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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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Evolution, analysis and modeling

Evolution takes place on multiple levels, from genome rearrangements to species extinctions and collapse of ecosystems. We are interested in mathematical descriptions of the interplay between the evolution of the genome of individual species and the stresses imposed by the environment. We both work with abstract models of evolution, as well as with characterization of the interplay between molecular network structure and the function they are evolved to do.

Publications

Per Bak and Kim Sneppen
Punctuated equilibrium and criticality in a simple model of evoluton
Phys. Rev. Lett. 71 (1993)

K.S. Korolev, Mikkel Avlund, Oskar Hallatschek, David R. Nelson
Genetic Demixing and Evolutionary Forces in the One-Dimensional Stepping Stone Model
Review of Modern Physics 82 (2010)
0904.4625

Alexander Hunziker, Csaba Tuboly, Péter Horváth, Sandeep Krishna, and Szabolcs Semsey
Genetic flexibility of regulatory networks
Proc. Natl. Acad. Sci. USA 107 (2010)

Sneppen K, Trusina A, Jensen MH, and Bornholdt S
A minimal model for multiple epidemics and immunity spreading.
Plos One 5 (2010)

Namiko Mitarai, Joachim Mathiesen, Kim Sneppen
Emergence of diversity in a model ecosystem
Phys. Rev. E 86 (2012)
1204.3398

Kim Sneppen and Namiko Mitarai
Multistability with a Metastable Mixed State
Phys. Rev. Lett. 109 (2012)

Sergei Maslov, Kim Sneppen
Diversity waves in collapse-driven population dynamics
Plos Computational Biology 11 (2015)
1503.00529

Sergei Maslov and Kim Sneppen
Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems
Scientific Reports 7 (2017)

Jan O. Haerter, Namiko Mitarai, and Kim Sneppen
Theory of invasion extinction dynamics in minimal food webs
Phys. Rev. E 97 (2018)

Sergei Maslov, Sandeep Krishna, Tin Yau Pang and Kim Sneppen
Toolbox model of evolution of prokaryotic metabolic networks and their regulation
PNAS 106 (2009)

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

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

Sergei Maslov, Kim Sneppen, Kasper A. Eriksen, Koon-Kiu Yan
Upstream Plasticity and Downstream Robustness in Evolution of Molecular Networks.
BMC Evolutionary Biology 4 (2004)

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

Pernille Yde, Mogens Hogh Jensen, and Ala Trusina
Analyzing inflammatory response as excitable media
Phys. Rev. E 84 (2011)

Jakob Enemark, Kim Sneppen
Analyzing a stochastic model for evolving regulatory networks by unbiased gene duplication
JSTAT 0 (2007)
0704.3808

Jacob Bock Axelsen, Koon-Kiu Yan, Sergei Maslov
Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins
Biology Direct 2 (2007)
q-bio/0507032

Stefan Bornholdt, Kim Sneppen, and Hildegard Westphal
Longevity of orders is related to the longevity of their constituent genera rather than genus richness
Theory in Biosciences: doi: 10.1007/s12064-008-0053-9 0 (2009)
q-bio.PE/0608033

Silja Heilmann, Kim Sneppen and Sandeep Krishna
Sustainability of Virulence in a Phage-Bacterial Ecosystem
Journal of Virology 84 (2010)

Derek Ping, Tong Wang, David T. Fraebel, Sergei Maslov, Kim Sneppen, Seppe Kuehn
Hitchhiking, collapse and contingency in phage infections of migrating bacterial populations
BioRxiv 0 (2018)