📄 node19.html
字号:
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN"><!--Converted with LaTeX2HTML 98.1p1 release (March 2nd, 1998)originally by Nikos Drakos (nikos@cbl.leeds.ac.uk), CBLU, University of Leeds* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan* with significant contributions from: Jens Lippmann, Marek Rouchal, Martin Wilck and others --><HTML><HEAD><TITLE>Bibliography</TITLE><META NAME="description" CONTENT="Bibliography"><META NAME="keywords" CONTENT="FEBS98-html"><META NAME="resource-type" CONTENT="document"><META NAME="distribution" CONTENT="global"><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1"><LINK REL="STYLESHEET" HREF="FEBS98-html.css"><LINK REL="next" HREF="node20.html"><LINK REL="previous" HREF="node18.html"><LINK REL="up" HREF="FEBS98-html.html"><LINK REL="next" HREF="node20.html"></HEAD><BODY BGCOLOR=#FFDEAD TEXT=#202020 LINK=#800000 ALINK=#ffff00 VLINK=#353976><!--Navigation Panel--><A NAME="tex2html271" HREF="node20.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html268" HREF="FEBS98-html.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html262" HREF="node18.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html270" HREF="node1.html"><IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents" SRC="img/contents_motif.gif"></A> <BR><B> Next:</B> <A NAME="tex2html272" HREF="node20.html">About this document ...</A><B> Up:</B> <A NAME="tex2html269" HREF="FEBS98-html.html">Algorithms and Thermodynamics for</A><B> Previous:</B> <A NAME="tex2html263" HREF="node18.html">Acknowledgment</A><BR><BR><!--End of Navigation Panel--><H2><A NAME="SECTIONREF">Bibliography</A></H2><DL COMPACT><DD><P></P><DT><A NAME="MACP9001"><STRONG>1</STRONG></A><DD><U>P.M. MacDonald.</U><BR><EM>Bicoid</EM> mRNA localization signal: phylogenetic conservation of function and RNA secondary structure.<BR><EM>Development</EM>, 110:161-171, 1990.<P></P><DT><A NAME="SMIM9001"><STRONG>2</STRONG></A><DD><U>M.H. de Smit and J. van Duin.</U><BR>Control of prokaryotic translation initiation by mRNA secondary structure.<BR><EM>Progress in Nucleic Acid Research in Molecular Biology</EM>, 38:1-35, 1990.<P></P><DT><A NAME="MILD9001"><STRONG>3</STRONG></A><DD><U>D.R. Mills, C. Priano, P.A. Merz, and B.D. Binderow.</U><BR>Q<IMG WIDTH="13" HEIGHT="29" ALIGN="MIDDLE" BORDER="0" SRC="img127.gif" ALT="$\beta$">RNA bacteriophage: mapping cis-acting elements within an RNA genome.<BR><EM>J. Virol.</EM>, 64:3872-3881, 1990.<P></P><DT><A NAME="BRAC9001"><STRONG>4</STRONG></A><DD><U>C.I. Brannan, E.C. Dees, R.S. Ingram, and S.M. Tilghman.</U><BR>The product of the h19 gene may function as an RNA.<BR><EM>Mol. Cell. Biol.</EM>, 10:28-36, 1990.<P></P><DT><A NAME="BROC9101"><STRONG>5</STRONG></A><DD><U>C.J. Brown, A. Ballabio, J.L. Rupert, R.G. Lafreniere, M. Grompe, R. Tonlorenzi, and H.F. Willard.</U><BR>A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome.<BR><EM>Nature</EM>, 349:38-44, 1991.<P></P><DT><A NAME="CECT8601"><STRONG>6</STRONG></A><DD><U>T.R. Cech and B.L. Bass.</U><BR>Biological catalysis by RNA.<BR><EM>Ann. Rev. Biochem.</EM>, 55:599-629, 1986.<P></P><DT><A NAME="CECT9001"><STRONG>7</STRONG></A><DD><U>T.R. Cech.</U><BR>Self-splicing of group I introns.<BR><EM>Ann. Rev. Biochem.</EM>, 59:543-568, 1990.<P></P><DT><A NAME="DARS9201"><STRONG>8</STRONG></A><DD><U>S.C. Darr, J.W. Brown, and N.R. Pace.</U><BR>The varieties of Ribonuclease P.<BR><EM>Trends Biochem. Sci.</EM>, 17:178-182, 1992.<P></P><DT><A NAME="KIMS7401"><STRONG>9</STRONG></A><DD><U>S.H. Kim, F.L. Suddath, G.J. Quigley, A. McPherson, and J.L. Sussman.</U><BR>Three dimensional tertiary structure of yeast phenylalanine transfer RNA.<BR><EM>Science</EM>, 185:435-440, 1974.<P></P><DT><A NAME="ROBJ7401"><STRONG>10</STRONG></A><DD><U>J.D. Robertus, J.E. Ladner, J.T. Finch, D. Rhodes, and R.S. Brown.</U><BR>Structure of yeast phenylalanine tRNA at 3 Å resolution.<BR><EM>Nature</EM>, 250:546-551, 1974.<P></P><DT><A NAME="PLEH9401"><STRONG>11</STRONG></A><DD><U>H.W. Pley, K.M Flaherty, and D.B. McKay.</U><BR>Three-dimensional structure of a hammerhead ribozyme.<BR><EM>Nature</EM>, 372:68-74, 1994.<P></P><DT><A NAME="GUTR9501"><STRONG>12</STRONG></A><DD><U>R.R. Gutell, 1995.</U><BR>personal communication.<P></P><DT><A NAME="MICF9001"><STRONG>13</STRONG></A><DD><U>F. Michel and E. Westhof.</U><BR>Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis.<BR><EM>J. Mol. Biol.</EM>, 216:585-610, 1990.<P></P><DT><A NAME="MAJF9101"><STRONG>14</STRONG></A><DD><U>F. Major, M. Turcotte, D. Gautheret, G. Lapalme, E. Fillion, and R.J. Cedergren.</U><BR>The combination of symbolic and numerical computation for three- dimensional modeling of RNA.<BR><EM>Science</EM>, 253:1255-1260, 1991.<P></P><DT><A NAME="MAJF9301"><STRONG>15</STRONG></A><DD><U>F. Major, D. Gautheret, and R. Cedergren.</U><BR>Reproducing the three-dimensional structure of a tRNA molecule from structural constraints.<BR><EM>Proc. Natl. Acad. Sci. USA</EM>, 90:9408-9412, 1993.<P></P><DT><A NAME="ZUKM8901"><STRONG>16</STRONG></A><DD><U>M. Zuker.</U><BR>On finding all suboptimal foldings of an RNA molecule.<BR><EM>Science</EM>, 244:48-52, 1989.<P></P><DT><A NAME="JAEJ8901"><STRONG>17</STRONG></A><DD><U>J.A. Jaeger, D.H. Turner, and M. Zuker.</U><BR>Improved predictions of secondary structures for RNA.<BR><EM>Proc. Natl. Acad. Sci. USA.</EM>, 86:7706-7710, 1989.<P></P><DT><A NAME="JAEJ9001"><STRONG>18</STRONG></A><DD><U>J.A. Jaeger, D.H. Turner, and M. Zuker.</U><BR>Predicting optimal and suboptimal secondary structure for RNA.<BR><EM>Meth. Enzymol.</EM>, 183:281-306, 1990.<P></P><DT><A NAME="ZUKM9401"><STRONG>19</STRONG></A><DD><U>M. Zuker.</U><BR><EM>Prediction of RNA Secondary Strcture by Energy Minimization.</EM>, volume 25 of <EM>Computer Analysis of Sequence Data, Part II, A.M. Griffin & H.G Griffin, Eds.</EM>, chapter 23, pages 267-294.<BR>CRC Press, Inc., Totowa, NJ, 1994.<P></P><DT><A NAME="MATD9801"><STRONG>20</STRONG></A><DD><U>D.H. Mathews, T.C. Andre, J. Kim, D.H. Turner, and M. Zuker.</U><BR><EM>An Updated Recursive Algorithm for RNA Secondary Structure Prediction with Improved Free Energy Parameters.</EM>, chapter 15, pages 246-257.<BR>American Chemical Society Symposium Series 682. American Chemical Society, Washington, DC, 1998.<P></P><DT><A NAME="SAND8301"><STRONG>21</STRONG></A><DD><U>D. Sankoff, J.B. Kruskal, S. Mainville, and R.J. Cedergren.</U><BR><EM>Fast algorithms to determine RNA secondary structures containing multiple loops.</EM>, chapter 3, pages 93-120.<BR>Time warps, string edits, and macromolecules: the theory and practice of sequence comparison, Sankoff D., Kruskal J.B., Eds. Addison-Wesley, Reading, MA, 1983.<P></P><DT><A NAME="ZUKM8401"><STRONG>22</STRONG></A><DD><U>M. Zuker and D. Sankoff.</U><BR>RNA secondary structures and their prediction.<BR><EM>Bull. Math. Biol.</EM>, 46:591-621, 1984.<P></P><DT><A NAME="ZUKM8601"><STRONG>23</STRONG></A><DD><U>M. Zuker.</U><BR>RNA folding prediction: The continued need for interaction between biologists and mathematicians.<BR><EM>Lectures on Mathematics in the Life Sciences</EM>, 17:86-123, 1986.<P></P><DT><A NAME="PLEC8901"><STRONG>24</STRONG></A><DD><U>C.W. Pleij and L. Bosch.</U><BR>RNA pseudoknots: structure, detection, and prediction.<BR><EM>Meth. Enzymol.</EM>, 180:289-303, 1989.<P></P><DT><A NAME="ABRJ9001"><STRONG>25</STRONG></A><DD><U>J.P.Abrahams, M. van den Berg, E. van Batenburg, and C.W. Pleij.</U><BR>Prediction of RNA secondary structure, including pseudoknotting, by computer simulation.<BR><EM>Nucleic Acids Res.</EM>, 18:3035-3044, 1990.<P></P><DT><A NAME="GUTR9001"><STRONG>26</STRONG></A><DD><U>R.R. Gutell and C.R. Woese.</U><BR>Higher order structural elements in ribosomal RNAs: Pseudo-knots and the use of noncanonical pairs.<BR><EM>Proc. Natl. Acad. Sci. USA</EM>, 87:663-667, 1990.<P></P><DT><A NAME="DAME9201"><STRONG>27</STRONG></A><DD><U>E. Dam, K. Pleij, and D. Draper.</U><BR>Structural and functional aspects of RNA pseudoknots.<BR><EM>Biochemistry</EM>, 31:11665-11676, 1992.<P></P><DT><A NAME="PLEC9401"><STRONG>28</STRONG></A><DD><U>C.W. Pleij.</U><BR>RNA pseudoknots.<BR><EM>Curr. Opin. Struct. Biol.</EM>, 4:337-344, 1994.<P></P><DT><A NAME="DUZ9601"><STRONG>29</STRONG></A><DD><U>Z. Du, D.P. Giedroc, and D.W. Hoffman.</U><BR>Structure of the autoregulatory pseudoknot within the gene 32 messenger RNA of bacteriophages T2 and T6: A model for a possible family of structurally related RNA pseudoknots.<BR><EM>Biochemistry</EM>, 35(13):4187-4198, 1996.<P></P><DT><A NAME="JACH5001"><STRONG>30</STRONG></A><DD><U>H. Jacobson and W.H. Stockmayer.</U><BR>Intramolecular reaction in polycondensations. I. The theory of linear systems.<BR><EM>J. Chem. Phys.</EM>, 18:1600-1606, 1950.<P></P><DT><A NAME="FRES8601"><STRONG>31</STRONG></A><DD><U>S.M. Freier, R. Kierzek, J.A. Jaeger, N. Sugimoto, M.H. Caruthers, T. Neilson, and D.H. Turner.</U><BR>Improved free-energy parameters for predictions of RNA duplex stability.<BR><EM>Proc. Natl. Acad. Sci. USA</EM>, 83:9373-9377, 1986.<P></P><DT><A NAME="TURD8701"><STRONG>32</STRONG></A><DD><U>D.H. Turner, N. Sugimoto, J.A. Jaeger, C.E. Longfellow, S.M. Freier, and R. Kierzek.</U><BR>Improved parameters for prediction of RNA structure.<BR><EM>Cold Spring Harb. Symp. Quant. Biol.</EM>, 52:123-133, 1987.<P></P><DT><A NAME="TURD8801"><STRONG>33</STRONG></A><DD><U>D.H. Turner, N. Sugimoto, and S.M. Freier.</U><BR>RNA structure prediction.<BR><EM>Annu. Rev. Biophys. Biophys. Chem.</EM>, 17:167-192, 1988.<P></P><DT><A NAME="WUM9501"><STRONG>34</STRONG></A><DD><U>M. Wu, J.A. McDowell, and D.H. Turner.</U><BR>A periodic table of symmetric tandem mismatches in RNA.<BR><EM>Biochemistry</EM>, 34:3204-3211, 1995.<P></P><DT><A NAME="WALA9401"><STRONG>35</STRONG></A><DD><U>A.E. Walter, D.H. Turner, J. Kim, M.H. Lyttle, P. Muller, D.H. Mathews, and M. Zuker.</U><BR>Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.<BR><EM>Proc Natl Acad Sci USA</EM>, 91:9218-9222, 1994.<P></P><DT><A NAME="SANJ9801"><STRONG>36</STRONG></A><DD><U>J.Jr. SantaLucia.</U><BR>A unified view of polymer, dumbbell, and oligonucleotide DNAnearest-neighbor thermodynamics.<BR><EM>Proc. Natl. Acad. Sci. USA</EM>, 95:1460-1465, 1998.<P></P><DT><A NAME="SUGN9501"><STRONG>37</STRONG></A><DD><U>N. Sugimoto, S. Nakano, M. Katoh, A. Matsumura, H. Nakamuta, T. Ohmichi, M. Yoneyama, and M. Sasaki.</U><BR>Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes.<BR><EM>Biochemistry</EM>, 34:11211-11216, 1995.<P></P><DT><A NAME="ZUKM9801"><STRONG>38</STRONG></A><DD><U>M. Zuker and A.B. Jacobson.</U><BR>Using Reliability Information to Annotate RNA Secondary Structures.<BR><EM>RNA</EM>, 4:669-679, 1998.<P></P><DT><A NAME="BEAR8101"><STRONG>39</STRONG></A><DD><U>R.C. Beach.</U><BR><EM>The Unified Graphics System for Fortran 77 Programming Manual.</EM><BR>Stanford Linear Accelerator Center Computational Research Group, Stanford, CA, 1981.<BR>Technical Memo 203.<P></P><DT><A NAME="ZUKM9102"><STRONG>40</STRONG></A><DD><U>M. Zuker, J.A. Jaeger, and D.H. Turner.</U><BR>A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison.<BR><EM>Nucleic Acids Res.</EM>, 19:2707-2714, 1991.<P></P><DT><A NAME="BRUR8801"><STRONG>41</STRONG></A><DD><U>R.E. Bruccoleri and G. Heinrich.</U><BR>An improved algorithm for nucleic acid secondary structure display.<BR><EM>Comput. Appl. Biosci.</EM>, 4:167-173, 1988.</DL><P><BR><HR><ADDRESS><TABLE><TR><TD><IMG SRC=img/shield16.gif HSPACE=20></TD><TD><I>Michael Zuker <BR>Institute for Biomedical Computing<BR>Washington University in St. Louis<BR>1998-12-05</I></TD></TR></TABLE></ADDRESS></BODY></HTML>⌨️ 快捷键说明
复制代码
Ctrl + C
搜索代码
Ctrl + F
全屏模式
F11
切换主题
Ctrl + Shift + D
显示快捷键
?
增大字号
Ctrl + =
减小字号
Ctrl + -