dorman, Ph.D.
    • Xun Gu, Ph.D.
    • Xiaoqiu Huang, Ph.D.
• Bachelor of Science with Departmental Honors in Biology; Summa Cum Laude; University of Kentucky; Lexington, Kentucky, U.S.A.; May 2002.
• Associate in Science with High Distinction; Somerset Community College; Somerset, Kentucky, U.S.A.; December 1998.

Research Interests:

My research efforts at Iowa State University addressed eukaryotic gene structure prediction and molecular evolution.

Research Experience:

Research Computational Biologist: Spring 2009 - Present. United States Department of Agriculture.

Postdoctoral Research: Spring 2008 - Fall 2008. Volker Brendel, Ph.D., Genetics, Development, and Cell Biology, Iowa State University.

Graduate Research: Spring 2003 - Fall 2007. Volker Brendel, Ph.D., Genetics, Development, and Cell Biology, Iowa State University.

I developed algorithms and software systems for eukaryotic gene structure prediction.

Graduate Research: Fall 2004 - Summer 2005. Jonathan F. Wendel, Ph.D., Ecology, Evolution, and Organismal Biolgy, Iowa State University.

I studied patterns of molecular evolution in a variety of angiosperm lineages.

Undergraduate Research: Summer 2000, Summer 2001 - Spring 2002. Brian Rymond, Ph.D., Department of Biological Sciences, University of Kentucky.

Characterization of splicing factors in Saccharomyces cerevisiae was conducted using a variety of biochemical and molecular genetic tools.

Undergraduate Research: Summer 1999 - Spring 2000. Tim McClintock, Ph.D., Department of Physiology, College of Medicine, University of Kentucky.

I studied the role of G-proteins in olfactory signal transduction pathways of the lobster, Homarus americanus.

Teaching Experience:

Co-Instructor: (BCB 568, Computational Molecular Biology) Spring 2008. Iowa State University.

Graduate Mentor: (NIH-NSF Computational and Systems Biology Summer Institute) Summer 2007. Guided senior Computer Science major throughout a two-month research project, culminating with oral presentation. Iowa State University.

Graduate Teaching Assistant: (BCB 594, Computational Molecular Biology) Spring 2004, Spring 2005. Iowa State University.

Graduate Teaching Assistant: (NIH-NSF BBSI Summer Institute in Bioinformatics and Computational Biology) Summer 2004, Summer 2005. Iowa State University.

Undergraduate Teaching Assistant: (Principles of Biology I Lab) Summer 2001. Department of Biological Sciences, University of Kentucky.

Publications:

• Journal Papers:
  • Sparks, M.E. and Brendel, V. (2008) MetWAMer: eukaryotic translation initiation site prediction. BMC Bioinformatics. 9:381.
    [Abstract] [Print PDF]
  • Udall, J.A., Swanson, J.M., Haller, K., Rapp, R.A., Sparks, M.E., Hatfield, J., Yu, Y., Wu, Y., Dowd, C., Arpat, A.B., Sickler, B.A., Wilkins, T.A., Guo, J.Y., Chen, X.Y., Scheffler, J., Taliercio, E., Turley, R., McFadden, H., Payton, P., Klueva, N., Allen, R., Zhang, D., Haigler, C., Wilkerson, C., Suo, J., Schulze, S.R., Pierce, M.L., Essenberg, M., Kim, H., Llewellyn, D.J., Dennis, E.S., Kudrna, D., Wing, R., Paterson, A.H., Soderlund, C., and Wendel, J.F. (2006) A global assembly of cotton ESTs. Genome Research. 16:441-450.
    [Abstract] [Print PDF]
  • Gremme, G., Brendel, V., Sparks, M.E. and Kurtz, S. (2005) Engineering a software tool for gene structure prediction in higher organisms. Information and Software Technology. 47:965-978.
    [Abstract] [Print PDF]
  • Sparks, M.E. and Brendel, V. (2005) Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants. Bioinformatics. 21:iii20-iii30.
    [Abstract] [Print PDF]
• Refereed Conference Publications:
  • Sparks, M.E., Brendel, V. and Dorman, K.S. (2007) Markov model variants for appraisal of coding potential in plant DNA. Lecture Notes in Bioinformatics. 4463:394-405.
    [Abstract] [Print PDF]
• Book Chapters and Theses:
  • Brendel, V., Pan, X. and Sparks, M.E. (2004) Bioinformatics: The interpretation of genomic information. In R.F. Wilson, H.T. Stalker and C. Brummer (eds.), Legume Crop Genomics, pp. 255-266. Am. Oil Chem. Soc. Press, Champaign, IL, U.S.A.
  • Sparks, M.E. (2007) Computational annotation of eukaryotic gene structures: algorithms development and software systems. Ph.D. Thesis, Iowa State University.
    [ISU Library Holdings]

Recent Presentations:

• Departmental Seminar, Department of Statistics. 3 November 2008. Iowa State University. (oral presentation, abstract)
• International Symposium on Bioinformatics Research and Applications. 7-10 May 2007. Georgia State University. Atlanta, Georgia, U.S.A. (oral presentation)
• VIGRE-Bioinformatics and Genetic Statistics. 2 November 2006. Iowa State University. (oral presentation, abstract)
• International Botanical Congress. 17-23 July 2005. Vienna, Austria. (poster)
• International BCB-Workshop on Gene Annotation Analysis and Alternative Splicing. 13-14 December 2004. Berlin, Germany. (oral presentation)
• RECOMB. 10-13 April 2003. Berlin, Germany. (poster)

Academic Software:

• That I've exclusively (or primarily) developed:
  • MetWAMer: Translation initiation site prediction in eukaryotes.
  • IMMpractical: Markov chain models for coding fragment recognition.
  • gthXML-tools: Utilities for post-processing gthXML data.
  • BSSM4GSQ: Training of splice site models.
  • PASIF: Gene structure prediction in eukaryotes.
  • miscellaneous code
• That I've contributed to:
  • GenomeThreader: Spliced alignment-based gene annotation.
  • GeneSeqer: Spliced alignment-based gene annotation.

Computer Skills:

• Programming Languages:
  • Primary: Common Lisp, C, Python, Perl, Bash
  • Secondary: Java, Fortran, C++
• Meta-languages: XML
• Utilities: LaTeX, Octave/Matlab, R
• Operating Systems: FreeBSD, GNU/Linux

Graduate Coursework (for-credit):

• Computational Biology and/or Computer Science:
  • Computational Molecular Biology (Volker Brendel, Spring 2003)
  • Fundamental Algorithms in Computational Biology (David Fernández-Baca and Srinivas Aluru, Fall 2003)
  • Computational Techniques for Genome Assembly and Analysis (Xiaoqiu Huang, Fall 2003)
  • Principles of Artificial Intelligence (Vasant Honavar, Fall 2006)
  • Machine Learning (Vasant Honavar, Spring 2007)
• Molecular and/or Evolutionary Biology:
  • Molecular Genetics (Kristen Johansen and Tom Peterson, Spring 2003)
  • Plant Transformation Techniques (Kan Wang, Spring 2004)
  • Molecular Evolution (Jonathan F. Wendel, Fall 2004)
  • Molecular Phylogenetics (Dennis Lavrov, Spring 2006)
• Statistics:
  • Statistical Theory for Research Workers (Mark Kaiser, Fall 2002)
  • Statistical Methods in Computational Biology (Xun Gu, Spring 2004)

Supplementary Training:

• Oligonucleotide Microarray Workshop. 10-15 May 2004. University of Arizona. Tucson, Arizona, U.S.A.

International Study:

• Prof. Dr. Stefan Kurtz. Zentrum für Bioinformatik Hamburg, Universität Hamburg, Germany. June 2003.
• Dr. John W.S. Brown and Dr. Craig G. Simpson. Scottish Crop Research Institute, Dundee, Scotland. July 2003.

Funding:

• USDA MGET Fellowship Addendum, Iowa State University (Spring 2006)
• Research Assistantship with Volker Brendel, Iowa State University (Fall 2004 - present)
• USDA MGET Graduate Training Fellowship, Iowa State University (Summer 2002 - Summer 2004)

Personal:

• My wife, Wendy, studies virology.
• I have trained with the Iowa State Judo and Hapkido clubs.
• In high school, I disrupted classrooms with improvised rock bass solos (circa 1994): 1 2

References:

• Volker Brendel, Ph.D., Bergdahl Professor of Bioinformatics (mail), Department of Genetics, Development, and Cell Biology, Iowa State University.
• Jonathan F. Wendel, Ph.D., Professor and Chair (mail), Department of Ecology, Evolution, and Organismal Biology, Iowa State University.
• Karin S. Dorman, Ph.D., Associate Professor (mail), Department of Statistics, Iowa State University.

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