Molecular noise of innate immunity shapes bacteria-phage ecologies
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Jakob Ruess | Gašper Tkačik | Maroš Pleška | Cǎlin C Guet | G. Tkačik | J. Ruess | C. Guet | Maroš Pleška
[1] Daniel M. Stoebel,et al. The Cost of Expression of Escherichia coli lac Operon Proteins Is in the Process, Not in the Products , 2008, Genetics.
[2] M. Touchon,et al. Regulation of genetic flux between bacteria by restriction–modification systems , 2016, Proceedings of the National Academy of Sciences.
[3] W. Huisinga,et al. Solving the chemical master equation for monomolecular reaction systems analytically , 2006, Journal of mathematical biology.
[4] A Danchin,et al. Evolutionary role of restriction/modification systems as revealed by comparative genome analysis. , 2001, Genome research.
[5] I. Kobayashi. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. , 2001, Nucleic acids research.
[6] B. Levin,et al. Phage–host population dynamics promotes prophage acquisition in bacteria with innate immunity , 2018, Nature Ecology & Evolution.
[7] M. Touchon,et al. The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts , 2014, Nucleic acids research.
[8] P. Sharp. Molecular evolution of bacteriophages: evidence of selection against the recognition sites of host restriction enzymes. , 1986, Molecular biology and evolution.
[9] G. Bertani,et al. HOST CONTROLLED VARIATION IN BACTERIAL VIRUSES , 1953, Journal of bacteriology.
[10] N. Murray. 2001 Fred Griffith review lecture. Immigration control of DNA in bacteria: self versus non-self. , 2002, Microbiology.
[11] D. Dubnau,et al. Noise in Gene Expression Determines Cell Fate in Bacillus subtilis , 2007, Science.
[12] E. Seneta,et al. On quasi-stationary distributions in absorbing continuous-time finite Markov chains , 1967, Journal of Applied Probability.
[13] E. Kussell,et al. Evolutionary dynamics of restriction site avoidance. , 2012, Physical review letters.
[14] William Bialek,et al. Information processing in living systems , 2014, 1412.8752.
[15] A. Buckling,et al. Diversity of locust gut bacteria protects against pathogen invasion , 2005 .
[16] Stanislas Leibler,et al. Dynamic Persistence of Antibiotic-Stressed Mycobacteria , 2013, Science.
[17] Johan Paulsson,et al. Non-genetic heterogeneity from stochastic partitioning at cell division , 2011, Nature Genetics.
[18] James Gurney,et al. Why put up with immunity when there is resistance: an excursion into the population and evolutionary dynamics of restriction–modification and CRISPR-Cas , 2018, bioRxiv.
[19] B. Levin,et al. Sensitivity of naturally occurring coliphages to type I and type II restriction and modification. , 1993, Journal of general microbiology.
[20] Sylvain Moineau,et al. Bacteriophage resistance mechanisms , 2010, Nature Reviews Microbiology.
[21] A. Arkin,et al. It's a noisy business! Genetic regulation at the nanomolar scale. , 1999, Trends in genetics : TIG.
[22] A. Buckling,et al. The diversity-generating benefits of a prokaryotic adaptive immune system , 2016, Nature.
[23] V. Nagaraja,et al. Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense , 2013, Microbiology and Molecular Reviews.
[24] A. Witczak,et al. Natural tuning of restriction endonuclease synthesis by cluster of rare arginine codons , 2019, Scientific Reports.
[25] V. Nagaraja,et al. Restriction endonuclease triggered bacterial apoptosis as a mechanism for long time survival , 2017, Nucleic acids research.
[26] Jeffrey W. Smith,et al. Stochastic Gene Expression in a Single Cell , .
[27] J. Lygeros,et al. Decision Making I , 2014 .
[28] S. Leibler,et al. Strongly deterministic population dynamics in closed microbial communities , 2015 .
[29] S. Leibler,et al. Contingency and Statistical Laws in Replicate Microbial Closed Ecosystems , 2012, Cell.
[30] Tobias Bergmiller,et al. Bacterial Autoimmunity Due to a Restriction-Modification System , 2016, Current Biology.
[31] C. Guet,et al. Effects of mutations in phage restriction sites during escape from restriction–modification , 2017, Biology Letters.
[32] O Shoval,et al. Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space , 2012, Science.
[33] A. Novick,et al. ENZYME INDUCTION AS AN ALL-OR-NONE PHENOMENON. , 1957, Proceedings of the National Academy of Sciences of the United States of America.
[34] T. Thingstad. Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems , 2000 .
[35] Irene Otero-Muras,et al. Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality. , 2017, ACS synthetic biology.
[36] M. Gelfand,et al. Restriction-modification systems and bacteriophage invasion: who wins? , 2010, Journal of theoretical biology.
[37] S. Leibler,et al. Bacterial Persistence as a Phenotypic Switch , 2004, Science.
[38] B. Levin,et al. PHAGE‐MEDIATED SELECTION AND THE EVOLUTION AND MAINTENANCE OF RESTRICTION‐MODIFICATION , 1993, Evolution; international journal of organic evolution.
[39] Abhyudai Singh,et al. First-passage time approach to controlling noise in the timing of intracellular events , 2017, Proceedings of the National Academy of Sciences.
[40] P. Swain,et al. Stochastic Gene Expression in a Single Cell , 2002, Science.
[41] Peter Buchholz,et al. Input Modeling with Phase-Type Distributions and Markov Models: Theory and Applications , 2014 .
[42] I. Kobayashi,et al. To be or not to be: regulation of restriction–modification systems and other toxin–antitoxin systems , 2013, Nucleic acids research.
[43] G. Bell,et al. Diversity peaks at intermediate productivity in a laboratory microcosm , 2000, Nature.
[44] A. Arkin,et al. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. , 1998, Genetics.
[45] Jean Sippy,et al. Decision Making at a Subcellular Level Determines the Outcome of Bacteriophage Infection , 2010, Cell.
[46] Allan Campbell,et al. CONDITIONS FOR THE EXISTENCE OF BACTERIOPHAGE , 1961 .
[47] U. Alon,et al. Optimality and evolutionary tuning of the expression level of a protein , 2005, Nature.
[48] A. Arkin,et al. Stochastic mechanisms in gene expression. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[49] W Arber,et al. DNA modification and restriction. , 1969, Annual review of biochemistry.
[50] C. Rao,et al. Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm , 2003 .
[51] F. M. Stewart,et al. Resource-Limited Growth, Competition, and Predation: A Model and Experimental Studies with Bacteria and Bacteriophage , 1977, The American Naturalist.
[52] D. Dryden,et al. The biology of restriction and anti-restriction. , 2005, Current opinion in microbiology.
[53] E V Koonin,et al. Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes. , 1997, Nucleic acids research.
[54] Jose M. G. Vilar,et al. Modeling network dynamics: the lac operon, a case study , 2004 .