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 Mapping the Regulatory Network for Salmonella enterica Serovar Typhimurium Invasion
    Carol Smith
    Wadsworth Center, New York State Department of Health, Albany, New York, USA
    MBio 7:. 2016
  6. pmc SuhB Associates with Nus Factors To Facilitate 30S Ribosome Biogenesis in Escherichia coli
    Navjot Singh
    Wadsworth Center, New York State Department of Health, Albany, New York, USA
    MBio 7:e00114. 2016
  7. 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
  8. 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
  9. pmc Comprehensive mapping of the Escherichia coli flagellar regulatory network
    Devon M Fitzgerald
    Department of Biomedical Sciences, University at Albany, Albany, New York, United States of America
    PLoS Genet 10:e1004649. 2014
  10. doi request reprint Chemical Inhibition of Kynureninase Reduces Pseudomonas aeruginosa Quorum Sensing and Virulence Factor Expression
    Stephen H Kasper
    Colleges of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, New York, United States
    ACS Chem Biol 11:1106-17. 2016

Collaborators

  • Kevin Struhl
  • Donald L Court
  • Ivan Erill
  • Zhen Zhang
  • Richard P Bonocora
  • Anne M Stringer
  • Carol Smith
  • Brianna L Petrone
  • Navjot Singh
  • Devon M Fitzgerald
  • Michael J Palumbo
  • Stephen H Kasper
  • James E Dornenburg
  • Nikos B Reppas
  • Daniel B Hall
  • Nathaniel C Cady
  • Mikhail Bubunenko
  • David M Abbott
  • Ronald Shi
  • Chunhong Mao
  • Rabi Ann Musah
  • Pascal Lapierre
  • Andrew A Reilly
  • Salvatore Currenti
  • Catherine Baranowski
  • Jayaleka J Amarasinghe
  • Lucia Reyes-Diaz
  • Anastasiya Yermakova
  • Nicholas J Mantis
  • Anne M Devita
  • George M Church

Detail Information

Publications19

  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 Mapping the Regulatory Network for Salmonella enterica Serovar Typhimurium Invasion
    Carol Smith
    Wadsworth Center, New York State Department of Health, Albany, New York, USA
    MBio 7:. 2016
    ..Our data are freely available through an intuitive online browser and represent a valuable resource for the bacterial research community...
  6. pmc SuhB Associates with Nus Factors To Facilitate 30S Ribosome Biogenesis in Escherichia coli
    Navjot Singh
    Wadsworth Center, New York State Department of Health, Albany, New York, USA
    MBio 7:e00114. 2016
    ..This occurs through formation of a SuhB-mediated loop between NusB/E/BoxA and RNAP/NusA/G. Thus, we have reassigned the function of these proteins at rRNA and identified another key player in this complex...
  7. 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. ..
  8. 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
    ....
  9. pmc Comprehensive mapping of the Escherichia coli flagellar regulatory network
    Devon M Fitzgerald
    Department of Biomedical Sciences, University at Albany, Albany, New York, United States of America
    PLoS Genet 10:e1004649. 2014
    ..Together, our data redefine the E. coli flagellar regulatory network, and provide new insight into the temporal orchestration of gene expression that coordinates the flagellar assembly process. ..
  10. doi request reprint Chemical Inhibition of Kynureninase Reduces Pseudomonas aeruginosa Quorum Sensing and Virulence Factor Expression
    Stephen H Kasper
    Colleges of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, New York, United States
    ACS Chem Biol 11:1106-17. 2016
    ..aeruginosa QS and virulence factor expression; however, this is the first study to show that targeted inhibition of KynU affects P. aeruginosa gene expression and QS, suggesting a potential antivirulence strategy. ..
  11. pmc Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding
    Richard P Bonocora
    Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
    PLoS Genet 11:e1005552. 2015
    ..We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic σ54 promoters that drive transcription of mRNAs with unusually long 5' UTRs. ..
  12. doi request reprint ChIP-seq for genome-scale analysis of bacterial DNA-binding proteins
    Richard P Bonocora
    Division of Genetics, Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA
    Methods Mol Biol 1276:327-40. 2015
    ..In this chapter we outline the steps to generate ChIP-seq libraries from bacterial samples and briefly discuss basic analysis of the data. ..
  13. 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...
  14. 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...
  15. 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...
  16. 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...
  17. 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...
  18. 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...