Publications
by J Elf
2009
Paul Sjoberg, Otto G Berg, Johan Elf
(2009) Taking the reaction-diffusion master equation to the microscopic limit
arXiv arXiv:0905.4629v1
Gene-Wei Li, Otto G. Berg, Johan Elf (2009) Effects of macromolecular crowding and DNA looping on gene regulation kinetics
Nature Physics doi: 10.1038/nphys1222
Gene-Wei Li, Johan Elf (2009) Single molecule approaches to transcription factor kinetics in living cells
FEBS letters http://dx.doi.org/10.1016/j.febslet.2009.11.035
Sjöberg P, Lötstedt P and Elf J (2009) Fokker-Planck
approximation of the master equation in molecular biology
Computing and Visualization in Science
2007
Elf et al. (2007) Probing Transctiption Factor Dynamics at the Single Molecule Level a Living Cell
Science 316 1191-4
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2006
Elf et al. (2006) Bi-stable bacterial growth rate in response to antibiotics with low membrane permeability
Physical Review letters 97:258104
Fange D and Elf J (2006) Noise induced Min phenotypes in E. coli
PLoS computational biology
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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
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pdf
Elf J and Ehrenberg M (2005) What makes ribosome mediated
transcriptional attenuation sensitive? PLoS Computational
Biology 1
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pdf
Hattne J, Fange D, and Elf J (2005) Stochastic
reaction-diffusion simulation with MesoRD Bioinformatics
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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
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pdf
Dittmar K, Sřrensen M, Elf J, Ehrenberg M, Pan T, (2005)
Microarrays reveal selective charging of tRNA isoacceptors
during amino acid starvation. EMBO reports 6
151-157
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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
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2004
Elf, J and Ehrenberg, M (2004) Spontaneous separation of
bi-stable biochemical systems into spatial domains of opposite
phases Systems Biology 2
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Supplementary
Material: Next Subvolume Method
Thesis:
Intracellular Flows and Fluctuation was awarded Bjurzons
premium for outstanding thesis by the faculty of Science and
Technology, Uppsala University
2003
Elf, J and Ehrenberg, M (2003) Fast evaluation of fluctuations
in biochemical networks with the linear noise approximation
Genome Research 13 2475-2484.
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Elf, J, Nilsson, D, Tenson, T and Ehrenberg, M. (2003).
Selective charging of tRNA isoacceptors explains patterns of
codon usage Science 300 1718-1722
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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
112 131-140
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pdf
Elf J., Paulsson J., Berg O. & Ehrenberg M.(2003)
Near-critical phenomena in intracellular metabolite pools
Biophysical Journal 84 154-170
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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
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pdf
Elf, J, Doncic, A & Ehrenberg, M (2003) Mesoscopic
reaction-diffusion in intracellular signaling Proceedings for
SPIE's "First International Symposium on fluctuations and
noise"
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pdf
Elf, J, Lötstedt, P, and Sjöberg, P (2003). Problems of high
dimension in molecular biology. Proceedings of the 17th
GAMM-Seminar 1-10
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<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:
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 in
Systems Modeling in Cellular Biology
MIT
press
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 and
Perspectives Springer-Verlag GmbH
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pdf
Ehrenberg, M, Elf, J , Aurell, E,Sandberg, R and Tegnér, J
(2003) Systems Biology is Taking Off Genome Research
13 2377-2380.
Ehrenberg, M, Elf, J , Aurell, E,Sandberg, R and Tegnér, J
(2003) Systems Biology is Taking Off Genome Research
13 2377-2380.
Aurell, E, Elf, J and Jeppsson, J. (eds.) (2002) Systems Biology
- The logic of life. Proceedings of the 3rd international
conference on Systems Biology