Early Replicons: Origin and Evolution

[1]  Hermann Haken,et al.  Synergetics: An Introduction , 1983 .

[2]  E. Seneta.  Non-negative Matrices and Markov Chains , 2008 .

[3]  S. Cavicchi,et al.  Fitness variation in response to artificial selection for reduced cell area, cell number and wing area in natural populations of Drosophila melanogaster , 2007, BMC Evolutionary Biology.

[4]  J. J. Bull,et al.  Theory of Lethal Mutagenesis for Viruses , 2007, Journal of Virology.

[5]  P. Hogeweg,et al.  Error-threshold exists in fitness landscapes with lethal mutants , 2007, BMC Evolutionary Biology.

[6]  E. Shakhnovich,et al.  Semiconservative quasispecies equations for polysomic genomes: the haploid case. , 2006, Journal of theoretical biology.

[7]  J. William Schopf,et al.  Fossil evidence of Archaean life , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[8]  Paul A. Serbinowski,et al.  A structural basis for discriminating between self and nonself double-stranded RNAs in mammalian cells , 2006, Nature Biotechnology.

[9]  P. Schuster.  Prediction of RNA secondary structures: from theory to models and real molecules , 2006 .

[10]  M. Deem,et al.  Quasispecies theory for multiple-peak fitness landscapes. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[11]  Chin-Kun Hu,et al.  Exact solution of the Eigen model with general fitness functions and degradation rates. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[12]  S. Klußmann,et al.  The aptamer handbook : functional oligonucleotides and their applications , 2006 .

[13]  P. Dittrich,et al.  Determinants of simulated RNA evolution. , 2006, Journal of theoretical biology.

[14]  B. Palsson.  Systems Biology: Properties of Reconstructed Networks , 2006 .

[15]  M. Huynen.  Exploring phenotype space through neutral evolution , 1996, Journal of Molecular Evolution.

[16]  Victor Fok,et al.  The RNA World , 2006 .

[17]  P. Stadler,et al.  Replicator Dynamics in Protocells , 2006 .

[18]  Claus O Wilke,et al.  Quasispecies theory in the context of population genetics , 2005, BMC Evolutionary Biology.

[19]  Axel Kowald,et al.  Systems Biology in Practice: Concepts, Implementation and Application , 2005 .

[20]  E. Domingo.  Antiviral strategy on the horizon , 2005 .

[21]  Stuart Kauffman,et al.  Adaptive walks with noisy fitness measurements , 1995, Molecular Diversity.

[22]  P. Schuster,et al.  Stages of emerging life —Five principles of early organization , 2005, Journal of Molecular Evolution.

[23]  Terry L. Marsh,et al.  Rna catalysis and the origin of life , 2005, Origins of life and evolution of the biosphere.

[24]  A. Serganov,et al.  Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation , 2005, Nature Structural &Molecular Biology.

[25]  P. Hogeweg,et al.  Phenotypic error threshold; additivity and epistasis in RNA evolution , 2005, BMC Evolutionary Biology.

[26]  Andrés Moya,et al.  Validating viral quasispecies with digital organisms: a re-examination of the critical mutation rate , 2005, BMC Evolutionary Biology.

[27]  Liangjiang Wang,et al.  The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants , 2005, BMC Evolutionary Biology.

[28]  L. Loeb,et al.  Viral error catastrophe by mutagenic nucleosides. , 2004, Annual review of microbiology.

[29]  H. Suga,et al.  Reduction of an aldehyde by a NADH/Zn2+ -dependent redox active ribozyme. , 2004, Journal of the American Chemical Society.

[30]  J. Mattick.  RNA regulation: a new genetics? , 2004, Nature Reviews Genetics.

[31]  E. Holmes,et al.  The population genetics and evolutionary epidemiology of RNA viruses , 2004, Nature Reviews Microbiology.

[32]  N. Packard,et al.  Transitions from Nonliving to Living Matter , 2004, Science.

[33]  Peter F. Stadler,et al.  Proto-Organism Kinetics: Evolutionary Dynamics of Lipid Aggregates with Genes and Metabolism , 2004, Origins of life and evolution of the biosphere.

[34]  Eric J. Deeds,et al.  Semiconservative replication in the quasispecies model. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[35]  L. Orgel.  Some Consequences of the RNA World Hypothesis , 2003, Origins of life and evolution of the biosphere.

[36]  Peter Schuster,et al.  A principle of natural self-organization , 1977, Naturwissenschaften.

[37]  M. Eigen.  Selforganization of matter and the evolution of biological macromolecules , 1971, Naturwissenschaften.

[38]  Thomas A Steitz,et al.  RNA, the first macromolecular catalyst: the ribosome is a ribozyme. , 2003, Trends in biochemical sciences.

[39]  Martin Nilsson,et al.  Bridging Nonliving and Living Matter , 2003, Artificial Life.

[40]  Peter F. Stadler,et al.  Molecular Replicator Dynamics , 2003, Adv. Complex Syst..

[41]  P. Campos.  Error threshold transition in the random-energy model. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[42]  Manfred Eigen,et al.  Error catastrophe and antiviral strategy , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Michael T. McManus,et al.  Gene silencing in mammals by small interfering RNAs , 2002, Nature Reviews Genetics.

[44]  A. Steele,et al.  Questioning the evidence for Earth's oldest fossils , 2002, Nature.

[45]  Edward C. Holmes,et al.  Is the Quasispecies Concept Relevant to RNA Viruses? , 2002, Journal of Virology.

[46]  E. Domingo,et al.  Quasispecies Theory in Virology , 2002, Journal of Virology.

[47]  T. Cavalier-smith.  Obcells as Proto-Organisms: Membrane Heredity, Lithophosphorylation, and the Origins of the Genetic Code, the First Cells, and Photosynthesis , 2001, Journal of Molecular Evolution.

[48]  E. Baake,et al.  Mutation-selection models solved exactly with methods of statistical mechanics. , 2001, Genetical research.

[49]  J. McCaskill,et al.  Error threshold for spatially resolved evolution in the quasispecies model. , 2001, Physical review letters.

[50]  E. Holmes,et al.  Evidence for the non-quasispecies evolution of RNA viruses [corrected]. , 2001, Molecular biology and evolution.

[51]  R. Solé,et al.  Field theory for a reaction-diffusion model of quasispecies dynamics. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[52]  Claus O. Wilke,et al.  SELECTION FOR FITNESS VERSUS SELECTION FOR ROBUSTNESS IN RNA SECONDARY STRUCTURE FOLDING , 2001, Evolution; international journal of organic evolution.

[53]  Christian M. Reidys,et al.  Neutrality in fitness landscapes , 2001, Appl. Math. Comput..

[54]  Claus O. Wilke,et al.  Dynamic fitness landscapes in molecular evolution , 1999, physics/9912012.

[55]  C V Forst,et al.  Replication and mutation on neutral networks , 2001, Bulletin of mathematical biology.

[56]  P. Schuster,et al.  Dynamics of autocatalytic replicator networks based on higher-order ligation reactions , 2000, Bulletin of mathematical biology.

[57]  Christopher Ronnewinkel,et al.  Dynamic fitness landscapes: expansions for small mutation rates , 2000, physics/0010045.

[58]  T. Steitz,et al.  The structural basis of ribosome activity in peptide bond synthesis. , 2000, Science.

[59]  T. Steitz,et al.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. , 2000, Science.

[60]  S. Elena,et al.  The evolution of RNA viruses: A population genetics view. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[61]  T. Jukes,et al.  The neutral theory of molecular evolution. , 2000, Genetics.

[62]  B. Salvato,et al.  Isomorphism of quasispecies and percolation models. , 2000, Journal of theoretical biology.

[63]  J. Drake,et al.  Mutation rates among RNA viruses. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[64]  Robert Happel,et al.  Autocatalytic replication in a CSTR and constant organization , 1999, Journal of mathematical biology.

[65]  A. Jäschke,et al.  A small catalytic RNA motif with Diels-Alderase activity. , 1999, Chemistry & biology.

[66]  S A Kauffman,et al.  Selection dynamics in autocatalytic systems: templates replicating through binary ligation. , 1998, Bulletin of mathematical biology.

[67]  P. Schuster,et al.  Shaping space: the possible and the attainable in RNA genotype-phenotype mapping. , 1998, Journal of theoretical biology.

[68]  A. Ferré-D’Amaré,et al.  Crystal structure of a hepatitis delta virus ribozyme , 1998, Nature.

[69]  T. Cech,et al.  Peptidyl-transferase ribozymes: trans reactions, structural characterization and ribosomal RNA-like features. , 1998, Chemistry & biology.

[70]  P. Schuster,et al.  IR-98-039 / April Continuity in Evolution : On the Nature of Transitions , 1998 .

[71]  J. Fontanari,et al.  Error threshold in finite populations , 1997, cond-mat/9709247.

[72]  M. Famulok,et al.  A novel ribozyme with ester transferase activity. , 1998, Chemistry & biology.

[73]  Yohei Yokobayashi,et al.  Emergence of symbiosis in peptide self-replication through a hypercyclic network , 1997, Nature.

[74]  T. Cech,et al.  Peptide bond formation by in vitro selected ribozymes , 1997, Nature.

[75]  E. Szathmáry,et al.  An extremum principle for parabolic competition , 1997 .

[76]  P. Schuster.  Landscapes and molecular evolution , 1997 .

[77]  A. Schwartz.  Speculation on the RNA precursor problem. , 1997, Journal of theoretical biology.

[78]  T. Gánti.  Biogenesis itself. , 1997, Journal of theoretical biology.

[79]  John Maynard Smith,et al.  From replicators to reproducers: the first major transitions leading to life. , 1997, Journal of theoretical biology.

[80]  Kay Severin,et al.  Peptide Self-Replication via Template-Directed Ligation , 1997 .

[81]  G. Schwarz,et al.  Re: Manfred Eigen's 70th birthday. , 1997, Biophysical chemistry.

[82]  J. McCaskill,et al.  Spatially resolved in vitro molecular ecology. , 1997, Biophysical chemistry.

[83]  P. Schuster,et al.  Genotypes with phenotypes: adventures in an RNA toy world. , 1997, Biophysical chemistry.

[84]  Thomas Wiehe,et al.  Model dependency of error thresholds: the role of fitness functions and contrasts between the finite and infinite sites models , 1997 .

[85]  P. Schuster,et al.  Generic properties of combinatory maps: neutral networks of RNA secondary structures. , 1997, Bulletin of mathematical biology.

[86]  E. Domingo,et al.  RNA virus mutations and fitness for survival. , 1997, Annual review of microbiology.

[87]  H. Noller,et al.  Ribosomes and translation. , 1997, Annual review of biochemistry.

[88]  D. Patel,et al.  Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex. , 1997, Chemistry & biology.

[89]  J. McCaskill,et al.  A molecular predator and its prey: coupled isothermal amplification of nucleic acids. , 1997, Chemistry & biology.

[90]  L. Peliti,et al.  Error threshold in simple landscapes , 1996, cond-mat/9610028.

[91]  L. Gold,et al.  In vitro selection of a novel catalytic RNA: characterization of a sulfur alkylation reaction and interaction with a small peptide. , 1996, RNA.

[92]  C. Kundrot,et al.  Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing , 1996, Science.

[93]  Juan R. Granja,et al.  A self-replicating peptide , 1996, Nature.

[94]  David P. Bartel,et al.  RNA-catalysed RNA polymerization using nucleoside triphosphates , 1996, Nature.

[95]  J. Szostak,et al.  Ribozyme-catalysed amino-acid transfer reactions , 1996, Nature.

[96]  Fontanari,et al.  Population genetics approach to the quasispecies model. , 1996, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[97]  M. Huynen,et al.  Smoothness within ruggedness: the role of neutrality in adaptation. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[98]  Kenso Soai,et al.  Asymmetric autocatalysis and amplification of enantiomeric excess of a chiral molecule , 1995, Nature.

[99]  Eörs Szathmáry,et al.  The Major Transitions in Evolution , 1997 .

[100]  J. Szostak,et al.  Kinetic and thermodynamic characterization of the reaction catalyzed by a polynucleotide kinase ribozyme. , 1995, Biochemistry.

[101]  J W Szostak,et al.  Structurally complex and highly active RNA ligases derived from random RNA sequences. , 1995, Science.

[102]  A. Klug,et al.  The crystal structure of an AII-RNAhammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage , 1995, Cell.

[103]  J. Szostak,et al.  A DNA metalloenzyme with DNA ligase activity , 1995, Nature.

[104]  Jack W. Szostak,et al.  In vitro evolution of a self-alkylatlng ribozyme , 1995, Nature.

[105]  S. Wain-Hobson,et al.  Hypermutagenesis of RNA using human immunodeficiency virus type 1 reverse transcriptase and biased dNTP concentrations. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[106]  K. Flaherty,et al.  Three-dimensional structure of a hammerhead ribozyme , 1994, Nature.

[107]  Pier Luigi Luisi,et al.  Enzymatic RNA Synthesis in Self-Reproducing Vesicles: An Approach to the Construction of a Minimal Synthetic Cell , 1994 .

[108]  Jon R. Lorsch,et al.  In vitro evolution of new ribozymes with polynucleotide kinase activity , 1994, Nature.

[109]  P. Schultz,et al.  Expanding the scope of RNA catalysis. , 1994, Science.

[110]  R R Breaker,et al.  Emergence of a replicating species from an in vitro RNA evolution reaction. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[111]  K. Nicolaou,et al.  Chemical self-replication of palindromic duplex DNA , 1994, Nature.

[112]  P. Schuster,et al.  From sequences to shapes and back: a case study in RNA secondary structures , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[113]  L. Peliti,et al.  An evolutionary version of the random energy model , 1993 .

[114]  G. Wagner,et al.  What is the difference between models of error thresholds and Muller's ratchet? , 1993 .

[115]  D. Bartel,et al.  Isolation of new ribozymes from a large pool of random sequences [see comment]. , 1993, Science.

[116]  P. Schuster,et al.  Statistics of RNA secondary structures , 1993, Biopolymers.

[117]  J. Drake.  Rates of spontaneous mutation among RNA viruses. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[118]  J. Schopf,et al.  Microfossils of the Early Archean Apex Chert: New Evidence of the Antiquity of Life , 1993, Science.

[119]  A. Eschenmoser,et al.  Hexose nucleic acids , 1993 .

[120]  Günter von Kiedrowski,et al.  Minimal Replicator Theory I: Parabolic Versus Exponential Growth , 1993 .

[121]  W. Ebeling.  Chemical evolution. Origin of the elements, molecules and living systems. Von S. F. Mason. Clarendon Press, Oxford, 1991. IX, 317 S., geb. £19.50. – ISBN 0-19-855272-6 , 1992 .

[122]  G. F. Joyce,et al.  Directed evolution of an RNA enzyme. , 1992, Science.

[123]  H. Noller,et al.  Unusual resistance of peptidyl transferase to protein extraction procedures. , 1992, Science.

[124]  Pier Luigi Luisi,et al.  Autocatalytic self-replicating micelles as models for prebiotic structures , 1992, Nature.

[125]  Tarazona.  Error thresholds for molecular quasispecies as phase transitions: From simple landscapes to spin-glass models. , 1992, Physical review. A, Atomic, molecular, and optical physics.

[126]  L. Orgel,et al.  Molecular replication , 1992, Nature.

[127]  M. Eigen,et al.  The hypercycle. Coupling of RNA and protein biosynthesis in the infection cycle of an RNA bacteriophage. , 1991, Biochemistry.

[128]  Julius Rebek,et al.  Kinetic studies and modeling of a self-replicating system , 1991 .

[129]  T. Gingeras,et al.  Self-sustained sequence replication (3SR): an isothermal transcription-based amplification system alternative to PCR. , 1991, PCR methods and applications.

[130]  G. F. Joyce,et al.  The rise and fall of the RNA world. , 1991, The New biologist.

[131]  S. Mason,et al.  Chemical Evolution: Origins of the Elements, Molecules, and Living Systems , 1991 .

[132]  B. Derrida,et al.  Evolution in a flat fitness landscape , 1991 .

[133]  Stuart A. Kauffman,et al.  The origins of order , 1993 .

[134]  P. Stadler.  Complementary replication. , 1991, Mathematical biosciences.

[135]  K. Mullis.  The unusual origin of the polymerase chain reaction. , 1990, Scientific American.

[136]  R Rusting,et al.  Safe passage? Study fuels debate over safety of birth centers. , 1990, Scientific American.

[137]  Julius Rebek,et al.  Self-replicating system , 1990 .

[138]  T. Cech.  Self-splicing of group I introns. , 1990, Annual review of biochemistry.

[139]  L. A. Segel,et al.  The Quasi-Steady-State Assumption: A Case Study in Perturbation , 1989, SIAM Rev..

[140]  Schuster,et al.  Physical aspects of evolutionary optimization and adaptation. , 1989, Physical review. A, General physics.

[141]  E. Szathmáry,et al.  Sub-exponential growth and coexistence of non-enzymatically replicating templates. , 1989, Journal of theoretical biology.

[142]  M. Nowak,et al.  Error thresholds of replication in finite populations mutation frequencies and the onset of Muller's ratchet. , 1989, Journal of theoretical biology.

[143]  T. Cech.  RNA as an enzyme. , 1986, Biochemistry international.

[144]  D. Goeddel,et al.  A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction , 1989 .

[145]  M. Schidlowski.  A 3,800-million-year isotopic record of life from carbon in sedimentary rocks , 1988, Nature.

[146]  Peter Schuster,et al.  Stationary mutant distributions and evolutionary optimization , 1988 .

[147]  P. Schuster,et al.  Stationary mutant distributions and evolutionary optimization. , 1988, Bulletin of mathematical biology.

[148]  O. Uhlenbeck.  A small catalytic oligoribonucleotide , 1987, Nature.

[149]  I. Leuthäusser,et al.  Statistical mechanics of Eigen's evolution model , 1987 .

[150]  P. Schuster,et al.  A computer model of evolutionary optimization. , 1987, Biophysical chemistry.

[151]  L E Orgel,et al.  Evolution of the genetic apparatus: a review. , 1987, Cold Spring Harbor symposia on quantitative biology.

[152]  B. Ganem.  RNA world , 1987, Nature.

[153]  L E Orgel,et al.  RNA catalysis and the origins of life. , 1986, Journal of theoretical biology.

[154]  M. Veltman.  THE HIGGS BOSON , 1986 .

[155]  Günter von Kiedrowski,et al.  A Self‐Replicating Hexadeoxynucleotide , 1986 .

[156]  W. Gilbert.  Origin of life: The RNA world , 1986, Nature.

[157]  Peter Schuster,et al.  Dynamics of Evolutionary Optimization , 1985 .

[158]  K Sigmund,et al.  Polynucleotide evolution and branching processes , 1985, Bulletin of mathematical biology.

[159]  S. Swain.  Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences , 1984 .

[160]  J. S. McCaskill,et al.  A localization threshold for macromolecular quasispecies from continuously distributed replication rates , 1984 .

[161]  D. Yevick,et al.  Laser theory , 1984, IEEE Journal of Quantum Electronics.

[162]  N. Pace,et al.  The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme , 1983, Cell.

[163]  T. Cech.  RNA splicing: Three themes with variations , 1983, Cell.

[164]  Valerie Isham,et al.  Non‐Negative Matrices and Markov Chains , 1983 .

[165]  P. Schuster,et al.  Self-replication with errors. A model for polynucleotide replication. , 1982, Biophysical chemistry.

[166]  H. Nürnberg.  The Hypercycle. A Principle of Natural Self Organization. , 1981 .

[167]  Josef Hofbauer,et al.  On the occurrence of limit cycles in the Volterra-Lotka equation , 1981 .

[168]  Josef Hofbauer,et al.  Competition and cooperation in catalytic selfreplication , 1981 .

[169]  M. Eigen,et al.  The Hypercycle: A principle of natural self-organization , 2009 .

[170]  H. D. PFLUG,et al.  Combined structural and chemical analysis of 3,800-Myr-old microfossils , 1979, Nature.

[171]  Charles Weissmann,et al.  Nucleotide sequence heterogeneity of an RNA phage population , 1978, Cell.

[172]  D. Gillespie.  Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[173]  M. Eigen,et al.  The hypercycle. A principle of natural self-organization. Part A: Emergence of the hypercycle. , 1977, Die Naturwissenschaften.

[174]  I. Prigogine,et al.  Formative Processes. (Book Reviews: Self-Organization in Nonequilibrium Systems. From Dissipative Structures to Order through Fluctuations) , 1977 .

[175]  Daniel T. Gillespie,et al.  Concerning the validity of the stochastic approach to chemical kinetics , 1977 .

[176]  D. Gillespie.  A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions , 1976 .

[177]  Richard H. Enns,et al.  On the theory of selection of coupled macromolecular systems , 1976 .

[178]  F. Kramer,et al.  Evolution in vitro: sequence and phenotype of a mutant RNA resistant to ethidium bromide. , 1974, Journal of molecular biology.

[179]  Colin J. Thompson,et al.  On Eigen's theory of the self-organization of matter and the evolution of biological macromolecules , 1974 .

[180]  C. Weissmann,et al.  The making of a phage , 1974, FEBS letters.

[181]  F. Schlögl.  Chemical reaction models for non-equilibrium phase transitions , 1972 .

[182]  S. Fox,et al.  Molecular evolution and the origin of life , 1972 .

[183]  S. Spiegelman,et al.  An approach to the experimental analysis of precellular evolution , 1971, Quarterly Reviews of Biophysics.

[184]  L. Orgel.  Evolution of the genetic apparatus. , 1968, Journal of molecular biology.

[185]  D. Mills,et al.  An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule. , 1967, Proceedings of the National Academy of Sciences of the United States of America.

[186]  F. Frank,et al.  On spontaneous asymmetric synthesis. , 1953, Biochimica et biophysica acta.

[187]  A. M. Turing,et al.  The chemical basis of morphogenesis , 1952, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.