Zasha Weinberg

Summary

Affiliation: Yale University
Country: USA

Publications

  1. pmc 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
  2. pmc Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
    Zasha Weinberg
    Howard Hughes Medical Institute, Yale University, New Haven, CT 06520 8103, USA
    Genome Biol 11:R31. 2010
  3. pmc R2R--software to speed the depiction of aesthetic consensus RNA secondary structures
    Zasha Weinberg
    Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520 8103, USA
    BMC Bioinformatics 12:3. 2011
  4. pmc 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
  5. pmc 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
  6. pmc Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'
    Michelle M Meyer
    Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
    BMC Genomics 10:268. 2009
  7. pmc 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
  8. doi request reprint Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis
    Zasha Weinberg
    Howard Hughes Medical Institute, New Haven, Connecticut 06520 8103, USA
    Nature 462:656-9. 2009
  9. doi request reprint An allosteric self-splicing ribozyme triggered by a bacterial second messenger
    Elaine R Lee
    Department of Molecular, Cellular, and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520 8103, USA
    Science 329:845-8. 2010
  10. doi request reprint Widespread genetic switches and toxicity resistance proteins for fluoride
    Jenny L Baker
    Department of Chemistry, Yale University, Box 208103, New Haven, CT 06520, USA
    Science 335:233-5. 2012

Collaborators

Detail Information

Publications21

  1. pmc 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...
  2. pmc Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
    Zasha Weinberg
    Howard Hughes Medical Institute, Yale University, New Haven, CT 06520 8103, USA
    Genome Biol 11:R31. 2010
    ..Structured RNAs can be detected by comparative genomics, in which homologous sequences are identified and inspected for mutations that conserve RNA secondary structure...
  3. pmc R2R--software to speed the depiction of aesthetic consensus RNA secondary structures
    Zasha Weinberg
    Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520 8103, USA
    BMC Bioinformatics 12:3. 2011
    ..Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams...
  4. pmc 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...
  5. pmc 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...
  6. pmc Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'
    Michelle M Meyer
    Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
    BMC Genomics 10:268. 2009
    ..The genome of 'Candidatus Pelagibacter ubique' HTCC 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. It is also small, contains little non-coding DNA, and has strikingly low GC content...
  7. pmc 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...
  8. doi request reprint Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis
    Zasha Weinberg
    Howard Hughes Medical Institute, New Haven, Connecticut 06520 8103, USA
    Nature 462:656-9. 2009
    ....
  9. doi request reprint An allosteric self-splicing ribozyme triggered by a bacterial second messenger
    Elaine R Lee
    Department of Molecular, Cellular, and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520 8103, USA
    Science 329:845-8. 2010
    ..Our findings indicate that some self-splicing ribozymes are not selfish elements but are harnessed by cells as metabolite sensors and genetic regulators...
  10. doi request reprint Widespread genetic switches and toxicity resistance proteins for fluoride
    Jenny L Baker
    Department of Chemistry, Yale University, Box 208103, New Haven, CT 06520, USA
    Science 335:233-5. 2012
    ..Our findings indicate that most organisms are naturally exposed to toxic levels of fluoride and that many species use fluoride-sensing RNAs to control the expression of proteins that alleviate the deleterious effects of this anion...
  11. pmc A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate
    Tyler D Ames
    Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520 8103, USA
    Chem Biol 17:681-5. 2010
    ..These findings expand the number of coenzymes that are directly sensed by RNA and reveal possible riboswitch-controlled regulons that respond to changes in single-carbon metabolism...
  12. pmc Riboswitches in eubacteria sense the second messenger c-di-AMP
    James W Nelson
    Department of Chemistry, Yale University, New Haven, Connecticut, USA
    Nat Chem Biol 9:834-9. 2013
    ..Our findings resolve the mystery regarding the primary ligand for this extremely common riboswitch class and expose a major portion of the super-regulon of genes that are controlled by the widespread bacterial second messenger c-di-AMP. ..
  13. pmc Identification of hammerhead ribozymes in all domains of life reveals novel structural variations
    Jonathan Perreault
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
    PLoS Comput Biol 7:e1002031. 2011
    ..In rare instances, nucleotide variation occurs at positions within the catalytic core that are otherwise strictly conserved, suggesting that core mutations are occasionally tolerated or preferred...
  14. pmc A widespread self-cleaving ribozyme class is revealed by bioinformatics
    Adam Roth
    1 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA 2 Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA 3
    Nat Chem Biol 10:56-60. 2014
    ..The twister ribozyme motif provides another example of a natural RNA catalyst and calls attention to the potentially varied biological roles of this and other classes of widely distributed self-cleaving RNAs. ..
  15. pmc Fluoride resistance and transport by riboswitch-controlled CLC antiporters
    Randy B Stockbridge
    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02454, USA
    Proc Natl Acad Sci U S A 109:15289-94. 2012
    ..Finally, F(-)/H(+) exchange occurs with 1:1 stoichiometry, in contrast to the usual value of 2:1...
  16. ncbi request reprint 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...
  17. pmc Small, highly active DNAs that hydrolyze DNA
    Hongzhou Gu
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
    J Am Chem Soc 135:9121-9. 2013
    ....
  18. pmc 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...
  19. ncbi request reprint 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...
  20. ncbi request reprint 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
    ..Previous tools fall short of this goal...
  21. ncbi request reprint 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...