Michael Zuker

Summary

Affiliation: Rensselaer Polytechnic Institute
Country: USA

Publications

  1. ncbi RNAML: a standard syntax for exchanging RNA information
    Allison Waugh
    Stanford Medical Informatics, Stanford University Medical Center, California 94305, USA
    RNA 8:707-17. 2002
  2. ncbi UNAFold: software for nucleic acid folding and hybridization
    Nicholas R Markham
    Xerox Litigation Services, Albany, NY, USA
    Methods Mol Biol 453:3-31. 2008
  3. ncbi Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
  4. ncbi DINAMelt web server for nucleic acid melting prediction
    Nicholas R Markham
    Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY 12180-3590, USA
    Nucleic Acids Res 33:W577-81. 2005
  5. ncbi Prediction of hybridization and melting for double-stranded nucleic acids
    Roumen A Dimitrov
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
    Biophys J 87:215-26. 2004
  6. ncbi OligoArray: genome-scale oligonucleotide design for microarrays
    Jean Marie Rouillard
    Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109 2136, USA
    Bioinformatics 18:486-7. 2002
  7. ncbi OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
    Jean Marie Rouillard
    Department of Chemical Engineering, University of Michigan, H H Dow, Ann Arbor, MI 48109, USA
    Nucleic Acids Res 31:3057-62. 2003
  8. ncbi Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    David H Mathews
    Center for Human Genetics and Molecular Pediatric Disease, The Aab Institute of Biomedical Sciences, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 703, Rochester, NY 14642, USA
    Proc Natl Acad Sci U S A 101:7287-92. 2004
  9. ncbi RNA secondary structure prediction
    David H Mathews
    University of Rochester, Rochester, New York, USA
    Curr Protoc Nucleic Acid Chem . 2007

Research Grants

  1. ALGORITHMS, THERMODYNAMICS AND STATISTICS FOR RNA FOLDIN
    Michael Zuker; Fiscal Year: 2003

Collaborators

Detail Information

Publications9

  1. ncbi RNAML: a standard syntax for exchanging RNA information
    Allison Waugh
    Stanford Medical Informatics, Stanford University Medical Center, California 94305, USA
    RNA 8:707-17. 2002
    ..In addition to the various generic packages that exist to read and interpret XML formats, an XML processor was developed and put in the open-source MC-Core library for nucleic acid and protein structure computer manipulation...
  2. ncbi UNAFold: software for nucleic acid folding and hybridization
    Nicholas R Markham
    Xerox Litigation Services, Albany, NY, USA
    Methods Mol Biol 453:3-31. 2008
    ..Users are encouraged to create their own scripts to supplement what comes with the package. This evolving software is available for download at http://www.bioinfo.rpi.edu/applications/hybrid/download.php ...
  3. ncbi Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
    ..The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'...
  4. ncbi DINAMelt web server for nucleic acid melting prediction
    Nicholas R Markham
    Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY 12180-3590, USA
    Nucleic Acids Res 33:W577-81. 2005
    ..This server is connected to an active research program and should evolve as new theory and software are developed. The server URL is http://www.bioinfo.rpi.edu/applications/hybrid/...
  5. ncbi Prediction of hybridization and melting for double-stranded nucleic acids
    Roumen A Dimitrov
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
    Biophys J 87:215-26. 2004
    ....
  6. ncbi OligoArray: genome-scale oligonucleotide design for microarrays
    Jean Marie Rouillard
    Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109 2136, USA
    Bioinformatics 18:486-7. 2002
    ..AVAILABILITY: The program code is distributed under the GNU General Public License and is freely available for non-profit use via request from the authors...
  7. ncbi OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
    Jean Marie Rouillard
    Department of Chemical Engineering, University of Michigan, H H Dow, Ann Arbor, MI 48109, USA
    Nucleic Acids Res 31:3057-62. 2003
    ..OligoArray 2.0 was used to design 75 764 oligonucleotides representing 26 140 transcripts from Arabidopsis thaliana. Among this set, we provide at least one specific oligonucleotide for 93% of these transcripts...
  8. ncbi Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    David H Mathews
    Center for Human Genetics and Molecular Pediatric Disease, The Aab Institute of Biomedical Sciences, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 703, Rochester, NY 14642, USA
    Proc Natl Acad Sci U S A 101:7287-92. 2004
    ..For the 11 sequences with <6% pseudoknotted base pairs, structures predicted with constraints from chemical modification contain on average 84% of known canonical base pairs...
  9. ncbi RNA secondary structure prediction
    David H Mathews
    University of Rochester, Rochester, New York, USA
    Curr Protoc Nucleic Acid Chem . 2007
    ..The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted. Prediction of high-affinity oligonucleotide binding sites to a structured RNA target is also presented...

Research Grants4

  1. ALGORITHMS, THERMODYNAMICS AND STATISTICS FOR RNA FOLDIN
    Michael Zuker; Fiscal Year: 2003
    ..Partition function computations will be extended to allow folding constraints and to compute probabilities of foldings similar to a given one. ..