Loading...

Petzold Linda

TitleCNSI-UCSB
InstitutionUniversity of California Los Angeles
DepartmentCalifornia NanoSystems Institute
Address5106 Harold Frank Hall
Santa Barbara CA 93106
Phone(805) 893-5435
vCardDownload vCard
    Other Positions
    TitleProfessor


    Collapse Research 
    Collapse Research Activities and Funding
    Stochastic Simulation Service: A Cloud Computing Framework for Modeling and Simul
    NIH/NIBIB R01EB014877May 15, 2012 - Apr 30, 2015
    Role: Principal Investigator
    MECHANISMS AND MODELING OF NETWORKED CIRCADIAN PACEMAKER SYNCHRONIZATION
    NIH/NIGMS R01GM096873Aug 1, 2011 - Jul 31, 2015
    Role: Co-Principal Investigator
    Multiscale Modeling &Analysis of Circadian Rhythm Generation &Synchronization
    NIH/NIGMS R01GM078993May 11, 2006 - Apr 30, 2011
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. Nowakowski TJ, Rani N, Golkaram M, Zhou HR, Alvarado B, Huch K, West JA, Leyrat A, Pollen AA, Kriegstein AR, Petzold LR, Kosik KS. Regulation of cell-type-specific transcriptomes by microRNA networks during human brain development. Nat Neurosci. 2018 Nov 19. PMID: 30455455.
      View in: PubMed
    2. Ghaffari H, Petzold LR. Identification of influential proteins in the classical retinoic acid signaling pathway. Theor Biol Med Model. 2018 10 16; 15(1):16. PMID: 30322383.
      View in: PubMed
    3. McBride D, Petzold L. Model-based Inference of a Directed Network of Circadian Neurons. J Biol Rhythms. 2018 Aug 07; 748730418790402. PMID: 30084298.
      View in: PubMed
    4. 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 Comput Biol. 2018 06; 14(6):e1006241. PMID: 29889845.
      View in: PubMed
    5. Wu TB, Wu S, Buoni M, Orfeo T, Brummel-Ziedins K, Cohen M, Petzold L. Computational Model for Hyperfibrinolytic Onset of Acute Traumatic Coagulopathy. Ann Biomed Eng. 2018 Apr 19. PMID: 29675813.
      View in: PubMed
    6. Banavar SP, Gomez C, Trogdon M, Petzold LR, Yi TM, Campàs O. Mechanical feedback coordinates cell wall expansion and assembly in yeast mating morphogenesis. PLoS Comput Biol. 2018 Jan; 14(1):e1005940. PMID: 29346368.
      View in: PubMed
    7. Doostparast Torshizi A, Petzold LR. Graph-based semi-supervised learning with genomic data integration using condition-responsive genes applied to phenotype classification. J Am Med Inform Assoc. 2018 Jan 01; 25(1):99-108. PMID: 28505320.
      View in: PubMed
    8. Bales B, Petzold L, Goodlet BR, Lenthe WC, Pollock TM. Bayesian inference of elastic properties with resonant ultrasound spectroscopy. J Acoust Soc Am. 2018 Jan; 143(1):71. PMID: 29390755.
      View in: PubMed
    9. Hellander S, Hellander A, Petzold L. Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning. J Chem Phys. 2017 Dec 21; 147(23):234101. PMID: 29272930.
      View in: PubMed
    10. Carmona-Alcocer V, Abel JH, Sun TC, Petzold LR, Doyle FJ, Simms CL, Herzog ED. Ontogeny of Circadian Rhythms and Synchrony in the Suprachiasmatic Nucleus. J Neurosci. 2018 Feb 07; 38(6):1326-1334. PMID: 29054877.
      View in: PubMed
    11. Golkaram M, Jang J, Hellander S, Kosik KS, Petzold LR. The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation. Sci Rep. 2017 Oct 17; 7(1):13307. PMID: 29042584.
      View in: PubMed
    12. Drawert B, Griesemer M, Petzold LR, Briggs CJ. Using stochastic epidemiological models to evaluate conservation strategies for endangered amphibians. J R Soc Interface. 2017 Aug; 14(133). PMID: 28855388.
      View in: PubMed
    13. Doostparast Torshizi A, Petzold L. Sparse Pathway-Induced Dynamic Network Biomarker Discovery for Early Warning Signal Detection in Complex Diseases. IEEE/ACM Trans Comput Biol Bioinform. 2017 Mar 27. PMID: 28368826.
      View in: PubMed
    14. Hellander S, Petzold L. Reaction rates for reaction-diffusion kinetics on unstructured meshes. J Chem Phys. 2017 Feb 14; 146(6):064101. PMID: 28201913.
      View in: PubMed
    15. 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, Krintz C, Petzold LR. Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist. PLoS Comput Biol. 2016 Dec; 12(12):e1005220. PMID: 27930676.
      View in: PubMed
    16. Golkaram M, Hellander S, Drawert B, Petzold LR. Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion. PLoS Comput Biol. 2016 Nov; 12(11):e1005122. PMID: 27893768.
      View in: PubMed
    17. Drawert B, Hellander S, Trogdon M, Yi TM, Petzold L. A framework for discrete stochastic simulation on 3D moving boundary domains. J Chem Phys. 2016 Nov 14; 145(18):184113. PMID: 27846706.
      View in: PubMed
    18. Zhang Y, Wu TB, Daigle BJ, Cohen M, Petzold L. Identification of disease states associated with coagulopathy in trauma. BMC Med Inform Decis Mak. 2016 Sep 22; 16(1):124. PMID: 27658851.
      View in: PubMed
    19. Abel JH, Drawert B, Hellander A, Petzold LR. GillesPy: A Python Package for Stochastic Model Building and Simulation. IEEE Life Sci Lett. 2016 Sep; 2(3):35-38. PMID: 28630888.
      View in: PubMed
    20. 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 J Sci Comput. 2016; 38(3):C179-C202. PMID: 28190948.
      View in: PubMed
    21. 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. Proc Natl Acad Sci U S A. 2016 Apr 19; 113(16):4512-7. PMID: 27044085; PMCID: PMC4843423 [Available on 10/19/16].
    22. Hellander S, Petzold L. Reaction rates for a generalized reaction-diffusion master equation. Phys Rev E. 2016 Jan; 93(1):013307. PMID: 26871190; PMCID: PMC4854577.
    23. Pourzanjani A, Herzog ED, Petzold LR. On the Inference of Functional Circadian Networks Using Granger Causality. PLoS One. 2015; 10(9):e0137540. PMID: 26413748; PMCID: PMC4586144.
    24. Wu S, Fu J, Petzold LR. Adaptive deployment of model reductions for tau-leaping simulation. J Chem Phys. 2015 May 28; 142(20):204108. PMID: 26026435; PMCID: PMC4449353.
    25. Lawson MJ, Petzold L, Hellander A. Accuracy of the Michaelis-Menten approximation when analysing effects of molecular noise. J R Soc Interface. 2015 May 06; 12(106). PMID: 25833240; PMCID: PMC4424680.
    26. Thakur GS, Daigle BJ, Dean KR, Zhang Y, Rodriguez-Fernandez M, Hammamieh R, Yang R, Jett M, Palma J, Petzold LR, Doyle FJ. Systems biology approach to understanding post-traumatic stress disorder. Mol Biosyst. 2015 Apr; 11(4):980-93. PMID: 25627823.
      View in: PubMed
    27. Hellander S, Hellander A, Petzold L. Reaction rates for mesoscopic reaction-diffusion kinetics. Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Feb; 91(2):023312. PMID: 25768640; PMCID: PMC4854576.
    28. Daigle BJ, Soltani M, Petzold LR, Singh A. Inferring single-cell gene expression mechanisms using stochastic simulation. Bioinformatics. 2015 May 01; 31(9):1428-35. PMID: 25573914; PMCID: PMC4492418.
    29. Fu J, Wu S, Li H, Petzold LR. The Time Dependent Propensity Function for Acceleration of Spatial Stochastic Simulation of Reaction-Diffusion Systems. J Comput Phys. 2014 Oct 01; 274:524-549. PMID: 26609185.
      View in: PubMed
    30. Griesemer M, Young C, Robinson AS, Petzold L. BiP clustering facilitates protein folding in the endoplasmic reticulum. PLoS Comput Biol. 2014 Jul; 10(7):e1003675. PMID: 24991821; PMCID: PMC4081015.
    31. Hellander A, Lawson MJ, Drawert B, Petzold L. Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting. J Comput Phys. 2014 Jun 01; 266:89-100. PMID: 26865735.
      View in: PubMed
    32. Gillespie DT, Petzold LR, Seitaridou E. Validity conditions for stochastic chemical kinetics in diffusion-limited systems. J Chem Phys. 2014 Feb 07; 140(5):054111. PMID: 24511926; PMCID: PMC3977787.
    33. 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. Proc Natl Acad Sci U S A. 2013 Nov 12; 110(46):E4355-61. PMID: 24167276; PMCID: PMC3832006.
    34. Yang R, Daigle BJ, Muhie SY, Hammamieh R, Jett M, Petzold L, Doyle FJ. Core modular blood and brain biomarkers in social defeat mouse model for post traumatic stress disorder. BMC Syst Biol. 2013 Aug 20; 7:80. PMID: 23962043; PMCID: PMC3751782.
    35. Lawson MJ, Drawert B, Khammash M, Petzold L, Yi TM. Spatial stochastic dynamics enable robust cell polarization. PLoS Comput Biol. 2013; 9(7):e1003139. PMID: 23935469; PMCID: PMC3723497.
    36. Sturrock M, Hellander A, Aldakheel S, Petzold L, Chaplain MA. The role of dimerisation and nuclear transport in the Hes1 gene regulatory network. Bull Math Biol. 2014 Apr; 76(4):766-98. PMID: 23686434; PMCID: PMC3999905.
    37. Gillespie DT, Hellander A, Petzold LR. Perspective: Stochastic algorithms for chemical kinetics. J Chem Phys. 2013 May 07; 138(17):170901. PMID: 23656106; PMCID: PMC3656953.
    38. Kolpas A, Busch M, Li H, Couzin ID, Petzold L, Moehlis J. How the spatial position of individuals affects their influence on swarms: a numerical comparison of two popular swarm dynamics models. PLoS One. 2013; 8(3):e58525. PMID: 23555585.
      View in: PubMed
    39. Wu S, Fu J, Li H, Petzold L. Automatic identification of model reductions for discrete stochastic simulation. J Chem Phys. 2012 Jul 21; 137(3):034106. PMID: 22830682.
      View in: PubMed
    40. Daigle BJ, Roh MK, Petzold LR, Niemi J. Accelerated maximum likelihood parameter estimation for stochastic biochemical systems. BMC Bioinformatics. 2012 May 01; 13:68. PMID: 22548918; PMCID: PMC3496601.
    41. Hellander S, Hellander A, Petzold L. Reaction-diffusion master equation in the microscopic limit. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Apr; 85(4 Pt 1):042901. PMID: 22680526.
      View in: PubMed
    42. Harang R, Bonnet G, Petzold LR. WAVOS: a MATLAB toolkit for wavelet analysis and visualization of oscillatory systems. BMC Res Notes. 2012 Mar 26; 5:163. PMID: 22448897; PMCID: PMC3353168.
    43. Yang R, Daigle BJ, Petzold LR, Doyle FJ. Core module biomarker identification with network exploration for breast cancer metastasis. BMC Bioinformatics. 2012 Jan 18; 13:12. PMID: 22257533; PMCID: PMC3349569.
    44. Roh MK, Daigle BJ, Gillespie DT, Petzold LR. State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events. J Chem Phys. 2011 Dec 21; 135(23):234108. PMID: 22191865; PMCID: PMC3264419.
    45. 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. J Biol Rhythms. 2011 Aug; 26(4):353-62. PMID: 21775294; PMCID: PMC3472003.
    46. Sanft KR, Wu S, Roh M, Fu J, Lim RK, Petzold LR. StochKit2: software for discrete stochastic simulation of biochemical systems with events. Bioinformatics. 2011 Sep 01; 27(17):2457-8. PMID: 21727139; PMCID: PMC3157925.
    47. Wu S, Fu J, Cao Y, Petzold L. Michaelis-Menten speeds up tau-leaping under a wide range of conditions. J Chem Phys. 2011 Apr 07; 134(13):134112. PMID: 21476748; PMCID: PMC3087420.
    48. Daigle BJ, Roh MK, Gillespie DT, Petzold LR. Automated estimation of rare event probabilities in biochemical systems. J Chem Phys. 2011 Jan 28; 134(4):044110. PMID: 21280690; PMCID: PMC3045218.
    49. Luni C, Shoemaker JE, Sanft KR, Petzold LR, Doyle FJ. Confidence from uncertainty--a multi-target drug screening method from robust control theory. BMC Syst Biol. 2010 Nov 24; 4:161. PMID: 21106087; PMCID: PMC3277951.
    50. Roh MK, Gillespie DT, Petzold LR. State-dependent biasing method for importance sampling in the weighted stochastic simulation algorithm. J Chem Phys. 2010 Nov 07; 133(17):174106. PMID: 21054005; PMCID: PMC3188645.
    51. Taylor SR, Webb AB, Smith KS, Petzold LR, Doyle FJ. Velocity response curves support the role of continuous entrainment in circadian clocks. J Biol Rhythms. 2010 Apr; 25(2):138-49. PMID: 20348465.
      View in: PubMed
    52. Drawert B, Lawson MJ, Petzold L, Khammash M. The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation. J Chem Phys. 2010 Feb 21; 132(7):074101. PMID: 20170209; PMCID: PMC2905448.
    53. Gillespie DT, Roh M, Petzold LR. Refining the weighted stochastic simulation algorithm. J Chem Phys. 2009 May 07; 130(17):174103. PMID: 19425765; PMCID: PMC2832048.
    54. Lampoudi S, Gillespie DT, Petzold LR. The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems. J Chem Phys. 2009 Mar 07; 130(9):094104. PMID: 19275393; PMCID: PMC2671688.
    55. Gillespie DT, Cao Y, Sanft KR, Petzold LR. The subtle business of model reduction for stochastic chemical kinetics. J Chem Phys. 2009 Feb 14; 130(6):064103. PMID: 19222263; PMCID: PMC2675560.
    56. Lampoudi S, Gillespie DT, Petzold LR. Effect of excluded volume on 2D discrete stochastic chemical kinetics. J Comput Phys. 2009; 228(10):3656-3668. PMID: 19360139.
      View in: PubMed
    57. Resat H, Petzold L, Pettigrew MF. Kinetic modeling of biological systems. Methods Mol Biol. 2009; 541:311-35. PMID: 19381542; PMCID: PMC2877599.
    58. Bagheri N, Taylor SR, Meeker K, Petzold LR, Doyle FJ. Synchrony and entrainment properties of robust circadian oscillators. J R Soc Interface. 2008 Aug 06; 5 Suppl 1:S17-28. PMID: 18426774; PMCID: PMC2706452.
    59. Cao Y, Petzold L. Slow Scale Tau-leaping Method. Comput Methods Appl Mech Eng. 2008 Aug 01; 197(43-44):3472-3479. PMID: 19794828.
      View in: PubMed
    60. 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. Biophys J. 2008 Oct; 95(8):3535-58. PMID: 18641066; PMCID: PMC2553102.
    61. Taylor SR, Doyle FJ, Petzold LR. Oscillator model reduction preserving the phase response: application to the circadian clock. Biophys J. 2008 Aug; 95(4):1658-73. PMID: 18487303; PMCID: PMC2483761.
    62. Taylor SR, Gunawan R, Petzold LR, Doyle FJ. Sensitivity Measures for Oscillating Systems: Application to Mammalian Circadian Gene Network. IEEE Trans Automat Contr. 2008 Jan 01; 53:177-188. PMID: 19593456.
      View in: PubMed
    63. Li H, Cao Y, Petzold LR, Gillespie DT. Algorithms and software for stochastic simulation of biochemical reacting systems. Biotechnol Prog. 2008 Jan-Feb; 24(1):56-61. PMID: 17894470; PMCID: PMC2664303.
    64. Liu T, Papagiannakopoulos T, Puskar K, Qi S, Santiago F, Clay W, Lao K, Lee Y, Nelson SF, Kornblum HI, Doyle F, Petzold L, Shraiman B, Kosik KS. Detection of a microRNA signal in an in vivo expression set of mRNAs. PLoS One. 2007 Aug 29; 2(8):e804. PMID: 17726534; PMCID: PMC1950084.
    65. Cao Y, Gillespie DT, Petzold LR. Adaptive explicit-implicit tau-leaping method with automatic tau selection. J Chem Phys. 2007 Jun 14; 126(22):224101. PMID: 17581038.
      View in: PubMed
    66. Gillespie DT, Lampoudi S, Petzold LR. Effect of reactant size on discrete stochastic chemical kinetics. J Chem Phys. 2007 Jan 21; 126(3):034302. PMID: 17249866.
      View in: PubMed
    67. 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. J Chem Phys. 2006 Feb 14; 124(6):64904. PMID: 16483241.
      View in: PubMed
    68. Cao Y, Gillespie DT, Petzold LR. Efficient step size selection for the tau-leaping simulation method. J Chem Phys. 2006 Jan 28; 124(4):044109. PMID: 16460151.
      View in: PubMed
    69. Cao Y, Gillespie DT, Petzold LR. Accelerated stochastic simulation of the stiff enzyme-substrate reaction. J Chem Phys. 2005 Oct 08; 123(14):144917. PMID: 16238434.
      View in: PubMed
    70. Cao Y, Gillespie DT, Petzold LR. Avoiding negative populations in explicit Poisson tau-leaping. J Chem Phys. 2005 Aug 01; 123(5):054104. PMID: 16108628.
      View in: PubMed
    71. Gunawan R, Cao Y, Petzold L, Doyle FJ. Sensitivity analysis of discrete stochastic systems. Biophys J. 2005 Apr; 88(4):2530-40. PMID: 15695639; PMCID: PMC1305350.
    72. Cao Y, Gillespie DT, Petzold LR. The slow-scale stochastic simulation algorithm. J Chem Phys. 2005 Jan 01; 122(1):14116. PMID: 15638651.
      View in: PubMed
    73. Cao Y, Petzold LR, Rathinam M, Gillespie DT. The numerical stability of leaping methods for stochastic simulation of chemically reacting systems. J Chem Phys. 2004 Dec 22; 121(24):12169-78. PMID: 15606235.
      View in: PubMed
    74. Cao Y, Li H, Petzold L. Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. J Chem Phys. 2004 Sep 01; 121(9):4059-67. PMID: 15332951.
      View in: PubMed