Brian Tjaden

Summary

Affiliation: Wellesley College
Country: USA

Publications

  1. pmc Computational analysis of bacterial RNA-Seq data
    Ryan McClure
    Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
    Nucleic Acids Res 41:e140. 2013
  2. doi request reprint Computational identification of sRNA targets
    Brian Tjaden
    Computer Science Department, Wellesley College, Wellesley, MA, USA
    Methods Mol Biol 905:227-34. 2012
  3. pmc An approach for clustering gene expression data with error information
    Brian Tjaden
    Computer Science Department, Wellesley College, Wellesley, MA 02481, USA
    BMC Bioinformatics 7:17. 2006
  4. pmc Target prediction for small, noncoding RNAs in bacteria
    Brian Tjaden
    Computer Science Department, Wellesley College, Wellesley, MA 02481, USA
    Nucleic Acids Res 34:2791-802. 2006
  5. ncbi request reprint Prediction of small, noncoding RNAs in bacteria using heterogeneous data
    Brian Tjaden
    Computer Science Department, Wellesley College, Wellesley, MA 02481, USA
    J Math Biol 56:183-200. 2008
  6. pmc TargetRNA: a tool for predicting targets of small RNA action in bacteria
    Brian Tjaden
    Computer Science Department, Wellesley College, Wellesley, MA 02481, USA
    Nucleic Acids Res 36:W109-13. 2008
  7. ncbi request reprint Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis
    Brian Tjaden
    Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195, USA
    Bioinformatics 18:S337-44. 2002
  8. pmc Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays
    Brian Tjaden
    Department of Computer Science, University of Washington, Seattle, WA 98195, USA
    Nucleic Acids Res 30:3732-8. 2002
  9. pmc A novel fur- and iron-regulated small RNA, NrrF, is required for indirect fur-mediated regulation of the sdhA and sdhC genes in Neisseria meningitidis
    J R Mellin
    Department of Medicine, Section of Molecular Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
    J Bacteriol 189:3686-94. 2007

Research Grants

Collaborators

Detail Information

Publications9

  1. pmc Computational analysis of bacterial RNA-Seq data
    Ryan McClure
    Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
    Nucleic Acids Res 41:e140. 2013
    ..Our results suggest that Rockhopper can be used for efficient and accurate analysis of bacterial RNA-seq data, and that it can aid with elucidation of bacterial transcriptomes. ..
  2. doi request reprint Computational identification of sRNA targets
    Brian Tjaden
    Computer Science Department, Wellesley College, Wellesley, MA, USA
    Methods Mol Biol 905:227-34. 2012
    ..In this chapter, we provide a detailed guide on how to use TargetRNA to identify targets of sRNA regulation...
  3. pmc An approach for clustering gene expression data with error information
    Brian Tjaden
    Computer Science Department, Wellesley College, Wellesley, MA 02481, USA
    BMC Bioinformatics 7:17. 2006
    ..One of the challenges is to incorporate the measurement error information into downstream analyses of gene expression data, such as traditional clustering techniques...
  4. pmc Target prediction for small, noncoding RNAs in bacteria
    Brian Tjaden
    Computer Science Department, Wellesley College, Wellesley, MA 02481, USA
    Nucleic Acids Res 34:2791-802. 2006
    ..Our results show that TargetRNA is a useful tool for finding mRNA targets of sRNAs, although its rate of success varies between sRNAs...
  5. ncbi request reprint Prediction of small, noncoding RNAs in bacteria using heterogeneous data
    Brian Tjaden
    Computer Science Department, Wellesley College, Wellesley, MA 02481, USA
    J Math Biol 56:183-200. 2008
    ..We demonstrate that sRNAFinder improves upon current tools for identifying small, noncoding genes in bacteria...
  6. pmc TargetRNA: a tool for predicting targets of small RNA action in bacteria
    Brian Tjaden
    Computer Science Department, Wellesley College, Wellesley, MA 02481, USA
    Nucleic Acids Res 36:W109-13. 2008
    ..The predictive performance of TargetRNA has been validated experimentally in several bacterial organisms. TargetRNA is freely available at http://snowwhite.wellesley.edu/targetRNA...
  7. ncbi request reprint Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis
    Brian Tjaden
    Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195, USA
    Bioinformatics 18:S337-44. 2002
    ..The operon elements we identify correspond to documented operons with 99% specificity and 63% sensitivity. Similarly we find that our 5' UTR results accurately coincide with experimentally verified promoter regions for most genes...
  8. pmc Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays
    Brian Tjaden
    Department of Computer Science, University of Washington, Seattle, WA 98195, USA
    Nucleic Acids Res 30:3732-8. 2002
    ..Through the experimental identification of all RNAs expressed under a specific condition, we gain a more thorough understanding of all cellular processes...
  9. pmc A novel fur- and iron-regulated small RNA, NrrF, is required for indirect fur-mediated regulation of the sdhA and sdhC genes in Neisseria meningitidis
    J R Mellin
    Department of Medicine, Section of Molecular Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
    J Bacteriol 189:3686-94. 2007
    ..This study is the first report of small RNAs in N. meningitidis and the first to use a bioinformatics approach to identify, a priori, regulatory targets of a small RNA...

Research Grants1

  1. Methods for characterizing noncoding RNAs in bacteria
    Brian Tjaden; Fiscal Year: 2006
    ..While the bioinformatics approaches developed in this project will be applicable to prokaryotes more broadly, the approaches will be validated experimentally in Escherichia coli and Pseudomonas aeruginosa. ..