Zasha Weinberg

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. ncbi Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy
    Zasha Weinberg
    Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
    Bioinformatics 20:i334-41. 2004
  2. ncbi Sequence-based heuristics for faster annotation of non-coding RNA families
    Zasha Weinberg
    Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
    Bioinformatics 22:35-9. 2006
  3. ncbi A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes
    Zizhen Yao
    Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA
    PLoS Comput Biol 3:e126. 2007
  4. ncbi CMfinder--a covariance model based RNA motif finding algorithm
    Zizhen Yao
    Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195 2350, USA
    Bioinformatics 22:445-52. 2006
  5. ncbi Finding non-coding RNAs through genome-scale clustering
    Huei Hun Tseng
    Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195 2350, USA
    J Bioinform Comput Biol 7:373-88. 2009
  6. ncbi 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter
    Jeffrey E Barrick
    Department of Molecular, Cellular, and Developmental Biology, Yale University, P O Box 208103, New Haven, CT 06520, USA
    RNA 11:774-84. 2005
  7. ncbi Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline
    Zasha Weinberg
    Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520 8103, USA
    Nucleic Acids Res 35:4809-19. 2007
  8. ncbi A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism
    Elizabeth E Regulski
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Mol Microbiol 68:918-32. 2008
  9. ncbi A glycine-dependent riboswitch that uses cooperative binding to control gene expression
    Maumita Mandal
    Department of Molecular, Cellular, and Developmental Biology, Yale University, Post Office Box 208103, New Haven, CT 06520 8103, USA
    Science 306:275-9. 2004
  10. ncbi The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches
    Zasha Weinberg
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 8103, USA
    RNA 14:822-8. 2008

Detail Information

Publications11

  1. ncbi Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy
    Zasha Weinberg
    Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
    Bioinformatics 20:i334-41. 2004
    ..Current heuristic filters are also expected to perform poorly on such families...
  2. ncbi Sequence-based heuristics for faster annotation of non-coding RNA families
    Zasha Weinberg
    Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
    Bioinformatics 22:35-9. 2006
    ..However, these rigorous filters make searches slower than heuristics could be...
  3. ncbi A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes
    Zizhen Yao
    Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA
    PLoS Comput Biol 3:e126. 2007
    ..Of the ncRNA candidates not in Rfam, we find compelling evidence that some of them are functional, and analyze several potential ribosomal protein leaders in depth...
  4. ncbi CMfinder--a covariance model based RNA motif finding algorithm
    Zizhen Yao
    Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195 2350, USA
    Bioinformatics 22:445-52. 2006
    ..We have used this approach to obtain highly accurate covariance models of known RNA motifs based on small numbers of related sequences, which identified homologs in deeply-diverged species...
  5. ncbi Finding non-coding RNAs through genome-scale clustering
    Huei Hun Tseng
    Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195 2350, USA
    J Bioinform Comput Biol 7:373-88. 2009
    ..Hence, our method shows promise for discovering new families of ncRNA...
  6. ncbi 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter
    Jeffrey E Barrick
    Department of Molecular, Cellular, and Developmental Biology, Yale University, P O Box 208103, New Haven, CT 06520, USA
    RNA 11:774-84. 2005
    ..coli ygfA gene encoding a putative methenyltetrahydrofolate synthetase. The prevalence and robust expression of 6S RNAs emphasize their critical role in bacterial adaptation...
  7. ncbi Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline
    Zasha Weinberg
    Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520 8103, USA
    Nucleic Acids Res 35:4809-19. 2007
    ..These candidate RNAs add to the growing list of RNA motifs involved in multiple cellular processes, and suggest that many additional RNAs remain to be discovered...
  8. ncbi A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism
    Elizabeth E Regulski
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Mol Microbiol 68:918-32. 2008
    ..Furthermore, we identify variants of this RNA that are likely to be triggered by the related tungsten cofactor (Tuco), which carries tungsten in place of molybdenum as the metal constituent...
  9. ncbi A glycine-dependent riboswitch that uses cooperative binding to control gene expression
    Maumita Mandal
    Department of Molecular, Cellular, and Developmental Biology, Yale University, Post Office Box 208103, New Haven, CT 06520 8103, USA
    Science 306:275-9. 2004
    ..Thus, riboswitches perform key regulatory roles and exhibit complex performance characteristics that previously had been observed only with protein factors...
  10. ncbi The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches
    Zasha Weinberg
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 8103, USA
    RNA 14:822-8. 2008
    ..Our findings support the view that RNA has considerable structural versatility and reveal that riboswitches exploit this potential to expand the scope of RNA in genetic regulation...
  11. ncbi Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote
    Jonathan A Eisen
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Biol 4:e286. 2006
    ..thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance...