2. Publications

Publications:

Updated citation information is available at
http://scholar.google.com/citations?user=Ryq7X_0AAAAJ&hl=en


Journal Publications

  1. J. Martinez-Picado, R. Zurakowski, M.J. Buzon, M. Stevenson.  Episomal HIV-1 DNA and its relationship to other markers of HIV-1 persistence. 2018, Retrovirology Vol 15(1). 10.1186/s12977-018-0398-1
  2. E. Fabian Cardozo, Michael J. Piovoso, and Ryan Zurakowski.  Increased inflammation in sanctuary sites may explain viral blips in HIV infection.  2016, IET Systems Biology Vol 10(4), pp. 153-166.  10.1049/iet-syb.2015.0066
  3. Ryan Zurakowski. Using the Tools we Have: Low-efficacy Vaccines and HIV.  2016, EBioMedicine Vol. 2(12), pp. 1867-1868.  doi:10.1016/j.ebiom.2015.12.007
  4. Bethany Allik, Cory Miller, Michael J Piovoso, and Ryan Zurakowski. The Tobit Kalman Filter: An Estimator for Censored Measurements. 2015, IEEE Trans. of Control Systems Technology Vol. 24(1), pp. 365-371. 10.1109/TCST.2015.2432155
  5. Maria Buzon, Florencia Pareyra, Enrique Martin-Gayo, Zhengyu Ouyang, Hon Sun, Jonathan Li, Michael Piovoso, Amy Shaw, Judith Dalmau, Nadine Zangger, Javier Martinez-Picado, Ryan Zurakowski, Xu G Yu, Amalio Telenti, Bruce D. Walker, Eric S. Rosenberg, and Mathias Lichterfeld. Long-term Antiretroviral Treatment Initiated in Primary HIV-1 Infection Affects the Size, Composition and Decay Kinetics of the Reservoir of HIV-1 Infected CD4 T Cells.  2014, Journal of Virology, Vol. 88(17), pp. 10056-10065.  http://dx.doi.org/10.1128/JVI.01046-14
  6. Maria J Buzon, Hong Sun, Chun Li, Amy Shaw, Katherine Seiss, Zhengyu Ouyang, Enrique Martin-Gayo, Jin Leng, Timothy J Henrich, Jonathan Z Li, Florencia Pereyra, Ryan Zurakowski, Bruce D Walker, Eric S Rosenberg, Xu G Yu and Mathias Lichterfeld, HIV-1 persistence in CD4+ T cells with stem cell like properties.  2014, Nature Medicine, Vol. 20, pp. 139-142. http://dx.doi.org/10.1038/nm.3445
  7. E. Fabian Cardozo, Rutao Luo, Michael J. Piovoso and Ryan Zurakowski, Spatial modeling of HIV cryptic viremia and 2-LTR formation during raltegravir intensification.  2014, Journal of Theoretical Biology, Vol. 345, pp. 61-69. http://dx.doi.org/10.1016/j.jtbi.2013.12.020
  8. Bethany Allik, Mark Ilg and Ryan Zurakowski, Ballistic Roll Estimation Using EKF Frequency Tracking and Adaptive Noise Cancellation, 2013, IEEE Trans. Aerospace and Electronic Systems Vol. 49 No. 4 pp. 2546-2553. http://dx.doi.org/10.1109/TAES.2013.6621835
  9. Rutao Luo, E. Fabian Cardozo, Michael J Piovoso, Hulin Wu, Maria J Buzon, Javier Martinez-Picado, Ryan Zurakowski, Modelling HIV-1 2-LTR dynamics following raltegravir intensification.  J. Royal Society Interface, 2013 10(84) pp. 20130186. http://dx.doi.org/10.1098/rsif.2013.0186
  10. Rutao Luo, Michael J. Piovoso and Ryan Zurakowski, Modeling Uncertainty in Single-Copy Assays for HIV.  Journal of Clinical Microbiology, 2012 50(10):3382-3383. http://dx.doi.org/10.1128/JCM.01254-12
  11. Rutao Luo, Michael J. Piovoso,  Javier Martinez-Picado, Ryan Zurakowski, HIV Model Parameter Estimates from Interruption Trial Data Including Drug Efficacy and Reservoir Dynamics.  PLoS ONE 7(7):2012 e40198. http://dx.doi.org/10.1371/journal.pone.0040198
  12. E Fabian Cardozo and Ryan Zurakowski, Robust Closed-Loop Minimal Sampling Method for HIV Therapy Switching Strategies, IEEE Trans. Biomedical Engineering, 2012, Vol. 59, No. 8, pp. 2227-2234.  http://dx.doi.org/10.1109/TBME.2012.2201479
  13. Rutao Luo, Michael J. Piovoso, Javier Martinez-Picado, Ryan Zurakowski, Optimal antiviral switching to minimize resistance risk in HIV therapy.  PLoS ONE 6(11):2011 e27047. http://dx.doi.org/10.1371/journal.pone.0027047
  14. Ryan Zurakowski, Nonlinear observer output-feedback MPC treatment scheduling for HIV, Biomedical Engineering Online, 2011, Vol. 10, No. 40,  pp. 1-16.  http://dx.doi.org/10.1186/1475-925X-10-40
  15. Rutao Luo, LaMont Cannon, Jason Hernandez, Michael J. Piovoso, Ryan Zurakowski, Controlling the Evolution of Resistance.  Journal of Process Control.  2011. Vol. 21, No. 3, pp. 367-378. http://dx.doi.org/10.1016/j.jprocont.2010.11.010
  16. Ryan Zurakowski, Dominik Wodarz, Model-driven approaches for in Vitro combination therapy using ONYX-015 replicating oncolytic adenovirus. Journal of Theoretical Biology, 2007. Vol. 245, pp. 1–8 . http://dx.doi.org/10.1016/j.jtbi.2006.09.029
  17. Ryan Zurakowski and Andrew R. Teel,  A model predictive control based scheduling method for HIV therapy. Journal of Theoretical Biology, 2006. Vol. 238, No. 2, pp. 368-82. http://dx.doi.org/10.1016/j.jtbi.2005.05.004
  18. Ryan Zurakowski, Michael J. Messina, Sezai E. Tuna and Andrew R. Teel, Treatment scheduling for HIV using nonlinear model predictive control.  Australian Journal of Electrical and Electronics Engineering, 2005, Vol. 2, No. 1.

Refereed Conference Publications

  1. Joshua A. Blotnick, Cesar A. Vargas-Garcia, John J. Dennehy, Ryan Zurakowski and Abhyudai Singh, The effect of multiplicity of infection on the temperateness of a bacteriophage: Implications for viral fitness.  IEEE Conference on Decision and Control 2017, pp. 1641-1645. 10.1109/CDC.2017.8263885
  2. Aditya Jagarapu, LaMont Cannon and Ryan Zurakowski, Experiment design for early molecular events in HIV infection.  American Control Conference 2017, pp. 122-127.  10.23919/ACC.2017.7962941
  3. LaMont Cannon, Aditya Jagarapu, Cesar A. Vargas-Garcia, Michael J. Piovoso and Ryan Zurakowski, Implications of measurement assay type in design of HIV experiments.  IEEE Conference on Decision and Control 2017 pp. 4106-4111.  10.1109/CDC.2017.8264262
  4. Bethany Allik, Michael J. Piovoso, and Ryan Zurakowski, Recursive Estimation with Quantized and Censored Measurements.  American Control Conference, 2016 pp. 5130-5135. 10.1109/ACC.2016.7526473
  5. LaMont Cannon, Cesar A. Vargas-Garcia, Michael J. Piovoso, and Ryan Zurakowski, Prospective HIV clinical trial comparison by expected Kullback-Leibler divergence.  American Control Conference, 2016 pp. 1295-1300. 10.1109/ACC.2016.7525096
  6. Bethany Allik, Cory Miller, Michael J. Piovoso and Ryan Zurakowski, Nonlinear Estimators for Censored Data: A Comparison of the EKF, the UKF and the Tobit Kalman Filter. American Control Conference, 2015 pp. 5146-5151. 10.1109/ACC.2015.7172142
  7. Cory Miller, Bethany Allik, Michael J. Piovoso and Ryan Zurakowski, Estimation of Mobile Vehicle Range & Position Using the Tobit Kalman Filter.  53rd IEEE Conference on Decision and Control, 2014 pp. 5001-5007. http://dx.doi.org/10.1109/CDC.2014.7040170
  8. Cesar A. Vargas-Garcia, LaMont Cannon, Abhyudai Singh and Ryan Zurakowski, Optimal multi-drug approaches for reduction of the latent pool in HIV.  Proc. 19th IFAC World Congress, 2014, pp. 784-789. http://dx.doi.org/10.3182/20140824-6-ZA-1003.02720
  9. Michael J. Piovoso and Ryan Zurakowski, Evaluation of HIV 2-LTR formation models using monotone system theory.  American Control Conference, 2014, pp. 2747-2752. http://dx.doi.org/10.1109/ACC.2014.6858730
  10. E. Fabian Cardozo, Ryan Zurakowski and Nii Attoh-Okine, Analysis of HIV-1 Compartmental Model Parameters using Bayesian MCMC Estimation.  American Control Conference, 2014, pp. 2765-2770. http://dx.doi.org/10.1109/ACC.2014.6859111
  11. Bethany Allik, Cory Miller, Michael J. Piovoso and Ryan Zurakowski, Estimation of Saturated Data Using the Tobit Kalman Filter.  American Control Conference, 2014, pp. 4151-5146. http://dx.doi.org/10.1109/ACC.2014.6859251
  12. Cesar Augusto Vargas-Garcia, Ryan Zurakowski, and Abhyudai Singh, Conditions for invasion of synapse-forming HIV variants.  52nd IEEE Conference on Decision and Control, 2013 pp. 7193-7198. http://dx.doi.org/10.1109/CDC.2013.6761030
  13. E Fabian Cardozo, Cesar A. Garcia and Ryan Zurakowski, A Compartment Based Model for the Formation of 2-LTR Circles after Raltegravir Intensification.  51st IEEE Conference on Decision and Control, 2012, pp. 4924-4929. http://dx.doi.org/10.1109/CDC.2012.6426088
  14. Cory Miller, Bethany Allik, Mark Ilg and Ryan Zurakowski, Kalman Filter-based Tracking of Multiple Similar Objects from a Moving Camera Platform.  51st IEEE Conference on Decision and Control, 2012, pp. 5679-5684. http://dx.doi.org/10.1109/CDC.2012.6425956
  15. Liliana Mabel Peinado Cortes and Ryan Zurakowski, Resistance Evolution in HIV – Modeling When to Intervene.  American Control Conference, 2012, pp. 4053-4058. http://dx.doi.org/10.1109/ACC.2012.6315693
  16. E. Fabian Cardozo and Ryan Zurakowski, Measurement error robustness of a closed-loop minimal sampling method for HIV therapy switching.  33rd International Conference of the IEEE EMBS, 2011, pp. 116-119. http://dx.doi.org/10.1109/IEMBS.2011.6089910
  17. Rutao Luo, Michael J. Piovoso and Ryan Zurakowski,  Quantitative analysis of viral persistence and transient viral load rebound from HIV clinical data.  33rd International Conference of the IEEE EMBS, 2011, pp. 3585-3588. http://dx.doi.org/10.1109/IEMBS.2011.6090599
  18. LaMont Cannon, Jason Hernandez and Ryan Zurakowski, Modeling and Analysis of Gene-Therapeutic Combination Chemotherapy for Pancreatic Cancer.  Proc. 18th IFAC World Congress, 2011, pp. 14217-14222. http://dx.doi.org/10.3182/20110828-6-IT-1002.03162
  19. Ryan Zurakowski, Matthew Churgin, Camilo Perez, Matthew Rodriguez, Approximate-model closed-loop minimal sampling method for HIV viral-load minima detection.  American Control Conference, 2011, pp. 5418-5419. http://dx.doi.org/10.1109/ACC.2011.5991281
  20. Rutao Luo, Michael J. Piovoso, Ryan Zurakowski, Modeling-error robustness of a viral-load preconditioning strategy for HIV treatment switching.  Proc. American Control Conference 2010, Baltimore, MD.  pp. 5155-5160. http://dx.doi.org/10.1109/ACC.2010.5530483
  21. Esteban Rosero, Ryan Zurakowski, Closed-loop minimal sampling method for determining viral-load minima during switching.  Proc. American Control Conference 2010, Baltimore, MD.  pp. 460-461. http://dx.doi.org/10.1109/ACC.2010.5530993
  22. Rutao Luo, Michael J Piovoso and Ryan Zurakowski, A generalized multi-strain model of HIV evolution with implications for drug-resistance management.  Proc. American Control Conference, 2009 St. Louis, MO pp. 2295-2300.  http://dx.doi.org/10.1109/ACC.2009.5160358
  23. Rutao Luo and Ryan Zurakowski, Resistance risk management in HIV therapy switching with explicit quiescent T-cell modeling.  Proc.  17th IFAC World Congress, 2008 Seoul, Korea, pp. 10325-10330.  http://dx.doi.org/10.3182/20080706-5-KR-1001.01747
  24. Rutao Luo and Ryan Zurakowski,  A new strategy to decrease risk of resistance emerging during therapy switching in HIV treatment. Proc. American Control Conference, 2008 Seattle, WA pp. 2112-2117.  http://dx.doi.org/10.1109/ACC.2008.4586804
  25. Ryan Zurakowski, Dominik Wodarz, Treatment interruptions to decrease risk of resistance emerging during therapy switching in HIV treatment. Proc. 2007 Conference on Decision and Control pp. 5174-5179. http://dx.doi.org/10.1109/CDC.2007.4434887
  26. Ryan Zurakowski and Dominik Wodarz,  Modeling and control for in Vitro combination therapy using ONYX-015 replicating adenovirus. Proc. American Control Conference, 2006, Minneapolis, MN, pp.4794-4799. http://dx.doi.org/10.1109/ACC.2006.1657479
  27. Ryan Zurakowski, An output-feedback MPC-based scheduling method for enhancing immune response to HIV. Proc. American Control Conference, 2006, Minneapolis, MN, pp. 4800-4805. http://dx.doi.org/10.1109/ACC.2006.1657480
  28. Ryan Zurakowski, Michael J. Messina, Sezai E. Tuna, and Andrew R. Teel, HIV treatment scheduling via robust nonlinear model predictive control.  Proc. Asian Control Conference, 2004, Vol. 1, pp. 25-32. Keynote. http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=1425932
  29. Ryan Zurakowski, Andrew R. Teel, and Dominik Wodarz, Utilizing alternate target cells in treating HIV infection through scheduled treatment interruptions.  Proc. American Control Conference,2004, Vol. 1, pp. 946-951. http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=1383729
  30. Ryan Zurakowski and Andrew R. Teel, Enhancing immune response to HIV infection using MPC-based treatment scheduling. Proc. American Control Conference, 2003, Vol. 2, pp. 1182-1187. http://dx.doi.org/10.1109/ACC.2003.1239748

Published Abstracts

  1. Joshua T. Morgan, Ryan Zurakowski, and Jason P. Gleghorn. Automated methodology for the detection and quantification of branching events in epithelial tissues.  The 2015 ASCB Annual Meeting, San Diego, CA December 12-16.
  2. Ryan Zurakowski, LaMont Cannon and Michael J. Piovoso.  Interpreting the outcome of integrase-inhibitor intensification experiments. Strategies for an HIV Cure 2014, NIH Main Campus, Bethesda, MD October 15-17, 2014.
  3. E. Fabian Cardozo, Rutao Luo, Michael J. Piovoso and Ryan Zurakowski.  Modeling Drug-Privileged Lymphoid Sites: Necessary Conditions for Persistence HIV Replication. 6th International Workshop of HIV Persistence During Therapy.  Miami, FL December 3-6 2013.
  4. Cesar A. Vargas-Garcia, Ryan Zurakowski and Abhyudai Singh.  Conditions for invasion of synapse-forming HIV variants.  International Conference on Computational Cell Biology, Blacksburg, VA August 14-16, 2013.
  5. E. Fabian Cardozo, Rutao Luo, Michael J. Piovoso and Ryan Zurakowski.  A Spatial Model of 2-LTR Formation and Cryptic Viremia following Raltegravir Intensification.  IABS International Scientific Workshop on New Cells, New Vaccines VII, Wilmington, DE March 17-20, 2013.
  6. E. Fabian Cardozo and Ryan Zurakowski.  Modeling Cryptic Viremia.  Inaugural Fraunhofer – Delaware Technology Summit, Newark, DE March 5-6 2013.
  7. Rutao Luo, Michael J. Piovoso, Hulin Wu, Maria J. Buzon, Javier Martinez-Picado and Ryan Zurakowski. Quantifying Virus Dynamics From Measured HIV-1 2-LTR Circles From Peripheral Blood Mononuclear Cells Following Raltegravir Intensification In Subjects With Sustained Viral Suppression. 19th International HIV Dynamics and Evolution, Asheville, NC April 25-28, 2012.
  8. Ryan Zurakowski, Rutao Luo, and Michael J. Piovoso. Modeling HIV DNA artifact formation in integrase inhibitor therapy.  1080th Meeting of the AMS, Washington, DC March 17-18, 2012.
  9. Ryan Zurakowski, Rutao Luo, Michael J. Piovoso, Maria J. Buzon, and Javier Martinez-Picado. HIV Reservoirs, DNA Circles, and Differential Equations.  1st Annual CBCB Research Symposium in Bioinformatics and Systems Biology, Newark, DE May 27, 2011.
  10. Ryan Zurakowski, Rutao Luo, Michael J. Piovoso, Maria J. Buzon, and Javier Martinez-Picado. Quantifying HIV Reservoir Rates from 2-LTR Circle Measurements.  3rd Annual DHSA Research Symposium, Wilmington, DE May 17, 2011.
  11. Michael J. Piovoso, Rutao Luo, and Ryan Zurakowski.  HIV Treatment Optimization for Resistance Risk Management.  Proc. Foundations of Systems Biology in Engineering, Denver, CO August 9-12, 2009.
  12. Ryan Zurakowski, Optimal Management of Drug Resistance in Suppressive Therapy. Proc. Eighth SIAM Conference on Control and its Applications, June 29 – July 1, 2007.
  13. Ryan Zurakowski and Dominik Wodarz, Modeling and control for in vitro oncolytic virus therapies. Proc. Sixth SIAM Conference on Control and its Applications, July 11-14, 2005.

Theses and Dissertations

  1. Cory Miller, Estimation and control with censored data.  Ph.D. Dissertation, 2014, University of Delaware.
  2. Bethany Allik, The Tobit Kalman filter: an estimator for censored data.  Ph.D. Disseration, 2014, University of Delaware.
  3. E. Fabian Cardozo, Multi-compartmental modeling of HIV-1 cryptic viremia.  Ph.D. Dissertation, 2014, University of Delaware.
  4. Shannon Kung, Determining optimal chemotherapy schedules using ODE modeling and control.  M.S. Thesis, 2013, University of Delaware.
  5. Rutao Luo, HIV model parameter estimates from interruption trial data. M.S. Thesis, 2012, University of Delaware.
  6. LaMont Cannon, Dynamic suicide gene therapy control.  M.S. Thesis, 2010, University of Delaware.
  7. Jason Hernandez, Controlling resistance evolution in cancer gene therapy. M.S. Thesis, 2010, University of Delaware.
  8. Ryan Zurakowski, Exploiting Immune Response Dynamics in HIV Therapy.  Ph.D. Dissertation, 2004, University of California, Santa Barbara.
  9. Ryan Zurakowski.  A Lyapunov Method for Nonsmooth Optimization.  M.S. Thesis, 2000, University of California, Santa Barbara.

Invited Talks

October 10, 2013, 4th International Symposium on Hot Topics in HIV: Vaccines, Immune Recovery and Eradication, Barcelona, Spain “Modeling Dynamic Measures of Viral Persistence”

September 18, 2013, Johns Hopkins University  “Interpretation of 2-LTR data from raltegravir intensification trials”

March 5, 2013, Fraunhofer – Delaware Technology Summit, Newark DE, Panel Member  “Step Ahead Together: Creative Collaborating as an Approach to Building and Sustaining a Pharma R&D Pipeline”

Jan 11, 2013, Merck Sharp & Dohme Corp., West Point, PA, “Interpretation of 2-LTR data from raltegravir intensification trials”

May 9, 2012, Pennsylvania/Mid-Atlantic AIDS Education Training Center, Christiana Care Health Services, Advanced Lecture Series, “Modeling Cryptic Viremia in HIV: Evidence and Implications”

July 13, 2011, Pennsylvania/Mid-Atlantic AIDS Education Training Center, Christiana Care Health Services, Advanced Lecture Series, “Model-based measurement: HIV Reservoir dynamic rates from 2-LTR measurements with treatment implications”

Nov 19, 2010, National University of Colombia, Bogota, “Controlling the Evolution of Resistance”

June 24, 2010, DARPA Prophecy East Teaming Conference, “Model-Driven Interventions to Prevent the Emergence of Antiviral-Resistant Strains in HIV Therapy.”

Nov 10, 2009, Pennsylvania State University, Great Valley Campus, Engineering Division Lecture Series, “HIV Strain Competition Modeling with Treatment Applications”

April 20, 2009, Center for Translational Cancer Research, “Dynamic effects and unexpected results in combination chemotherapies”

March 14, 2006, Johns Hopkins University, “Disease Modeling and Control Theoretic Approaches to Treatment:  Applications to HIV and Colon Cancer”