Autocatalytic recombination systems: A reaction network perspective
Tài liệu tham khảo
Alberts, 2002
Kauffman, 1986, Autocatalytic sets of proteins, J. Theoret. Biol., 119, 1, 10.1016/S0022-5193(86)80047-9
Kauffman, 1993
Robertson, 2000, Minimal self-replicating systems, Chem. Soc. Rev., 29, 141, 10.1039/a803602k
Eilertsen, 2018, A theory of reactant-stationary kinetics for a mechanism of zymogen activation, Biophys. Chem., 242, 34, 10.1016/j.bpc.2018.08.003
Tyczynska, 2020
Eigen, 1971, Self-organization of matter and the evolution of biological macromolecules, Naturwissenschaften, 58, 465, 10.1007/BF00623322
Eigen, 1977, A principle of natural self-organization, Naturwissenschaften, 64, 541, 10.1007/BF00450633
Eigen, 1982, Stages of emerging life — Five principles of early organization, J. Mol. Evol., 19, 47, 10.1007/BF02100223
Schuster, 1983, Replicator dynamics, J. Theoret. Biol., 100, 533, 10.1016/0022-5193(83)90445-9
Hofbauer, 1998
Joshi, 2021, Autocatalytic networks: An intimate relation between network topology and dynamics, SIAM J. Appl. Math., 81, 1623, 10.1137/20M1342720
Hofbauer, 1981, A general cooperation theorem for hypercycles, Mon.hefte Math., 91, 233, 10.1007/BF01301790
Schuster, 1978, Dynamical systems under constant organization I. Topological analysis of a family of non-linear differential equations — a model for catalytic hypercycles, Bull. Math. Biol., 40, 743
Hofbauer, 1980, Dynamical systems under constant organization II: Homogeneous growth functions of degree p=2, SIAM J. Appl. Math., 38, 282, 10.1137/0138025
Schuster, 1979, Dynamical systems under constant organization. III. Cooperative and competitive behavior of hypercycles, J. Differ. Equ., 32, 357, 10.1016/0022-0396(79)90039-1
Hofbauer, 1984, A difference equation model for the hypercycle, SIAM J. Appl. Math., 44, 762, 10.1137/0144054
Craciun, 2013, Persistence and permanence of mass-action and power-law dynamical systems, SIAM J. Appl. Math., 73, 305, 10.1137/100812355
Pantea, 2012, On the persistence and global stability of mass-action systems, SIAM J. Math. Anal., 44, 1636, 10.1137/110840509
Anderson, 2011, A proof of the global attractor conjecture in the single linkage class case, SIAM J. Appl. Math., 71, 1487, 10.1137/11082631X
Gopalkrishnan, 2014, A geometric approach to the global attractor conjecture, SIAM J. Appl. Dyn. Syst., 13, 758, 10.1137/130928170
Craciun, 2009, Toric dynamical systems, J. Symb. Comput., 44, 1551, 10.1016/j.jsc.2008.08.006
Gunawardena, 2003
Feinberg, 1989, Necessary and sufficient conditions for detailed balancing in mass action systems of arbitrary complexity, Chem. Eng. Sci., 44, 1819, 10.1016/0009-2509(89)85124-3
Feinberg, 1987, Chemical reaction network structure and the stability of complex isothermal reactors — I. The deficiency zero and deficiency one theorems, Chem. Eng. Sci., 42, 2229, 10.1016/0009-2509(87)80099-4
Feinberg, 1988, Chemical reaction network structure and the stability of complex isothermal reactors–II. Multiple steady states for networks of deficiency one, Chem. Eng. Sci., 43, 1, 10.1016/0009-2509(88)87122-7
Feinberg, 1972, On chemical kinetics of a certain class, Arch. Ration. Mech. Anal., 46, 1, 10.1007/BF00251866
Craciun, 2015
Craciun, 2019, Polynomial dynamical systems, reaction networks, and toric differential inclusions, SIAGA, 3, 87
Craciun, 2019
Feinberg, 2019
Hárs, 1981, On the inverse problem of reaction kinetics, 363
Craciun, 2020, An efficient characterization of complex-balanced, detailed-balanced, and weakly reversible systems, SIAM J. Appl. Math., 80, 183, 10.1137/19M1244494
Hordijk, 2004, Detecting autocatalytic, self-sustaining sets in chemical reaction systems, J. Theoret. Biol., 227, 451, 10.1016/j.jtbi.2003.11.020
Hordijk, 2011, Required levels of catalysis for emergence of autocatalytic sets in models of chemical reaction systems, Int. J. Mol. Sci., 12, 3085, 10.3390/ijms12053085
Kauffman, 1996
Hordijk, 2010, Autocatalytic sets and the origin of life, Entropy, 12, 1733, 10.3390/e12071733
Hofbauer, 1988
Eigen, 2012
Hofbauer, 1991, Stable periodic solutions for the hypercycle system, J. Dynam. Differential Equations, 3, 423, 10.1007/BF01049740
Kuehn, 2015
Rieger, 2012
Stadler, 1993, Random catalytic reaction networks, Physica D, 63, 378, 10.1016/0167-2789(93)90118-K
Sung, 2006, Mechanism of homologous recombination: mediators and helicases take on regulatory functions, Nat. Rev. Mol., 7, 739, 10.1038/nrm2008
Vasquez, 2001, Manipulating the mammalian genome by homologous recombination, Proc. Natl. Acad. Sci. USA, 98, 8403, 10.1073/pnas.111009698
Capecchi, 2005, Gene targeting in mice: functional analysis of the mammalian genome for the twenty-first century, Nat. Rev. Genet., 6, 507, 10.1038/nrg1619
Capecchi, 1989, Altering the genome by homologous recombination, Science, 244, 1288, 10.1126/science.2660260
Gerlai, 2016, Gene targeting using homologous recombination in embryonic stem cells: the future for behavior genetics?, Front. Genet., 7, 43, 10.3389/fgene.2016.00043
Wilson, 2006, Nonhomologous end-joining: mechanisms, conservation and relationship to illegitimate recombination, 487
Rockafellar, 2015
Boros, 2020, Permanence of weakly reversible mass-action systems with a single linkage class, SIAM J. Appl. Dyn. Syst., 19, 352, 10.1137/19M1248431
Hordijk, 2012, Predicting template-based catalysis rates in a simple catalytic reaction model, J. Theoret. Biol., 295, 132, 10.1016/j.jtbi.2011.11.024
Deshpande, 2014, Autocatalysis in reaction networks, Bull. Math. Biol., 76, 2570, 10.1007/s11538-014-0024-x
Qian, 2011, A simple DNA gate motif for synthesizing large-scale circuits, J. R. Soc. Interface, 8, 1281, 10.1098/rsif.2010.0729
Phillips, 2009, A programming language for composable DNA circuits, J. R. Soc. Interface, 6, S419, 10.1098/rsif.2009.0072.focus
Soloveichik, 2010, DNA as a universal substrate for chemical kinetics, Proc. Natl. Acad. Sci. USA, 107, 5393, 10.1073/pnas.0909380107
Angeli, 2007, A Petri net approach to persistence analysis in chemical reaction networks, 181