Software: MesoRD
Publications:
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 in press
Elf J and Ehrenberg M (2005) What makes ribosome mediated transcriptional attenuation sensitive? PLoS Computational Biology 1
Hattne J, Fange D, and Elf J (2005) Stochastic reaction-diffusion simulation with MesoRD Bioinformatics
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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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Dittmar K, Sørensen 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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Elf, J and Ehrenberg, M (2004) 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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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
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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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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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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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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Books and Reviews:
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 Springer-Verlag GmbH
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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
Teaching:
Molecular
Systems Analysis
