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Papers

2017
07843624.pdf Abel, J., Drawert, B., Hellander, A. & Petzold, L. R. (2017). GillesPy: A Python Package for Stochastic Model Building and Simulation. IEEE Life Sciences Letters, Vol. 2, No. 3, pp. 35-38.
1-s2.0-s0925231217305581-main.pdf Torshizi, A. D., Petzold, L., & Cohen, M. (2017). Multivariate Soft Repulsive System Identification for Constructing Rule-based Classification Systems: Application to Trauma Clinical Data. To appear Neurocomputing
main.pdf Hellander, S. & Petzold, L. (2017). Reaction Rates for Reaction-Diffusion Kinetics on Unstructured Meshes. J. Chem. Phys. 146, 064101
balesetal_2017_modelling_simul._mater._sci._eng._10.1088_1361-651x_aa67b9.pdf Bales, B., Pollock, T., & Petzold, L. (2017). Segmentation-Free Image Processing and Analysis of Precipitate Shapes in 2D and 3D. To appear Modelling Simul. Mater. Sci. Eng.
07887681.pdf Torshizi, A. D. & Petzold, L. (2017). Sparse Pathway-Induced Dynamic Network Biomarker Discovery for Early Warning Signal Detection in Complex Diseases. To appear IEEE/ACM Transactions on Computational Biology and Bioinformatics
main.pdf Zhang, Y., Jiang, R., & Petzold, L. (2017). Survival Topic Models for Predicting Outcomes for Trauma Patients. To Appear HDMM 2017
2016
1.4967338.pdf Drawert, B., Hellander, S., Trogdon, M., Yi, T-M, & Petzold, L. (2016). A Framework for Discrete Stochastic Simulation on 3D Moving Boundary Domains. J. Chem. Phys., 145, 184113.
aes_paper.pdf Lim, R. K., Petzold, L. R., & Koc, C. K. (2016). Bitsliced High-Performance AES-ECB on GPUs. LNCS 9100, pp. 125-133
pnas-2016-abel-1521178113.pdf Abel, J. H., Meeker, K., Granados-Fuentes, D., St. John, P. C., Wang, T. J., Bales, B. B., Doyle III, F. J., Herzog, E. D., & Petzold L. R. (2016). Functional Network Inference of the Suprachiasmatic Nucleus. Proceedings of the National Academy of Science.
art3a10.11862fs12911-016-0360-x.pdf Zhang, Y. Wu, T. B., Daigle, Jr., B. J., Cohen, M., & Petzold, L. (2016). Identification of Disease States Associated with Coagulopathy in Trauma. BMC Medical Informatics and Decision Making, 16:124
pcbi.1005122.pdf Golkaram, M., Hellander, S., Drawert, B., & Petzold, L. R. (2016). Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion. PLoS Comput. Biol. 12(11):e1005122
15m1014784.pdf Drawert, B., Trogdon, M., Toor, S., Petzold, L., & Hellander, A. (2016). MOLNs: A Cloud Platform for Interactive, Reproducible, and Scalable Spatial Stochastic Computational Experiments in Systems Biology Using PyURDME. SIAM J. Sci. Comput., 38(3), C179-C202
ec11568_final.pdf Hellander, S., & Petzold, L. (2016). Reaction Rates for a Generalized Reaction-Diffusion Master Equation. Phys. Rev. E 93, 013307.
journal.pcbi_.1005220.pdf Drawert, B., Hellander, A., Bales, B., Banerjee, D., Bellesia, G., Daigle, Jr., B. J., Douglas, G., Gu, M., Gupta, A., Hellander, S., Horuk, C., Nath, D., Takkar, A., Wu, S., Lötstedt, P., Krintz, C., & Petzold, L. R. (2016). Stochastic Simulation Service: Bridging the Gap Between the Compuational Expert and the Biologist. PLoS Comput. Biol. 12(12): e1005220
2015
interface_latex.pdf Lawson, M. J., Petzold, L., & Hellander, A. (2015). Accuracy of the Michaelis-Menten Approximation When Analysing Effects of Molecular Noise. J. R. Soc. Interface 12:20150054.
1.4921638.pdf Wu, S., Fu, J., & Petzold, L. R. (2015). Adaptive Deployment of Model Reductions for Tau-Leaping Simulation. J. Chem. Phys. 142, 204108
temporal_opdetection-2.pdf Bhattacharjee, K., & Petzold, L. (2015, December). Detecting Opinions in a Temporally Evolving Conversation on Twitter. Proceedings of the International Conference on Social Informatics (SocInfo), Beijing, China.
b325.pdf Doostparast, A. Petzold, L., & Cohen, M. (2015, November). Direct Higher Order Fuzzy Rule-based Classification System: Application in Mortality Prediction. Proceedings of the IEEE International Conference on Bioinformatics & Biomedicine (IEEE BIBM 2015), Washington D. C.
abel-gillespy-fosbe-vf.pdf Abel, J. H., Drawert, B., Hellander, A., & Petzold, L. R. (2015, August). GillesPy: A Python Package for Stochastic Model Building and Simulation. FOSBE 2015 Conference Proceedings, Boston, MA.
gpubasedsims.pdf Pro, J. W., Lim, R. K., Petzold, L. R., Utz, M., & Begley, M. R. (2015). GPU-Based Simulations of Fracture in Idealized Brick and Mortar Composites. J. Mech. Phys. Solids 80, 68-85.
international_journal_of_high_performance_computing_applications-2015-lim-1094342015593395.pdf Lim, R. K., Pro, J. W., Begley, M. R., Utz, M., & Petzold, L. R. (2015). High-performance Simulation of Fracture in Idealized "Brick and Mortar" Composites Using Adaptive Monte Carlo Minimization on the GPU. Int. J. High Perform. C. 1-14
btv007.pdf Daigle, Jr., B. J., Soltani, M., Petzold, L. R. & Singh, A. (2015). Inferring Single-Cell Gene Expression Mechanisms Using Stochastic Simulation. Bioinformatics, 31(9), 2015, 1428-1435
manuscript.pdf Pourzanjani, A., Herzog, E. D., & Petzold, L. R. (2015). On the Inference of Functional Circadian Networks Using Granger Causality. PLoS ONE 10(9):e0137540
physreve.91.023312.pdf Hellander, S., Hellander, A., & Petzold, L. (2015). Reaction Rates for Mesoscopic Reaction-Diffusion Kinetics. Phys. Rev. E 91, 023312.
thakur_etal_molbiosystems_2015.pdf Thakur, G. S., Daigle Jr., B. J., Dean, K. R., Zhang, Y., Rodriguez-Fernandez, M., Hammamieh, R., Yang, R., Jett, M., Palma, J., Petzold, L. R., & Doyle III, F. J. (2015). Systems Biology Approach to Understanding Post-Traumatic Stress Disorder. Mol. BioSyst., 2015, 11, 980.

doi:10.1039/C4MB00404C  |  PMID: 25627823 [PubMed - in process]

1-s2.0-s2352431615001054-main.pdf Pro, J. W., Lim, R. K., Petzold, L. R., Utz, M., & Begley, M. R. (2015). The Impact of Stochastic Microstructures on the Macroscopic Fracture Properties of Brick and Mortar Composites. Extreme Mechanics Letters 5 (2015) 1-9
2014
IFAC14_2031_FI.pdf Thakur, G., Daigle Jr., B., Petzold, L. R. & Doyle, F. (2014). A Multivariate Ensemble Approach for Identification of Biomarkers: Application to Breast Cancer. Proceedings of the 19th IFAC World Congress.
ELFPT_main.pdf Bezzola, A., Bales, B. B., Alkire, R. C. & Petzold, L. R. (2014). An Exact and Efficient First Passage Time Algorithm for Reaction-Diffusion Processes on a 2D-Lattice. J. Comp. Phys., 256, pp. 183-197.
BiPClustering.pdf Griesemer, M., Young, C., Robinson, A. S. & Petzold, L. R. (2014). BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum. PLoS Comput. Biol. 10(7): e1003675.
main.pdf Zhang, Y., Daigle, Jr., B. J., Ferrigno, L., Cohen, M., & Petzold, L. (2014). Data-Driven Mortality Prediction for Trauma Patients. Invited Refereed Presentation at NIPS MLCB Workshop
LocalError.pdf Hellander, A., Lawson, M., Drawert, B. & Petzold, L. (2014). Local Error Estimates for Adaptive Simulation of the Reaction-Diffusion Master Equation via Operator Splitting. J. Comp. Phys. 266, pp. 89-100.
NumericalScaling.pdf Bezzola, A., Bales, B. B., Petzold, L. R. & Alkire, R. C. (2014). Numerical Scaling Studies of Kinetically-Limited Electrochemical Nucleation and Growth with Accelerated Stochastic Simulations. J. Electrochem. Soc. 161(8), E3001-E3008.
OpinionMining.pdf Bhattacharjee, K. & Petzold, L. R. (2014). Probabilistic User-level Opinion Detection on Online Social Networks. Proceedings of the International Conference on Social Informatics (SocInfo).
Hes1_dimerisation.pdf Sturrock, M., Hellander, A., Aldakheel, S., Petzold, L. R. & Chaplain, M. A. J. (2014). The Role of Dimerisation and Nuclear Transport in the Hes1 Gene Regulatory Network. Bull. Math Biol. 76(4):766-98.
TimeDependentPropensity.pdf Fu, J., Wu, S., Li, H. & Petzold, L. R. (2014). The Time Dependent Propensity Function for Acceleration of Spatial Stochastic Simulation of Reaction-Diffusion Systems. J. Comp. Phys. 274, pp. 524–549.
Validity.pdf Gillespie, D., Petzold, L. R. & Seitaridou, E. (2014). Validity Conditions for Stochastic Chemical Kinetics in Diffusion-Limited Systems. J. Chem. Phys. 140, 054111.

© 2014 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the authors and the American Institute of Physics. Journal Version  |  PMCID: PMC3977787

2013
Neuropeptide.pdf An, S., Harang, R., Meeker, K., Granados-Fuentes, D., Tsai, C., Mazuski, C., Kim, J., Doyle III, F. J., Petzold, L. R. & Herzog, E. D. (2013). A Neuropeptide Speeds Circadian Entrainment by Reducing Intercellular Synchrony. Proceedings of the National Academy of Sciences.
Mouse_Model.pdf Yang, R., Daigle, Jr., B. J., Muhie, S. Y., Hammamieh, R., Jett, M., Petzold, L. & Doyle III, F. J. (2013). Core Modular Blood and Brain Biomarkers in Social Defeat Mouse Model for Post Traumatic Stress Disorder. BMC Systems Biology 2013, 7:80.
Pub199-1.pdf Kolpas, A., Busch, M., Li, H., Couzin, I. D., Petzold, L. R. & Moehlis, J. (2013). How the Spatial Position of Individuals Affects Their Influence on Swarms: A Numerical Comparison of Two Popular Swarm Dynamics Models. PLoS ONE 8(3): e58525.
I_Act.pdf Macropol, K., Bogdanov, P., Singh, A. K., Petzold, L. R. & Yan, X. (2013). I Act, Therefore I Judge: Network Sentiment Dynamics Based on User Activity Change. Proceedings of IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining.
Perspective.pdf Gillespie, D. T., Hellander, A. & Petzold, L. R. (2013). Perspective: Stochastic Algorithms for Chemical Kinetics. J. Chem. Phys. 138, 170901.

© 2013 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the authors and the American Institute of Physics. Journal Version  |  PMCID: PMC3656953

Polarization.pdf Lawson, M. J., Drawert, B., Khammash, M., Petzold, L. R. & Yi, T. (2013). Spatial Stochastic Dynamics Enable Robust Cell Polarization. PLoS Comput. Biol. 9(7): e1003139.
Time_Dependent.pdf Fu, J., Wu, S. & Petzold, L. R. (2013). Time Dependent Solution for Acceleration of Tau-Leaping. J. Comp. Phys. 235, 446-457.
2012
URDME_StratUm.pdf Östberg, P., Hellander, A., Drawert, B., Elmroth, E., Holmgren, S. & Petzold, L. R. (2012). Abstractions for Scaling eScience Applications to Distributed Computing Environments: A StratUm Integration Case Study in Molecular Systems Biology. Proceedings of Bioinformatics 2012, International Conference on Bioinformatics Models, Methods, and Algorithms.
Accelerated.pdf Daigle, Jr., B. J., Roh, M. K., Petzold, L. R. & Niemi, J. (2012). Accelerated Maximum Likelihood Parameter Estimation for Stochastic Biochemical Systems. BMC Bioinformatics 2012, 13:68.
Automatic_Id.pdf Wu, S., Fe, J., Li, H. & Petzold, L. R. (2012). Automatic Identification of Model Reductions for Discrete Stochastic Simulation. J. Chem. Phys. 137(3), 034106.
COMBINER.pdf Yang, R., Daigle Jr., B., Petzold, L. R. & Doyle III, F. J. (2012). Core Module Biomarker Identification with Network Exploration for Breast Cancer Metastasis. BMC Bioinfomatics 13:12.
Core_module.pdf Yang, R., Daigle, Jr., B. J., Petzold, L. R. & Doyle III, F. J. (2012). Core Module Network Construction for Breast Cancer Metastasis. Proceedings of the 10th World Congress on Intelligent Control and Automation, Beijing, China.
Language_Runtime.pdf Bunch, C., Drawert, B., Chohan, N., Krintz, C., Petzold, L. R. & Shams, K. (2012). Language and Runtime Support for Automatic Configuration and Deployment of Scientific Computing Software over Cloud Fabrics. J. Grid Computing 10(1) 23-46
Wallace, E., Gillespie, D. T., Sanft, K. R., & Petzold, L. R. (2012). Linear Noise Approximation is Valid Over Limited Times for any Chemical System that is Sufficiently Large. IET Systems Biology 6(4) 102-115.
Hellander, S., Hellander, A. & Petzold, L. (2012). Reaction-diffusion Master Equation in the Microscopic Limit. Phys. Rev. E 85(4), 042901.
Reducing_MSGC.pdf Östberg, P., Hellander, A., Drawert, B., Elmroth, E., Holmgren, S. & Petzold, L. R. (2012). Reducing Complexity in Management of eScience Computations. Proceedings of CCGrid 2012, 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing.
Spatial_Local_Final.pdf Griesemer, M., Young, C., Robinson, A. & Petzold, L. (2012). Spatial Localization of Chaperone Distribution in the Endoplasmic Reticulum of Yeast. IET Systems Biology 6(2):54-63.
URDME_BMCsysbio.pdf Drawert, B., Engblom, S. & Hellander, A. (2012). URDME: A Modular Framework for Stochastic Simulation of Reaction-Transport Processes in Complex Geometries. BMC Syst. Biol. 6:76.
Harang, R., Bonnet, G. & Petzold, L. R. (2012). WAVOS: a MATLAB Toolkit for Wavelet Analysis and Visualization of Oscillatory Systems. BMC Research Notes 5:163.
2011
JCPSA61344044110_1.pdf Daigle, B., Roh, M., Gillespie, D. & Petzold, L. (2011). Automated Estimation of Rare Event Probabilities in Biochemical Systems. J. Chem. Phys. 134, 044110.
© 2011 American Institute of Physics. The article may be downloaded for personal use only. Any other use requires prior permission of the authors and the American Institute of Physics. Journal Version
tbme_paper_020311.pdf Abdur-Rahim, J. A., Petzold, L. R., Grafton, S. T. & Doyle III, F. J. (2011). Identifying Learning in a Visuomotor Skill. Transactions on Biomedical Engineering, Submitted
stoch_2011.pdf Sanft, K. R., Gillespie, D. T. & Petzold, L. R. (2011). Legitimacy of the Stochastic Michaelis-Menten Approximation. IET Systems Biology, 5(1), 58-69.
© The Institution of Engineering and Technology 2011 Journal version
JCPSA613413134112_1.pdf Wu, S., Fu, J., Cao, Y. & Petzold, L. (2011). Michaelis-Menten Speeds up Tau-leaping Under a Wide Range of Conditions. J. Chem. Phys. 134, 134112.
© 2011 American Institute of Physics. The article may be downloaded for personal use only. Any other use requires prior permission of the authors and the American Institute of Physics. Journal Version
sdwSSA_ver3.1.pdf Roh, M., Daigle Jr., B., Gillespie, D. & Petzold, L. R. (2011). State-dependent Doubly Weighted Stochastic Simulation Algorithm for Automatic Characterization of Stochastic Biochemical Rare Events. J. Chem. Phys. 135(23):234108.
© 2011 American Institute of Physics. The article may be downloaded for personal use only. Any other use requires prior permission of the authors and the American Institute of Physics. Journal Version
Sanft, K. R., Wu, S., Roh, M., Fu, J., Lim, R. K. & Petzold, L. R. (2011). StochKit2: Software for Discrete Stochastic Simulation of Biochemical Systems with Events. Bioinformatics (2011) 27(17): 2457-2458.
© The Authors 2011. Published by Oxford University Press. Journal Version
SIREVCSE.pdf Turner, P. & Petzold, L., Co-Chairs, Shiflet, A., Vakalis, I., Jordan, K. & St. John, S., SIAM Working Group on CSE Undergraduate Education (2011). Undergraduate Computational Science and Engineering Education. SIAM Review 53(3), 561-574.
JBRWavelet.pdf Meeker, K., Harang, R., Webb, A. B., Welsh, D. K., Doyle III, F. J., Bonnet, G., Herzog, E. D. & Petzold, L. R. (2011). Wavelet Measurement Suggests Cause of Period Instability in Mammalian Circadian Neurons. J. of Biological Rhythms 26(4):353-62.
2010
Buoni_2009_Journal-of-Computational-Physics.pdf Buoni, M. & Petzold, L. (2010). An Algorithm for Simulation of Electrochemical Systems with Surface-Bulk Coupling Strategies. J. Comp. Phys. 229(2), pp. 379-398
Pub178.pdf Luni, C., Shoemaker, J., Sanft, K., Petzold, L., Doyle, F. (2010). Confidence from Uncertainty - A Multi-Target Drug Screening Method from Robust Control Theory. BMC Systems Biology 4:161
Luni_Dycops-1.pdf Luni, C., Sanft, K., Petzold, L., Doyle III, F. (2010). Modelling of Detailed Insulin Receptor Kinetics Affects Sensitivity and Noise in the Downstream Signalling Pathway. DYCOPS2010, 9th IFAC Symposium on Dynamics and Control of Process Systems, Leuven, Belgium
wSSA_state-dependent-biasing_2010.pdf Roh, M., Gillespie, D., Petzold, L. (2010). State-Dependent Biasing Method for Importance Sampling in the Weighted Stochastic Simulation Algorithm. J. Chem. Phys. 133, p. 174106
DFSP.pdf Drawert, B., Lawson, M. J., Petzold, L. & Khammash, M. (2010). The Diffusive Finite State Projection Algorithm for Efficient Simulation of the Stochastic Reaction-Diffusion Master Equation. J. Chem. Phys. 132(7), 074101 (12 pages)
© 2010 American Institute of Physics Journal version
Pub173.pdf Taylor, S., Webb, A., Smith, K., Petzold, L., Doyle III, F. (2010). Velocity Response Curves Support the Role of Continuous Entrainment in Circadian Clocks. J. Biological Rhythms 25(2):138-149
2009
projection_methods.pdf Zheng, Z., Petzold, L. & Simeon, B. (2009). A Framework for the Analysis of Second Order Projection Methods. Submitted
simeonserbanpetzold.pdf Simeon, B., Serban, R. & Petzold, L. (2009). A Model of Macroscale Deformation and Microvibration in Skeletal Muscle Tissue. M2AN 43, pp. 805-823
Gillespie_FOSBE.pdf Gillespie, D., Cao, Y., Sanft, K. & Petzold, L. (2009). Abridging Chemical Reaction Networks: It's a Subtle Business. Proc. 2009 FOSBE Conference
An_Algorithm.pdf Buoni, M. & Petzold, L. (2009). An Algorithm for Simulation of Electrochemical Systems with Surface-Bulk Coupling Strategies. 18th IMACS CONGRESS MODSIM
JCompPhys_122208.pdf Lampoudi, S., Gillespie, D. & Petzold, L. (2009). Effect of excluded volume on 2D discrete stochastic chemical kinetics. J. Comp. Phys. 228(10), pp. 3656-3668
Pub161.pdf Li, H. & Petzold, L. (2009). Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems on the Graphics Processing Unit. Int. J. of High Performance Computing Applications 24(2), pp. 107-116

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