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Publications
by J Elf

2013

  • Fredrik Persson, Irmeli Barkefors and Johan Elf (2013) Single molecule methods with applications in living cells. Current Opinion in Biotechnology . Accepted for publication.
  • Fredrik Persson, Martin Lindén, Cecilia Unoson and Johan Elf (2013) Extracting intracellular diffusive states and transition rates from single molecule tracking data. Nature Methods 10, 265-269. Download pdf

    • 2012

  • Anel Mahmutovic, David Fange, Otto Berg and Johan Elf (2012) Lost in presumption: stochastic reactions in spatial models. Nature Methods . Vol. 9 no. 12 pp. 1163-1166. Download pdf
  • David Fange, Anel Mahmutovic and Johan Elf (2012) MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit. Bioinformatics doi:10.1093/bioinformatics/bts584. Download pdf
  • Petter Hammar, Prune Leroy, Anel Mahmutovic, Erik G. Marklund, Otto G. Berg, Johan Elf (2012) The lac repressor displays facilitated diffusion in living cells. Science 22 June 2012: Vol. 336 no. 6088 pp. 1595-1598. Download pdf
      • Related Media Coverage:
    • Nature: Research Highlights (2012) Molecular Biology: Transcription factors slide to find binding sites in vivo. Download pdf
    • Nature Review Microbiology: Research Highlights (2012) Bacterial transcription: Transcription factor sliding in live bacteria. Download pdf
    • Nature Review Genetics: Research Highlights (2012) Gene regulation: Protein crawls on chromosome. Download pdf
  • G. Ullman, M. Wallden, E. G. Marklund, A. Mahmutovic, I. Razinkov, J. Elf (2012) Hi-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking. Philosophical Transactions B. Download pdf
  • Viktoriya Shyp, Stoyan Tankov, Andrey Ermakov, Pavel Kudrin, Brian P English, Mĺns Ehrenberg, Tanel Tenson, Johan Elf & Vasili Hauryliuk1 (2012) Positive allosteric feedback regulation of the stringent response enzyme RelA by its product. EMBO reports 20 July, 2012. Download pdf
      Related Media Coverage:
    • Nature Chemical Biology: Research Highlights (2012) Regulation: Positively alarming. Download pdf
  • Arash Sanamrad, Fredrik Persson, and Johan Elf (2012) Isotropic diffusion of the small ribosomal subunit in Escherichia coli. ArXiv. Download pdf

    • 2011

  • Anton Kuzmenko, Stoyan Tankov, Brian P. English, Ivan Tarassov, Tanel Tenson, Piotr Kamenski, Johan Elf & Vasili Hauryliuk (2011) Single molecule tracking fluorescence microscopy in mitochondria reveals highly dynamic but confined movement of Tom40. Sci Rep. 2011; 1: 195. Download pdf
  • Andreas Grönlund, Per Lötstedt & Johan Elf (2011) Delay induced anomalous fluctuations in intracellular regulation. Nature Communications 2011 Aug 9;2:419. Download pdf
  • Brian English , Vasili Hauryliuk , Arash Sanamrad , Stoyan Tankov , Nynke Dekker & Johan Elf (2011) Single Molecule Investigations of the Stringent Response Machinery in Living Bacterial Cells.PNAS 108(31):E365-73. Download pdf
  • Mats Wallden & Johan Elf (2011) Studying Transcriptional Interactions in Single Cells at Sufficinet Resolution.Current Opinion in Biotechnology 22:81-6. Download pdf

    • 2010

  • David Fange, Otto G. Berg, Paul Sjöberg & Johan Elf (2010) Stochastic reaction-diffusion kinetics in the microscopic limit. PNAS 107:19820-5. Download pdf
  • Fender A, Elf J, Hampel K, Zimmermann B & Wagner EG (2010) RNAs actively cycle on the Sm-like protein Hfq.Genes & Development 24:2621-6. Download pdf
  • Andreas Grönlund, Per Lötstedt, Johan Elf (2010) The costs and constraints from time-delayed feed-back in small gene regulatory motifs. PNAS 107:8171-8176. Download pdf
  • Brian P. English, Arash Sanamrad, Stoyan Tankov, Vasili Hauryliuk, Johan Elf (2010) Tracking of individual freely diffusing fluorescent protein molecules in the bacterial cytoplasm. ArXiv:1003.2110. Download pdf

    • 2009

  • Paul Sjoberg, Otto G Berg, Johan Elf(2009) Taking the reaction-diffusion master equation to the microscopic limit. ArXiv:0905.4629v1. Download pdf
  • Gene-Wei Li, Otto G. Berg, Johan Elf (2009) Effects of macromolecular crowding and DNA looping on gene regulation kinetics. Nature Physics 5, 294 - 297. Download pdf
  • Gene-Wei Li, Johan Elf (2009) Single molecule approaches to transcription factor kinetics in living cells. FEBS Letters 583: 3979-3983. Download pdf
  • Sjöberg P, Lötstedt P and Elf J (2009) Fokker-Planck approximation of the master equation in molecular biology. Computing and Visualization in Science 12:37-50. Download pdf

    • 2007

  • Johan Elf, Gene-Wei Li, and X. Sunney Xie (2007) Probing Transctiption Factor Dynamics at the Single Molecule Level a Living Cell Science 316(5828): 1191-1194. Download pdf
      Related Media Coverage:
    • Nature Methods Special Feature: Method of the Year (2008) Watching single molecules in cells Download pdf
    • JCB Research Roundup (2007) Imaging individual transcription factors. Download pdf
    • C&E News Cover Story: Peeking into cells (July 4 2007)
    • NatureTechnology Feature: Close-up on cell biology. 446, 937-940.

    2006

  • Elf J, Nilsson K, Tenson T amd Ehrenberg M. (2006) Bi-stable bacterial growth rate in response to antibiotics with low membrane permeability. Physical Review letters 2006 Dec 22;97(25):258104.
  • Fange D and Elf J (2006) Noise induced Min phenotypes in E. coli. PLoS computational biology Jun 30;2(6):e80. Download pdf

    • 2005

  • Sřrensen MA, Elf J, Bouakaz E, Tenson T, Sanyal S, Björk GR, and Ehrenberg M (2005) Over expression of a tRNA-Leu isoacceptor changes charging pattern of leucine tRNAs and reveals new codon reading. J Mol Biol 354, 16-24. Download pdf
  • Elf J and Ehrenberg M (2005) What makes ribosome mediated transcriptional attenuation sensitive? PLoS Computational Biology 1(1): e2. Download pdf
  • Hattne J, Fange D, and Elf J (2005) Stochastic reaction-diffusion simulation with MesoRD. Bioinformatics Vol.21 no.12, pages 2923-2924. Download pdf
  • Lindsley D, Bonthuis P, Gallant J, Tofoleanu T, Elf J and Ehrenberg M (2005) Ribosome By-passing At Serine Codons as a Test of the Model of Selective tRNA Charging. EMBO reports 6:147-150. Download pdf
  • Dittmar K, Sřrensen M, Elf J, Ehrenberg M, Pan T, (2005) Selective charging of tRNA isoacceptors during amino acid starvation. EMBO reports 6:151-157. Download pdf
  • Elf, J and Ehrenberg, M (2005) Near-critical behavior of aminoacyl-tRNA pools in E. coli at rate limiting supply of amino acids. Biophys. J 88:132-46. Download pdf

    2004

  • Elf, J and Ehrenberg, M (2004) Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases. Systems Biology Vol.1, No.2, Dec. Download pdf Supplementary Material
  • Thesis: Intracellular Flows and Fluctuation (2004) Was awarded Bjurzons premium for outstanding thesis by the faculty of Science and Technology, Uppsala University. Download pdf

    2003

  • Elf, J and Ehrenberg, M (2003) Fast evaluation of fluctuations in biochemical networks with the linear noise approximation. Genome Research 13:2475-2484. Download pdf
  • Elf, J, Nilsson, D, Tenson, T and Ehrenberg, M. (2003). Selective charging of tRNA isoacceptors explains patterns of codon usage Science 300: 1718-1722. Download pdf
  • Pedersen, K., Zavialov, A., Pavlov, M., Elf, J., Gerdes, K. and Ehrenberg, M. (2003). The bacterial toxin RelE displays codon specific cleavage of mRNAs in the ribosomal A-site. Cell Volume 112, Issue 1, 131-140. Download pdf
  • Elf J., Paulsson J., Berg O. & Ehrenberg M.(2003) Near-critical phenomena in intracellular metabolite pools Biophysical Journal 84:154-170. Download pdf
  • Elf, J, Doncic, A & Ehrenberg, M (2003) Mesoscopic reaction-diffusion in intracellular signaling. Proceedings of the SPIE Volume 5110, pp. 114-124. Download pdf
  • Elf, J, Lötstedt, P, and Sjöberg, P (2003). Problems of high dimension in molecular biology. Proceedings of the 17th GAMM-Seminar pp 1-10. Download pdf

    <2003

  • Elf, J., Berg, O.G. & Ehrenberg, M. (2001) Comparison of repressor and transcriptional attenuator systems for control of amino acid biosynthetic operons. J. Mol. Biol, 313(5):941-954. Download pdf
  • Elf J, Fried G, Lilja L, Meister B, Bark C. (2000) Differential sorting of SNAP-25a and SNAP-25b proteins in neuroblastoma cells. Eur J Cell Biol.79:781-9.

    Books and Reviews:  MIT press

  • Jie, Elf, Li, Yu, and Xie (2007) Imaging Gene Expression in Living Cells at the Single-Molecule Level in Single Molecule Techniques: A Laboratory Manual, Cold Spring Harbor Laboratory Press.
  • Paulsson J and Elf J (Spring 2006) Stochastic Modeling inSystems Modeling in Cellular Biology MITpress
  • Kruse K and Elf J (Spring 2006) Kinetics in Spatially Extended Systems in Systems Modeling in Cellular Biology MIT press
  • Elf, J, Paulsson, J, Berg, OG & Ehernberg, M (2005). Mesoscopic kinetics and its applications in protein synthesis.Topics in Current Genetics:Systems Biology: Definitions andPerspectives Springer-Verlag GmbH Download pdf
  • Ehrenberg, M, Elf, J , Aurell, E,Sandberg, R and Tegnér, J(2003) Systems Biology is Taking Off Genome Research 13:2377-2380. Download pdf
  • Aurell, E, Elf, J and Jeppsson, J. (eds.) (2002) Systems Biology - The logic of life. Proceedings of the 3rd international conference on Systems Biology
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