BioInfo 4U


Steve's Quick Links


Steve's Home page

Steve's SGCEP Courses: Introductory Biology I and Biology II, and Environmental Science

Steve's VSU nonmajors introductory General Biology courses: I and II

Steve's VSU graduate level Molecular Phylogenetics course

Steve's FSU Introduction to Bioinformatics Laboratory course

Steve's FSU Comparative Genomics Outline

Steve's FSU GCG Workshops

Florida State University Department of Scientific Computing

High Performance Computing at Florida State University

Florida State University Biology Department

Guide to Online Higher Education in the United States

 

The end of my first private trip down the Colorado River through the Grand Canyon, AZ, USA (June 2000).

  Steven M. Thompson: Curriculum Vitae

DBA BioInfo 4U

Internet:  stevet@bio.fsu.edu

 http://www.bioinfo4u.net/

 2538 Winnwood Circle, Valdosta, GA, 31601-7953

 229-249-9751

 Personal: 6'4", 230 lbs.

 Birth date: 1-18-1956

 Spouse: Theresa M. Thompson, Ph.D.
since 12-21-1985

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, instruction, and writing and editorial assistance, with curricular implementation at all levels of higher education.

Experience

Independent Bioinformatics Consultant, Instructor, Author and Editor -- BioInfo 4U: Current client, Edanz Group Global Ltd., freelance scientific editing (hired October 2013). Previous clients have included Florida State University, Tallahassee, FL, College of Medicine, Institute of Molecular Biophysics, and Department of Chemistry and Biochemistry (April 1999-September 2010); University of Florida, Gainesville, FL. Interdisciplinary Center for Biotechnology Research (April 1999-June 2000); and the Genetics Computer Group, Madison, WI (January 2000-March 2000). Services include scientific writing and editing, research consultation/collaboration, data-mining, bioinformatics computational analyses, and the design and implementation of sequence analysis workshops, particularly those emphasizing molecular evolution.

Instructor: South Georgia College Entry Program, Valdosta, GA (January 2012-May 2012). Taught non-major, undergraduate students first semester and second semester introductory general biology, and environmental science.

Instructor: Valdosta State University Department of Biology, Valdosta, GA (August 2009-May 2011). Taught non-major, undergraduate students first and second semester introductory general biology, and a graduate-level molecular phylogenetics course (Spring 2010).

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 - included 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, Florida State University, Tallahassee, FL (non-tenure track faculty August 2001-April 2009, visiting scientist September 2000-May 2001). Provided 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, Washington State University, Pullman, WA (August 1990-May 1998). Responsibilities included user assistance, consultation, and collaboration; software evaluation and installation; facilities maintenance; resource administration; technical writing; public relations; formal and informal instruction; and curriculum development, particularly of self-paced tutorials.

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

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

Project Associate: Biochemistry/Biophysics Department, Washington State University, Pullman, WA (September 1988-August 1990). Responsibilities included 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 (September 1983- May 1985). Responsibiliies included 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:
     Visit the links for full curriculum in most cases.

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 previous 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

Valdosta State University, Department of Biology , 1500 N Patterson, Valdosta, GA 31698-00115:
Teaching and research colleagues: David L. Bechler,229-293-6063;
John F. Elder, 229-333-5762;
Theresa Grove, 229-333-5226;
Leslie S. Jones, 229-219-1337;
Jonghoon Kang, 229-333-7140; and
Brian C. Ring, 229-249-4841.

Florida State University, 600 W. College Avenue, Tallahassee, FL 32306:
Department of Scientific Computing, 400 Dirac Science Library, FSU Mail Code 4120:
Director: Max Gunzburger, 850-644-7060.
And previous Director: Joseph Travis, Department of Biological Sciences, FSU Mail Code 4295, 850-644-5434.
Supervisor while employed at DSC: Jim Wilgenbusch, 850-645-0307.
Former teaching colleagues:
Gavin Naylor, now at the College of Charleston, Biology Department,
66 George Street, Charleston, SC 29424, 843-953-5991; and
David Swofford, now at Duke University's Institute for Genome Sciences and Policy, Center for Evolutionary Genomics,
Duke Box 90338, Durham, NC 27708, 919-613-7458.
Institute of Molecular Biophysics, 91 Chieftan Way, FSU Mail Code 4380:
Previous Director: W. Ross Ellington, Department of Biological Sciences, FSU Mail Code 1330, 850-645-6900.
Research clients at Florida State University included:
Hank W. Bass, Department of Biological Sciences, 850-644-9711;
Michael Blaber, College of Medicine, 850-644-3361;
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; and
Brian G. Miller, Department of Chemistry and Biochemistry, 850-645-6570.

Workshop on Molecular Evolution
Current Co-Directors: David Hillis
University of Texas, Department of Integrative Biology,
1 University Station CO930, 2415 Speedway,
Austin, TX 78712-1095, 512-471-5792; and
Mitchell L. Sogin
Marine Biological Laboratory, The Josephine Bay Paul Center,
7 MBL Street, Woods Hole, MA 02543-1015, 508-289-7246.
Previous Director: Michael Cummings
University of Maryland, Laboratory of Molecular Evolution,
College Park, MD 20742-3360, 508-540-2736.
And previous Co-Director: Daniel B. Davison
Bristol-Myers Squibb PRI, Bioinformatics Dept. 502,
5 Research Parkway, Wallingford, CT 06492, 203-284-7958.

Interdisciplinary Center for Biotechnology Research
Associate Director: William Farmerie
University of Florida, PO Box 103622, Gainesville, FL 32610, 352-273-8030.

Center for Visualization, Analysis, and Design in the Molecular Sciences
Contact: Michael D. Griswold
Washington State University, School of Molecular Biosciences
Biotechnoloy Life Sciences 247, Pullman, WA 99164, 509-335-6281.
Supervisor while employed at VADMS: Susan J. Johns
11118 Little River Road, Glide, OR 97443, 541-496-0716.

Publications and Meeting Presentations

Thompson, S.M. (2014) Computational Biology: the Fundamentals of Sequence Based Techniques. In Computing Handbook, Third Edition: Computer Science and Software Engineering, Volume I. Diaz-Herrera, J., Gonzalez, T. and Tucker, A. editors, Taylor & Francis Group, Chapman and Hall/CRC Press, Boca Raton, FL USA.

Kang, J. and Thompson, S.M. (2012) A Little Mathematics in an Undergraduate Cell Biology Course. Biomolecules, 1(2): 1000e103.

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, 2: 97-113 .

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.

 
   
 
© 2013 Steven M. Thompson, acknowledgements and thanks to the Florida State University Biology Department for generously extending Web hosting and e-mail services beyond my FSU tenure. stevet@bio.fsu.edu
fsu seal