Home > College of Arts and Sciences > Biology > Steve Thompson
Biology Department Instructor Steve Thompson
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Curriculum Vitae |
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http://www.valdosta.edu/~stthompson/ |
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229-249-9751 |
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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
Instructor: Valdosta State University Biology Department, Valdosta, GA (August 2009-present). Teach non-major, undergraduate students general biology in two lectures and one laboratory course:
- BIOL 1010 Introduction to Biology: The Evolution and Diversity of Life Section C -- Lectures.
- BIOL 1030 Introduction to Biology: Organismal Biology Section B and Section D -- Lectures.
- BIOL 1040L Organismal Biology Lab Section M. Lectures, where applicable, are found through appropriate links in the above list.
Independent BioInformatics Consultant/Instructor: BioInfo 4U.
Present clients --
Dr.
Susanne Cappendijk, Florida Sate
University, College of Medicine,
850-645-1483; and Dr.
Brian G. Miller, Florida Sate
University, Department of
Chemistry and Biochemistry, 850-645-6570
(both, from May 2009-present).
Previous clients have included -- 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 --
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, and individual
research consultation and collaboration.
Course Faculty Member/Laboratory Instructor: The Workshop on Molecular Evolution, at the Marine Biological Laboratory, Woods Hole, MA (1992-present, every 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 are graduate candidates, post-doctoral fellows, and university faculty members from worldwide, diverse scientific backgrounds. Computational techniques taught include 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 (not currently being taught):
- 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).
- 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. As well as a hour and half workshop
on Command-line
Phylogenetics -- Computing Basics (Fall 2005).
- Florida State University,
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).
- Marine Biological Laboratory
Workshop on
Molecular Evolution: Delivered a new
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 (every 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.
- Valdosta State
University, Valdosta, GA: Delivered 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).
- 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, also available as a Microsoft
PowerPoint
file
(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).
- Washington State University 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.
- Washington State University "Summer Workshop on Plant Biochemistry:" Design of afternoon computer tutorial for workshop, "BioInformatics: A Quick Tour with the RuBisCO Large SubUnit," (1996 & 1997).
- Washington State University 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).
- 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).
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.
- 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.
- microscopy and cytogenetics; immunochemistry; chromatography;
- Pedagogy includes --
- instructional methodology, curriculum development and
implementation,
- task analysis, experimental design, and evaluation procedures and construction.
cash and inventory control, employee supervision, public relations.
heavy equipment, chain saw, and skiing skills.
maintenance, use, repair -- all construction equipment.
automotive parts, sales and service.
audio/visual technician, graphics, darkroom, and photography skills.
backcountry skiing, hiking, backpacking, hunting, fishing, and camping;
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
- Department of Scientific Computing (DSC)
- Florida State University
- Tallahassee, FL 32306-4120
- 850-644-1010
- current Director: Dr. Max Gunzburger
- and previous Director: Dr. Joseph Travis
- immediate Supervisor: Dr. Jim Wilgenbusch
- Institute of Molecular Biophysics (IMB)
- Florida State University
- Tallahassee, FL 32306-3050
- 850-644-4764
- previous Director: Dr. W. Ross Ellington
- Teaching colleague at Florida State University:
- Dr. Gavin Naylor
- Department of Scientific Computing, 850-645-0314
- And former Florida State University teaching colleague, now at Duke University:
- Dr. David Swofford
- Institute for Genome Sciences and Policy, Center for Evolutionary Genomics, 919-613-7458
- Research clients at Florida State University include:
- Dr. Hank W. Bass
- Department of Biological Sciences, 850-644-9711
- Dr. Michael Blaber
- College of Medicine, 850-644-3361
- Dr. Susanne Cappendijk
- College of Medicine, 850-645-1483
- Dr. David M. Gilbert
- Department of Biological Sciences, 850-645-7583
- Dr. Hong Li
- Department of Chemistry and Biochemistry, 850-644-6785
- Dr. Brian G. Miller
- Department of Chemistry and Biochemistry, 850-645-6570
- Workshop on Molecular Evolution
- current Director: Dr. Michael Cummings
- Center for Bioinformatics and Computational Biology
- University of Maryland
- College Park, MD 20742-3360
- 508-540-2736
- and previous Director: Dr. Mitchell L. Sogin
- Marine Biological Laboratory
- 7 MBL Street, Woods Hole, MA 02543-1015
- 508-289-7246
- and previous CoDirector: Dr. 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: Dr. Sheldon M. Schuster
- Center for Visualization, Analysis, and Design
- in the Molecular Sciences (VADMS)
- Washington State University
- Mail Stop 4660
- Pullman, WA 99164
- contact: Dr. Michael D. Griswold
- 509-335-1276
- and former Supervisor: Susan J. Johns
- 1623 47th Ave. San Francisco, CA 94122
- 415-759-5284
- Florida State University
Publications and Meeting Presentations
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.