Jonathan E Allen

Summary

Affiliation: Lawrence Livermore National Laboratory
Country: USA

Publications

  1. ncbi Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
    Brian J Haas
    J Craig Venter Institute, The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Biol 9:R7. 2008
  2. ncbi DNA signatures for detecting genetic engineering in bacteria
    Jonathan E Allen
    Lawrence Livermore National Lab, Livermore, CA 94550, USA
    Genome Biol 9:R56. 2008
  3. ncbi Conserved amino acid markers from past influenza pandemic strains
    Jonathan E Allen
    Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA
    BMC Microbiol 9:77. 2009
  4. ncbi Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
    Jane M Carlton
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 419:512-9. 2002
  5. ncbi Computational gene prediction using multiple sources of evidence
    Jonathan E Allen
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 14:142-8. 2004
  6. ncbi The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans
    Brendan J Loftus
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 307:1321-4. 2005
  7. ncbi JIGSAW: integration of multiple sources of evidence for gene prediction
    Jonathan E Allen
    Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, College Park, MD 20742, USA
    Bioinformatics 21:3596-603. 2005
  8. ncbi JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions
    Jonathan E Allen
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 7:S9.1-13. 2006

Detail Information

Publications8

  1. ncbi Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
    Brian J Haas
    J Craig Venter Institute, The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Biol 9:R7. 2008
    ..Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation...
  2. ncbi DNA signatures for detecting genetic engineering in bacteria
    Jonathan E Allen
    Lawrence Livermore National Lab, Livermore, CA 94550, USA
    Genome Biol 9:R56. 2008
    ..Such DNA signatures could be important in detecting genetically engineered bacteria in environmental samples...
  3. ncbi Conserved amino acid markers from past influenza pandemic strains
    Jonathan E Allen
    Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA
    BMC Microbiol 9:77. 2009
    ..Influenza proteomes from distinct viral phenotype classes were searched for class specific amino acid mutations conserved in past pandemics, using reverse engineered linear classifiers...
  4. ncbi Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
    Jane M Carlton
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 419:512-9. 2002
    ..This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease...
  5. ncbi Computational gene prediction using multiple sources of evidence
    Jonathan E Allen
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 14:142-8. 2004
    ..Our results show that combining gene prediction evidence consistently outperforms even the best individual gene finder and, in some cases, can produce dramatic improvements in sensitivity and specificity...
  6. ncbi The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans
    Brendan J Loftus
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 307:1321-4. 2005
    ..neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes...
  7. ncbi JIGSAW: integration of multiple sources of evidence for gene prediction
    Jonathan E Allen
    Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, College Park, MD 20742, USA
    Bioinformatics 21:3596-603. 2005
    ..Genome annotation pipelines collect a variety of types of evidence about gene structure and synthesize the results, which can then be refined further through manual, expert curation of gene models...
  8. ncbi JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions
    Jonathan E Allen
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 7:S9.1-13. 2006
    ..We relate these findings to our current plans for future research...