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    Lev Tsimring

    TitleResearcher
    SchoolUniversity of California, San Diego
    DepartmentBiocircuits Institute
    Address9500 Gilman Drive #0328
    CA La Jolla 92093
    Phone858-534-0816
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      Collapse Research 
      Collapse Research Activities and Funding
      Network-Driven Dynamics of Replicative Aging
      NIH/NIA R01AG056440Aug 1, 2017 - May 31, 2022
      Role: Co-Principal Investigator
      The q-bio Summer School
      NIH/NIGMS R25GM105608Apr 1, 2013 - Jan 31, 2017
      Role: Principal Investigator
      Delays and variability in single-cell NFkB signaling
      NIH/NIGMS R01GM089976May 1, 2010 - Apr 30, 2014
      Role: Principal Investigator
      San Diego Center for Systems Biology: From Maps to Models
      NIH/NIGMS P50GM085764Jul 1, 2008 - May 31, 2019
      Role: Co-Investigator
      Engineered gene circuits for basic science and biotechnology
      NIH/NIGMS R01GM069811Dec 1, 2003 - Jul 31, 2020
      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.
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      1. Didovyk A, Tonooka T, Tsimring L, Hasty J. Rapid and Scalable Preparation of Bacterial Lysates for Cell-Free Gene Expression. ACS Synth Biol. 2017 Aug 21. PMID: 28795570.
        View in: PubMed
      2. Jiang Y, AkhavanAghdam Z, Tsimring L, Hao N. Coupled feedback loops control the stimulus-dependent dynamics of the yeast transcription factor Msn2. J Biol Chem. 2017 Jul 28; 292(30):12366-12372. PMID: 28637875.
        View in: PubMed
      3. Scott SR, Din MO, Bittihn P, Xiong L, Tsimring L, Hasty J. A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis. Nat Microbiol. 2017 Jun 12; 2:17083. PMID: 28604679.
        View in: PubMed
      4. Didovyk A, Tsimring L. Synthetic Gene Circuits Learn to Classify. Cell Syst. 2017 Feb 22; 4(2):151-153. PMID: 28231449.
        View in: PubMed
      5. Humphries J, Xiong L, Liu J, Prindle A, Yuan F, Arjes HA, Tsimring L, Süel GM. Species-Independent Attraction to Biofilms through Electrical Signaling. Cell. 2017 Jan 12; 168(1-2):200-209.e12. PMID: 28086091.
        View in: PubMed
      6. Bittihn P, Hasty J, Tsimring L. Suppression of Beneficial Mutations in Dynamic Microbial Populations. Phys Rev Lett. 2017 Jan 13; 118(2):028102. PMID: 28128631.
        View in: PubMed
      7. Steiner PJ, Williams RJ, Hasty J, Tsimring L. Criticality and Adaptivity in Enzymatic Networks. Biophys J. 2016 Sep 06; 111(5):1078-87. PMID: 27602735.
        View in: PubMed
      8. Borek B, Hasty J, Tsimring L. Correction: Turing Patterning Using Gene Circuits with Gas-Induced Degradation of Quorum Sensing Molecules. PLoS One. 2016; 11(7):e0160272. PMID: 27467885.
        View in: PubMed
      9. Didovyk A, Borek B, Tsimring L, Hasty J. Transcriptional regulation with CRISPR-Cas9: principles, advances, and applications. Curr Opin Biotechnol. 2016 Aug; 40:177-184. PMID: 27344519; PMCID: PMC4975649 [Available on 08/01/17].
      10. Borek B, Hasty J, Tsimring L. Turing Patterning Using Gene Circuits with Gas-Induced Degradation of Quorum Sensing Molecules. PLoS One. 2016; 11(5):e0153679. PMID: 27148743; PMCID: PMC4858293.
      11. Kanakov O, Laptyeva T, Tsimring L, Ivanchenko M. Spatiotemporal dynamics of distributed synthetic genetic circuits. Physica D. 2016 Apr 01; 318-319:116-123. PMID: 26955203.
        View in: PubMed
      12. Didovyk A, Borek B, Hasty J, Tsimring L. Orthogonal Modular Gene Repression in Escherichia coli Using Engineered CRISPR/Cas9. ACS Synth Biol. 2016 Jan 15; 5(1):81-8. PMID: 26390083.
        View in: PubMed
      13. Hardy MD, Yang J, Selimkhanov J, Cole CM, Tsimring L, Devaraj NK. Self-reproducing catalyst drives repeated phospholipid synthesis and membrane growth. Proc Natl Acad Sci U S A. 2015 Jul 07; 112(27):8187-92. PMID: 26100914; PMCID: PMC4500204.
      14. Kanakov O, Kotelnikov R, Alsaedi A, Tsimring L, Huerta R, Zaikin A, Ivanchenko M. Multi-input distributed classifiers for synthetic genetic circuits. PLoS One. 2015; 10(5):e0125144. PMID: 25946237; PMCID: PMC4450813.
      15. Davis-Turak JC, Allison K, Shokhirev MN, Ponomarenko P, Tsimring L, Glass CK, Johnson TL, Hoffmann A. Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing. Nucleic Acids Res. 2015 Jan; 43(2):699-707. PMID: 25541195; PMCID: PMC4333389.
      16. Selimkhanov J, Taylor B, Yao J, Pilko A, Albeck J, Hoffmann A, Tsimring L, Wollman R. Systems biology. Accurate information transmission through dynamic biochemical signaling networks. Science. 2014 Dec 12; 346(6215):1370-3. PMID: 25504722; PMCID: PMC4813785.
      17. Didovyk A, Kanakov OI, Ivanchenko MV, Hasty J, Huerta R, Tsimring L. Distributed classifier based on genetically engineered bacterial cell cultures. ACS Synth Biol. 2015 Jan 16; 4(1):72-82. PMID: 25349924; PMCID: PMC4304444.
      18. Mather W, Hasty J, Tsimring L. Synchronization of degrade-and-fire oscillations via a common activator. Phys Rev Lett. 2014 Sep 19; 113(12):128102. PMID: 25279645; PMCID: PMC4494757.
      19. Prindle A, Selimkhanov J, Li H, Razinkov I, Tsimring L, Hasty J. Rapid and tunable post-translational coupling of genetic circuits. Nature. 2014 Apr 17; 508(7496):387-91. PMID: 24717442; PMCID: PMC4142690.
      20. Tsimring L. Noise in biology. Rep Prog Phys. 2014; 77(2):026601. PMID: 24444693; PMCID: PMC4033672.
      21. Razinkov IA, Baumgartner BL, Bennett MR, Tsimring L, Hasty J. Measuring competitive fitness in dynamic environments. J Phys Chem B. 2013 Oct 24; 117(42):13175-81. PMID: 23841812; PMCID: PMC3808460.
      22. Longo DM, Selimkhanov J, Kearns JD, Hasty J, Hoffmann A, Tsimring L. Dual delayed feedback provides sensitivity and robustness to the NF-?B signaling module. PLoS Comput Biol. 2013; 9(6):e1003112. PMID: 23825938; PMCID: PMC3694842.
      23. Mather WH, Hasty J, Tsimring L, Williams RJ. Translational cross talk in gene networks. Biophys J. 2013 Jun 04; 104(11):2564-72. PMID: 23746529; PMCID: PMC3672881.
      24. Fernandez B, Tsimring L. Typical trajectories of coupled degrade-and-fire oscillators: from dispersed populations to massive clustering. J Math Biol. 2014 Jun; 68(7):1627-52. PMID: 23639980; PMCID: PMC3858518.
      25. Harvey CW, Alber M, Tsimring L, Aranson IS. Continuum modeling of clustering of myxobacteria. New J Phys. 2013 Mar; 15. PMID: 23712128.
        View in: PubMed
      26. Kolnik M, Tsimring L, Hasty J. Vacuum-assisted cell loading enables shear-free mammalian microfluidic culture. Lab Chip. 2012 Nov 21; 12(22):4732-7. PMID: 22961584; PMCID: PMC3510264.
      27. Mather WH, Hasty J, Tsimring L. Fast stochastic algorithm for simulating evolutionary population dynamics. Bioinformatics. 2012 May 01; 28(9):1230-8. PMID: 22437850; PMCID: PMC3338019.
      28. Cookson NA, Mather WH, Danino T, Mondragón-Palomino O, Williams RJ, Tsimring L, Hasty J. Queueing up for enzymatic processing: correlated signaling through coupled degradation. Mol Syst Biol. 2011 Dec 20; 7:561. PMID: 22186735; PMCID: PMC3737734.
      29. Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring L, Hasty J. A sensing array of radically coupled genetic 'biopixels'. Nature. 2011 Dec 18; 481(7379):39-44. PMID: 22178928; PMCID: PMC3259005.
      30. Baumgartner BL, Bennett MR, Ferry M, Johnson TL, Tsimring L, Hasty J. Antagonistic gene transcripts regulate adaptation to new growth environments. Proc Natl Acad Sci U S A. 2011 Dec 27; 108(52):21087-92. PMID: 22160690; PMCID: PMC3248483.
      31. Selimkhanov J, Hasty J, Tsimring L. Recent advances in single-cell studies of gene regulation. Curr Opin Biotechnol. 2012 Feb; 23(1):34-40. PMID: 22154220; PMCID: PMC3273644.
      32. Fernandez B, Tsimring L. Corepressive interaction and clustering of degrade-and-fire oscillators. Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Nov; 84(5 Pt 1):051916. PMID: 22181453; PMCID: PMC4813716.
      33. Danino T, Volfson D, Bhatia SN, Tsimring L, Hasty J. In-silico patterning of vascular mesenchymal cells in three dimensions. PLoS One. 2011; 6(5):e20182. PMID: 21633504; PMCID: PMC3102094.
      34. Boyer D, Mather W, Mondragón-Palomino O, Orozco-Fuentes S, Danino T, Hasty J, Tsimring L. Buckling instability in ordered bacterial colonies. Phys Biol. 2011 Apr; 8(2):026008. PMID: 21358041; PMCID: PMC3767764.
      35. Mather WH, Cookson NA, Hasty J, Tsimring L, Williams RJ. Correlation resonance generated by coupled enzymatic processing. Biophys J. 2010 Nov 17; 99(10):3172-81. PMID: 21081064; PMCID: PMC2980735.
      36. Mather W, Mondragón-Palomino O, Danino T, Hasty J, Tsimring L. Streaming instability in growing cell populations. Phys Rev Lett. 2010 May 21; 104(20):208101. PMID: 20867071; PMCID: PMC2947335.
      37. Danino T, Mondragón-Palomino O, Tsimring L, Hasty J. A synchronized quorum of genetic clocks. Nature. 2010 Jan 21; 463(7279):326-30. PMID: 20090747; PMCID: PMC2838179.
      38. Cookson NA, Cookson SW, Tsimring L, Hasty J. Cell cycle-dependent variations in protein concentration. Nucleic Acids Res. 2010 May; 38(8):2676-81. PMID: 20019065; PMCID: PMC2860113.
      39. Cookson NA, Tsimring L, Hasty J. The pedestrian watchmaker: genetic clocks from engineered oscillators. FEBS Lett. 2009 Dec 17; 583(24):3931-7. PMID: 19903483; PMCID: PMC2921805.
      40. Melhus MF, Aranson IS, Volfson D, Tsimring L. Effect of noise on solid-to-liquid transition in small granular systems under shear. Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Oct; 80(4 Pt 1):041305. PMID: 19905306.
        View in: PubMed
      41. Longo DM, Hoffmann A, Tsimring L, Hasty J. Coherent activation of a synthetic mammalian gene network. Syst Synth Biol. 2010 Mar; 4(1):15-23. PMID: 19757189; PMCID: PMC2816225.
      42. Mather W, Bennett MR, Hasty J, Tsimring L. Delay-induced degrade-and-fire oscillations in small genetic circuits. Phys Rev Lett. 2009 Feb 13; 102(6):068105. PMID: 19257639; PMCID: PMC2924583.
      43. Stricker J, Cookson S, Bennett MR, Mather WH, Tsimring L, Hasty J. A fast, robust and tunable synthetic gene oscillator. Nature. 2008 Nov 27; 456(7221):516-9. PMID: 18971928.
        View in: PubMed
      44. Volfson D, Cookson S, Hasty J, Tsimring L. Biomechanical ordering of dense cell populations. Proc Natl Acad Sci U S A. 2008 Oct 07; 105(40):15346-51. PMID: 18832176; PMCID: PMC2563119.
      45. Aranson IS, Tsimring L, Malloggi F, Clément E. Nonlocal rheological properties of granular flows near a jamming limit. Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Sep; 78(3 Pt 1):031303. PMID: 18851027.
        View in: PubMed
      46. Bennett MR, Pang WL, Ostroff NA, Baumgartner BL, Nayak S, Tsimring L, Hasty J. Metabolic gene regulation in a dynamically changing environment. Nature. 2008 Aug 28; 454(7208):1119-22. PMID: 18668041; PMCID: PMC2654342.
      47. Fernandez B, Tsimring L. Athermal dynamics of strongly coupled stochastic three-state oscillators. Phys Rev Lett. 2008 Apr 25; 100(16):165705. PMID: 18518222.
        View in: PubMed
      48. Kudrolli A, Lumay G, Volfson D, Tsimring L. Swarming and swirling in self-propelled polar granular rods. Phys Rev Lett. 2008 Feb 08; 100(5):058001. PMID: 18352433.
        View in: PubMed
      49. Karpeev D, Aranson IS, Tsimring L, Kaper HG. Interactions of semiflexible filaments and molecular motors. Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Nov; 76(5 Pt 1):051905. PMID: 18233685.
        View in: PubMed
      50. Aranson IS, Volfson D, Tsimring L. Swirling motion in a system of vibrated elongated particles. Phys Rev E Stat Nonlin Soft Matter Phys. 2007 May; 75(5 Pt 1):051301. PMID: 17677048.
        View in: PubMed
      51. Bennett MR, Volfson D, Tsimring L, Hasty J. Transient dynamics of genetic regulatory networks. Biophys J. 2007 May 15; 92(10):3501-12. PMID: 17350994; PMCID: PMC1853127.
      52. Dyhrfjeld-Johnsen J, Santhakumar V, Morgan RJ, Huerta R, Tsimring L, Soltesz I. Topological determinants of epileptogenesis in large-scale structural and functional models of the dentate gyrus derived from experimental data. J Neurophysiol. 2007 Feb; 97(2):1566-87. PMID: 17093119.
        View in: PubMed
      53. Aranson IS, Tsimring L. Theory of self-assembly of microtubules and motors. Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Sep; 74(3 Pt 1):031915. PMID: 17025675.
        View in: PubMed
      54. Volfson D, Meerson B, Tsimring L. Thermal collapse of a granular gas under gravity. Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jun; 73(6 Pt 1):061305. PMID: 16906820.
        View in: PubMed
      55. Volfson D, Marciniak J, Blake WJ, Ostroff N, Tsimring L, Hasty J. Origins of extrinsic variability in eukaryotic gene expression. Nature. 2006 Feb 16; 439(7078):861-4. PMID: 16372021.
        View in: PubMed
      56. Bratsun D, Volfson D, Tsimring L, Hasty J. Delay-induced stochastic oscillations in gene regulation. Proc Natl Acad Sci U S A. 2005 Oct 11; 102(41):14593-8. PMID: 16199522; PMCID: PMC1253555.
      57. Volkovskii AR, Tsimring L, Rulkov NF, Langmore I. Spread spectrum communication system with chaotic frequency modulation. Chaos. 2005 Sep; 15(3):33101. PMID: 16252975.
        View in: PubMed
      58. Aranson IS, Tsimring L. Pattern formation of microtubules and motors: inelastic interaction of polar rods. Phys Rev E Stat Nonlin Soft Matter Phys. 2005 May; 71(5 Pt 1):050901. PMID: 16089514.
        View in: PubMed
      59. Gabbay M, Larsen ML, Tsimring L. Globally coupled noisy oscillators with inhomogeneous periodic forcing. Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Dec; 70(6 Pt 2):066212. PMID: 15697489.
        View in: PubMed
      60. Volfson D, Kudrolli A, Tsimring L. Anisotropy-driven dynamics in vibrated granular rods. Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Nov; 70(5 Pt 1):051312. PMID: 15600608.
        View in: PubMed
      61. Volfson D, Tsimring L, Aranson IS. Stick-slip dynamics of a granular layer under shear. Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Mar; 69(3 Pt 1):031302. PMID: 15089281.
        View in: PubMed
      62. Volfson D, Tsimring L, Aranson IS. Partially fluidized shear granular flows: continuum theory and molecular dynamics simulations. Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Aug; 68(2 Pt 1):021301. PMID: 14524963.
        View in: PubMed
      63. Volfson D, Tsimring L, Aranson IS. Order parameter description of stationary partially fluidized shear granular flows. Phys Rev Lett. 2003 Jun 27; 90(25 Pt 1):254301. PMID: 12857136.
        View in: PubMed
      64. Aranson IS, Tsimring L. Model of coarsening and vortex formation in vibrated granular rods. Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Feb; 67(2 Pt 1):021305. PMID: 12636669.
        View in: PubMed
      65. Tenny R, Tsimring L, Larson L, Abarbanel HD. Using distributed nonlinear dynamics for public key encryption. Phys Rev Lett. 2003 Jan 31; 90(4):047903. PMID: 12570462.
        View in: PubMed
      66. Seliger P, Tsimring L, Rabinovich MI. Dynamics-based sequential memory: winnerless competition of patterns. Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Jan; 67(1 Pt 1):011905. PMID: 12636530.
        View in: PubMed
      67. Huerta R, Tsimring L. Contact tracing and epidemics control in social networks. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Nov; 66(5 Pt 2):056115. PMID: 12513564.
        View in: PubMed
      68. Aranson IS, Tsimring L. Continuum theory of partially fluidized granular flows. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Jun; 65(6 Pt 1):061303. PMID: 12188712.
        View in: PubMed
      69. Seliger P, Young SC, Tsimring L. Plasticity and learning in a network of coupled phase oscillators. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Apr; 65(4 Pt 1):041906. PMID: 12005872.
        View in: PubMed