The end of my first private trip down the Colorado River through the Grand Canyon, AZ, USA (June 2000).	Steven M. Thompson: Curriculum Vitae
	BioInfo 4U - BookMarks
	Internet:  stevet@bio.fsu.edu
	http://www.bio.fsu.edu/~stevet/cv.html
	2538 Winnwood Circle, Valdosta, GA, 31601-7953
	229-249-9751
	Personal: 6'4", 225 lbs.
	Birth date: 1-18-56
	Spouse: Theresa M. Thompson, Ph.D. since 12-21-85

Objective

Primary professional ambition: contribute to the understanding of fundamental questions in molecular biology -- evolution, structure/function, development, and regulation -- with computer-aided genomics and sequence analysis tools, and make these powerful bioinformatics resources available to the scientific community through cooperative collaboration and instruction with curricular implementation at all levels of higher education.

Experience

Independent BioInformatics Consultant/Instructor: BioInfo 4U. Clients have included -- Susanne Cappendijk Florida Sate University, College of Medicine, 850-645-1483 (May 2009-Sept. 2010); Brian G. Miller, Florida Sate University, Department of Chemistry and Biochemistry, 850-645-6570 (May 2009-Sept. 2010); the Institute of Molecular Biophysics, at Florida State University, Tallahassee, FL (April 1999-June 2000); the Interdisciplinary Center for Biotechnology Research, at the University of Florida, Gainesville, FL (April 1999-June 2000); and the Genetics Computer Group, then in Madison, WI (January 2000-March 2000).

Services -- Research consultation/collaboration, data-mining, bioinformatics computational analyses, and the design and implementation of sequence analysis workshops, particularly using the Genetics Computer Group's (GCG, a 'retired' subsidiary of Accelrys, Inc.) Wisconsin Package SeqLab interface.

Course Faculty Member/Laboratory Instructor: The Workshop on Molecular Evolution, at the Marine Biological Laboratory, Woods Hole, MA (1992-2009, each late July/earlyAugust); and at the Centers for Disease Control and Prevention, Atlanta, GA (February, 2008).

Responsibilities -- lecture, instruction, and assistance in the computer laboratory portion of the course, particularly that related to multiple sequence alignment and analysis. Students were graduate candidates, post-doctoral fellows, and university faculty members from worldwide, diverse scientific backgrounds. Computational techniques taught included GCG's SeqLab, SeaView, MAFFT, T-Coffee, PAUP*, PHYLIP, PAML, and MrBayes.

Assistant in Research: the Department of Scientific Computing (DSC), at Florida State University, Tallahassee, FL (non-tenure track faculty August 2001-April 2009; visiting scientist September 2000-May 2001). Bioinformatics support -- research collaboration; curriculum development, instruction, and coordination (workshops, modules, and two different courses: An Introduction to Bioinformatics and Comparative Genomics); and maintenance and management of bioinformatics software and databases.

US CRDF Peer Reviewer: U.S. Civilian Research & Development Foundation Cooperative Grants Program competition (2005). Member grant proposal review committee.

Staff Scientist, Consultant, and Instructor: Center for Visualization, Analysis, and Design in the Molecular Sciences (VADMS), Washington State University, Pullman, WA (August 1990-May 1998). User assistance, consultation, and collaboration; software evaluation and installation; facilities maintenance; resource administration; technical writing; and public relations. Formal and informal instruction, and curriculum development, particularly self-paced tutorials.

Section Co-Chair: Pacific Symposium on Biocomputing -- Education Sessions (January 1996 & 1997). Organization, participant correspondence, and direction of symposium subsection concerned with the methodology, pedagogy, and curricula for teaching bioinformatics and computational biology.

USDA NRICGP Peer Reviewer: Mechanisms of Animal Disease Program (1993) and Sustaining Animal Health and Well-Being Program (1997 & 1998). Member ad hoc grant proposal review committee.

Project Associate: Biochemistry/Biophysics Department, Washington State University, Pullman, WA (September 1988-August 1990). Independent site-directed mutagenesis research on isocitrate lyase; general laboratory management and maintenance; radiation safety and control.

Graduate Assistant: Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ (1983-1985). Set up and teaching of undergraduate laboratory courses: Cellular & Molecular Biology, Medical Anatomy & Physiology, General Genetics, General Biology, and Microbiology.

Classes, workshops, seminars, and course modules:

• Valdosta State University: Taught undergraduate, non-major biology in two different courses, and one laboratory course -- BIOL 1010 "Introduction to Biology: The Evolution and Diversity of Life" Spring 2011 syllabus and lectures; BIOL 1030 "Introduction to Biology: Organismal Biology" Spring 2011 syllabus and lectures; and BIOL 1040L "Organismal Biology Lab" Fall 2009 syllabus (all three, Fall semester 2009, Biol 1010 and 1030, Spring 2010 through Spring 2011).

  I also taught a graduate student molecular phylogenetics course -- BIOL 7020 "Special Topics in Cell/Molecular Biology: Molecular Phylogenetics" syllabus and lectures (Spring 2010).

  And I developed and delivered an overview human, medical bioinformatics summary "Bioinformatics for the Naive Novice" for the VSU Continuing Education program Learning In Retirement.

  Furthermore, I delivered a lecture, "My View of Life," on deep evolution and the diversity of life for a multidisciplinary English Department course entitled "Global Images of Nature" (May, 2005 & 2008); and an overview survey seminar on bioinformatics for a mixed, diverse audience: "A Post-Genomics BioInformatics Survey . . . a whirlwind tour" (October, 2002).

• Florida State University: Developed, coordinated, and and team-taught: "An Introduction to Bioinformatics" Spring 2002 through Spring 2009; and helped to develop and team-teach Experimental Biology: "Comparative Genomics" (Fall 2004 through Spring 2007, Course Statement).

  I also developed and delivered several introductory bioinformatics course modules and seminars: including a lecture for Biomedical Sciences 5525, Bioregulation (Spring 2008); a two part, part 1 and part 2, presentation, and a condensed version for Biochemistry 5405, Molecular Biology and Biotechnology (Spring 2007, 2008 & 2009); a lecture and PowerPoint presentation for Biochemistry 5425, Molecular Biology (Spring 2001, 2002 & 2005); a presentation for the FSU undergraduate Howard Hughes Medical Institute Fellowship recipients (Summer 2003); a presentation for Library and Information Studies 4722, Information Representation (Spring 2001 & 2002); and a presentation for the Mathematics Department colloquium series concerning the development of bioinformatics curricula at Florida State University (Spring 2001); as well as an hour and half workshop for the Biology Department on Command-line Phylogenetics -- Computing Basics (Fall 2005).

• Florida State University (1999-2007) and the University of Florida (1999 & 2000), multi-hour, stand-alone, sequence analysis workshops. 1) A lecture; and a tutorial, "A Brief Introduction to Multiple Sequence Analysis through GCG's SeqLab" with its Appendices "The Genetics Computer Group" and "A Basic Guide to UNIX for Neophytes:" Basic bioinformatics with particular emphasis on multiple sequence alignment techniques using GCG's SeqLab system. 2) "Computational Methods for Rational Primer Design and Analysis:" Two scenarios, HPV L1 DNA, strain specificity design, and primate prion protein, guessmer methods. 3) "Advanced DataBase Searching Techniques and PairWise Comparisons:" The algorithms and methodology of database searching and alignment significance. 4) "A Brief Introduction to Molecular Evolutionary Phylogenetic Inference:" The rationale, methodology, and interpretation of molecular phylogenetic inference software.

• Marine Biological Laboratory Workshop on Molecular Evolution: Delivered a presentation and tutorial presenting multiple sequence alignment theory and technique particularly on using Kazutaka Katoh's alignment program MAFFT within Manolo Gouy's SeaView graphical multiple sequence alignment editor (late July/early August 2008 & 2009).

  The previous curricula -- a presentation; a tutorial, "A Brief Introduction to Multiple Sequence Analysis through GCG's SeqLab;" and its supplement, "BioInformatics -- A SeqLab Introduction" -- provided a general introduction to basic bioinformatics sequence analysis, particularly multiple sequence alignment techniques using GCG's SeqLab (each late July/early August, 1993-2007).

  "Gene Discovery and Analysis in Contig3000, a 5.4Kb Stretch of the Giardia lamblia Genome," was a four day workshop for the Josephine Bay Paul Center in comparative molecular biology and evolution using GCG's SeqLab for genome analysis, multiple sequence alignment, and feature annotation (July, 1999).

• Centers for Disease Control and Prevention Workshop on Molecular Evolution: Special Session on Phylogenetics: Presented a survey lecture on multiple sequence alignment techniques, and a tutorial on using Manolo Gouy's graphical alignment editor SeaView along with Kazutaka Katoh's alignment program MAFFT (February, 2008).

• Fort Valley State University, Fort Valley, GA: Led a two day bioinformatics survey workshop emphasizing efficient use of the GCG SeqLab graphical user interface for sequence analysis (July, 2008): PowerPoint lecture, introduction, and tutorial.

• NSF Chautauqua Course Evolutionary Bioinformatics Education, sponsored by BioQUEST and hosted by Clark Atlanta University, Atlanta, GA: Presentation and discussion of methods and issues for Multiple Sequence Alignment and Analysis, also avalaible as a PowerPoint file (May, 2003).

• North Georgia College and State University, Dahlonega, GA: Delivered seminar on setting up an undergraduate Bioinformatics Curriculum (May, 2003).

• Woods Hole Oceanographic Institution, Woods Hole, MA: Presented "Biomolecular Sequence Alignment and Analysis, Part I -- BioInformatics: A SeqLab Introduction and Part II -- A GCG Wisconsin Package SeqLab Tutorial for the Woods Hole Oceanographic Institution." This was a two day seminar consisting of an introductory lecture and a detailed tutorial for WHOI staff and faculty introducing the basics of sequence analysis and multiple sequence alignment using GCG's SeqLab (February, 2003).

• Iowa State University, Ames, IA, the Bioinformatics and Computational Biology Program and the Laurence H. Baker Center for Bioinformatics and Biological Statistics: Presented "Biomolecular Sequence Alignment and Analysis, Part I -- BioInformatics: A SeqLab Introduction and Part II -- A GCG Wisconsin Package SeqLab Tutorial for Iowa State University." This was a three day seminar consisting of an introductory lecture and a detailed tutorial for ISU graduate students, staff, and faculty introducing the basics of sequence analysis and multiple sequence alignment using GCG's SeqLab (November, 2001 & 2002).

• Washington State University: Biochemistry/Biophysics 378 and 578, "Molecular Biology Computer Techniques:" An undergraduate, introductory-level survey course, and an intensive, graduate-level, project-oriented version respectively -- lectures and computer tutorials on bioinformatics and sequence analysis, including UNIX and MacOS usage, database access, PCR primer design, fragment assembly, gene discovery, dynamic programming, dot matrixes, similarity search algorithms, multiple sequence alignment, structure prediction, molecular evolutionary phylogenetics, and a mock-professional meeting poster session final examination (in 578) (378: 1996 & 1997, 578: 1990-1998).

  Biochemistry/Biophysics 576 and 577, "Molecular Biology Techniques:" Design and delivery of one day computer techniques workshops in introductory prokaryotic sequence analysis (1993) and PCR primer design, 'universal' versus strain discriminatory, (1997 & 1998) for these wet-lab methodology courses.

  "Summer Workshop on Plant Biochemistry:" Design of afternoon computer tutorial for workshop, "BioInformatics: A Quick Tour with the RuBisCO Large SubUnit," (1996 & 1997).

  Veterinary Pharmacology 537, "Physiology and Biochemistry of Neuropeptides:" Design and implementation of afternoon workshop containing a hands-on computerized demonstration of sequence analysis applications in the pharmacology of neuropeptides and their receptors (1993 & 1996).

• Battelle Pacific Northwest Laboratory, "A JumpStart Primer:" Design and delivery of one day workshop -- bacterial genomics, environmental remediation, and getting from sequences to phylogenies (1995).

Specialized methods and techniques:

Computational sequence analysis and data mining --


including the GCG Wisconsin Package and SeqLab, EMBOSS, BLAST, FastA, SeaView, ClustalW/X, Muscle, T-Coffee, MAFFT, Mummer, Mauve, HMMer, and MEME/MAST;


Phylogenetic inference and coalescence analysis --


including PAUP*, PHYLIP, Tree-Puzzle, PhyML, RAxML, GARLI, MrBayes, PAML, ModelTest, ProtTest, Migrate-n, and Lamarc;


Genetics and sequence database maintenance --


including GCG, SRS, and ACeDB format;


Internet BioInformatics resource expertise --


including ftp/sftp/scp, telnet/ssh, X-Windowing, and WWW;


in Macintosh, DOS/MS Windows, UNIX/Linux, OpenVMS, and html environments.


Laboratory skills --


recombinant DNA technology; radioisotope methods; spectroscopy;


microscopy and cytogenetics; immunochemistry; chromatography;


cell propagation and culture; ultracentrifugation; electrophoresis.


Pedagogy includes --


instructional methodology, curriculum development and implementation,


task analysis, experimental design, and evaluation procedures and construction.

Miscellaneous experience:

Manager: Imported Auto Parts, Flagstaff, AZ (1985-1988);
   cash and inventory control, employee supervision, public relations.

Trail crew/logging operation: Fairfield Snowbowl, Flagstaff, AZ (1983-1984);
   heavy equipment, chain saw, and skiing skills.

Coconino Equipment Rental, Flagstaff, AZ (1980-1982);
   maintenance, use, repair -- all construction equipment.

Yellowfront, Flagstaff & Tempe, AZ (1977-1980);
   automotive parts, sales and service.

Northern Arizona University, Flagstaff, AZ (1974-1977);
   audio/visual technician, graphics, darkroom, and photography skills.

Personal interests:

outdoor activities -- whitewater boating, dual sport motorcycling, bicycling,
backcountry skiing, hiking, backpacking, hunting, fishing, and camping;

home and automobile -- restoration and maintenance;

culinary arts and event host -- restaurant chef much of student life in AZ and full-time cook at home.

Education

Master of Arts in the Teaching of Biology (May 1988), Northern Arizona University. Admitted to program, February, 1983; supported Fall Semester, 1983 through Spring, 1985 with tuition waivers and Graduate Assistantships. 52 graduate hours: 31 biology/microbiology, 6 chemistry, 3 computer programming, and 12 community college education. Major emphasis: molecular and cellular biology, minor: community college education. Graduate GPA: 3.9.

Bachelor of Science in Biology and Chemistry, Magna Cum Laude (May 1978), Northern Arizona University, Flagstaff, AZ; supported by Raymond and Frier foundation scholarships throughout undergraduate terms. Inaugurated to Phi Kappa Phi (October 1977). 130 undergraduate hours: 48 biology, 26 chemistry/physics, 12 calculus, 44 liberal studies education.

Public school education, Mesa, AZ (1962-1974); graduated Mesa High School, 17 of 700.

References

Biology Department

Valdosta State University

Valdosta, GA 31698

229-333-5759

Teaching and research colleagues: David L. Bechler, John F. Elder, Theresa Grove, Leslie S. Jones, Jonghoon Kang, and Brian C. Ring.

Department of Scientific Computing (DSC)

Florida State University

Tallahassee, FL 32306-4120

850-644-1010

current Director: Max Gunzburger

and previous Director: Joseph Travis

immediate Supervisor: Jim Wilgenbusch

Institute of Molecular Biophysics (IMB)

Florida State University

Tallahassee, FL 32306-3050

850-644-4764

previous Director: W. Ross Ellington

Former teaching colleague at Florida State University:

Gavin Naylor, now at the College of Charleston.

And former Florida State University teaching colleague:

David Swofford, now at Duke University's

Institute for Genome Sciences and Policy, Center for Evolutionary Genomics, 919-613-7458

Research clients at Florida State University include:

Hank W. Bass

Department of Biological Sciences, 850-644-9711

Michael Blaber

College of Medicine, 850-644-3361

Dr. Susanne Cappendijk

College of Medicine, 850-645-1483

David M. Gilbert

Department of Biological Sciences, 850-645-7583

Hong Li

Department of Chemistry and Biochemistry, 850-644-6785

Brian G. Miller

Department of Chemistry and Biochemistry, 850-645-6570

Workshop on Molecular Evolution

current Director: Mitchell L. Sogin

Marine Biological Laboratory

7 MBL Street, Woods Hole, MA 02543-1015

508-289-7246

and previous Director: Michael Cummings

Center for Bioinformatics and Computational Biology

University of Maryland

College Park, MD 20742-3360

508-540-2736

and previous CoDirector: Daniel B. Davison

Bristol-Myers Sqibb PRI, Bioinformatics Dept. 502

5 Research Parkway, Wallingford, CT 06492

203-284-7958

Interdisciplinary Center for Biotechnology Research (ICBR)

University of Florida

PO Box 110580

Gainesville, FL 32611

352-273-8030

previous Director: Sheldon M. Schuster

Center for Visualization, Analysis, and Design

in the Molecular Sciences (VADMS)

Washington State University

Mail Stop 4660

Pullman, WA 99164

contact: Michael D. Griswold

509-335-1276

and former Supervisor: Susan J. Johns

1623 47th Ave. San Francisco, CA 94122

415-759-5284

Publications and Meeting Presentations

Johnson, G.T., Elder, J.F., Thompson, S.M., Hightower, P., and Bechler, D. (2011) Phylogeny of the Freshwater Crayfish Subfamily Cambarinae Based on 16S rDNA Gene Analysis. Current Trends in Ecology, in press.

Elder, J.F., Thompson, S.M., and Kang, J. (2011) The Molecular Biology/Immunology Paradigm Extended to Bioinformatics. Journal of Clinical & Cellular Immunology, 2:1000111. 1-2.

Conejo, M.S., Thompson, S.M., and Miller, B.G. (2010) Evolutionary Bases of Carbohydrate Recognition and Substrate Discrimination in the ROK Protein Family. Journal of Molecular Evolution, 70: 545-556.

Thompson, S.M. (2009) An Introduction to Multiple Sequence Alignment -- and the T-Coffee Shop. Beyond just aligning sequences: How good can you make your alignment, and so what? In Bioinformatics for Systems Biology. Krawetz, S.A., editor, Humana Press, Totowa, NJ USA.

Larion, M., Moore, L.B., Thompson, S.M., and Miller, B.G. (2007) Divergent Evolution of Function in the ROK Sugar Kinase Superfamily: Role of Enzyme Loops in Substrate Specificity. Biochemistry 46: 13564-13572.

Thompson, S.M. (2004) Multiple Sequence Alignment and Analysis: Part I -- An Introduction to the Theory and Application of Multiple Sequence Analysis, in Computational Genomics: Theory and Application. Grant, R.P., editor, Horizon Scientific Press, Norfolk, UK.

Thompson, S.M. (2004) Multiple Sequence Alignment and Analysis: Part II -- A Practical Tour of SeqLab, the Accelrys GCG Wisconsin Package Graphical User Interface, in Computational Genomics: Theory and Application. Grant, R.P., editor, Horizon Scientific Press, Norfolk, UK.

Thompson, S.M. (2003) An Introduction to Multiple Sequence Alignment and Analysis, in Introduction to Bioinformatics, A Theoretical And Practical Approach. Krawetz, S.A. and Womble, D.D., editors, Humana Press, Totowa, NJ USA.

Thompson, S.M. (2003) Multiple Sequence Alignment and Analysis: The SeqLab Interface -- a Practical Guide, in Introduction to Bioinformatics, A Theoretical And Practical Approach. Krawetz, S.A. and Womble, D.D., editors, Humana Press, Totowa, NJ USA.

Thompson, S.M. (2003) Constructing and Refining Multiple Sequence Alignments with PileUp, SeqLab, and the GCG Suite, in Current Protocols in Bioinformatics. Baxevanis, A.D., Davison, D.B., Page, R.D., Petsko, G.A., Stormo, G.D. and Leonard, S.A., editors, John Wiley & Sons, Hoboken, NJ USA.

Bernett, M.J., Blaber, S.I., Scarisbrick, I.A., Dhanarajan, P. Thompson, S.M., and Blaber, M. (2002) Crystal Structure and Biochemical Characterization of Human Kallikrein 6 Reveals that a Trypsin-like Kallikrein is Expressed in the Central Nervous System. Journal of Biological Chemistry, 277: 24562-24570.

Ristow, S.S., Grabowski, L.D., Thompson, S.M., Warr, G.W., Kaattari, S.L., de Avila, J.M., and Thorgaard, G.H. (1999) Coding Sequences of the MHC II Beta Chain of Homozygous Rainbow Trout (Oncorhynchus mykiss). Developmental and Comparative Immunology, 23: 51-60.

Thompson, S.M. and Speth, R.C. (June, 1997) G-Protein Coupled Receptors: Comparative Analysis and Phylogeny, poster presentation at Gordon Research Conference on Ligand Recognition and Molecular Gating, Sandberg, K., chair, Plymouth State College, Plymouth, NH USA.

Johns, S.J., Thompson, S.M., and Dunker, A.K. (1995) An Introductory Course in Computational Molecular Biology: Rationale, History, Observations, and Course Description, in Proceedings of the 1996 Pacific Symposium on Biocomputing. Hunter, L. and Klein, T.E., editors, World Scientific, River Edge, NJ USA.

Speth, R.C., Thompson, S.M., and Johns, S.J. (1995) Angiotensin II Receptors: Structural and Functional Considerations, in Tissue Renin--Angiotensin Systems. Mukhopadhyay, A. and Raizada, M.K., editors, Plenum Press, New York, NY USA.

Thompson, S.M., Johns, S.J., and Dunker, A.K. (1995) Educational Issues in Biocomputing, Session Introduction, in Proceedings of the 1996 Pacific Symposium on Biocomputing. Hunter, L. and Klein, T.E., editors, World Scientific, River Edge, NJ USA.

Suarez, C.E., Thompson, S.M., McElwain, T.F., Hines, S.A., and Palmer, G.H. (1994) Conservation of Oligopeptide Motifs in Rhoptry Proteins from Erythroparasitic Protozoa. Experimental Parasitology, 78: 246-251.