Stephan Watkins

Full CV / Resume

EDUCATIONAL EXPERIENCE:
1)University of California Irvine-Irvine, CA, USA. BS, Biology, BA-Modern Chinese
2)Netherlands Cancer Institute, University of Amsterdam-Amsterdam, Netherlands. 1999-2002. Graduate University
courses, X-ray Crystallographic training.
3)University of Bern-Bern, Switzerland. MS student in Cell Biology, Dr. Daniel Schümperli October 2007-
December 2008. MS-Biology Awarded December 2008.
4)University of Bern-Bern, Switzerland, PhD, Inselspital and University Bern Cell and Molecular Biology
September 2010- October 2013. Thesis “ Computational and Cellular Analysis of Non-Covalent Pharmaceutical
Interactions With Immune Receptors Causing Adverse Drug Reactions: T Cell Receptors and Sulfamethoxazole as a
Case Study”.
WORK EXPERIENCE:
University of California Irvine Medical Center- Chao Cancer Center-Dr. Kenneth Chang, Orange California. April
1997-December 1997. Assisting in colon cancer biopsy processing and storage of cancer cell lines.
University of California-Department of Biophysics and Physiology, Irvine, California. January 1998- March 2000.
Purification of proteins, Crystallization of Proteins and structure elucidation. Work on X-ray data collection at
synchrotron sources.
Netherlands Cancer Institute-Amsterdam, Netherlands. March 2000-March 2002. Worked in Structural Biology and
Biophysics. Crystallization of protein/DNA complexes X-ray structure elucidation from synchrotron data
University of California Irvine-Department of Biophysics, Irvine, California. April 2002-December 2002. Structural
solution of varied sugar digesting enzymes. Work on crystallization of Annexins with lipids via novel techniques,
and in lipid cubic phase.
University of Bern-Department of Cell biology, Bern, Switzerland September 2007-December 2008. Purification of
RNA binding proteins, synthesis of RNA oligos, Protein-RNA binding studies, Radio labeling and Phosphor
imaging of RNA, RNA-Protein adducts.
University of Bern-Bern, Switzerland, PhD, Inselspital and University Bern Cell and Molecular Biology April 2010-
June 2013. Primary blood cell isolation, cell culture, diagnostic cell work, FACS, B and T cell transfection, Ca2++
assays, cell proliferation assays. Computational work, molecular biophysics (molecular dynamics and analysis),
docking, protein model generation and analysis, programming biological software, Java, C++, Python.
Oregon State University, Plant Pathology and Botany, Corvallis, Oregon April 2014-June 2015. Molecular
dynamics of phytopthora plant pathogenic proteins on lipid membrane systems. Surface plasmon resonance, light
polarization, protein purification and cloning.
Sea of Green Analytic, Newport, Oregon October 2015-February 2016. Set up mass-spectrometer, testing for
pesticides. General cannabis preparation and testing for pesticides, and cannabinoid concentration.
LANGUAGES: English, German.
COMPUTER SKILLS: Programming in C++, Python, JAVA, Tcl/Tk limited Fortran and PERL. Experience with structural, crystallography (xplor, yassara, CCP4, Arp/Warp) and molecular dynamics software (Gromacs, NAMD, LAMMPS).
EQUIPMENT EXPERIENCE: FACS, Plasmon Resonance, ELISpot, ITC, Rygaku X-ray machines, Fluorescence Plate,
Scintillation Machines, Mass Spectrometer Quad, Absorption/Emission Machines (Plate Based), Microscopes, Fluorescence
Microscope, Spectrophotometer, Cell Scintillation Machines, FPLC, HPLC, and assorted general lab equipment.
1
PUBLICATIONS:
Online PhD Thesis: , published draft was edited for graduation
1) , H. Van Poudroyen, T. Sixma. The Structure of Transposon Tc3a Bipartite Domain Bound to DNA
Oligo. Nucleic Acids Res. August 13, 2004,32(14):4306-12
2) Heffron, , Rhonda Moeller, Aise Taban, R. Butowt, D. DellaPenna, F. Jurnak. Resolving the Space
Group Ambiguity of Crystals of Tomato fruit Polygalacturhonase S. Acta Cryst. D Biol Crystallogr. 2003
Dec;59(Pt12):2088-93
3) Activating Interactions of Sulfanilamides with T Cell Receptors. S. Watkins, Pichler, Open J.
Immunology, September, 3(3)2013:139-157
4) S. Watkins, Pichler. T Cell Receptors Containing Variable Domain β20-1 Harbor a Nucleotide Binding
Pocket in the CDR2β Loop. Open J. Immunology, September, 3(3)2013:165-175
5) S. Watkins, Pichler Sulfamethoxazole Induces a Switch Mechanism in T cell Receptors Containing
TCRVβ20-1, Altering pHLA Recognition. PlosOne 2013 Oct 7;8(10):e76211. Doi:

6) J. Adam, N. Wuillemin, S. Watkins, H. Jamin, K. K. Eriksson, P. Villiger, S. Fontana, Pichler, D. Yerly.
Abacavir Induced T Cell Reactivity Represents an Allo-immune Response. PLoS One. 2014 Apr 21;9(4):e95339.
doi: E Collection 2014.
7) Adam, J., Wüllemin, N., Watkins, S. Yerli, D., Pichler, Drug hypersensitivity: how drugs stimulate T cells
via pharmacological interaction with immune receptors. International Archives of Allergy and Immunology,
Nov. 3rd, 2015;168:13–24.
8) Pichler, WJ , Watkins, S Interaction of small molecules with specific immune receptors: The p-i concept and
its consequences. Current Immunology Reviews, April 27th, 2014 vol 10, issue 1.
9) Molecular Dynamics Simulations of Phytopthora sojae Avirulence Factor 5, PsAvh5, Define Membrane
Binding and Inositolphosphate-3′-phosphate Interactions and Protein Mechanics Watkins, Stephan L., Tyler, Brett
( ).
10) Biophysical Analysis From Computational Refolding of Avirulence Protein Avh5 Gives Insight Into
Functional Aspects of Unstructured Sequence. Watkins, Stephan L., Tyler, Brett (unpublished)
Lectures:
Guest Lecture, ADH5 Drug Hypersensitivity Meeting, Munich, Germany, 11 – 14 April 2012. T Cell Mediated
Drug Hypersensitivity.
Student Lecturer 24th Meeting of the Swiss Immunology PhD students February, 2012. Computational,
Biochemical and Cellular Elucidation of Non-hapten Pharmaceutical Interactions (p-i) in Adverse Drug
Hypersensitivity
Student Presentation CUSO CHUV, Lausanne, 2011, 5-10 September . Emerging Pathogens, Swine Reston
Ebola Virus, Epidemiology and Spread in the Philippines.
Bern July, 2010 . Immunology Department Lecture. Can Computational Biology Using Molecular Models Help
Explain the p-i Concept in Drug Allergy?
Posters:
ADH4 Drug Hypersensitivity Meeting Rome, Italy, 22-25 April 2010, Modeling of sulfamethoxazole (SMX) binding to
sulfamethoxazole specific T cell receptor (TCR)
Graduate Cell Biology annual Presentation. January 2011. Molecular Interactions of Pharmaceuticals With T cells Causing
Drug Allergy.
Annual Congress SSAI-SGAI: Advances in immunology and allergology: from research to diagnosis and therapy, Lugano,
Switzerland, March 17th to 18th, 2011. Molecular Interactions of Sulphamethoxazole with the T cell Receptor: Deciphering
Molecular Mechanisms in Drug Hypersensitivity.
Graduate Cell Biology annual Presentation. January 2012. Computational, Biochemical and Cellular Elucidation of Nonhapten
Pharmaceutical Interactions (p-i interactions) in Adverse Drug Hypersensitivity
CGRB annual seminar, Corvallis, Oregon, February 2015. Refolding Phytophthora Sojae Avh5 Requires N-terminal
Acetylation, and Cleavage in the RxLR Motif.