A Framework to Think About Evolving Genetic Regulatory Systems

The aim of this article is to suggest a framework to study the expected regulatory connections and coordinated patterns of gene expression in large genetic systems undergoing persistent mutation and selection.

[1]  S. Kauffman Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.

[2]  R. Axel,et al.  Analysis of the complexity and diversity of mRNA from chicken liver and oviduct , 1976, Cell.

[3]  A. D. Hershey,et al.  The Bacteriophage Lambda. , 1971 .

[4]  B. Mcclintock,et al.  Controlling elements and the gene. , 1956, Cold Spring Harbor symposia on quantitative biology.

[5]  S. Kauffman The large scale structure and dynamics of gene control circuits: an ensemble approach. , 1974, Journal of theoretical biology.

[6]  T. Humphreys,et al.  Similarity of hnRNA sequences in blastula and pluteus stage sea urchin embryos , 1977, Cell.

[7]  R. Britten,et al.  Sequence complexity of heterogeneous nuclear RNA in sea urchin embryos , 1975, Cell.

[8]  K. Tartof Unequal mitotic sister chromatid exchange and disproportionate replication as mechanisms regulating ribosomal RNA gene redundancy. , 1974, Cold Spring Harbor symposia on quantitative biology.

[9]  G. P. Smith,et al.  Unequal crossover and the evolution of multigene families. , 1974, Cold Spring Harbor symposia on quantitative biology.

[10]  C. Helms,et al.  A chromosomal translocation causing overproduction of iso-2-cytochrome c in yeast. , 1978, Genetics.

[11]  H. D. Berendes Gene activities in the Malphigian tubules of Drosophila hydei at different developmental stages , 1966 .

[12]  R. Britten,et al.  Distinct single-copy sequence sets in sea urchin nuclear RNAs. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[13]  R. Milkman Perspectives On Evolution , 1982 .

[14]  E. Dubois,et al.  Mating signals control expression of mutations resulting from insertion of a transposable repetitive element adjacent to diverse yeast genes , 1980, Cell.

[15]  W. Beermann Developmental Studies on Giant Chromosomes , 2013, Results and Problems in Cell Differentiation.

[16]  N. Sueoka,et al.  Sequence complexity of nuclear RNAs in adult rat tissues , 1978, Cell.

[17]  W. Gilbert Why genes in pieces? , 1978, Nature.

[18]  Marvin Minsky,et al.  Computation : finite and infinite machines , 2016 .

[19]  J. August,et al.  Polypeptides of cells transformed by RNA or DNA tumor viruses. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[20]  M. Ashburner Puffing patterns in Drosophila melanogaster and related species. , 1972, Results and problems in cell differentiation.

[21]  G. Rubin,et al.  Drosophila genome organization: conserved and dynamic aspects. , 1981, Annual review of genetics.

[22]  W. J. Dickinson Complex cis-acting regulatory genes demonstrated in Drosophila hybrids , 1979 .

[23]  M. M. Green Transposable elements in Drosophila and other Diptera. , 1980, Annual review of genetics.

[24]  Peterson Pa Instability among the components of a regulatory element transposon in maize. , 1981 .

[25]  R. A. Sherlock,et al.  Analysis of the behaviour of Kauffman binary networks—II. The state cycle fraction for networks of different connectivities , 1979 .

[26]  G. Fink,et al.  Genetic events associated with an insertion mutation in yeast , 1980, Cell.

[27]  R. A. Sherlock Analysis of the behaviour of Kauffman binary networks—I. State space description and the distribution of limit cycle lengths , 1979 .

[28]  J. Bishop,et al.  The gene numbers game. , 1974, Cell.

[29]  J. Darnell Implications of RNA-RNA splicing in evolution of eukaryotic cells. , 1978, Science.

[30]  R. Britten,et al.  Repetitive and Non-Repetitive DNA Sequences and a Speculation on the Origins of Evolutionary Novelty , 1971, The Quarterly Review of Biology.

[31]  Françoise Fogelman-Soulié,et al.  Specific roles of the different Boolean mappings in random networks , 1982 .

[32]  R. Britten,et al.  Regulation of gene expression: possible role of repetitive sequences. , 1979, Science.

[33]  Brown Dd Gene expression in eukaryotes. , 1981 .

[34]  L. Sachs,et al.  Molecular dissection of differentiation in normal and leukemic myeloblasts: separately programmed pathways of gene expression. , 1980, Developmental biology.

[35]  R. Axel,et al.  Integration, transcription, and control of a Drosophila heat shock gene in mouse cells. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Claude Berge,et al.  The theory of graphs and its applications , 1962 .

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

[38]  Alan E. Gelfand,et al.  A system theoretic approach to the management of complex organizations: Management by exception, priority, and input span in a class of fixed‐structure models , 1979 .

[39]  S. Kauffman Emergent properties in random complex automata , 1984 .

[40]  Ronald W. Davis,et al.  Evidence for transposition of dispersed repetitive DNA families in yeast , 1979, Cell.

[41]  R. Britten,et al.  Gene regulation for higher cells: a theory. , 1969, Science.

[42]  J. August,et al.  Polypeptide maps of cells infected with murine type C leukemia or sarcoma oncovirus , 1978, Cell.

[43]  S. Wolfram Statistical mechanics of cellular automata , 1983 .

[44]  W. S. Hayward,et al.  Activation of a cellular onc gene by promoter insertion in ALV-induced lymphoid leukosis , 1981, Nature.

[45]  T. Ohta On the evolution of multigene families. , 1983, Theoretical population biology.

[46]  W. Ewens Mathematical Population Genetics , 1980 .

[47]  A. Wilson,et al.  Rapid speciation and chromosomal evolution in mammals. , 1977, Proceedings of the National Academy of Sciences of the United States of America.