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

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Molecular switches and epigenetics

Cells carry information handed down from their ancestors and are able to pass on information to their descendants. In many cases this ``memory" is epigenetic -- not stored in the DNA sequence -- allowing cells with identical DNA to maintain distinct properties. Epigenetic cell memory implies alternative states that are stable over time and are inherited through cell division. Mechanism for epigenetic cell memory invokes positive feedback loops, either on genes with mutual repression or, for eucaryotes, through recruited modifications of DNA bound nucleosomes.

Publications

E. Aurell and K. Sneppen
Epigenetics as a first exit problem
Phys. Rev. Lett 88 (2002)
cond-mat/0103080

Victor Olariu, Cecilia Lövkvist and Kim Sneppen
Nanog, Oct4 and Tet1 interplay in establishing pluripotency
Scientific Reports 6 (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 (2015)

Namiko Mitarai, Mogens Hřgh Jensen, Szabolcs Semsey
Coupled Positive and Negative Feedbacks Produce Diverse Gene Expression Patterns in Colonies
mBio 6 (2015)

Kamilla Norregaard, Magnus Andersson, Kim Sneppen, Peter Eigil Nielsen, Stanley Brown, Lene B Oddershede
Effect of supercoiling on the lambda switch
Bacteriophage 4 (2014)

Ilaria Cataudella, Kim Sneppen, Kenn Gerdes, Namiko Mitarai
Conditional Cooperativity of Toxin - Antitoxin Regulation Can Mediate Bistability between Growth and Dormancy
PLoS Comput Biol 9 (2013)

Ilaria Cataudella, Ala Trusina, Kim Sneppen, Kenn Gerdes, and Namiko Mitarai
Conditional cooperativity in toxin–antitoxin regulation prevents random toxin activation and promotes fast translational recovery
Nuc. Acids Res. 40 (2012)

Kim Sneppen, Sandeep Krishna, Szabolcs Semsey
Simplified Models of Biological Networks
Annual Review of Biophysics 39 (2010)

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

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

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

Hiizu Nakanishi, Margit Pedersen, Anne K. Alsing and Kim Sneppen
Modeling of the Genetic Switch of Bacteriophage TP901-1: A Heteromer of CI and MOR Ensures Robust Bistability
J. Mol. Biol. 394 (2009)
0908.4145

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

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

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 (2005)
q-bio.MN/0511047

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 (2005)

E. Aurell, S. Brown, J. Johansen, K. Sneppen
Stability puzzles in lambda phage
Phys. Rev. E 65 (2002)
cond-mat/0010286

Michaela J. Obersriebnig, Emil M. H. Pallesen, Kim Sneppen, Ala Trusina and Genevičve Thon
Nucleation and spreading of a heterochromatic domain in fission yeast
Nature Communications 7 (2016)