Mihaela Pertea

Summary

Affiliation: University of Maryland
Country: USA

Publications

  1. 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
  2. pmc A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana
    Mihaela Pertea
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Bioinformatics 8:159. 2007
  3. pmc Detection of lineage-specific evolutionary changes among primate species
    Mihaela Pertea
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
    BMC Bioinformatics 12:274. 2011
  4. pmc OperonDB: a comprehensive database of predicted operons in microbial genomes
    Mihaela Pertea
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Nucleic Acids Res 37:D479-82. 2009
  5. doi request reprint Using GlimmerM to find genes in eukaryotic genomes
    Mihaela Pertea
    The Institute for Genomic Research, Rockville, Maryland, USA
    Curr Protoc Bioinformatics . 2002
  6. pmc Between a chicken and a grape: estimating the number of human genes
    Mihaela Pertea
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 11:206. 2010
  7. 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
  8. pmc DIAMUND: direct comparison of genomes to detect mutations
    Steven L Salzberg
    Center for Computational Biology, Johns Hopkins School of Medicine, Baltimore, Maryland, 21205 McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, 21205
    Hum Mutat 35:283-8. 2014
  9. pmc Do-it-yourself genetic testing
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 11:404. 2010
  10. 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

Detail Information

Publications15

  1. 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...
  2. pmc A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana
    Mihaela Pertea
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Bioinformatics 8:159. 2007
    ..However exonic splicing enhancers have been shown to enhance the utilization of nearby splice sites...
  3. pmc Detection of lineage-specific evolutionary changes among primate species
    Mihaela Pertea
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
    BMC Bioinformatics 12:274. 2011
    ..Because the primate genomes are highly similar to one another, methods developed for analysis of more divergent species do not always detect signs of evolutionary selection...
  4. pmc OperonDB: a comprehensive database of predicted operons in microbial genomes
    Mihaela Pertea
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Nucleic Acids Res 37:D479-82. 2009
    ..The new database is updated regularly as additional genomes become available in public archives. OperonDB can be accessed at: http://operondb.cbcb.umd.edu...
  5. doi request reprint Using GlimmerM to find genes in eukaryotic genomes
    Mihaela Pertea
    The Institute for Genomic Research, Rockville, Maryland, USA
    Curr Protoc Bioinformatics . 2002
    ..A unique feature of the system compared to other eukaryotic gene finders is a module that allows users to provide their own data and train GlimmerM for any organism...
  6. pmc Between a chicken and a grape: estimating the number of human genes
    Mihaela Pertea
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 11:206. 2010
    ..Many people expected the question 'How many genes in the human genome?' to be resolved with the publication of the genome sequence in 2001, but estimates continue to fluctuate...
  7. 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
    ....
  8. pmc DIAMUND: direct comparison of genomes to detect mutations
    Steven L Salzberg
    Center for Computational Biology, Johns Hopkins School of Medicine, Baltimore, Maryland, 21205 McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, 21205
    Hum Mutat 35:283-8. 2014
    ..We demonstrate our results on several example cases, including two family trios in which it correctly found the disease-causing variant while excluding thousands of harmless variants that standard methods had identified. ..
  9. pmc Do-it-yourself genetic testing
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 11:404. 2010
    ..ABSTRACT : We developed a computational screen that tests an individual's genome for mutations in the BRCA genes, despite the fact that both are currently protected by patents...
  10. 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...
  11. pmc GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders
    William H Majoros
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 31:3601-4. 2003
    ..Cases have been found where each of the genefinders outperforms each of the others, demonstrating the collective value of this ensemble of genefinders. These programs are all accessible through webservers at http://www.tigr.org/software...
  12. ncbi request reprint Computational gene finding in plants
    Mihaela Pertea
    Institute for Genome Research, Rockville, MD 20850, USA
    Plant Mol Biol 48:39-48. 2002
    ..This paper reviews some of the most widely used algorithms for gene finding in plants, including technical descriptions of how they work and recent measurements of their success on the genomes of Arabidopsis thaliana and rice...
  13. pmc Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species
    C Robin Buell
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 15:1284-91. 2005
    ....
  14. pmc Efficient decoding algorithms for generalized hidden Markov model gene finders
    William H Majoros
    Bioinformatics Department, The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD, USA
    BMC Bioinformatics 6:16. 2005
    ..Unfortunately, the task of implementing an efficient GHMM-based gene finder is already a nontrivial one, and it can be expected that this task will only grow more onerous as our models increase in complexity...
  15. 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...