Linda Petzold - Publications

Affiliations: 
University of California, Santa Barbara, Santa Barbara, CA, United States 
Area:
Systems Biology and Discovery Tools

82 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Matthew S, Carter F, Cooper J, Dippel M, Green E, Hodges S, Kidwell M, Nickerson D, Rumsey B, Reeve J, Petzold LR, Sanft KR, Drawert B. GillesPy2: A Biochemical Modeling Framework for Simulation Driven Biological Discovery. Letters in Biomathematics. 10: 87-103. PMID 37655179  0.8
2022 Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, ... ... Petzold LR, et al. BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research. PMID 35524558 DOI: 10.1093/nar/gkac331  0.741
2022 Doering GN, Drawert B, Lee C, Pruitt JN, Petzold LR, Dalnoki-Veress K. Noise resistant synchronization and collective rhythm switching in a model of animal group locomotion. Royal Society Open Science. 9: 211908. PMID 35291326 DOI: 10.1098/rsos.211908  0.712
2022 Lawson MJ, Drawert B, Petzold L, Yi TM. A positive feedback loop involving the Spa2 SHD domain contributes to focal polarization. Plos One. 17: e0263347. PMID 35134079 DOI: 10.1371/journal.pone.0263347  0.709
2021 Jiang RM, Wrede F, Singh P, Hellander A, Petzold LR. Accelerated regression-based summary statistics for discrete stochastic systems via approximate simulators. Bmc Bioinformatics. 22: 339. PMID 34162329 DOI: 10.1186/s12859-021-04255-9  0.321
2021 Jacob B, Drawert B, Yi TM, Petzold L. An arbitrary Lagrangian Eulerian smoothed particle hydrodynamics (ALE-SPH) method with a boundary volume fraction formulation for fluid-structure interaction. Engineering Analysis With Boundary Elements. 128: 274-289. PMID 34040286 DOI: 10.1016/j.enganabound.2021.04.006  0.709
2021 Jiang R, Jacob B, Geiger M, Matthew S, Rumsey B, Singh P, Wrede F, Yi TM, Drawert B, Hellander A, Petzold L. Epidemiological modeling in StochSS Live! Bioinformatics (Oxford, England). PMID 33512399 DOI: 10.1093/bioinformatics/btab061  0.742
2021 Banavar SP, Trogdon M, Drawert B, Yi TM, Petzold LR, Campàs O. Coordinating cell polarization and morphogenesis through mechanical feedback. Plos Computational Biology. 17: e1007971. PMID 33507956 DOI: 10.1371/journal.pcbi.1007971  0.707
2019 Doering GN, Sheehy KA, Lichtenstein JLL, Drawert B, Petzold LR, Pruitt JN. Sources of intraspecific variation in the collective tempo and synchrony of ant societies. Behavioral Ecology : Official Journal of the International Society For Behavioral Ecology. 30: 1682-1690. PMID 31723317 DOI: 10.1093/Beheco/Arz135  0.696
2019 Drawert B, Jacob B, Li Z, Yi TM, Petzold L. Validation data for a hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) method. Data in Brief. 22: 11-15. PMID 30581900 DOI: 10.1016/J.Dib.2018.11.103  0.758
2018 Trogdon M, Drawert B, Gomez C, Banavar SP, Yi TM, Campàs O, Petzold LR. The effect of cell geometry on polarization in budding yeast. Plos Computational Biology. 14: e1006241. PMID 29889845 DOI: 10.1371/Journal.Pcbi.1006241  0.719
2018 Wu TB, Wu S, Buoni M, Orfeo T, Brummel-Ziedins K, Cohen M, Petzold L. Computational Model for Hyperfibrinolytic Onset of Acute Traumatic Coagulopathy. Annals of Biomedical Engineering. PMID 29675813 DOI: 10.1007/S10439-018-2031-9  0.729
2018 Bales B, Petzold L, Goodlet BR, Lenthe WC, Pollock TM. Bayesian inference of elastic properties with resonant ultrasound spectroscopy. The Journal of the Acoustical Society of America. 143: 71. PMID 29390755 DOI: 10.1121/1.5017840  0.31
2017 Hellander S, Hellander A, Petzold L. Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning. The Journal of Chemical Physics. 147: 234101. PMID 29272930 DOI: 10.1063/1.5002773  0.409
2017 Drawert B, Griesemer M, Petzold LR, Briggs CJ. Using stochastic epidemiological models to evaluate conservation strategies for endangered amphibians. Journal of the Royal Society, Interface. 14. PMID 28855388 DOI: 10.1098/Rsif.2017.0480  0.751
2017 Hellander S, Petzold L. Reaction rates for reaction-diffusion kinetics on unstructured meshes. The Journal of Chemical Physics. 146: 064101. PMID 28201913 DOI: 10.1063/1.4975167  0.357
2017 Torshizi AD, Petzold L, Cohen M. Multivariate soft repulsive system identification for constructing rule-based classification systems Neurocomputing. 245: 77-85. DOI: 10.1016/J.Neucom.2017.03.043  0.305
2016 Abel JH, Drawert B, Hellander A, Petzold LR. GillesPy: A Python Package for Stochastic Model Building and Simulation. Ieee Life Sciences Letters. 2: 35-38. PMID 28630888 DOI: 10.1109/LLS.2017.2652448  0.762
2016 Drawert B, Trogdon M, Toor S, Petzold L, Hellander A. MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME. Siam Journal On Scientific Computing : a Publication of the Society For Industrial and Applied Mathematics. 38: C179-C202. PMID 28190948 DOI: 10.1137/15M1014784  0.746
2016 Drawert B, Hellander A, Bales B, Banerjee D, Bellesia G, Daigle BJ, Douglas G, Gu M, Gupta A, Hellander S, Horuk C, Nath D, Takkar A, Wu S, Lötstedt P, ... ... Petzold LR, et al. Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist. Plos Computational Biology. 12: e1005220. PMID 27930676 DOI: 10.1371/Journal.Pcbi.1005220  0.749
2016 Golkaram M, Hellander S, Drawert B, Petzold LR. Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion. Plos Computational Biology. 12: e1005122. PMID 27893768 DOI: 10.1371/Journal.Pcbi.1005122  0.727
2016 Drawert B, Hellander S, Trogdon M, Yi TM, Petzold L. A framework for discrete stochastic simulation on 3D moving boundary domains. The Journal of Chemical Physics. 145: 184113. PMID 27846706 DOI: 10.1063/1.4967338  0.77
2016 Abel JH, Meeker K, Granados-Fuentes D, St John PC, Wang TJ, Bales BB, Doyle FJ, Herzog ED, Petzold LR. Functional network inference of the suprachiasmatic nucleus. Proceedings of the National Academy of Sciences of the United States of America. PMID 27044085 DOI: 10.1073/Pnas.1521178113  0.759
2016 Hellander S, Petzold L. Reaction rates for a generalized reaction-diffusion master equation. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 93: 013307. PMID 26871190 DOI: 10.1103/Physreve.93.013307  0.354
2015 Wu S, Fu J, Petzold LR. Adaptive deployment of model reductions for tau-leaping simulation. The Journal of Chemical Physics. 142: 204108. PMID 26026435 DOI: 10.1063/1.4921638  0.537
2015 Lawson MJ, Petzold L, Hellander A. Accuracy of the Michaelis-Menten approximation when analysing effects of molecular noise. Journal of the Royal Society, Interface / the Royal Society. 12. PMID 25833240 DOI: 10.1098/Rsif.2015.0054  0.415
2015 Hellander S, Hellander A, Petzold L. Reaction rates for mesoscopic reaction-diffusion kinetics. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 91: 023312. PMID 25768640 DOI: 10.1103/Physreve.91.023312  0.376
2014 Hellander A, Lawson MJ, Drawert B, Petzold L. Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting. Journal of Computational Physics. 266: 89-100. PMID 26865735 DOI: 10.1016/J.Jcp.2014.02.004  0.76
2014 Fu J, Wu S, Li H, Petzold LR. The Time Dependent Propensity Function for Acceleration of Spatial Stochastic Simulation of Reaction-Diffusion Systems. Journal of Computational Physics. 274: 524-549. PMID 26609185 DOI: 10.1016/J.Jcp.2014.06.025  0.535
2014 Griesemer M, Young C, Robinson AS, Petzold L. BiP clustering facilitates protein folding in the endoplasmic reticulum. Plos Computational Biology. 10: e1003675. PMID 24991821 DOI: 10.1371/Journal.Pcbi.1003675  0.769
2014 Sturrock M, Hellander A, Aldakheel S, Petzold L, Chaplain MA. The role of dimerisation and nuclear transport in the Hes1 gene regulatory network. Bulletin of Mathematical Biology. 76: 766-98. PMID 23686434 DOI: 10.1007/S11538-013-9842-5  0.388
2014 Bezzola A, Bales BB, Petzold LR, Alkire RC. Numerical scaling studies of kinetically-limited electrochemical nucleation and growth with accelerated stochastic simulations Journal of the Electrochemical Society. 161: E3001-E3008. DOI: 10.1149/2.001408Jes  0.778
2014 Bezzola A, Bales BB, Alkire RC, Petzold LR. An exact and efficient first passage time algorithm for reaction-diffusion processes on a 2D-lattice Journal of Computational Physics. 256: 183-197. DOI: 10.1016/J.Jcp.2013.08.053  0.787
2014 Griesemer M, Young C, Robinson AS, Petzold L. Enhanced Chaperone Clustering Facilitates Protein Folding in the Endoplasmic Reticulum of Yeast Biophysical Journal. 106: 247a. DOI: 10.1016/J.Bpj.2013.11.1448  0.768
2013 An S, Harang R, Meeker K, Granados-Fuentes D, Tsai CA, Mazuski C, Kim J, Doyle FJ, Petzold LR, Herzog ED. A neuropeptide speeds circadian entrainment by reducing intercellular synchrony. Proceedings of the National Academy of Sciences of the United States of America. 110: E4355-61. PMID 24167276 DOI: 10.1073/Pnas.1307088110  0.756
2013 Lawson MJ, Drawert B, Khammash M, Petzold L, Yi TM. Spatial stochastic dynamics enable robust cell polarization. Plos Computational Biology. 9: e1003139. PMID 23935469 DOI: 10.1371/Journal.Pcbi.1003139  0.728
2013 Fu J, Wu S, Petzold LR. Time dependent solution for acceleration of tau-leaping Journal of Computational Physics. 235: 446-457. DOI: 10.1016/J.Jcp.2012.10.036  0.479
2012 Wallace EW, Gillespie DT, Sanft KR, Petzold LR. Linear noise approximation is valid over limited times for any chemical system that is sufficiently large. Iet Systems Biology. 6: 102-15. PMID 23039691 DOI: 10.1049/Iet-Syb.2011.0038  0.742
2012 Wu S, Fu J, Li H, Petzold L. Automatic identification of model reductions for discrete stochastic simulation. The Journal of Chemical Physics. 137: 034106. PMID 22830682 DOI: 10.1063/1.4733563  0.615
2012 Hellander S, Hellander A, Petzold L. Reaction-diffusion master equation in the microscopic limit. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 85: 042901. PMID 22680526 DOI: 10.1103/Physreve.85.042901  0.356
2012 Daigle BJ, Roh MK, Petzold LR, Niemi J. Accelerated maximum likelihood parameter estimation for stochastic biochemical systems. Bmc Bioinformatics. 13: 68. PMID 22548918 DOI: 10.1186/1471-2105-13-68  0.757
2012 Griesemer M, Young C, Robinson A, Petzold L. Spatial localisation of chaperone distribution in the endoplasmic reticulum of yeast Iet Systems Biology. 6: 54-63. PMID 22519358 DOI: 10.1049/Iet-Syb.2011.0006  0.76
2011 Roh MK, Daigle BJ, Gillespie DT, Petzold LR. State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events. The Journal of Chemical Physics. 135: 234108. PMID 22191865 DOI: 10.1063/1.3668100  0.746
2011 Meeker K, Harang R, Webb AB, Welsh DK, Doyle FJ, Bonnet G, Herzog ED, Petzold LR. Wavelet measurement suggests cause of period instability in mammalian circadian neurons. Journal of Biological Rhythms. 26: 353-62. PMID 21775294 DOI: 10.1177/0748730411409863  0.763
2011 Sanft KR, Wu S, Roh M, Fu J, Lim RK, Petzold LR. StochKit2: software for discrete stochastic simulation of biochemical systems with events. Bioinformatics (Oxford, England). 27: 2457-8. PMID 21727139 DOI: 10.1093/Bioinformatics/Btr401  0.786
2011 Wu S, Fu J, Cao Y, Petzold L. Michaelis-Menten speeds up tau-leaping under a wide range of conditions. The Journal of Chemical Physics. 134: 134112. PMID 21476748 DOI: 10.1063/1.3576123  0.537
2011 Daigle BJ, Roh MK, Gillespie DT, Petzold LR. Automated estimation of rare event probabilities in biochemical systems. The Journal of Chemical Physics. 134: 044110. PMID 21280690 DOI: 10.1063/1.3522769  0.754
2011 Sanft KR, Gillespie DT, Petzold LR. Legitimacy of the stochastic Michaelis-Menten approximation. Iet Systems Biology. 5: 58. PMID 21261403 DOI: 10.1049/Iet-Syb.2009.0057  0.773
2010 Luni C, Shoemaker JE, Sanft KR, Petzold LR, Doyle FJ. Confidence from uncertainty--a multi-target drug screening method from robust control theory. Bmc Systems Biology. 4: 161. PMID 21106087 DOI: 10.1186/1752-0509-4-161  0.746
2010 Roh MK, Gillespie DT, Petzold LR. State-dependent biasing method for importance sampling in the weighted stochastic simulation algorithm. The Journal of Chemical Physics. 133: 174106. PMID 21054005 DOI: 10.1063/1.3493460  0.75
2010 Drawert B, Lawson MJ, Petzold L, Khammash M. The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation. The Journal of Chemical Physics. 132: 074101. PMID 20170209 DOI: 10.1063/1.3310809  0.77
2010 Luni C, Sanft KR, Petzold LR, Doyle FJ. Modelling of detailed insulin receptor kinetics affects sensitivity and noise in the downstream signalling pathway Ifac Proceedings Volumes (Ifac-Papersonline). 9: 326-331. DOI: 10.3182/20100705-3-Be-2011.00054  0.752
2010 Li H, Petzold L. Efficient parallelization of the stochastic simulation algorithm for chemically reacting systems on the graphics processing unit International Journal of High Performance Computing Applications. 24: 107-116. DOI: 10.1177/1094342009106066  0.307
2010 Buoni M, Petzold L. An algorithm for simulation of electrochemical systems with surface-bulk coupling strategies Journal of Computational Physics. 229: 379-398. DOI: 10.1016/J.Jcp.2009.09.032  0.769
2009 Gillespie DT, Roh M, Petzold LR. Refining the weighted stochastic simulation algorithm. The Journal of Chemical Physics. 130: 174103. PMID 19425765 DOI: 10.1063/1.3116791  0.756
2009 Resat H, Petzold L, Pettigrew MF. Kinetic modeling of biological systems. Methods in Molecular Biology (Clifton, N.J.). 541: 311-35. PMID 19381542 DOI: 10.1007/978-1-59745-243-4_14  0.428
2009 Lampoudi S, Gillespie DT, Petzold LR. Effect of excluded volume on 2D discrete stochastic chemical kinetics. Journal of Computational Physics. 228: 3656-3668. PMID 19360139 DOI: 10.1016/J.Jcp.2009.02.002  0.785
2009 Lampoudi S, Gillespie DT, Petzold LR. The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems. The Journal of Chemical Physics. 130: 094104. PMID 19275393 DOI: 10.1063/1.3074302  0.795
2009 Gillespie DT, Cao Y, Sanft KR, Petzold LR. The subtle business of model reduction for stochastic chemical kinetics. The Journal of Chemical Physics. 130: 064103. PMID 19222263 DOI: 10.1063/1.3072704  0.781
2009 Li H, Kolpas A, Petzold L, Moehlis J. Parallel simulation for a fish schooling model on a general-purpose graphics processing unit Concurrency Computation Practice and Experience. 21: 725-737. DOI: 10.1002/Cpe.V21:6  0.309
2008 Cao Y, Petzold L. Slow Scale Tau-leaping Method. Computer Methods in Applied Mechanics and Engineering. 197: 3472-3479. PMID 19794828 DOI: 10.1016/J.Cma.2008.02.024  0.364
2008 Hildebrandt S, Raden D, Petzold L, Robinson AS, Doyle FJ. A top-down approach to mechanistic biological modeling: application to the single-chain antibody folding pathway. Biophysical Journal. 95: 3535-58. PMID 18641066 DOI: 10.1529/Biophysj.107.125039  0.348
2008 Bagheri N, Taylor SR, Meeker K, Petzold LR, Doyle FJ. Synchrony and entrainment properties of robust circadian oscillators. Journal of the Royal Society, Interface / the Royal Society. 5: S17-28. PMID 18426774 DOI: 10.1098/Rsif.2008.0045.Focus  0.768
2008 Kwei E, Sanft K, Petzold L, Doyle F. Systems analysis of the insulin signaling pathway Ifac Proceedings Volumes (Ifac-Papersonline). 17. DOI: 10.3182/20080706-5-Kr-1001.02686  0.743
2008 Zheng Z, Simeon B, Petzold L. A stabilized explicit Lagrange multiplier based domain decomposition method for parabolic problems Journal of Computational Physics. 227: 5272-5285. DOI: 10.1016/J.Jcp.2008.01.057  0.551
2008 Zheng Z, Stephens RM, Braatz RD, Alkire RC, Petzold LR. A hybrid multiscale kinetic Monte Carlo method for simulation of copper electrodeposition Journal of Computational Physics. 227: 5184-5199. DOI: 10.1016/J.Jcp.2008.01.056  0.579
2008 Kwei EC, Sanft KR, Shoemaker JE, Petzold LR, Doyle FJ. Stochastic simulation and systems analysis of insulin-stimulated GLUT4 translocation Aiche Annual Meeting, Conference Proceedings 0.746
2007 Gillespie DT, Lampoudi S, Petzold LR. Effect of reactant size on discrete stochastic chemical kinetics. The Journal of Chemical Physics. 126: 034302. PMID 17249866 DOI: 10.1063/1.2424461  0.767
2007 Buoni M, Petzold L. An efficient, scalable numerical algorithm for the simulation of electrochemical systems on irregular domains Journal of Computational Physics. 225: 2320-2332. DOI: 10.1016/J.Jcp.2007.03.025  0.763
2006 Zheng Z, Stroumpoulis D, Parra A, Petzold L, Tirrell M. A Monte Carlo simulation study of lipid bilayer formation on hydrophilic substrates from vesicle solutions. The Journal of Chemical Physics. 124: 64904. PMID 16483241 DOI: 10.1063/1.2166392  0.583
2006 Zheng Z, Petzold L. Runge-Kutta-Chebyshev projection method Journal of Computational Physics. 219: 976-991. DOI: 10.1016/J.Jcp.2006.07.005  0.549
2006 Cao Y, Petzold L. Accuracy limitations and the measurement of errors in the stochastic simulation of chemically reacting systems Journal of Computational Physics. 212: 6-24. DOI: 10.1016/J.Jcp.2005.06.012  0.358
2005 Gunawan R, Cao Y, Petzold L, Doyle FJ. Sensitivity analysis of discrete stochastic systems. Biophysical Journal. 88: 2530-40. PMID 15695639 DOI: 10.1529/Biophysj.104.053405  0.357
2005 Cao Y, Gillespie D, Petzold L. Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems Journal of Computational Physics. 206: 395-411. DOI: 10.1016/J.Jcp.2004.12.014  0.41
2005 El Samad H, Khammash M, Petzold L, Gillespie D. Stochastic modelling of gene regulatory networks International Journal of Robust and Nonlinear Control. 15: 691-711. DOI: 10.1002/Rnc.1018  0.407
2004 Cao Y, Li H, Petzold L. Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. The Journal of Chemical Physics. 121: 4059-67. PMID 15332951 DOI: 10.1063/1.1778376  0.378
2002 Cao Y, Li S, Petzold L. Adjoint sensitivity analysis for differential-algebraic equations: Algorithms and software Journal of Computational and Applied Mathematics. 149: 171-191. DOI: 10.1016/S0377-0427(02)00528-9  0.323
2000 Li S, Petzold L. Software and algorithms for sensitivity analysis of large-scale differential algebraic systems Journal of Computational and Applied Mathematics. 125: 131-145. DOI: 10.1016/S0377-0427(00)00464-7  0.335
1999 Li S, Petzold L, Zhu W. Sensitivity analysis of differential-algebraic equations: A comparison of methods on a special problem Applied Numerical Mathematics. 32: 161-174. DOI: 10.1016/S0168-9274(99)00020-3  0.312
1998 Li S, Petzold L, Ren Y. Stability of Moving Mesh Systems of Partial Differential Equations Siam Journal On Scientific Computing. 20: 719-738. DOI: 10.1137/S1064827596302011  0.306
1998 Yen J, Petzold L, Raha S. A time integration algorithm for flexible mechanism dynamics: The DAE α-method Computer Methods in Applied Mechanics and Engineering. 158: 341-355. DOI: 10.1016/S0045-7825(97)00261-2  0.343
1986 Lötstedt P, Petzold L. Numerical solution of nonlinear differential equations with algebraic constraints I: Convergence results for backward differentiation formulas Mathematics of Computation. 46: 491-516. DOI: 10.2307/2007989  0.309
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