Biomedical Engineering Reference
In-Depth Information
51. Han K, Kim D, Kim HJ. 1999. A vector-based method for drawing RNA secondary structure.
Bioinformatics
15
:286-297.
52. Haslinger C. 2001.
Prediction algorithms for restricted RNA pseudoknots
. PhD dissertation,
University of Vienna, Faculty of Sciences.
53. Höbartner C, Micura R. 2003. Bistable secondary structures of small RNAs and their structural
probing by comparative imino proton NMR spectroscopy.
J Mol Biol
325
:421-431.
54. Höchsmann M. 2001. Tree and forrest alignments: an algebraic dynamic programming ap-
proach for aligning trees and forests. MSc thesis. University of Bielefeld, Germany.
55. Hofacker IL, Fekete M, Stadler PF. 2002. Secondary structure prediction for aligned RNA
sequences.
J Mol Biol
319
:1059-1066.
56. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S, Tacker M, Schuster P. 1994. Fast folding
and comparison of RNA secondary structures.
Monatsh Chem
125
:167-188.
57. Hofacker IL, Huynen MA, Stadler PF, Stolorz PE. 1996. Knowledge discovery in RNA se-
quence families of HIV using scalable computers. In
Proceedings of the 2nd international con-
ference on knowledge discovery and data mining, Portland, OR
, pp. 20-25. Ed. E Simoudis, J
Han, U Fayyad. AAAI Press, Menlo Park, CA.
58. Hofacker IL, and PS, Stadler PF. 1998. Combinatorics of RNA secondary structures.
Discr
Appl Math
89
:177-207.
59. Hofacker IL, Fekete M, Flamm C, Huynen MA, Rauscher S, Stolorz PE, Stadler PF. 1998.
Automatic detection of conserved RNA structure elements in complete RNA virus genomes.
Nucleic Acids Res
26
:3825-3836.
60. Hofacker IL, Stadler PF. 1999. Automatic detection of conserved base pairing patterns in RNA
virus genomes.
Comput Chem
23
:401-414.
61. Hogeweg P, Hesper B. 1984. Energy directed folding of RNA sequences.
Nucleic Acids Res
12
:67-74.
62. Huez I, Créancier L, Audigier S, Gensac M-C, Prats A-C, Prats H. 1998. Two independent
internal ribosome entry sites are involved in translation initiation of vascular endothelial
growth factor mRNA.
Mol Cell Biol
18
:6178-6190.
63. Huynen MA, Stadler PF, Fontana W. 1996. Smoothness within ruggedness: the role of neutral-
ity in adaptation.
Proc Natl Acad Sci USA
93
:397-401.
64. Huynen MA, Perelson AS, Viera WA, Stadler PF. 1996. Base pairing probabilities in a com-
plete HIV-1 RNA.
J Comput Biol
3:253-274.
65. Huynen MA. 1996. Exploring phenotype space through neutral evolution.
J Mol Evol
43
:165-
169.
66. Isambert H, Siggia ED. 2000. Modeling RNA folding paths with pseudoknots: application to
hepatitis delta virus ribozyme.
Proc Natl Acad Sci USA
97
:6515-6520.
67. Jacobs GH, Rackham O, Stockwell PA, Tate W, and Brown CM. 2002. Transterm: a database
of mRNAs and translational control elements.
Nucleic Acids Res
30
:310-311.
68. Jacobson AB, Zuker M. 1993. Structural analysis by energy dot plot of large mRNA.
J Mol
Biol
233
:261-269.
69. Jaeger JA, Turner DH, Zuker M. 1989. Improved predictions of secondary structures for RNA.
Proc Natl Acad Sci USA
86
:7706-7710.
70. Juan V, Wilson C. 1999. RNA secondary structure prediction based on free energy and phy-
logenetic analysis.
J Mol Biol
289
:935-947.
71. Keefe AD, Szostak JW. 2001. Functional proteins from a random-sequence library.
Nature
410
:715-718.
72.
Keiler KC, Shapiro L, Williams KP. 2000. tmRNAs that encode proteolysis-inducing tags are
found in all known bacterial genomes: A two-piece tmRNA functions in
Caulobacter
.
Proc
Natl Acad Sci USA
97
:7778-7783.
73.
Kidd-Ljunggren K, Zuker M, Hofacker IL, Kidd AH. 2000. The hepatitis B virus pregenome:
prediction of RNA structure and implications for the emergence of deletions.
Intervirology
43
:154-164.
