Patrick William Nelson

Patrick W. Nelson

Research Professor Burroughs Wellcome Fellow

University of Michigan W: (734) 763-3408 Department of Mathematics F: (734) 763-0937 530 Church Street E: [email protected] Ann Arbor, MI 48109 http://www.math.lsa.umich.edu/~pwn

Education and Employment History

* Research Professor, (July 2008-present) Center for Computational Medicine and Biology, University of Michigan  Assistant Professor (tenure-track), Department of Mathematics, University of Michigan (Sept. 2002-June 2009)  Assistant Professor (non tenure-track), Department of Mathematics, University of Michigan (Sept. 2000-Aug 2002)  Post-doc, Center for Mathematics and Computation in the Life Sciences and Medicine, Department of Mathematics, Duke University (Sept. 1999-Aug 2000)  Post-doc, Institute for Mathematics and Its Applications, University of Minnesota (Sept 1998-Aug 1999)  Ph.D. in Applied Mathematics University of Washington, Seattle. Advisor: Professor James D. Murray, FRS. (June 1998)  M.Sc. in Applied Mathematics, University of Washington, Seattle. (Aug 1995)  B.S. in Mathematics, Arizona State University, Tempe. (May 1994)

Current NSF/AMS Grants and Career Awards (Total Amount: $1,756,735.00)

[1] NSF Nelson (PI), Jackson (co-PI, Math) and J. Schiefelbein (co-PI, Molecular, Cellular and Developmental Biology), UBM 905,000 2006-2011 [2] NSF Ulsoy (PI, Mech. Engineering) and Nelson (co-PI) Analysis of Time-Delayed Systems via Lambert Functions, DMS-CMS 258,735 2006-2009 [3] Burroughs Wellcome Career Award at the Scientific Interface: $538,000, 2002-2008 [4] CCMB, Nelson (PI), Jackson (co-PI), and Pietropola (co-PI), Modeling and Experiment with Diabetes, 50,000 2007-2008 [4] AMS, Michigan Math and Science Scholars Program, 5000.00, 2006

Fellowships and Past Funding

* Howard Hughes Bioinformatics Pilot Grant, Michigan: (2003-2004) $55,000 * Rackham Fellowship, Michigan: (2001) $7,000 * NSF Fellowship, University of Washington, Department of Zoology (1997)

Publications

[1] Perelson, A.S and Nelson, P.W. Mathematical Models of HIV-Dynamics in vivo. SIAM Review V41:1 1999, pgs3-44.

[2] Nelson, P.W., Murray, J.D., and Perelson, A.S. A model of HIV pathogenesis that includes an intracellular delay. Mathematical Biosciences V163:2 2000, pgs 201-215.

[3] Perelson, A.S. and Nelson, P.W. Modeling Viral Infections. In An Introduction to Mathematical Modeling in Physiology, Cell Biology and Immunology, J. Sneyd, ed., AMS , Providence, RI 2001

[4] Nelson, P.W., Mittler, J. and Perelson, A.S. Effect of drug efficacy and the eclipse phase of the viral life cycle on the estimates of HIV viral dynamic parameters. Journal of Aids V26:5 2001

[5] Nelson, P. and Hernandez, J. Modeling the immune response to parasitic infections: Leishmaniasis and Chagas disease. Comments on Theoretical Biology V6:2 2002

[6] Nelson, P.W. and Perelson, A.S. Mathematical Analysis of delay differential equations models of HIV-1 infection. Mathematical Biosciences V179:1 2002, pgs 73-94

[7] Criminale, W.O., Jackson, T.L.,and Nelson, P.W. Limit cycle-strange attractor competition. Studies in Applied Mathematics V112 2004, pages 133-60

[8] Bortz, D. and Nelson, P. Sensitivity Analysis of Nonlinear Lumped Parameter Models of HIV Infection Dynamics. Bulletin of Mathematical Biology V66 2004, pages 1009-26

[9] Nelson, P.W., Gilchrist, M., Coombs, D., Hyman, J., and Perelson, A.S. An Age-structured model of HIV infection that allows for variations in the production rate of viral particles and the death rate of productively infected cells. Mathematical Biosciences and Engineering V1:2, 2004, pages 267-88

[10] Forde, J. and Nelson, P. Applications of Sturm Sequences to Bifurcation Analysis of Delay Differential Equation Models. Journal of Mathematical Analysis and Applications, V300:2, 2004, pages 273-284

[11] Ciupe, S. , De Bivort, B., Bortz, D. and Nelson, P.. Estimating kinetic parameters from HIV primary infection data through the eyes of three different mathematical models. Mathematical Biosciences V200, 2006 pages 1 – 27.

[12] Bortz, D. and Nelson, P. Model Selection and Mixed-Effects Modeling of HIV Infection Dynamics. Bulletin of Mathematical Biology, V68(8), 2006, pages 2005-25. [13] Ciupe, S., Ribeiro, R., Nelson, P., Dusheiko, G., and Perelson, A.S. The role of cells refractory to productive infection in acute hepatitis B viral dynamics (Proceedings of the National Academy of Science, V104, 2007, pgs 5050-55)

[14] Yi, S., Nelson, P., and Ulsoy, G. Delay differential equations via the Matrix Lambert W Function and bifurcation analysis: Application to machine tool chatter, Mathematical Biosciences and Engineering, V4(2), 2007.

[15] Yi, S. Nelson, P. and Ulsoy, G. Controllability and Observability of Systems of Linear Delay Differential Equations via the Matrix Lambert W Function, Proceedings of the American Control Conference, 2007, pgs 5631-36.

[16] Yi, S., Ulsoy, G. and Nelson, P. Solution of systems of linear delay differential equations via Laplace Transformations, Proceedings 45th IEEE Conference on Decision and Control, 2006, pgs 2535-40.

[17] S. Yi, P. W. Nelson and A. G. Ulsoy, Chatter stability analysis using the matrix Lambert function and bifurcation analysis, Proc. International Conference on Manufacturing Science and Engineering, MSEC 2006, 2006.

[18] Greineder, Nelson, P. C., Dressel, A., Erba, H., and Younger, J. An in-vitro and in-silico analysis of the utility of Annexin V binding to lymphocytes as a biomarker in Emergency Department’s studies of Sepsis, Academic Emergency Medicine, V14(9), 2007, pgs 763-771

[19] Yi, S., Ulsoy, G. and Nelson, P. Analysis of systems of linear delay differential equations using the Matrix Lambert Function and the Laplace Transformation (to appear)

[20] Ciupe, S., Nelson, P., Rubiero, R. and Perelson, A. Modeling the mechanisms of acute hepatitis B virus infection, Journal of Theoretical Biology, V247(1), 2007, pgs 23-35

[21] S.Yi, P. W. Nelson and A. G. Ulsoy, Survey on analysis of time delayed systems via the Lambert W function, Dynamics of Continuous, Discrete and Impulsive Systems (Series A), 2007. (in press). [Also presented at Proc. 5th Int. Conf. on Differential Equations and Dynamical Systems, Edinburg, Texas, Dec. 2006]

[22] Yi, S., Ulsoy, G, and Nelson, P. Feedback control via Eigenvalue assignment for time delayed systems using the Lambert W Function (in press 2008), Journal of Vibration and Control

[23] S. Yi, P. W. Nelson and A. G. Ulsoy, Controllability and Observability of Systems of Linear Delay Differential Equations via the Matrix Lambert Function, IEEE Trans. Aut. Cont.,V53(3), 2008, pgs 854-60. [24] S. Yi, P. W. Nelson and A. G. Ulsoy, Eigenvalues and Sensitivity Analysis for a Model of HIV-1 Pathogenesis with an Intracellular Delay, ASME Dynamic Systems and Control Conference, (to appear 2008).

[25] S. Yi, P. W. Nelson and A. G. Ulsoy, Analysis and control of time delayed systems via the Lambert W function, IFAC, 2008, pgs 13414-19.

[26] S. Yi, P. W. Nelson and A. G. Ulsoy, Robust control and time-domain specifications for systems for delay differential equations via eigenvalue assignment, American Control Conference, 2008, ppgs 4928-33.

[27] Pietropaolo, M. and Surhigh, J. and Nelson, P. and Eisenbarth, G. Perspectives in Diabetes, Primer: Immunity and Autoimmunity, Diabetes, 2008, pgs 2872-82.

[28] Nelson, P., Smith, N., Ciupe, S., Zou, W. Omenn, G. and Pietropaolo, M. Modeling dynamic fluctuations in type 1 diabetes progression: Quantifying ß-cell variation after the appearance of islet marker antibodies (submitting)

[29] S, Yi, P. W. Nelson and A. G. Ulsoy, Effects of time-delays on stability and limits on stabilizing of first order time-delay systems, (submitted)

[30] L. Almassalha, A. Radhamohan, A. Cheng, D. Gammack, J. Schiefelbein, P. Nelson, Modeling pattern formation in the Arabidopsis Root, (submitting)

[31] S. Yi, Ulsoy, G. and Nelson, P. Controllability and Observability for HIV drug therapy models (submitting)

Professional Associations and Activities

* Director of the NSF-UBM (SUBMERGE) program at Michigan * Elected to Board of Directors, Society for Mathematical Biology, 2007 * Review Panelist, NSF (Mathematical Biology) 2006 * Review Panelist, NIH (Mathematical Biology) 2006 * External PhD reviewer, Arizona State U. and U. Western Ontario 2005 * Review Panelist, NSF/NIH 2004 * Assistant Director, Michigan Math and Science Scholars 2004-Present * Associate Editor, Mathematical Biosciences and Engineering 2004-Present * Chair, SMB's annual meeting, 2004 * Co-Organizer, Distinguished Lecture Series in Mathematical Biology 2004-2006 * Co-Director, University of Michigan's Mathematical Biology Research Group 2000- Present * Chairman, First Annual Conference on Mathematical Immunology, Duke University, April 23-26, 2000 * Reviewer, Mathematical Biosciences, JTB, JMB, BMB, Physica A and D, SIAM and IEEE 1998-Present * Book reviewer, Bulletin of Mathematical Biology and Siam Review 1999 * Visiting Research Scientist, Los Alamos National Lab, 1998-Present * Co-Organizer, sixth annual Pacific Northwest Workshop in Mathematical Biology 1998 * Member, SMB, SIAM, AMS, MAA

Invited/Contributed Talks

[2007] University of Arizona, Sept: Department of Mathematics, Plenary Speaker, World Congress on Engineering and Computer Sciences: International conference on modeling health advances, UC Berkeley [2006] SIAM Annual Meeting, Boston; University of Michigan. [2005] UM Alumni and Rotary Club of Battle Creek, MI,; Arizona State University; [2004] Michigan State University; University of Michigan; Society for Mathematical Biology’s Annual Meeting; AMS Annual Meeting. [2003] SIAM Annual Meeting, June: Montreal, CA: University of Iowa, March: Department of Mathematics [2002] Arizona State University, Nov: Department of Mathematics: University of Michigan, Oct: Bioinformatics: Rutgers University, DIMACS Workshop on The Pathogenesis of Infectious Diseases: Host-Pathogen Dynamics Piscataway, NJ, Sept: Burroughs Wellcome Meeting, Durham, NC, Aug. (Poster): Society for Mathematical Biology's Annual meeting, Knoxville, July: Symposia talk on Modeling HIV-1 Infection: Lawrence Technical University, April: Detroit [2001] International conference honoring John Jacquez, Oct: Ann Arbor: Arizona State University, December: University of Michigan, April: Applied and Interdisciplinary Seminar Series. AMS/MAA Joint Meeting, Jan.: New Orleans [2000] University of Michigan, Feb: Department of Mathematics: University of North Carolina, April: School of Public Health: Duke University, May: Workshop on Mathematical Biology [1999] Arizona State University, April: University of Minnesota, May: Duke University, May: Duke University, Oct [1998] Washington State University, January: Microbiology Colloquium, Department of Microbiology: Washington State University, January: Mathematics Colloquium, Department of Pure and Applied Mathematics: Pacific Northwest Workshop in Mathematical Biology, March: University of Minnesota Nov: IMA

Courses Taught

[2008] Math 462, Mathematical Modeling Math 463, Mathematical Biology [2007] Math 417, Linear Algebra, Math 463, Mathematical Biology [2006] Math 557, Methods of Applied Mathematics II Math 463, Mathematical Biology [2005] Math 558, Non-linear Dynamics [2004] Math 215, Calculus III Math 651, Applied Partial Differential Equations [2003] Math 651, Multiple Scales and Singular Perturbations Methods [2002] Math 462, Mathematical Modeling [2001] Math 404, Intermediate Differential Equations Math 450, Advanced Mathematics for Engineers Math 462, Mathematical Modeling [2000] Math 115, Introductory Calculus

Courses Developed and Supervised

2004 Math 651, Applied PDE’s and Multiple Scales 2001-present Math 462, Mathematical Modeling 2000-present Math 463, Mathematical Biology 1999 Duke University, Mathematical Immunology

Ph.D. Students (s), Post-docs (p) and Undergraduates (u)

[1s] Stanca Ciupe, Development and Applications of Mathematical Tools in models of infectious diseases and biological phenomenon (PhD 2005) [2s] Jonathan Forde, Delay Differenatial Equation Models in mathematical Biology (PhD 2005) [3s] Sun Yi (Ph.D. student Mechanical Engineering, Co-advisor with G. Ulsoy), 2005 – [1p] David Bortz (Post-doc) 2002-2006 [2p] David Gammack (Post-doc) 2003-2007 [1u] Tadashi Yamada (Undergraduate) 2000-2001 [2u] Louis Conlon (Undergraduate) 2003 [3u] Lydia Bilinsky (Undergraduate) 2005-2006 [4u] Noah Smith (Undergraduate) 2006 - 2008

Department Service

[2008] Undergraduate Advising, MMSS [2006] AIM Preliminary Exam Committee, Undergraduate Advising, MMSS, AIM Admissions, AIM Fellowships [2005] AIM Preliminary Exam Committee, Undergraduate Advising, Michigan Math and Science Scholars Program [2004] AIM Preliminary Exam Committee, Undergraduate Advising, MMSS Computing Committee [2003] Computing Committee, Undergraduate Advising, Mathematical Modeling Competition