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Mathematical Sciences
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Michael Zuker
Department of Mathematical Sciences Faculty:

Kristin Bennett
Jennifer Blue
Mohamed Boudjelkha
Margaret Cheney
Donald Drew
Joseph Ecker
Joseph E. Flaherty
Isom Herron
Mark Holmes
David Isaacson
Ashwani Kapila
Maya Kiehl
Gregor Kovacic
Peter Kramer
Fengyan Li
Chjan Lim
Yuri Lvov
Harry McLaughlin
Joyce McLaughlin
John Mitchell
Clifford Nolan
Bruce Piper
Victor Roytburd
Lester Rubenfeld
David Schmidt
Donald Schwendeman
William Siegmann
Michael Zuker

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Mathematical Sciences Faculty
Michael Zuker

Professor of Mathematical Sciences
Adjunct Professor, Institute for RNA Science and Technology, SUNY Albany

Education:

Ph.D in Mathematics, May 1974, Massachusetts Institute of Technology
B.Sc., May 1970, McGill University

Research Areas:

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.

Selected Publications:

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)

Web Servers:

DINAMelt   |   mfold

Download Software:

UNAFold & OligoArrayAux   |   mfold_util   (v 4.6)   |   mfold

Teaching:

MATH-4010   Abstract Algebra
MATH-4100   Linear Algebra
MATH-2800   Discrete Structures

Contact Information:

zukerm@rpi.edu
(518) 276-6382 (secretary)
Fax: (518) 276-4824

More Info:

UNAFold web server at the SUNY Albany Institute for RNA Science and Technology
http://mfold.rna.albany.edu

http://unafold.math.rpi.edu/ (Personal Home Page)

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