Adam M Phillippy

Summary

Affiliation: University of Maryland
Country: USA

Publications

  1. pmc On the evolving portfolio of community-standards and data sharing policies: turning challenges into new opportunities
    Susanna Assunta Sansone
    Oxford e Research Centre, University of Oxford, Oxford, UK
    Gigascience 1:10. 2012
  2. pmc The rise of a digital immune system
    Michael C Schatz
    Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
    Gigascience 1:4. 2012
  3. pmc Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
    Xiangyu Deng
    National Center for Food Safety and Technology, Illinois Institute of Technology, Summit, Illinois 60501, USA
    BMC Genomics 11:500. 2010
  4. pmc Comprehensive DNA signature discovery and validation
    Adam M Phillippy
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
    PLoS Comput Biol 3:e98. 2007
  5. pmc Genome assembly forensics: finding the elusive mis-assembly
    Adam M Phillippy
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 9:R55. 2008
  6. pmc Efficient oligonucleotide probe selection for pan-genomic tiling arrays
    Adam M Phillippy
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Bioinformatics 10:293. 2009
  7. pmc Insignia: a DNA signature search web server for diagnostic assay development
    Adam M Phillippy
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
    Nucleic Acids Res 37:W229-34. 2009
  8. pmc Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Genomics 9:204. 2008
  9. pmc Hawkeye: an interactive visual analytics tool for genome assemblies
    Michael C Schatz
    Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, University of Maryland, College Park, Maryland 20742, USA
    Genome Biol 8:R34. 2007
  10. doi request reprint Using MUMmer to identify similar regions in large sequence sets
    Arthur L Delcher
    The Institute for Genomic Research Rockville, Maryland and Computer Science Department, Loyola College in Maryland, Baltimore, Maryland, USA
    Curr Protoc Bioinformatics . 2003

Detail Information

Publications12

  1. pmc On the evolving portfolio of community-standards and data sharing policies: turning challenges into new opportunities
    Susanna Assunta Sansone
    Oxford e Research Centre, University of Oxford, Oxford, UK
    Gigascience 1:10. 2012
    ..It is time for all stakeholders to work together to reconcile cause and effect and make the data-sharing culture functional and efficient...
  2. pmc The rise of a digital immune system
    Michael C Schatz
    Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
    Gigascience 1:4. 2012
    ....
  3. pmc Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
    Xiangyu Deng
    National Center for Food Safety and Technology, Illinois Institute of Technology, Summit, Illinois 60501, USA
    BMC Genomics 11:500. 2010
    ..Two of these lineages predominantly cause human sporadic and epidemic infections, whereas the third lineage has never been implicated in human disease outbreaks despite its overall conservation of many known virulence factors...
  4. pmc Comprehensive DNA signature discovery and validation
    Adam M Phillippy
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
    PLoS Comput Biol 3:e98. 2007
    ..The Insignia system is freely accessible via a Web interface and has been released as open source software at: http://insignia.cbcb.umd.edu...
  5. pmc Genome assembly forensics: finding the elusive mis-assembly
    Adam M Phillippy
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 9:R55. 2008
    ..The software described is compatible with common assembly formats and is released, open-source, at http://amos.sourceforge.net...
  6. pmc Efficient oligonucleotide probe selection for pan-genomic tiling arrays
    Adam M Phillippy
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Bioinformatics 10:293. 2009
    ..Prior microarrays have included only a single strain per array or the conserved sequences of gene families. These arrays omit potentially important genes and sequence variants from the pan-genome...
  7. pmc Insignia: a DNA signature search web server for diagnostic assay development
    Adam M Phillippy
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
    Nucleic Acids Res 37:W229-34. 2009
    ..The Insignia website (http://insignia.cbcb.umd.edu) is free and open to all users and there is no login requirement. In addition, the source code for the computational pipeline is freely available...
  8. pmc Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Genomics 9:204. 2008
    ..We report here on the complete genome sequence of strain PXO99A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another...
  9. pmc Hawkeye: an interactive visual analytics tool for genome assemblies
    Michael C Schatz
    Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, University of Maryland, College Park, Maryland 20742, USA
    Genome Biol 8:R34. 2007
    ..Hawkeye is freely available and released as part of the open source AMOS project http://amos.sourceforge.net/hawkeye...
  10. doi request reprint Using MUMmer to identify similar regions in large sequence sets
    Arthur L Delcher
    The Institute for Genomic Research Rockville, Maryland and Computer Science Department, Loyola College in Maryland, Baltimore, Maryland, USA
    Curr Protoc Bioinformatics . 2003
    ..The system is particularly efficient at comparing highly similar sequences, such as alternative versions of fragment assemblies or closely related strains of the same bacterium...
  11. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  12. ncbi request reprint Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes
    Rekha Seshadri
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 307:105-8. 2005
    ..Genome analysis provides insights into the organism's complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph...