Joseph T Wade

Summary

Affiliation: Wadsworth Center
Country: USA

Publications

  1. pmc FRUIT, a scar-free system for targeted chromosomal mutagenesis, epitope tagging, and promoter replacement in Escherichia coli and Salmonella enterica
    Anne M Stringer
    Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
    PLoS ONE 7:e44841. 2012
  2. pmc Widespread antisense transcription in Escherichia coli
    James E Dornenburg
    Wadsworth Center, New York State Department of Health, Albany, New York, USA
    MBio 1:. 2010
  3. pmc Non-canonical protein-DNA interactions identified by ChIP are not artifacts
    Richard P Bonocora
    Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
    BMC Genomics 14:254. 2013
  4. pmc The transition from transcriptional initiation to elongation
    Joseph T Wade
    Wadsworth Center, New York State Department of Health, Albany, NY 12208, United States
    Curr Opin Genet Dev 18:130-6. 2008
  5. pmc Genome-Scale Analyses of Escherichia coli and Salmonella enterica AraC Reveal Noncanonical Targets and an Expanded Core Regulon
    Anne M Stringer
    Wadsworth Center, New York State Department of Health, Albany, New York, USA
    J Bacteriol 196:660-71. 2014
  6. pmc Identification of HilD-regulated genes in Salmonella enterica serovar Typhimurium
    Brianna L Petrone
    Wadsworth Center, New York State Department of Health, Albany, New York, USA
    J Bacteriol 196:1094-101. 2014
  7. ncbi request reprint Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization
    Joseph T Wade
    Department of Biological Chemistry and Molecular Pharmacology, Harvard University, Boston, MA 02115, USA
    Mol Microbiol 65:21-6. 2007
  8. ncbi request reprint The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting
    Nikos B Reppas
    Harvard University Biophysics Program, Harvard Medical School, Boston, Massachusetts 02115, USA
    Mol Cell 24:747-57. 2006
  9. ncbi request reprint Extensive functional overlap between sigma factors in Escherichia coli
    Joseph T Wade
    Department of Biological Chemistry and Molecular Pharmacology, Harvard University, Boston, Massachusetts 02115, USA
    Nat Struct Mol Biol 13:806-14. 2006
  10. pmc An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae
    Daniel B Hall
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell Biol 26:3672-9. 2006

Collaborators

  • Kevin Struhl
  • Ivan Erill
  • Zhen Zhang
  • Anne M Stringer
  • Brianna L Petrone
  • Richard P Bonocora
  • Michael J Palumbo
  • James E Dornenburg
  • Nikos B Reppas
  • Daniel B Hall
  • Salvatore Currenti
  • Catherine Baranowski
  • Andrew A Reilly
  • Devon M Fitzgerald
  • Anastasiya Yermakova
  • Navjot Singh
  • Jayaleka J Amarasinghe
  • Nicholas J Mantis
  • Lucia Reyes-Diaz
  • Anne M Devita
  • George M Church

Detail Information

Publications13

  1. pmc FRUIT, a scar-free system for targeted chromosomal mutagenesis, epitope tagging, and promoter replacement in Escherichia coli and Salmonella enterica
    Anne M Stringer
    Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
    PLoS ONE 7:e44841. 2012
    ..We have also used FRUIT to introduce constitutive and inducible promoters into the chromosome of E. coli K-12. Thus, FRUIT is a versatile, efficient recombineering approach that can be applied in multiple species of enteric bacteria...
  2. pmc Widespread antisense transcription in Escherichia coli
    James E Dornenburg
    Wadsworth Center, New York State Department of Health, Albany, New York, USA
    MBio 1:. 2010
    ..We propose that these transcripts are generated by promiscuous transcription initiation within genes and that many of them regulate expression of the overlapping gene...
  3. pmc Non-canonical protein-DNA interactions identified by ChIP are not artifacts
    Richard P Bonocora
    Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
    BMC Genomics 14:254. 2013
    ..Waldminghaus and Skarstad suggest specific changes to the standard ChIP procedure that reportedly eliminate the claimed artifacts...
  4. pmc The transition from transcriptional initiation to elongation
    Joseph T Wade
    Wadsworth Center, New York State Department of Health, Albany, NY 12208, United States
    Curr Opin Genet Dev 18:130-6. 2008
    ....
  5. pmc Genome-Scale Analyses of Escherichia coli and Salmonella enterica AraC Reveal Noncanonical Targets and an Expanded Core Regulon
    Anne M Stringer
    Wadsworth Center, New York State Department of Health, Albany, New York, USA
    J Bacteriol 196:660-71. 2014
    ....
  6. pmc Identification of HilD-regulated genes in Salmonella enterica serovar Typhimurium
    Brianna L Petrone
    Wadsworth Center, New York State Department of Health, Albany, New York, USA
    J Bacteriol 196:1094-101. 2014
    ..We also show that HilD-activated genes are frequently activated by HilC and RtsA, indicating extensive overlap of the HilD, HilC, and RtsA regulons. ..
  7. ncbi request reprint Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization
    Joseph T Wade
    Department of Biological Chemistry and Molecular Pharmacology, Harvard University, Boston, MA 02115, USA
    Mol Microbiol 65:21-6. 2007
    ..Here we review recent applications of ChIP-chip to the study of bacteria, which provide important and unexpected insights into transcription and chromosome organization...
  8. ncbi request reprint The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting
    Nikos B Reppas
    Harvard University Biophysics Program, Harvard Medical School, Boston, Massachusetts 02115, USA
    Mol Cell 24:747-57. 2006
    ..The genomic pattern of RNAP density in E. coli differs from that in yeast and mammalian cells...
  9. ncbi request reprint Extensive functional overlap between sigma factors in Escherichia coli
    Joseph T Wade
    Department of Biological Chemistry and Molecular Pharmacology, Harvard University, Boston, Massachusetts 02115, USA
    Nat Struct Mol Biol 13:806-14. 2006
    ..SigmaE-regulated promoters also overlap extensively with those for sigma70. These results suggest that extensive functional overlap between sigma factors is an important phenomenon...
  10. pmc An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae
    Daniel B Hall
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell Biol 26:3672-9. 2006
    ..We speculate that Hmo1 has a role in coordinating the transcription of rRNA and RP genes...
  11. ncbi request reprint The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes
    Joseph T Wade
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 432:1054-8. 2004
    ..Thus, Ifh1 association with promoters is the key regulatory step for coordinate expression of RP genes...
  12. pmc Association of RNA polymerase with transcribed regions in Escherichia coli
    Joseph T Wade
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 101:17777-82. 2004
    ..These observations suggest that in vivo association of sigma(70) and NusA with elongating RNAP is regulated by growth conditions...