David R Riley

Summary

Affiliation: University of Maryland
Country: USA

Publications

  1. pmc Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells
    Sheila Z Kimaro Mlacha
    Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya
    BMC Genomics 14:383. 2013
  2. pmc Transcriptional adaptation of pneumococci and human pharyngeal cells in the presence of a virus infection
    Sheila Z Kimaro Mlacha
    Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya
    BMC Genomics 14:378. 2013
  3. pmc Using Sybil for interactive comparative genomics of microbes on the web
    David R Riley
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
    Bioinformatics 28:160-6. 2012
  4. pmc Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species
    Claudio Donati
    Novartis Vaccines and Diagnostics, Via Fiorentina 1, 53100 Siena, Italy
    Genome Biol 11:R107. 2010
  5. pmc Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island
    Willem van Schaik
    Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
    BMC Genomics 11:239. 2010
  6. pmc CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing
    Samuel V Angiuoli
    Institute for Genome Sciences IGS, University of Maryland School of Medicine, Baltimore, Maryland, USA
    BMC Bioinformatics 12:356. 2011
  7. pmc Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi
    Panagiotis Ioannidis
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
    BMC Genomics 14:639. 2013
  8. pmc Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation
    Emmanuel F Mongodin
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    BMC Genomics 14:693. 2013
  9. pmc Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples
    David R Riley
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
    PLoS Comput Biol 9:e1003107. 2013
  10. pmc Genomic insights into the emerging human pathogen Mycobacterium massiliense
    Herve Tettelin
    Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
    J Bacteriol 194:5450. 2012

Collaborators

  • Julie C Dunning Hotopp
  • Claire M Fraser
  • Herve Tettelin
  • Samuel V Angiuoli
  • James Robert White
  • Yun Xu
  • Emmanuel F Mongodin
  • J Anthony G Scott
  • Adrian M Zelazny
  • W Florian Fricke
  • Sheila Z Kimaro Mlacha
  • Nikhil Kumar
  • Jacquelyn Sampson
  • George M Carlone
  • Sandra Romero-Steiner
  • Luke J Tallon
  • Nadeeza Ishmael
  • Panagiotis Ioannidis
  • Claudio Donati
  • Willem van Schaik
  • Todd H Creasy
  • Sandra Ott
  • Valerie Grinblat-Huse
  • Julie C Dunning Hotopp
  • Karen T Olarte
  • Jeremy M Foster
  • Xinyue Liu
  • Teresa C T Peret
  • Kelly L Johnston
  • Susan K Hollingshead
  • Dean D Erdman
  • Mark J Taylor
  • Umar Farooq
  • Cynthia S Goldsmith
  • Alessandro Muzzi
  • Morgens Kilian
  • Jos Boekhorst
  • Rob J L Willems
  • Janetta Top
  • E Richard Moxon
  • Antonello Covacci
  • Joyce E P Vrijenhoek
  • Rino Rappuoli
  • Tim J Mitchell
  • Claudia M E Schapendonk
  • Garth D Ehrlich
  • Nicholas J Croucher
  • Antoni P A Hendrickx
  • Stephen D Bentley
  • Vega Masignani
  • Fen Z Hu
  • Marco Oggioni
  • Marc J M Bonten
  • N Luisa Hiller
  • Isaac J Nijman

Detail Information

Publications10

  1. pmc Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells
    Sheila Z Kimaro Mlacha
    Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya
    BMC Genomics 14:383. 2013
    ..Understanding the molecular interactions between the bacterium and the host will contribute to the control and prevention of pneumococcal disease...
  2. pmc Transcriptional adaptation of pneumococci and human pharyngeal cells in the presence of a virus infection
    Sheila Z Kimaro Mlacha
    Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya
    BMC Genomics 14:378. 2013
    ..The objective of this study is to describe a comprehensive picture of the cellular interaction between the adhering bacteria and host cells in the presence or absence of a viral co-infection...
  3. pmc Using Sybil for interactive comparative genomics of microbes on the web
    David R Riley
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
    Bioinformatics 28:160-6. 2012
    ..In addition to scalability, comparative genomics tools must also provide user-friendly interfaces such that the research scientist can explore complex data with minimal technical expertise...
  4. pmc Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species
    Claudio Donati
    Novartis Vaccines and Diagnostics, Via Fiorentina 1, 53100 Siena, Italy
    Genome Biol 11:R107. 2010
    ..Streptococcus pneumoniae is one of the most important causes of microbial diseases in humans. The genomes of 44 diverse strains of S. pneumoniae were analyzed and compared with strains of non-pathogenic streptococci of the Mitis group...
  5. pmc Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island
    Willem van Schaik
    Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
    BMC Genomics 11:239. 2010
    ..The Gram-positive bacterium Enterococcus faecium is an important cause of nosocomial infections in immunocompromized patients...
  6. pmc CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing
    Samuel V Angiuoli
    Institute for Genome Sciences IGS, University of Maryland School of Medicine, Baltimore, Maryland, USA
    BMC Bioinformatics 12:356. 2011
    ..Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software...
  7. pmc Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi
    Panagiotis Ioannidis
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
    BMC Genomics 14:639. 2013
    ..Since extensive lateral gene transfer occurs frequently between Wolbachia and its hosts, we sought to measure the extent of such LGT in B. malayi by whole genome sequencing of Wolbachia-depleted worms...
  8. pmc Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation
    Emmanuel F Mongodin
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    BMC Genomics 14:693. 2013
    ..burgdorferi sensu stricto (B. burgdorferi s.s., 14 isolates), B. afzelii (2), B. garinii (2), B. "bavariensis" (1), B. spielmanii (1), B. valaisiana (1), B. bissettii (1), and B. "finlandensis" (1)...
  9. pmc Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples
    David R Riley
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
    PLoS Comput Biol 9:e1003107. 2013
    ..We anticipate that the application of our approach to additional cancer genome projects will lead to the more frequent detection of bacterial DNA integrations in tumors that are in close proximity to the human microbiome. ..
  10. pmc Genomic insights into the emerging human pathogen Mycobacterium massiliense
    Herve Tettelin
    Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
    J Bacteriol 194:5450. 2012
    ..Mycobacterium massiliense (Mycobacterium abscessus group) is an emerging pathogen causing pulmonary disease and skin and soft tissue infections. We report the genome sequence of the type strain CCUG 48898...