Tsute Chen

Summary

Affiliation: The Forsyth Institute
Country: USA

Publications

  1. pmc Comprehensive transcriptome analysis of the periodontopathogenic bacterium Porphyromonas gingivalis W83
    Hedda Høvik
    Department of Oral Biology, University of Oslo, Oslo, Norway
    J Bacteriol 194:100-14. 2012
  2. pmc Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays
    Hedda Høvik
    Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
    BMC Bioinformatics 11:82. 2010
  3. pmc The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information
    Tsute Chen
    The Forsyth Institute, Boston, MA 02115, USA
    Database (Oxford) 2010:baq013. 2010
  4. ncbi request reprint Detection, cloning, and sequence analysis of an indigenous plasmid from cellulolytic clostridial strain MCF1
    T Chen
    Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, 01003 5720, USA
    Plasmid 43:153-8. 2000
  5. ncbi request reprint DNA microarrays--an armory for combating infectious diseases in the new century
    T Chen
    Department of Molecular Genetics, The Forsyth Institute, Boston, MA 02115, USA
    Infect Disord Drug Targets 6:263-79. 2006
  6. pmc The bioinformatics resource for oral pathogens
    Tsute Chen
    The Forsyth Institute, 140 Fenway, Boston, MA 02115, USA
    Nucleic Acids Res 33:W734-40. 2005
  7. pmc Comparative whole-genome analysis of virulent and avirulent strains of Porphyromonas gingivalis
    Tsute Chen
    Department of Molecular Genetics, The Forsyth Institute, Boston, MA 02115, USA
    J Bacteriol 186:5473-9. 2004
  8. pmc Strand-specific transcriptome profiling with directly labeled RNA on genomic tiling microarrays
    Wen Han Yu
    Department of Molecular Genetics, The Forsyth Institute, Cambridge, MA, USA
    BMC Mol Biol 12:3. 2011
  9. pmc A hidden Markov support vector machine framework incorporating profile geometry learning for identifying microbial RNA in tiling array data
    Wen Han Yu
    Department of Molecular Genetics, The Forsyth Institute, Boston, MA 02115, USA
    Bioinformatics 26:1423-30. 2010
  10. pmc The canine oral microbiome
    Floyd E Dewhirst
    Department of Molecular Genetics, The Forsyth Institute, Cambridge, Massachusetts, USA
    PLoS ONE 7:e36067. 2012

Research Grants

Collaborators

  • Wen Han Yu
  • Ingar Olsen
  • Jacques Izard
  • Robert D Fleischmann
  • Margaret Duncan
  • Hedda Høvik
  • Floyd E Dewhirst
  • Richa Priyadarshini
  • Steven D Goodman
  • Annette Arndt
  • Mary E Davey
  • Natalia O Tjokro
  • Carla Cugini
  • Emily C Thompson
  • Erin A Klein
  • Catherine M F Buckley
  • Marie Lousie Bennett
  • Jessica M Blanton
  • Lisa Milella
  • Ian J Davis
  • Zoe V Marshall-Jones
  • Zeli Shen
  • Tahani Boumenna
  • Lauren N Stokes
  • Michael S Scimeca
  • Bruce J Paster
  • James G Fox

Detail Information

Publications13

  1. pmc Comprehensive transcriptome analysis of the periodontopathogenic bacterium Porphyromonas gingivalis W83
    Hedda Høvik
    Department of Oral Biology, University of Oslo, Oslo, Norway
    J Bacteriol 194:100-14. 2012
    ..gingivalis. The transcriptome profiles can be viewed at and downloaded from the Microbial Transcriptome Database website, http://bioinformatics.forsyth.org/mtd...
  2. pmc Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays
    Hedda Høvik
    Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
    BMC Bioinformatics 11:82. 2010
    ..This paper describes a comprehensive computational pipeline implemented specifically for designing tiling probe sets to study microbial transcriptome profiles...
  3. pmc The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information
    Tsute Chen
    The Forsyth Institute, Boston, MA 02115, USA
    Database (Oxford) 2010:baq013. 2010
    ..We provide HOMD as a conceptual model for the presentation of microbiome data for other human body sites. Database URL: http://www.homd.org...
  4. ncbi request reprint Detection, cloning, and sequence analysis of an indigenous plasmid from cellulolytic clostridial strain MCF1
    T Chen
    Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, 01003 5720, USA
    Plasmid 43:153-8. 2000
    ..The data suggest that pMCF1 belongs to the pC194 family of rolling-circle replicating plasmids and the ORF1 protein functions as its replication protein...
  5. ncbi request reprint DNA microarrays--an armory for combating infectious diseases in the new century
    T Chen
    Department of Molecular Genetics, The Forsyth Institute, Boston, MA 02115, USA
    Infect Disord Drug Targets 6:263-79. 2006
    ..Issues and challenges in the analysis, management and interpretation of microarray data are also addressed...
  6. pmc The bioinformatics resource for oral pathogens
    Tsute Chen
    The Forsyth Institute, 140 Fenway, Boston, MA 02115, USA
    Nucleic Acids Res 33:W734-40. 2005
    ..The concept of providing an integrated source of genomic data, as well as the data-mining model used in BROP can be applied to other organisms. BROP can be publicly accessed at http://www.brop.org...
  7. pmc Comparative whole-genome analysis of virulent and avirulent strains of Porphyromonas gingivalis
    Tsute Chen
    Department of Molecular Genetics, The Forsyth Institute, Boston, MA 02115, USA
    J Bacteriol 186:5473-9. 2004
    ....
  8. pmc Strand-specific transcriptome profiling with directly labeled RNA on genomic tiling microarrays
    Wen Han Yu
    Department of Molecular Genetics, The Forsyth Institute, Cambridge, MA, USA
    BMC Mol Biol 12:3. 2011
    ..To address this issue, we have developed an effective method using RNA that is directly labeled, thus by-passing the cDNA generation. This paper describes this method and its application to the mapping of transcriptome profiles...
  9. pmc A hidden Markov support vector machine framework incorporating profile geometry learning for identifying microbial RNA in tiling array data
    Wen Han Yu
    Department of Molecular Genetics, The Forsyth Institute, Boston, MA 02115, USA
    Bioinformatics 26:1423-30. 2010
    ..This article describes an efficient and accurate methodology to reveal complicated transcriptional architecture, including small regulatory RNAs, in microbial transcriptome profiles...
  10. pmc The canine oral microbiome
    Floyd E Dewhirst
    Department of Molecular Genetics, The Forsyth Institute, Cambridge, Massachusetts, USA
    PLoS ONE 7:e36067. 2012
    ..This report describes the diversity of the canine oral microbiome and provides a provisional 16S rRNA based taxonomic scheme for naming and identifying unnamed canine bacterial taxa...
  11. pmc The nucleoid-associated protein HUβ affects global gene expression in Porphyromonas gingivalis
    Richa Priyadarshini
    Department of Molecular Genetics, The Forsyth Institute, Cambridge, MA, USA
    Microbiology 159:219-29. 2013
    ..gingivalis; it affects not only production of capsular polysaccharides but also expression of genes involved in basic functions, such as cell wall synthesis, cell division and iron uptake...
  12. pmc Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: implications for phylogenetic inference and systematics
    Floyd E Dewhirst
    Department of Molecular Genetics, The Forsyth Institute, Boston, Massachusetts 02115, USA
    J Bacteriol 187:6106-18. 2005
    ..IVSs were found in helices 10, 25, and 45, as well as between helices 31' and 27'. Simultaneous insertion of IVSs at three sites was found in H. mesocricetorum...
  13. ncbi request reprint Gingipain adhesin domains mediate Porphyromonas gingivalis adherence to epithelial cells
    Tsute Chen
    Department of Molecular Genetics, The Forsyth Institute, 140 Fenway, Boston, MA 02115, USA
    Microb Pathog 36:205-9. 2004
    ..gingivalis adherence to epithelial cells is mediated by gingipain adhesin peptides...

Research Grants2

  1. Functional discovery of Porphyromonas gingivalis genes
    Tsute Chen; Fiscal Year: 2006
    ..abstract_text> ..