Education and Training

B.Sc. McGill University, May 1970

Ph.D. Massachusetts Institute of Technology, May 1974
Mathematics

Contact

E-mail: zukerm@rpi.edu
Website: http://frontend.bioinfo.rpi.edu/zukerm/home.html
Tel: (518) 276-6382
Fax: (518) 276-4824

Office: Amos Eaton Rm. 331

Rensselaer Polytechnic Institute
110 8th Street
Troy, NY 12180

Research Interests

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)