Lee Ann McCue

Summary

Affiliation: Wadsworth Center
Country: USA

Publications

  1. ncbi Factors influencing the identification of transcription factor binding sites by cross-species comparison
    Lee Ann McCue
    The Wadsworth Center, New York State Department of Health, Albany, New York 12201 0509, USA
    Genome Res 12:1523-32. 2002
  2. ncbi Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes
    Sean Conlan
    Wadsworth Center, New York State Department of Health, Center for Medical Sciences, 150 New Scotland Ave, Albany, NY 12208, USA
    Appl Environ Microbiol 71:7442-52. 2005
  3. ncbi A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction
    Lee A Newberg
    The Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
    Bioinformatics 23:1718-27. 2007
  4. ncbi Software to perform automated comparisons of pair-wise percent identities for microbial species
    Sean Conlan
    Wadsworth Center, Center for Medical Science, Albany, NY, USA
    Biotechniques 40:578, 580,582. 2006
  5. ncbi Characterization of Mycobacterium tuberculosis Rv3676 (CRPMt), a cyclic AMP receptor protein-like DNA binding protein
    Guangchun Bai
    Wadsworth Center, New York State Department of Health, Albany, 12201 2002, USA
    J Bacteriol 187:7795-804. 2005
  6. ncbi A family of acr-coregulated Mycobacterium tuberculosis genes shares a common DNA motif and requires Rv3133c (dosR or devR) for expression
    Matthew A Florczyk
    Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA
    Infect Immun 71:5332-43. 2003
  7. ncbi Identification of a Mycobacterium tuberculosis putative classical nitroreductase gene whose expression is coregulated with that of the acr aene within macrophages, in standing versus shaking cultures, and under low oxygen conditions
    Anjan Purkayastha
    Department of Biomedical Sciences, University of Albany School of Public Health, Albany, New York 12201-2002, USA
    Infect Immun 70:1518-29. 2002
  8. ncbi Making connections between novel transcription factors and their DNA motifs
    Kai Tan
    Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
    Genome Res 15:312-20. 2005
  9. ncbi Identification of mobile elements and pseudogenes in the Shewanella oneidensis MR-1 genome
    Margaret F Romine
    Pacific Northwest National Laboratory, MS P7 86, P O Box 999, Richland, WA 99352, USA
    Appl Environ Microbiol 74:3257-65. 2008
  10. ncbi Using the Gibbs Motif Sampler for phylogenetic footprinting
    William Thompson
    Center for Computational Molecular Biology, Brown Unversity
    Methods Mol Biol 395:403-24. 2007

Collaborators

Detail Information

Publications17

  1. ncbi Factors influencing the identification of transcription factor binding sites by cross-species comparison
    Lee Ann McCue
    The Wadsworth Center, New York State Department of Health, Albany, New York 12201 0509, USA
    Genome Res 12:1523-32. 2002
    ..The inclusion of a species very closely related to E. coli increased the number of statistically significant motif predictions, despite substantially increasing the critical MAP value...
  2. ncbi Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes
    Sean Conlan
    Wadsworth Center, New York State Department of Health, Center for Medical Sciences, 150 New Scotland Ave, Albany, NY 12208, USA
    Appl Environ Microbiol 71:7442-52. 2005
    ..In addition to predicting regulons, we identified a novel inverted repeat that likely forms a highly conserved stem-loop and that occurs downstream of over 100 genes...
  3. ncbi A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction
    Lee A Newberg
    The Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
    Bioinformatics 23:1718-27. 2007
    ..Comparative-genomics studies must be able to address the phylogenetic correlation in the data and efficiently explore the alignment space, in order to make specific and biologically relevant predictions...
  4. ncbi Software to perform automated comparisons of pair-wise percent identities for microbial species
    Sean Conlan
    Wadsworth Center, Center for Medical Science, Albany, NY, USA
    Biotechniques 40:578, 580,582. 2006
  5. ncbi Characterization of Mycobacterium tuberculosis Rv3676 (CRPMt), a cyclic AMP receptor protein-like DNA binding protein
    Guangchun Bai
    Wadsworth Center, New York State Department of Health, Albany, 12201 2002, USA
    J Bacteriol 187:7795-804. 2005
    ..tuberculosis, suggesting a role for cAMP signal transduction in M. tuberculosis and implicating CRP(Mt) as a cAMP-responsive global regulator...
  6. ncbi A family of acr-coregulated Mycobacterium tuberculosis genes shares a common DNA motif and requires Rv3133c (dosR or devR) for expression
    Matthew A Florczyk
    Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA
    Infect Immun 71:5332-43. 2003
    ..These findings are likely to be relevant to the in vivo environment and will contribute to our understanding of the pathogenesis of tuberculosis infection...
  7. ncbi Identification of a Mycobacterium tuberculosis putative classical nitroreductase gene whose expression is coregulated with that of the acr aene within macrophages, in standing versus shaking cultures, and under low oxygen conditions
    Anjan Purkayastha
    Department of Biomedical Sciences, University of Albany School of Public Health, Albany, New York 12201-2002, USA
    Infect Immun 70:1518-29. 2002
    ..We propose that these differences might be exploited for dissection of the regulatory factors that affect mycobacterial gene expression within the host...
  8. ncbi Making connections between novel transcription factors and their DNA motifs
    Kai Tan
    Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
    Genome Res 15:312-20. 2005
    ..Supporting evidence for some of the predicted pairs is presented. Functional annotations are made for 23 novel transcription factors based on the predicted transcription-factor-DNA-motif connections...
  9. ncbi Identification of mobile elements and pseudogenes in the Shewanella oneidensis MR-1 genome
    Margaret F Romine
    Pacific Northwest National Laboratory, MS P7 86, P O Box 999, Richland, WA 99352, USA
    Appl Environ Microbiol 74:3257-65. 2008
    ....
  10. ncbi Using the Gibbs Motif Sampler for phylogenetic footprinting
    William Thompson
    Center for Computational Molecular Biology, Brown Unversity
    Methods Mol Biol 395:403-24. 2007
    ..To illustrate this technique, we present examples that use Gibbs to detect binding sites for the transcription factor LexA in orthologous sequence data from representative species belonging to two different proteobacterial divisions...
  11. ncbi The Gibbs Centroid Sampler
    William A Thompson
    Center for Computational Molecular Biology and the Division of Applied Mathematics, Brown University, Providence, RI 02912, USA
    Nucleic Acids Res 35:W232-7. 2007
    ..The Gibbs Centroid Sampler, along with interactive tutorials, an online user manual, and information on downloading the software, is available at: http://bayesweb.wadsworth.org/gibbs/gibbs.html...
  12. ncbi Identification of a novel class in the alpha/beta hydrolase fold superfamily: the N-myc differentiation-related proteins
    Eudean Shaw
    Department of Chemical Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
    Proteins 47:163-8. 2002
    ..Unlike most of the other superfamily members, the N-myc downstream regulated proteins have never been proposed to possess the alpha/beta hydrolase fold and do not appear to be hydrolases...
  13. ncbi Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites
    Zhaohui S Qin
    Department of Statistics, Harvard University, Cambridge, MA 02138, USA
    Nat Biotechnol 21:435-9. 2003
    ....
  14. ncbi Comparative bacterial proteomics: analysis of the core genome concept
    Stephen J Callister
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
    PLoS ONE 3:e1542. 2008
    ....
  15. ncbi Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis
    Xiu Feng Wan
    Environmental Sciences Division, Oak Ridge National Laboratory, P O Box 2008, Oak Ridge, TN 37831 6038, USA
    J Bacteriol 186:8385-400. 2004
    ....
  16. ncbi Using the Gibbs motif sampler to find conserved domains in DNA and protein sequences
    William Thompson
    Brown University, Providence, Rhode Island, USA
    Curr Protoc Bioinformatics . 2005
    ..This unit describes the basic operation of the Web-based interface to Gibbs, along with advanced examples of its use, and the Web interface to dscan, a sequence database search program...
  17. ncbi Measuring global credibility with application to local sequence alignment
    Bobbie Jo M Webb-Robertson
    Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS Comput Biol 4:e1000077. 2008
    ....