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. ncbi request reprint Rail-RNA: scalable analysis of RNA-seq splicing and coverage
    Abhinav Nellore
    Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
    Bioinformatics . 2016
  5. pmc Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive
    Abhinav Nellore
    Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
    Genome Biol 17:266. 2016
  6. pmc Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce
    Abhinav Nellore
    Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
    Bioinformatics 32:2551-3. 2016
  7. ncbi request reprint Flexible expressed region analysis for RNA-seq with derfinder
    Leonardo Collado-Torres
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
    Nucleic Acids Res . 2016
  8. 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
  9. pmc Aligning short sequencing reads with Bowtie
    Ben Langmead
    Johns Hopkins University, Baltimore, Maryland, USA
    Curr Protoc Bioinformatics . 2010
  10. 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

Collaborators

Detail Information

Publications15

  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. ncbi request reprint Rail-RNA: scalable analysis of RNA-seq splicing and coverage
    Abhinav Nellore
    Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
    Bioinformatics . 2016
    ..Consequently, no information is gained from analyzing multiple samples together, and it requires extra work to obtain analysis products that incorporate data from across samples...
  5. pmc Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive
    Abhinav Nellore
    Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
    Genome Biol 17:266. 2016
    ..The impact of RNA-seq data on annotation has been confined to major projects like ENCODE and Illumina Body Map 2.0...
  6. pmc Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce
    Abhinav Nellore
    Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
    Bioinformatics 32:2551-3. 2016
    ..This is a major obstacle, impeding reproducibility and reducing the utility of archived data...
  7. ncbi request reprint Flexible expressed region analysis for RNA-seq with derfinder
    Leonardo Collado-Torres
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
    Nucleic Acids Res . 2016
    ..The package is available from Bioconductor at www.bioconductor.org/packages/derfinder...
  8. 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)...
  9. 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...
  10. 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
    ..We anticipate that ReCount will also be useful for investigators who wish to consider cross-study comparisons and alternative normalization strategies for RNA-seq...
  11. pmc Polyester: simulating RNA-seq datasets with differential transcript expression
    Alyssa C Frazee
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Center for Computational Biology and
    Bioinformatics 31:2778-84. 2015
    ..Since true differential expression status is often unknown in experimental datasets, artificially constructed datasets must be utilized, either by generating costly spike-in experiments or by simulating RNA-seq data...
  12. pmc Boiler: lossy compression of RNA-seq alignments using coverage vectors
    Jacob Pritt
    Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
    Nucleic Acids Res 44:e133. 2016
    ..Boiler also allows the user to pose fast and useful queries without decompressing the entire file. Boiler is free open source software available from github.com/jpritt/boiler. ..
  13. ncbi request reprint Widespread splicing of repetitive element loci into coding regions of gene transcripts
    Miranda M Darby
    Department of Pediatrics, Johns Hopkins University, Baltimore, USA
    Hum Mol Genet . 2016
    ..Our results demonstrate that RE expression is more complex than previously envisioned and raise the possibility that RE splicing might generate functional protein isoforms...
  14. pmc 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...
  15. 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...