Scott T. Cooper, Professor of Biology

Phone: (608)-785-6983    E-Mail: 


B.S. Biochemistry - Michigan State University, 1986

Ph.D. Biochemistry - University of Wisconsin-Madison, 1992

Courses Currently Taught: 

BIO 103 Introductory Biology

BIO 105 General Biology

BIO 433 Radiation Biology

BIO 435 Molecular Biology

BIO 436 Molecular Biology Lab

BIO 440 Bioinformatics

BIO 443 Molecular Mechanisms of Disease and Drug Action


Advisor for UWL Triathlon Club

Teaching interests:

Introductory Biology is a non-majors course that uses issues-based modules to teach the basic elements of biology.  Units include Ecology, Cells, Genetics, Evolution and Populations.  The lab is broken into three four-week units on Ecology, Cells, and Genetics.  Students work in groups to design experiments and write lab reports.

General Biology is a majors course that uses in-class problem-solving to give students a firm foundation in biology as a preparation for future science courses.  Units include Ecology, Cells, Genetics, Evolution and Populations.  The lab is broken into three four-week units on Ecology, Cells, and Genetics.  Students work in groups to design experiments and write lab reports.

Molecular Biology lecture consists of four sections. In the first we look at the central dogma and regulation of gene expression.  Next we focus on basic biotechnology techniques by examining the cloning and expression of human tissue plasminogen activator.   In the next section the course we examine cellular processes including cancer, developmental biology and the production of transgenic and cloned animals. Finally we explore the role of proteomics and genomics in elucidating the function of BRCA1.

In Molecular Biology Lab students work on two projects that are part of the research programs of other faculty in biochemistry or cell and molecular biology.  This allows the students to participate in a real research experiment. This also exposes them to several aspects of biotechnology research; yeast-two hybrid screening, site directed mutagenesis, cloning, and computer modeling. The students write their results in a peer-reviewed journal format. 

Bioinformatics is a team taught course that focuses on the many applications of bioinformatics and the theoretical algorithms underlying these computer programs.   There are four sections to the course; Databases, Phylogenetics, Genomics and Proteomics.

Molecular Basis of Disease and Drug Action examines the biological basis of many non-infectious and non-cancerous diseases and the drugs used to treat them.  For each disease the students are given three perspectives; pathology, pharmacology and clinical.  This course is team taught by Scott Cooper (pathology), Aaron Monte (pharmacology) and several M.D.s from local hospitals (clinical).  There are five units in the course; Pathology and Pharmacology, Inflammation, Cardiovascular, Neurological, and Genetics.  Students also give oral presentations on assigned diseases.

Radiation Biology is a course primarily for nuclear medical technology (NMT) and radiation therapy (RT) majors.  It focuses on the effects of radiation on biological systems.  The lab involves both exploring the properties of radiation, and the effects of radiation on biomolecules and cells.


Research interests:

Structure function studies of anticoagulants:  Uses of molecular tools in environmental sciences

Blood Clotting

My students are working on several projects related to understanding blood clotting

Environmental Science

My students have worked on several projects in collaboration with faculty in the River Studies Program at UWL.  Many of these use techniques used in medical diagnostics and forensics.


Graduate Student Theses: 

  1. Karl Richters, Effects of hibernation on blood clotting
  2. Travis Melin, The Protective Mechanism of Platelet Shape Change in Hibernating Thirteen-Lined Ground Squirrels (Spermophilus tridecemlineatus), 2009
  3. Geoff Pesanka, Screening for fungal anticoagulants
  4. Nate Susnik, Effects of methylmercury on fish reproduction, 2008
  5. Andrea Pierce, Role of antithrombin residues in cofactor activation and inhibition of thrombin bound to thrombomodulin
  6. Joe Balsanek, Microsatellite Analysis to differentiate between hatchery-bred and naturalized brown trout (Salmo trutta), 2007
  7. Patrick Gonzales, Shifting of the heparin binding site from the D-helix to the H-helix of human antithrombin, 2005
  8. Faye Ellis, Expression of protein C inhibitor with attached FLAG-tag in 293T cells, 2004
  9. Joshua D. Spencer, Role of the amino-terminal loop of antithrombin in cofactor activation and inhibition of thrombin bound to thrombomodulin, 2003
  10. Laureano Camacho, Conversion of the D- and H-helices of human antithrombin to resemble those of protein C inhibitor, 2002
  11. Tim Walston, Role of the H-helix in serpin inhibition of thrombin bound to thrombomodulin, 2000



Published Peer Reviewed Journal Articles:

  1. Patrick R. Gonzales, Timothy D. Walston, Laureano O. Camacho, Dana M. Kielar, Frank C. Church, Alireza R. Rezaie, Scott Cooper. Mutation of the H-helix in Antithrombin Decreases Heparin Stimulation of Protease Inhibition.  BBA Proteins and Proteomics, 1774 (11), pp 1431-1437, 2007.

  2. Fortenberry YM, Whinna HC, Cooper ST, Myles T, Leung LL, Church FC. Essential thrombin residues for inhibition by protein C inhibitor with the cofactors heparin and thrombomodulin. J Thromb Haemost, 5(7):1486-92, 2007.

  3. Scott Cooper, Robin Tyser, Mark Sandheinrich.  The Benefits of Linking Assignments to Online Quizzes in Introductory Biology Courses. Journal of Online Learning and Teaching, Vol. 3, No.3, pp. 214-221, 2007.

  4. Scott Cooper, Deborah Hanmer, Bill Cerbin. Problem Solving Modules in Large Introductory Biology Lectures Enhance Student Understanding.  American Biology Teacher, 68:524-9, 2006.
  5. Todd Weaver and Scott Cooper.  Exploring Protein Function and Evolution Using Free Online Bioinformatics Tools. Biochemistry and Molecular Biology Education. Vol. 33, No. 5, pp. 319-322, 2005.
  6. Scott Cooper.  The use of MERLOT in biochemistry and molecular biology education.  Biochemistry and Molecular Biology Education. Vol. 33, No. 5, pp. 323–324, 2005.
  7. Glasscock, L.N., S.M. Rehault, C.W. Gregory, Cooper, S.T., Jackson, T.P., Hoffman, M., and F.C. Church.  Protein C inhibitor (Plasminogen Activator Inhibitor-3) expression in the CWR22 prostate cancer xenograft. Exp. Molec. Pathol. 79(1):23-32, 2005.

  8. Réhault, S.M., Zechmeister-Machhart, M.,, Binz, N.M., Fortenberry, Y.M., Cooper, S.T., Geiger, M., and F.C. Church Characterization of recombinant human protein C inhibitor expressed in Escherichia coli. Biochimica Biophysica Acta.  1748: 57-65, 2005
  9. R.J. Haro, R. Gillis and S. T. Cooper. First Report of a Terrestrial Slug (Arion fasciatus) Living in an Aquatic Habitat. Journal of Malacologia. 45; 2004.

  10. Likui Yang, Chandrashekhara Manithody, Timothy D. Walston, Scott T. Cooper, and Alireza R. Rezaie. Thrombomodulin enhances the reactivity of thrombin with protein C inhibitor by providing both a binding-site for the serpin and allosterically modulating the activity of thrombin. J. Biol. Chem. 278; p. 37465-37470, 2003.

  11. Laura N. Glasscock, Bruce Gerlitz, Scott T. Cooper, Brian W. Grinnell and Frank C. Church. Basic residues in the 37-loop of activated protein C modulate inhibition by protein C inhibitor but not by 1-antitrypsin, BBA - Proteins and Proteomics 1649; 106-117, 2003.

  12. Cooper, S.T., Rezaie, A.R., Church, F.C., and Esmon, C.T.  Inhibition of a Thrombin Anion-Binding Exosite-2 Mutant by the Glycosaminoglycan-dependent Serpins Protein C Inhibitor and Heparin Cofactor II.  Thrombosis Reseach 16: 67-73, 2002.
  13.  Jackson, T.P., Cooper, S.T. and Church, F.C.  Assessment of the Protein C Inhibitor-Urokinase Interaction. J Protein Chem 16:  819-828, 1997.

  14. Cooper, S.T., Neese, L.L., Dicuccio, M., Liles, D.K., Hoffman, M. and Church, F.C.  Heparin-binding Serpins are not Released Following Intravenous Heparin Injection.  Clinical and Applied Thrombosis/Hemostasis 2: 185-191, 1996.

  15. Cooper, S.T., Whinna, H.C., Jackson, T.P. and Church, F.C.  Intermolecular Interactions Between Protein C Inhibitor and Coagulation Proteases.  Biochemistry 34, 12991-12997,  1995.

  16.  Rezaie, A.R., Cooper, S.T., Church, F.C., and Esmon, C.T.  Protein C Inhibitor is a Potent Inhibitor of the Thrombin-thrombomodulin Complex. J. Biol. Chem 270: 25336-9, 1995.

  17. Cooper, S.T. and Church, F.C.  Reactive Site Mutants of Recombinant Protein C Inhibitor.  Biochim. Biophys. Acta 1246. 29-33, 1995.

  18. Hoffman, M. and Cooper, S.T.  Thrombin Enhances Monocyte Secretion of Tumor Necrosis Factor and Interleukin-1 by Two Distinct Mechanisms.  Blood Cells, Molecules and Diseases 21: 156-167, 1995.

  19. Phillips, J.E., Cooper, S.T., Potter, E.E. and Church, F.C.  Mutagenesis of Recombinant Protein C Inhibitor Reactive Site Residues Alters Target Proteinase Specificity.  J. Biol. Chem. 26:  16696-16700, 1994.

  20. Cooper, S.T. and Attie, A.D.  Apolipoprotein R: A new member of the short consensus repeat family of proteins.  Biochemistry 31:  12328-12336, 1992.

  21. Cooper, S.T., Aiello, R.J., Checovich, W.J. and Attie, A.D.  Low density lipoprotein heterogeneity in spontaneously hypercholesterolemic pigs.  Mol. Cell. Biochem. 113: 133-140, 1992.

Published Non-Peer Reviewed Articles: 

  1. Cooper, S.T.  Integrating bioinformatics into undergraduate courses. Biochemistry and Molecular Biology Education 29:167-168, 2001

  2. Cooper, S.T. and Church, F.C.  PCI: Protein C Inhibitor? Adv Exp Med Biol 425: 45-54, 1997.



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