Biology Reference
In-Depth Information
[62] Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M,
Eisen MB. Conservation and evolution of cis-regulatory systems
in ascomycete fungi. PLOS Biol 2004;2:2202 e 19.
[63] Wray G, Hahn M, Abouheif E, Balhoff J, Pizer M, Rockman M,
et al. The evolution of transcriptional regulation in eukaryotes.
Mol Biol Evol 2003;20:1377 e 419.
[64] Ludwig MZ, Bergman C, Patel NH, Kreitman M. Evidence for
stabilizing selection in a eukaryotic enhancer element. Nature
2000;403:564 e 7.
[65] Maduro M, Pilgrim D. Conservation of function and expression of
unc-119 from two Caenorhabditis species despite divergence of
non-coding DNA. Gene 1996;183:77 e 85.
[66] Romano L, Wray G. Conservation of Endo16 expression in sea
urchins despite evolutionary divergence in both cis and trans-
acting components of transcriptional regulation. Development
2003;130:4187 e 99.
[67] Jaeger J, Surkova S, Blagov M, Janssens H, Kosman D, Kozlov K,
et al. Dynamic control of positional information in the early
Drosophila embryo. Nature 2004;430:368 e 71.
[68] Sanchez L, Chaouiya C, Thieffry D. Segmenting the fly embryo:
logical analysis of the role of the segment polarity cross-
regulatory module. Int J Dev Biol 2008;52:1059 e 75.
[69] Albert R, Othmer HG. The topology of the regulatory interactions
predicts the expression pattern of the segment polarity genes in
Drosophila melanogaster.
[82] Raman K, Wagner A. Evolvability and robustness in a complex
signaling circuit. Mol BioSyst 2011;7:1081
92.
[83] Ciliberti S, Martin OC, Wagner A. Innovation and robustness
in complex regulatory gene networks. Proc Natl Acad Sci USA
2007;104:13591 e 13596
[84] Ciliberti S, Martin OC, Wagner A. Circuit topology and the
evolution of robustness in complex regulatory gene networks.
PLOS Comput Biol 2007;3(2):e15.
[85] Maynard-Smith J. Natural selection and the concept of a protein
space. Nature 1970;255:563 e 4.
[86] Lipman D, Wilbur W. Modeling neutral and selective evolution of
protein folding. Proc R Soc Lon B 1991;245:7 e 11.
[87] Schuster P, FontanaW, Stadler P,Hofacker I. Fromsequences to shapes
and back e a case-study in RNA secondary structures. Proc R Soc Lon
B 1994;255:279 e 84.
[88] Berman H, Battistuz T, Bhat T, Bluhm W, Bourne P, Burkhardt K,
et al. The Protein Data Bank. Acta Crystallogr B Biol Crystallogr
2002;58:899 e 907.
[89] Hofacker I, Fontana W, Stadler P, Bonhoeffer L, Tacker M,
Schuster P. Fast folding and comparison of RNA secondary
structures. Monatshefte fuer Chemie 1994;125:167 e 88.
[90] Flamm C, Fontana W, Hofacker I, Schuster P. RNA folding at
elementary step resolution. RNA 2000;6:325 e 38.
[91] Fontana W, Schuster P. Shaping space:
e
the possible and the
Journal of Theoretical Biology
attainable in RNA genotype
phenotype mapping. J Theor Biol
e
2003;223:1
18.
515.
[92] Sumedha, Martin OC, Wagner A. New structural variation in
evolutionary searches of RNA neutral networks. BioSystems
2007;90:475 e 85.
[93] Wagner A. Robustness and evolvability: a paradox resolved. Proc
R Soc Lon B Biol Sci 2008;275:91 e 100.
[94] Jackson R, Kaminski A. Internal initiation of translation in
eukaryotes: The picornavirus paradigm and beyond. RNA
1995;1:985 e 1000.
[95] Mandl C, Holzmann H, Meixner T, Rauscher S, Stadler P,
Allison S, et al. Spontaneous and engineered deletions in the 3 0
noncoding region of tick-borne encephalitis virus: construction of
highly
1998;194:491
e
e
[70]
Ingolia NT. Topology and robustness in the Drosophila segment
polarity network. PLOS Biol 2004;2:805
15.
[71] MacCarthy T, Seymour R, Pomiankowski A. The evolutionary
potential of the Drosophila sex determination gene network. J
Theor Biol 2003;225:461 e 8.
[72] Mjolsness E, Sharp DH, Reinitz J. A connectionist model of
development. J Theor Biol 1991;152:429 e 53.
[73] Reinitz J, Mjolsness E, Sharp DH. Model for cooperative
control of positional information in Drosophila by bicoid and
maternal hunchback. J Exp Zool 1995;271:47 e 56.
[74] Reinitz J. Gene circuits for eve stripes: reverse engineering the
Drosophila segmentation gene network. Biophys J 1999;76:
A272 e A272.
[75] Sharp DH, Reinitz J. Prediction of mutant expression patterns
using gene circuits. BioSystems 1998;47:79 e 90.
[76] Azevedo RBR, Lohaus R, Srinivasan S, Dang KK, Burch CL.
Sexual reproduction selects for robustness and negative epistasis
in artificial gene networks. Nature 2006;440:87 e 90.
[77] Bornholdt S, Sneppen K. Robustness as an evolutionary principle.
Proc R Soc Lon B Biol Sci 2000;267:2281 e 6.
[78] Wagner A. Does evolutionary plasticity evolve? Evolution
1996;50:1008 e 23.
[79] Siegal M, Bergman A. Waddington's canalization revisited:
developmental stability and evolution. Proc Natl Acad Sci USA
2000;99:10528
e
attenuated mutants
of
a
flavivirus.
J Virol
1998;72:2132 e 40.
[96] Iserentant D, Fiers W. Secondary structure of messenger-RNA
and efficiency of translation initiation. Gene 1980;9:1 e 12.
[97] Feist AM, Palsson BO. The growing scope of applications of
genome-scale metabolic reconstructions using Escherichia coli.
Nat Biotech 2008;26:659 e 67.
[98] Cotterell J, Sharpe J. An atlas of gene regulatory networks reveals
multiple three-gene mechanisms for
interpreting morphogen
gradients. Mol Syst Biol 2010;6:425.
[99] Doolittle R. The origins and evolution of eukaryotic proteins.
Philos Trans Ro Soc B Biol Sci 1995;349:235
40.
[100] Thornton J, Orengo C, Todd A, Pearl F. Protein folds, functions
and evolution. J Mol Biol 1999;293:333
e
10532
[80] Bergman A, Siegal M. Evolutionary capacitance as a general
feature of complex gene networks. Nature 2003;424:549
42.
[101] Todd A, Orengo C, Thornton J. Evolution of protein function,
from a
e
e
52.
[81] Nochomovitz YD, Li H. Highly designable phenotypes and
mutational buffers emerge from a systematic mapping between
network topology and dynamic output. Proc Natl Acad Sci USA
2006;103:4180 e 5.
structural
perspective. Curr Opin Chem Biol
e
1999;3:548 e 56.
[102] Bastolla U, Porto M, Roman HE, Vendruscolo M. Connectivity
of neutral networks, overdispersion, and structural conservation
in protein evolution. J Mol Evol 2003;56:243 e 54.
Search WWH ::




Custom Search