Professor of Mathematical Sciences
Adjunct Professor, Institute for RNA Science and Technology,
Ph.D in Mathematics, May 1974, Massachusetts Institute of Technology
B.Sc., May 1970, McGill University
Dr. Zuker works on the development and implementation of algorithms
to predict nucleic acid folding and hybridization by free energy
minimization using empirically derived thermodynamic parameters.
Modeling and algorithm development have been closely coupled with the
derivation of nearest neighbor" and related energy rules.
Current work is focused on the computation of partition functions for
systems containing two molecules in solution that can fold as well as
hybridize with each other. Ensemble free energies, mole fractions of
different monomer and dimer species and base pair probabilities are
computed over a range of temperatures. These computations lead to the
prediction of UV absorbance (optical density) and heat capacity (Cp)
melting profiles that can be directly compared with experimental data.
A related project is the development of an algorithm named FASTH that
searches RNA or DNA sequence databases for optimal hybridization sites
for nucleic acid query sequences. Unlike traditional search algorithms,
such as BLASTN and FASTA, FASTH uses hybridization free energy as the
criterion for selection.
J. -M. Rouillard, C. J. Herbert & M. Zuker. OligoArray: Genome-scale oligonucleotide design for microarrays. Bioinformatics 18 (3), 486-487, (2002)
M. Zuker. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (13), 3406-3415, (2003)
R. A. Dimitrov & M. Zuker. Prediction of Hybridization and Melting for Double-Stranded Nucleic Acids. Biophysical J. 87, 215-226, (2004)
J. H. Mansfield, B. D. Harfe, R. Nissen, J. Obenauer, J. Srineel, A.
Chaudhuri, R. Farzan-Kashani, M. Zuker, A. E. Pasquinelli, G. Ruvkun, P.
A. Sharp, C. J. Tabin, M. T. McManus. MicroRNA-responsive 'sensor'
transgenes uncover Hox-like and other developmentally regulated patterns
of vertebrate microRNA expression. Nat Genet. 36 (10) 1079-83, (2004)
D. H. Mathews & M. Zuker. Predictive Methods Using RNA Sequences. In Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins A. Baxevanis and F. Ouellette eds., 3rd edition, John Wiley & Sons, New York, Chapter 7, (2005)
N. R. Markham & M. Zuker. DINAMelt Web Server for Nucleic Acid Melting Prediction. Nucleic Acids Res. 33, W577-W581, (2005)
UNAFold & OligoArrayAux
mfold_util (v 4.6) |
MATH-4010 Abstract Algebra
MATH-4100 Linear Algebra
MATH-2800 Discrete Structures
(518) 276-6382 (secretary)
Fax: (518) 276-4824
UNAFold web server at the SUNY Albany Institute for RNA Science and
http://unafold.math.rpi.edu/ (Personal Home Page)