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Items: 1 to 50 of 153

1.

Deconstructing the principles of ductal network formation in the pancreas.

Dahl-Jensen SB, Yennek S, Flasse L, Larsen HL, Sever D, Karremore G, Novak I, Sneppen K, Grapin-Botton A.

PLoS Biol. 2018 Jul 26;16(7):e2002842. doi: 10.1371/journal.pbio.2002842. eCollection 2018 Jul.

2.

Theory of invasion extinction dynamics in minimal food webs.

Haerter JO, Mitarai N, Sneppen K.

Phys Rev E. 2018 Feb;97(2-1):022404. doi: 10.1103/PhysRevE.97.022404.

PMID:
29548095
3.

Exploring the Link between Nucleosome Occupancy and DNA Methylation.

Lövkvist C, Sneppen K, Haerter JO.

Front Genet. 2018 Jan 12;8:232. doi: 10.3389/fgene.2017.00232. eCollection 2017.

4.

Existence and construction of large stable food webs.

Haerter JO, Mitarai N, Sneppen K.

Phys Rev E. 2017 Sep;96(3-1):032406. doi: 10.1103/PhysRevE.96.032406. Epub 2017 Sep 8.

PMID:
29346992
5.

A growing microcolony can survive and support persistent propagation of virulent phages.

Eriksen RS, Svenningsen SL, Sneppen K, Mitarai N.

Proc Natl Acad Sci U S A. 2018 Jan 9;115(2):337-342. doi: 10.1073/pnas.1708954115. Epub 2017 Dec 19.

6.

Severe population collapses and species extinctions in multihost epidemic dynamics.

Maslov S, Sneppen K.

Phys Rev E. 2017 Aug;96(2-1):022412. doi: 10.1103/PhysRevE.96.022412. Epub 2017 Aug 22.

PMID:
28950542
7.

Four simple rules that are sufficient to generate the mammalian blastocyst.

Nissen SB, Perera M, Gonzalez JM, Morgani SM, Jensen MH, Sneppen K, Brickman JM, Trusina A.

PLoS Biol. 2017 Jul 12;15(7):e2000737. doi: 10.1371/journal.pbio.2000737. eCollection 2017 Jul.

8.

Occlusion of the Ribosome Binding Site Connects the Translational Initiation Frequency, mRNA Stability and Premature Transcription Termination.

Eriksen M, Sneppen K, Pedersen S, Mitarai N.

Front Microbiol. 2017 Mar 14;8:362. doi: 10.3389/fmicb.2017.00362. eCollection 2017.

9.

Efficient chromosomal-scale DNA looping in Escherichia coli using multiple DNA-looping elements.

Hao N, Sneppen K, Shearwin KE, Dodd IB.

Nucleic Acids Res. 2017 May 19;45(9):5074-5085. doi: 10.1093/nar/gkx069.

10.

Models of life: epigenetics, diversity and cycles.

Sneppen K.

Rep Prog Phys. 2017 Apr;80(4):042601. doi: 10.1088/1361-6633/aa5aeb. Epub 2017 Jan 20. Review.

PMID:
28106010
11.

Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems.

Maslov S, Sneppen K.

Sci Rep. 2017 Jan 4;7:39642. doi: 10.1038/srep39642.

12.

Nucleosome dynamics and maintenance of epigenetic states of CpG islands.

Sneppen K, Dodd IB.

Phys Rev E. 2016 Jun;93(6):062417. doi: 10.1103/PhysRevE.93.062417. Epub 2016 Jun 28.

PMID:
27415308
13.

Three is much more than two in coarsening dynamics of cyclic competitions.

Mitarai N, Gunnarson I, Pedersen BN, Rosiek CA, Sneppen K.

Phys Rev E. 2016 Apr;93:042408. doi: 10.1103/PhysRevE.93.042408. Epub 2016 Apr 12.

PMID:
27176330
14.

A cross-immunization model for the extinction of old influenza strains.

Uekermann F, Sneppen K.

Sci Rep. 2016 May 13;6:25907. doi: 10.1038/srep25907.

15.

Nucleation and spreading of a heterochromatic domain in fission yeast.

Obersriebnig MJ, Pallesen EM, Sneppen K, Trusina A, Thon G.

Nat Commun. 2016 May 11;7:11518. doi: 10.1038/ncomms11518.

16.

Nanog, Oct4 and Tet1 interplay in establishing pluripotency.

Olariu V, Lövkvist C, Sneppen K.

Sci Rep. 2016 May 5;6:25438. doi: 10.1038/srep25438.

17.

Rapid Curtailing of the Stringent Response by Toxin-Antitoxin Module-Encoded mRNases.

Tian C, Roghanian M, Jørgensen MG, Sneppen K, Sørensen MA, Gerdes K, Mitarai N.

J Bacteriol. 2016 Jun 27;198(14):1918-1926. doi: 10.1128/JB.00062-16. Print 2016 Jul 15.

18.

Diffusion Retardation by Binding of Tobramycin in an Alginate Biofilm Model.

Cao B, Christophersen L, Kolpen M, Jensen PØ, Sneppen K, Høiby N, Moser C, Sams T.

PLoS One. 2016 Apr 21;11(4):e0153616. doi: 10.1371/journal.pone.0153616. eCollection 2016.

19.

Population Dynamics of Phage and Bacteria in Spatially Structured Habitats Using Phage λ and Escherichia coli.

Mitarai N, Brown S, Sneppen K.

J Bacteriol. 2016 May 27;198(12):1783-93. doi: 10.1128/JB.00965-15. Print 2016 Jun 15.

20.

DNA methylation in human epigenomes depends on local topology of CpG sites.

Lövkvist C, Dodd IB, Sneppen K, Haerter JO.

Nucleic Acids Res. 2016 Jun 20;44(11):5123-32. doi: 10.1093/nar/gkw124. Epub 2016 Feb 29.

21.

Stabilization of epigenetic states of CpG islands by local cooperation.

Sormani G, Haerter JO, Lövkvist C, Sneppen K.

Mol Biosyst. 2016 Jun 21;12(7):2142-6. doi: 10.1039/c6mb00044d.

PMID:
26923344
22.

Short-range growth inhibitory signals from the epithelium can drive non-stereotypic branching in the pancreas.

Dahl-Jensen SB, Figueiredo-Larsen M, Grapin-Botton A, Sneppen K.

Phys Biol. 2016 Feb 23;13(1):016007. doi: 10.1088/1478-3975/13/1/016007.

PMID:
26906913
23.

Food Web Assembly Rules for Generalized Lotka-Volterra Equations.

Haerter JO, Mitarai N, Sneppen K.

PLoS Comput Biol. 2016 Feb 1;12(2):e1004727. doi: 10.1371/journal.pcbi.1004727. eCollection 2016 Feb.

24.

Dynamic competition between transcription initiation and repression: Role of nonequilibrium steps in cell-to-cell heterogeneity.

Mitarai N, Semsey S, Sneppen K.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Aug;92(2):022710. Epub 2015 Aug 13.

PMID:
26382435
25.

Diversity Waves in Collapse-Driven Population Dynamics.

Maslov S, Sneppen K.

PLoS Comput Biol. 2015 Sep 14;11(9):e1004440. doi: 10.1371/journal.pcbi.1004440. eCollection 2015 Sep.

26.

Restriction modification systems as engines of diversity.

Sneppen K, Semsey S, Seshasayee AS, Krishna S.

Front Microbiol. 2015 Jun 2;6:528. doi: 10.3389/fmicb.2015.00528. eCollection 2015.

27.

Well-temperate phage: optimal bet-hedging against local environmental collapses.

Maslov S, Sneppen K.

Sci Rep. 2015 Jun 2;5:10523. doi: 10.1038/srep10523.

28.

Cooperative stabilization of the SIR complex provides robust epigenetic memory in a model of SIR silencing in Saccharomyces cerevisiae.

Sneppen K, Dodd IB.

Epigenetics. 2015;10(4):293-302. doi: 10.1080/15592294.2015.1017200. Epub 2015 Apr 1.

29.
30.

Phage and bacteria support mutual diversity in a narrowing staircase of coexistence.

Haerter JO, Mitarai N, Sneppen K.

ISME J. 2014 Nov;8(11):2317-26. doi: 10.1038/ismej.2014.80. Epub 2014 May 23.

31.

Speciation, diversification, and coexistence of sessile species that compete for space.

Mitarai N, Heinsalu E, Sneppen K.

PLoS One. 2014 May 12;9(5):e96665. doi: 10.1371/journal.pone.0096665. eCollection 2014.

32.

Effect of supercoiling on the λ switch.

Norregaard K, Andersson M, Sneppen K, Nielsen PE, Brown S, Oddershede LB.

Bacteriophage. 2014 Jan 1;4(1):e27517.

33.

Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states.

Haerter JO, Lövkvist C, Dodd IB, Sneppen K.

Nucleic Acids Res. 2014 Feb;42(4):2235-44. doi: 10.1093/nar/gkt1235. Epub 2013 Nov 27.

34.

DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch.

Norregaard K, Andersson M, Sneppen K, Nielsen PE, Brown S, Oddershede LB.

Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):17386-91. doi: 10.1073/pnas.1215907110. Epub 2013 Oct 7.

35.

Conditional cooperativity of toxin - antitoxin regulation can mediate bistability between growth and dormancy.

Cataudella I, Sneppen K, Gerdes K, Mitarai N.

PLoS Comput Biol. 2013;9(8):e1003174. doi: 10.1371/journal.pcbi.1003174. Epub 2013 Aug 29.

36.

Labyrinthine clustering in a spatial rock-paper-scissors ecosystem.

Juul J, Sneppen K, Mathiesen J.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Apr;87(4):042702. Epub 2013 Apr 8.

PMID:
23679446
37.

Genetic regulatory networks that count to 3.

Lehmann M, Sneppen K.

J Theor Biol. 2013 Jul 21;329:15-9. doi: 10.1016/j.jtbi.2013.03.023. Epub 2013 Apr 6.

PMID:
23567648
38.

Quality control system response to stochastic growth of amyloid fibrils.

Pigolotti S, Lizana L, Otzen D, Sneppen K.

FEBS Lett. 2013 May 2;587(9):1405-10. doi: 10.1016/j.febslet.2013.03.018. Epub 2013 Mar 21.

39.

Differentiation of developing olfactory neurons analysed in terms of coupled epigenetic landscapes.

Alsing AK, Sneppen K.

Nucleic Acids Res. 2013 May;41(9):4755-64. doi: 10.1093/nar/gkt181. Epub 2013 Mar 21.

40.

Spreading of multiple epidemics with cross immunization.

Uekermann F, Sneppen K.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Sep;86(3 Pt 2):036108. Epub 2012 Sep 13.

PMID:
23030981
41.

Emergence of diversity in a model ecosystem.

Mitarai N, Mathiesen J, Sneppen K.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jul;86(1 Pt 1):011929. Epub 2012 Jul 30.

PMID:
23005473
42.

Multistability with a metastable mixed state.

Sneppen K, Mitarai N.

Phys Rev Lett. 2012 Sep 7;109(10):100602. Epub 2012 Sep 5.

PMID:
23005273
43.

Clonal selection prevents tragedy of the commons when neighbors compete in a rock-paper-scissors game.

Juul J, Sneppen K, Mathiesen J.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jun;85(6 Pt 1):061924. Epub 2012 Jun 26.

PMID:
23005144
44.

Information spreading and development of cultural centers.

Dybiec B, Mitarai N, Sneppen K.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 May;85(5 Pt 2):056116. Epub 2012 May 18.

PMID:
23004830
45.

Specific contacts of the -35 region of the galP1 promoter by RNA polymerase inhibit GalR-mediated DNA looping repression.

Csiszovszki Z, Lewis DE, Le P, Sneppen K, Semsey S.

Nucleic Acids Res. 2012 Nov 1;40(20):10064-72. doi: 10.1093/nar/gks796. Epub 2012 Aug 31.

46.

A simple histone code opens many paths to epigenetics.

Sneppen K, Dodd IB.

PLoS Comput Biol. 2012;8(8):e1002643. doi: 10.1371/journal.pcbi.1002643. Epub 2012 Aug 16.

47.

Spatial structure and Lamarckian adaptation explain extreme genetic diversity at CRISPR locus.

Haerter JO, Sneppen K.

MBio. 2012 Jul 17;3(4):e00126-12. doi: 10.1128/mBio.00126-12. Print 2012.

48.

Coexistence of phage and bacteria on the boundary of self-organized refuges.

Heilmann S, Sneppen K, Krishna S.

Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12828-33. doi: 10.1073/pnas.1200771109. Epub 2012 Jul 17.

49.

Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery.

Cataudella I, Trusina A, Sneppen K, Gerdes K, Mitarai N.

Nucleic Acids Res. 2012 Aug;40(14):6424-34. doi: 10.1093/nar/gks297. Epub 2012 Apr 11.

50.

Protein localization with flexible DNA or RNA.

Bernhardsson S, Mitarai N, Sneppen K.

PLoS One. 2012;7(2):e29218. doi: 10.1371/journal.pone.0029218. Epub 2012 Feb 10.

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