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Results of
Professor Zuker's research has been very popular within the biotechnology
community, as their implications can help in invention of new drugs
and in optimizing old and designing new biotechnological methods.
For example, understanding mechanisms of RNA/protein complexes
formation can give leads to researchers to design drugs targeting
specific pathological processes. Also, nucleic acids folding data
is effectively used in the design of probes, PCR primers and molecular
beacons.
Recent work
in his laboratory includes the development of methods to predict
folding hybridization and melting curves for two strands of RNA
or DNA, and he is developing statistically based rules for RNA
folding. Algorithms invented by Professor Zuker are available on
applications pages section of
this site, which is so popular that the server registers as many
as 800,000 hits a month. Papers outlining his algorithms get cited
almost every day of the year. >> more
on Professor Zuker's research
Pioneering publications in Nucleic Acids Folding:
• P. Doty, H. Boedtker, J.R.
Fresco, R. Haselkorn and M. Litt, Secondary structure in ribonucleic
acids. Proc Natl Acad Sci USA 45 (1959), pp. 482–499.
• J.R. Fresco, B.M. Alberts and
P. Doty, Some molecular details of the secondary structure of ribonucleic
acid. Nature 188 (1960), pp. 98–101.
Online resources in Nucleic Acids Folding:
• Applications: M-Fold
Server
• Lectures on RNA
secondary structure prediction
Courses:
Various aspects of Nucleic Acid folding are covered in this
course given by Professor Zuker at RPI.
Publications of general interest:
Prof. Zuker's publications in Nucleic Acids Folding:
Journal article:
• M. Zuker. Calculating nucleic
acid secondary structure. Curr Opin Struct Biol. 10, 303-310, (2000)
•
M. Zuker. On Finding All Suboptimal Foldings of an RNA Molecule.
Science 244, 48-52 (1989)
•
A.B. Jacobson, R. Arora, M. Zuker, C. Priano, C.H. Lin &
D.R. Mills. Structural Plasticity in RNA and its Role in the Regulation
of Protein Translation in Coliphage Qß. J. Mol. Biol. 274,
589-600, (1998)
•
M. Zuker & A.B. Jacobson. Using Reliability Information
to Annotate RNA Secondary Structures. RNA 4, 669-679 (1998)
•
D.H. Mathews, J. Sabina, M. Zuker & DH Turner. Expanded
Sequence Dependence of Thermodynamic Parameters Improves Prediction
of RNA Secondary Structure J. Mol. Biol. 288, 911-940 (1999)
•
R.B. Lyngsø, M. Zuker & C.N.S. Pedersen. Fast evaluation
of internal loops in RNA secondary structure prediction. Bioinformatics
15, 440-445, (1999).
• V.
Moulton, M. Zuker, M. Steel, R. Pointon & D. Penny. Metrics
on RNA secondary structures. J. Computational Biology 7, 277-292,
(2000)
•
K. Kidd-Ljunggren, M. Zuker, I.L. Hofacker & A.H. Kidd.
The Hepatitis B Virus Pregenome: Prediction of RNA Structure and
Implications for the Emergence of Deletions. Intervirology 43,
154-164, (2000)
•
J.-M. Rouillard, C.J. Herbert & M. Zuker. OligoArray:
Genome-scale oligonucleotide design for microarrays. Bioinformatics
18 (3), 486-487, (2002)
•
A. Waugh, P. Gendron, R. Altman, J.W. Brown, D. Case, D. Gautheret,
S.C. Harvey, N. Leontis, J. Westbrook, E. Westhof, M. Zuker, F.
Major RNAML: A standard syntax for exchanging RNA information.
RNA 8 (6), 707-717, (2002)
Book chapters:
• M. Zuker, DH Mathews and DH
Turner, Algorithms and thermodynamics for RNA secondary structure
prediction: a practical guide. In: J. Barciszewski and B.F.C. Clark,
Editors, RNA Biochemistry and Biotechnology, Kluwer Academic Publishers,
Dordrecht (1999), pp. 11–43 [NATO Science Partnership Subseries
3: High Technology, Number 70.]
• M. Zuker, Prediction of RNA
secondary structure by energy minimization. In: A.M. Griffin and
H.G. Griffin, Editors, Computer Analysis of Sequence Data, part II,
vol 25, Humana Press Inc, Totowa, NJ (1994), pp. 267–294. .
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