Journal PDFs are provided below only within fair use, i.e. criticism, comment, news reporting, teaching (including multiple copies for classroom use), scholarship, or research, that is not an infringement of copyright.


  • Martin Linden and Johan Elf (2018) Variational algorithms for analyzing noisy multi-state diffusion trajectories. Biophysical Journal, 115(2), 276-282 Download pdf
  • Kalle Kipper, Nadja Eremina, Emil Marklund, Sumera Tubasum, Guanzhong Mao, Laura Christina Lehmann, Johan Elf, Sebastian Deindl (2018) Structure-guided approach to site-specific fluorophore labeling of the lac repressor LacI. PLoS ONE 13(6): e0198416 Download pdf
  • Ghosh A, Baltekin O, Waneskog M, Elkhalifa D, Hammarlof DL, Elf J, Koskiniemi S. (2018) Contact-dependent growth inhibition induces high levels of antibiotic-tolerant persister cells in clonal bacterial populations. EMBO J, 37(9), e98026. Download pdf
  • Ivan L. Volkov, Martin Linden, Javier Aguirre Rivera, Ka-Weng Ieong, Mikhail Metelev, Johan Elf and Magnus Johansson (2018) tRNA tracking for direct measurements of protein synthesis kinetics in live cells. Nature Chemical Biology, doi:10.1038/s41589-018-0063-y. Download pdf
  • 2017

  • Michael J Lawson, Daniel Camsund, Jimmy Larsson, Ozden Baltekin, David Fange and Johan Elf (2017) In situ genotyping of a pooled strain library after characterizing complex phenotypes. Molecular Systems Biology 2017 13, 947. Download pdf
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  • Daniel Lawson Jones*, Prune Leroy*, Cecilia Unoson*, David Fange, Vladimir Curic, Michael J. Lawson, Johan Elf (2017) Kinetics of dCas9 target search in Escherichia coli. Science 357 (6358) pp1420-1424. * Equal contribution. Download pdf
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  • Ozden Baltekin, Alexis Boucharin, Eva Tano, Dan I. Andersson, and Johan Elf (2017) Antibiotic susceptibility testing in less than 30 min using direct single-cell imaging. PNAS doi: 10.1073/pnas.1708558114 Download pdf
  • Martin Linden, Vladimir Curic, Elias Amselem & Johan Elf (2017) Pointwise error estimates in localization microscopy. Nature Communications 8: 15115. Download pdf Supplementary information Supplementary data
  • 2016

  • Francisco Balzarotti, Yvan Eilers, Klaus C. Gwosch, Arvid H. Gynna, Volker Westphal, Fernando D. Stefani, Johan Elf, Stefan W. Hell (2016) Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes. Science 10.1126/science.aak9913.
  • Kalle Kipper, Ebba G. Lundius, Vladimir Curic, Ivana Nikic, Manfred Wiessler, Edward A. Lemke, and Johan Elf (2016) Application of Noncanonical Amino Acids for Protein Labeling in a Genomically Recoded Escherichia coli. ACS Synthetic Biology 10.1021/acssynbio.6b00138 Download pdf
  • Johan Elf (2016) Hypothesis: Homologous Recombination Depends on Parallel Search. Cell Systems 3, 325-327 Download pdf
  • Johan Elf (2016) Staying Clear of the Dragons. Cell Systems 2, 219-220 Download pdf
  • Sanna Koskiniemi and Johan Elf (2016) Arming the Neighborhood. Dev. Cell 39, 5-6 Download pdf
  • Otto G Berg, Anel Mahmutovic, Emil Marklund and Johan Elf (2016) The helical structure of DNA facilitates binding. J. Phys. A: Math. Theor. 166, 729–739 Download pdf
  • Mats Wallden, David Fange, Ebba Gregorsson Lundius, Ozden Baltekin and Johan Elf (2016) The Synchronization of Replication and Division Cycles in Individual E. coli Cells. Cell 49 (2016) 364002 (17pp) Download pdf Get data
  • Martin Linden, Vladimir Curic, Alexis Boucharin, David Fange and Johan Elf (2016) Simulated single molecule microscopy with SMeagol. Bioinformatics doi: 10.1093/bioinformatics/btw109 Download pdf
  • 2015

  • Ahmad Paintdakhi, Bradley Parry, Manuel Campos, Irnov Irnov, Johan Elf, Ivan Surovtsev, Christine Jacobs-Wagner (2015) Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis. Mol. Micro. DOI: 10.1111/mmi.13264 Download pdf
  • Sajith Kecheril Sadanandan, Ozden Baltekin, Klas E. G. Magnusson, Alexis Boucharin, Petter Ranefall, Joakim Jalden, Johan Elf, Carolina Wahlby (2015) Segmentation and Track-analysis in Time-lapse Imaging of Bacteria. IEEE DOI 10.1109/JSTSP.2015.2491304 Download pdf
  • Anel Mahmutovic, Otto G Berg and Johan Elf (2015) What matters for lac repressor search in vivo - Sliding, Hopping, Intersegment Transfer, Crowding on DNA or Recognition? Nucleic Acid Research 43(7):3454-64 Download pdf
  • 2014

  • Arash Sanamrad, Fredrik Persson, Ebba G. Lundius, David Fange, Arvid H. Gynna and Johan Elf (2014) Single-particle tracking reveals that free ribosomal subunits are not excluded from the Escherichia coli nucleoid PNAS 10.1073/pnas.1411558111 Download pdf
  • Petter Hammar†, Mats Wallden†, David Fange, Fredrik Persson, Ozden Baltekin, Gustaf Ullman, Prune Leroy and Johan Elf (2014) Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation. Nature genetics doi:10.1038/ng.2905. † Equal contribution Download pdf
    • Related Media Coverage:
    • Science: Editors' Choice (Issue of 28 March 2014), Genetics: Tweaking a Switch


  • Erik G. Marklund, Anel Mahmutovic, Otto G. Berg, Petter Hammar, David van der Spoel, David Fange, and Johan Elf (2013) Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models PNAS; 110(49): 19796–19801. Download pdf
  • Andreas Gronlund, Per Lötstedt & Johan Elf (2013) Transcription factor binding kinetics constrain noise suppression via negative feedback. Nature Communications 4, 1864. Download pdf
  • Fredrik Persson, Martin Linden, 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

  • David Fange, Anel Mahmutovic, 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
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    • 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, Måns 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.


  • 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

  • Sørensen 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, Sørensen 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


  • 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


  • 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


  • 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

  • Jones D, Elf J. (2018). Bursting onto the scene? Exploring stochastic mRNA production in bacteria. Curr Opin Microbiol.45:124-130. Download pdf
  • Fredrik Persson, Irmeli Barkefors and Johan Elf (2013) Single molecule methods with applications in living cells. Current Opinion in Biotechnology 24. Download pdf
  • 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