Gabor T Marth

Summary

Affiliation: Boston College
Country: USA

Publications

  1. pmc The functional spectrum of low-frequency coding variation
    Gabor T Marth
    Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
    Genome Biol 12:R84. 2011
  2. pmc Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data
    Jiantao Wu
    Boston College, Boston, Chestnut Hill, MA, USA
    BMC Bioinformatics 13:305. 2012
  3. doi request reprint MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping
    Wan Ping Lee
    Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
    PLoS ONE 9:e90581. 2014
  4. pmc BamTools: a C++ API and toolkit for analyzing and managing BAM files
    Derek W Barnett
    Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
    Bioinformatics 27:1691-2. 2011
  5. pmc Variant discovery in targeted resequencing using whole genome amplified DNA
    Amit R Indap
    Department of Biology, Boston College, Chestnut Hill, MA, USA
    BMC Genomics 14:468. 2013
  6. pmc Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression
    Michele A Busby
    Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
    Bioinformatics 29:656-7. 2013
  7. ncbi request reprint Whole genome profiling of spontaneous and chemically induced mutations in Toxoplasma gondii
    Andrew Farrell
    Department of Biology, Boston College, Higgins Hall 355, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
    BMC Genomics 15:354. 2014
  8. pmc SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications
    Mengyao Zhao
    Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
    PLoS ONE 8:e82138. 2013
  9. pmc Targeted proteomic dissection of Toxoplasma cytoskeleton sub-compartments using MORN1
    Alexander Lorestani
    Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
    Cytoskeleton (Hoboken) 69:1069-85. 2012
  10. pmc Expression divergence measured by transcriptome sequencing of four yeast species
    Michele A Busby
    Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467 3961, USA
    BMC Genomics 12:635. 2011

Collaborators

Detail Information

Publications12

  1. pmc The functional spectrum of low-frequency coding variation
    Gabor T Marth
    Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
    Genome Biol 12:R84. 2011
    ....
  2. pmc Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data
    Jiantao Wu
    Boston College, Boston, Chestnut Hill, MA, USA
    BMC Bioinformatics 13:305. 2012
    ..However there has been little attention devoted to Copy Number Variation (CNV) detection from exome capture datasets despite the potentially high impact of CNVs in exonic regions on protein function...
  3. doi request reprint MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping
    Wan Ping Lee
    Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
    PLoS ONE 9:e90581. 2014
    ..MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me). ..
  4. pmc BamTools: a C++ API and toolkit for analyzing and managing BAM files
    Derek W Barnett
    Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
    Bioinformatics 27:1691-2. 2011
    ..However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research...
  5. pmc Variant discovery in targeted resequencing using whole genome amplified DNA
    Amit R Indap
    Department of Biology, Boston College, Chestnut Hill, MA, USA
    BMC Genomics 14:468. 2013
    ....
  6. pmc Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression
    Michele A Busby
    Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
    Bioinformatics 29:656-7. 2013
    ..A common question arises at the beginning of every experiment where RNA-Seq is used to detect differential gene expression between two conditions: How many reads should we sequence?..
  7. ncbi request reprint Whole genome profiling of spontaneous and chemically induced mutations in Toxoplasma gondii
    Andrew Farrell
    Department of Biology, Boston College, Higgins Hall 355, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
    BMC Genomics 15:354. 2014
    ....
  8. pmc SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications
    Mengyao Zhao
    Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
    PLoS ONE 8:e82138. 2013
    ..These issues make reusing these efficient Smith-Waterman implementations impractical...
  9. pmc Targeted proteomic dissection of Toxoplasma cytoskeleton sub-compartments using MORN1
    Alexander Lorestani
    Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
    Cytoskeleton (Hoboken) 69:1069-85. 2012
    ..Furthermore, we show that G-actin binding protein TgCAP is localized at the apical cap region in intracellular parasites, but quickly redistributes to a cytoplasmic localization pattern upon egress. © 2012 Wiley Periodicals, Inc...
  10. pmc Expression divergence measured by transcriptome sequencing of four yeast species
    Michele A Busby
    Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467 3961, USA
    BMC Genomics 12:635. 2011
    ..The evolution of gene expression is a challenging problem in evolutionary biology, for which accurate, well-calibrated measurements and methods are crucial...
  11. pmc A comprehensive map of mobile element insertion polymorphisms in humans
    Chip Stewart
    Department of Biology, Boston College, Chestnut Hill, Massachusetts, USA
    PLoS Genet 7:e1002236. 2011
    ..A direct comparison of MEI and SNP diversity levels suggests a differential mobile element insertion rate among populations...
  12. doi request reprint Pyrobayes: an improved base caller for SNP discovery in pyrosequences
    Aaron R Quinlan
    Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, Massachusetts 02467, USA
    Nat Methods 5:179-81. 2008
    ..Pyrobayes permits accurate single-nucleotide polymorphism (SNP) calling in resequencing applications, even in shallow read coverage, primarily because it produces more confident base calls than the native base calling program...