Swaine L Chen

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Codon usage between genomes is constrained by genome-wide mutational processes
    Swaine L Chen
    Department of Developmental Biology, Stanford University School of Medicine, Beckman Center, B300, Stanford, CA 94304, USA
    Proc Natl Acad Sci U S A 101:3480-5. 2004
  2. ncbi request reprint Genome-tools: a flexible package for genome sequence analysis
    William Lee
    Stanford University School of Medicine, Stanford, CA, USA
    Biotechniques 33:1334-41. 2002
  3. pmc Identification of long intergenic repeat sequences associated with DNA methylation sites in Caulobacter crescentus and other alpha-proteobacteria
    Swaine L Chen
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94304 5329, USA
    J Bacteriol 185:4997-5002. 2003
  4. pmc Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle
    Michael T Laub
    Department of Developmental Biology, Stanford University School of Medicine, Beckman Center, B300, 279 Campus Drive, Palo Alto, CA 94304 5329, USA
    Proc Natl Acad Sci U S A 99:4632-7. 2002
  5. pmc Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach
    Swaine L Chen
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 103:5977-82. 2006
  6. pmc Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cells
    Marios Giannakis
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 105:4358-63. 2008

Collaborators

Detail Information

Publications6

  1. pmc Codon usage between genomes is constrained by genome-wide mutational processes
    Swaine L Chen
    Department of Developmental Biology, Stanford University School of Medicine, Beckman Center, B300, Stanford, CA 94304, USA
    Proc Natl Acad Sci U S A 101:3480-5. 2004
    ..Our results suggest that, in general, genome-wide codon bias is determined primarily by mutational processes that act throughout the genome, and only secondarily by selective forces acting on translated sequences...
  2. ncbi request reprint Genome-tools: a flexible package for genome sequence analysis
    William Lee
    Stanford University School of Medicine, Stanford, CA, USA
    Biotechniques 33:1334-41. 2002
    ..The genome-tools Web interface is accessible at http://genome-tools.sourceforge.net, and the source code is available at http://sourceforge.net/projects/genome-tools...
  3. pmc Identification of long intergenic repeat sequences associated with DNA methylation sites in Caulobacter crescentus and other alpha-proteobacteria
    Swaine L Chen
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94304 5329, USA
    J Bacteriol 185:4997-5002. 2003
    ..The CIR1 and CIR2 motifs exhibit a conserved inverted repeat organization, with a CcrM site in the center of one of the repeats...
  4. pmc Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle
    Michael T Laub
    Department of Developmental Biology, Stanford University School of Medicine, Beckman Center, B300, 279 Campus Drive, Palo Alto, CA 94304 5329, USA
    Proc Natl Acad Sci U S A 99:4632-7. 2002
    ..Identification of additional regulatory genes activated by CtrA will serve to directly connect new regulatory modules to the network controlling cell cycle progression...
  5. pmc Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach
    Swaine L Chen
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 103:5977-82. 2006
    ..coli isolates from patients with UTI. These studies outline a computational approach that may be broadly applicable for studying strain-specific adaptation and pathogenesis in other bacteria...
  6. pmc Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cells
    Marios Giannakis
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 105:4358-63. 2008
    ..These results provide insights about how H. pylori may adapt to and influence stem cell biology and how its intracellular residency could contribute to gastric tumorigenesis...