Ben Langmead

Summary

Affiliation: Johns Hopkins Bloomberg School of Public Health
Country: USA

Publications

  1. pmc Fast gapped-read alignment with Bowtie 2
    Ben Langmead
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA
    Nat Methods 9:357-9. 2012
  2. pmc Searching for SNPs with cloud computing
    Ben Langmead
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA
    Genome Biol 10:R134. 2009
  3. pmc Cloud-scale RNA-sequencing differential expression analysis with Myrna
    Ben Langmead
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
    Genome Biol 11:R83. 2010
  4. pmc Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    Ben Langmead
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
    Genome Biol 10:R25. 2009
  5. pmc Aligning short sequencing reads with Bowtie
    Ben Langmead
    Johns Hopkins University, Baltimore, Maryland, USA
    Curr Protoc Bioinformatics . 2010
  6. pmc ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets
    Alyssa C Frazee
    Department of Biostatistics, The Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
    BMC Bioinformatics 12:449. 2011
  7. doi request reprint HISAT: a fast spliced aligner with low memory requirements
    Daehwan Kim
    1 Center for Computational Biology, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA 2 Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
    Nat Methods 12:357-60. 2015
  8. pmc Reversible switching between epigenetic states in honeybee behavioral subcastes
    Brian R Herb
    Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Nat Neurosci 15:1371-3. 2012

Detail Information

Publications8

  1. pmc Fast gapped-read alignment with Bowtie 2
    Ben Langmead
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA
    Nat Methods 9:357-9. 2012
    ..Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy...
  2. pmc Searching for SNPs with cloud computing
    Ben Langmead
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA
    Genome Biol 10:R134. 2009
    ..Crossbow is available from http://bowtie-bio.sourceforge.net/crossbow/...
  3. pmc Cloud-scale RNA-sequencing differential expression analysis with Myrna
    Ben Langmead
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
    Genome Biol 11:R83. 2010
    ..We apply Myrna to the analysis of publicly available data sets and assess the goodness of fit of standard statistical models. Myrna is available from http://bowtie-bio.sf.net/myrna...
  4. pmc Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    Ben Langmead
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
    Genome Biol 10:R25. 2009
    ..Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source (http://bowtie.cbcb.umd.edu)...
  5. pmc Aligning short sequencing reads with Bowtie
    Ben Langmead
    Johns Hopkins University, Baltimore, Maryland, USA
    Curr Protoc Bioinformatics . 2010
    ..It also includes protocols for building a genome index and calling consensus sequences from Bowtie alignments using SAMtools...
  6. pmc ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets
    Alyssa C Frazee
    Department of Biostatistics, The Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
    BMC Bioinformatics 12:449. 2011
    ..1..
  7. doi request reprint HISAT: a fast spliced aligner with low memory requirements
    Daehwan Kim
    1 Center for Computational Biology, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA 2 Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
    Nat Methods 12:357-60. 2015
    ..Despite its large number of indexes, HISAT requires only 4.3 gigabytes of memory. HISAT supports genomes of any size, including those larger than 4 billion bases. ..
  8. pmc Reversible switching between epigenetic states in honeybee behavioral subcastes
    Brian R Herb
    Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Nat Neurosci 15:1371-3. 2012
    ..Reverting foragers back to nurses reestablished methylation levels for a majority of genes and provides, to the best of our knowledge, the first evidence in any organism of reversible epigenetic changes associated with behavior...