Cole Trapnell

Summary

Affiliation: University of Maryland
Country: USA

Publications

  1. pmc TopHat: discovering splice junctions with RNA-Seq
    Cole Trapnell
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Bioinformatics 25:1105-11. 2009
  2. pmc How to map billions of short reads onto genomes
    Cole Trapnell
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
    Nat Biotechnol 27:455-7. 2009
  3. pmc Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    Cole Trapnell
    Department of Computer Science, University of Maryland, College Park, Maryland, USA
    Nat Biotechnol 28:511-5. 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. ncbi request reprint TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    Daehwan Kim
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
    Genome Biol 14:R36. 2013
  6. pmc Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Genomics 9:204. 2008
  7. pmc High-throughput sequence alignment using Graphics Processing Units
    Michael C Schatz
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
    BMC Bioinformatics 8:474. 2007

Detail Information

Publications7

  1. pmc TopHat: discovering splice junctions with RNA-Seq
    Cole Trapnell
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Bioinformatics 25:1105-11. 2009
    ..TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites...
  2. pmc How to map billions of short reads onto genomes
    Cole Trapnell
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
    Nat Biotechnol 27:455-7. 2009
    ..Mapping the vast quantities of short sequence fragments produced by next-generation sequencing platforms is a challenge. What programs are available and how do they work?..
  3. pmc Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    Cole Trapnell
    Department of Computer Science, University of Maryland, College Park, Maryland, USA
    Nat Biotechnol 28:511-5. 2010
    ..These results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation...
  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. ncbi request reprint TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    Daehwan Kim
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
    Genome Biol 14:R36. 2013
    ..TopHat2 is available at http://ccb.jhu.edu/software/tophat...
  6. pmc Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Genomics 9:204. 2008
    ..We report here on the complete genome sequence of strain PXO99A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another...
  7. pmc High-throughput sequence alignment using Graphics Processing Units
    Michael C Schatz
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
    BMC Bioinformatics 8:474. 2007
    ....