Jonathan E Allen

Summary

Affiliation: Lawrence Livermore National Laboratory
Country: USA

Publications

  1. ncbi request reprint 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
  2. ncbi request reprint 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
  3. pmc Scalable metagenomic taxonomy classification using a reference genome database
    Sasha K Ames
    Center for Applied Scientific Computing, Lawrence Livermore National Laboratory and Global Security Directorate, P O Box 808, Livermore, CA 94551, USA
    Bioinformatics 29:2253-60. 2013
  4. pmc 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
  5. pmc DNA signatures for detecting genetic engineering in bacteria
    Jonathan E Allen
    Lawrence Livermore National Lab, Livermore, CA 94550, USA
    Genome Biol 9:R56. 2008
  6. pmc 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
  7. pmc Ultra-deep sequencing of intra-host rabies virus populations during cross-species transmission
    Monica K Borucki
    Lawrence Livermore National Laboratory, Livermore, California, United States of America
    PLoS Negl Trop Dis 7:e2555. 2013
  8. pmc Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs
    Haiyin Chen-Harris
    Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, USA
    BMC Genomics 14:96. 2013
  9. pmc The role of viral population diversity in adaptation of bovine coronavirus to new host environments
    Monica K Borucki
    Lawrence Livermore National Laboratory, Livermore, CA, USA
    PLoS ONE 8:e52752. 2013
  10. pmc Microbial profiling of combat wound infection through detection microarray and next-generation sequencing
    Nicholas A Be
    Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
    J Clin Microbiol 52:2583-94. 2014

Detail Information

Publications13

  1. ncbi request reprint 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...
  2. ncbi request reprint 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...
  3. pmc Scalable metagenomic taxonomy classification using a reference genome database
    Sasha K Ames
    Center for Applied Scientific Computing, Lawrence Livermore National Laboratory and Global Security Directorate, P O Box 808, Livermore, CA 94551, USA
    Bioinformatics 29:2253-60. 2013
    ..Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge...
  4. pmc 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...
  5. pmc 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...
  6. pmc 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...
  7. pmc Ultra-deep sequencing of intra-host rabies virus populations during cross-species transmission
    Monica K Borucki
    Lawrence Livermore National Laboratory, Livermore, California, United States of America
    PLoS Negl Trop Dis 7:e2555. 2013
    ..These results suggest that analysis of rare variants within a viral population may yield clues to ancestral genomes and identify rare variants that have the potential to be selected for if environment conditions change. ..
  8. pmc Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs
    Haiyin Chen-Harris
    Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, USA
    BMC Genomics 14:96. 2013
    ..The challenge however, is to accurately model the errors in the sequencing data and differentiate real viral mutations, particularly those that exist at low frequencies, from sequencing errors...
  9. pmc The role of viral population diversity in adaptation of bovine coronavirus to new host environments
    Monica K Borucki
    Lawrence Livermore National Laboratory, Livermore, CA, USA
    PLoS ONE 8:e52752. 2013
    ....
  10. pmc Microbial profiling of combat wound infection through detection microarray and next-generation sequencing
    Nicholas A Be
    Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
    J Clin Microbiol 52:2583-94. 2014
    ..Future application of genomic protocols for assessing microbial content could allow application of specialized care through early and rapid identification and management of critical patterns in wound bioburden. ..
  11. pmc 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
    ....
  12. pmc 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...
  13. pmc 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...