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Center for Models of Life
Niels Bohr Institute
University of Copenhagen
Blegdamsvej 17
2100 Copenhagen Ø
Mail:  cmolnbi.dk

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Ian Dodd

Ian Dodd
Position: Visiting Professor
Email: ian.doddadelaide.edu.au
www: http://www.adelaide.edu.au/directory/ian.dodd

Publications:
Nan Hao, Kim Sneppen, Keith E. Shearwin, and Ian B. Dodd
Efficient chromosomal-scale DNA looping in Escherichia coli using multiple DNA-looping elements
Nucleic Acids Res 1:gkx069 (2017)

Cecilia Lövkvist, Ian B. Dodd, Kim Sneppen, and Jan O. Haerter
DNA methylation in human epigenomes depends on local topology of CpG sites
Nucl. Acids Res. 44:5123 (2016)

Kim Sneppen and Ian B. Dodd
Nucleosome dynamics and maintenance of epigenetic states of CpG islands
Physical Review E 93:062417 (2016)

Kim Sneppen and Ian B. Dodd
Cooperative stabilization of the SIR complex provides robust epigenetic memory in a model of SIR silencing in Saccharomyces cerevisiae
Epigenetics 10:293 (2015)

Haerter, Jan O., Cecilia Lövkvist, Ian B. Dodd, and Kim Sneppen
Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states
Nucleic Acids Research 27: (2013)

Kim Sneppen and Ian B. Dodd
A Simple Histone Code Opens Many Paths to Epigenetics
PLoS Comput Biol 8:e1002643 (2012)

Ian B. Dodd and Kim Sneppen
Barriers and Silencers: A Theoretical Toolkit for Control and Containment of Nucleosome-Based Epigenetic States
Journal of Molecular Biology 0: (2011)

Mille A. Micheelsen, Namiko Mitarai, Kim Sneppen, Ian. B. Dodd
Theory for stability and regulation of epigenetic landscapes
Phys. Biol. 7:026010 (2010)
1002.1600

Sneppen K, Pedersen S, Krishna S, Dodd I, Semsey S.
Economy of operon formation: cotranscription minimizes shortfall in protein complexes.
MBio 1: e00177 (2010)

Mikkel Avlund, Sandeep Krishna, Szabolcs Semsey, Ian B. Dodd, Kim Sneppen
Minimal Gene Regulatory Circuits for a Lysis-Lysogeny Choice in the Presence of Noise
PLoS ONE 5:e15037 (2010)

Mikkel Avlund, Ian B. Dodd, Szabolcs Semsey, Kim Sneppen, and Sandeep Krishna
Why Do Phage Play Dice
Journal of Virology 83:11416 (2009)

Mikkel Avlund, Ian B. Dodd, Kim Sneppen, and Sandeep Krishna
Minimal gene regulatory circuits that can count like bacteriophage lambda
J Mol Biol. 394:681 (2009)

Kim Sneppen, Mille A Micheelsen & Ian B Dodd
Ultrasensitive gene regulation by positive feedback loops in nucleosome modification
Molecular Systems Biology 4:182 (2008)

Namiko Mitarai, Ian B. Dodd, Michael T. Crooks, Kim Sneppen
The Generation of Promoter-Mediated Transcriptional Noise in Bacteria
PLoS Comput. Biol. 4:e1000109 (2008)

Ian B. Dodd, Mille A. Micheelsen, Kim Sneppen and Geneviève Thon
Theoretical Analysis of Epigenetic Cell Memory by Nucleosome Modification
Cell 129:813-822 (2007)

I.B. Dodd, K.E. Shearwin and K. Sneppen
Modelling transcriptional interference and DNA looping in gene regulation
J. Mol. Biol. 369:1200 (2007)

Martin Rosvall, Ian B. Dodd, Sandeep Krishna, Kim Sneppen
Network models of phage-bacteria coevolution
Phys. Rev. E 74:66105 (2006)
q-bio.PE/0609031

Sneppen K, Dodd IB, Shearwin KE, Palmer AC, Schubert RA, Callen BP, Egan JB
A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli
J. Mol. Biol. 346:399 (2005)

Ala Trusina, Kim Sneppen, I.B. Dodd, K.E. Shearwin and J.B. Egan.
Functional alignment of regulatory networks: A study of temerate phages
Plos Computational Biology 1:7 (2005)
q-bio.MN/0511047