Swaine L Chen
Affiliation: Stanford University
- Codon usage between genomes is constrained by genome-wide mutational processesSwaine 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...
- Genome-tools: a flexible package for genome sequence analysisWilliam 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...
- Identification of long intergenic repeat sequences associated with DNA methylation sites in Caulobacter crescentus and other alpha-proteobacteriaSwaine 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...
- Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycleMichael 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...
- Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approachSwaine 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...
- Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cellsMarios 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...