Steven L. Salzberg

Top papers

• Fast gapped-read alignment with Bowtie 2

  Ben Langmead, Steven L. Salzberg·2012·Nature Methods
  ↗ 60,243
• HISAT: a fast spliced aligner with low memory requirements

  Daehwan Kim, Ben Langmead, Steven L. Salzberg·2015·Nature Methods
  ↗ 25,712OA
• Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

  Ben Langmead, Cole Trapnell, Mihai Pop, et al.·2009·Genome biology
  ↗ 22,852OA
• Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

  Cole Trapnell, Brian A. Williams, Geo Pertea, et al.·2010·Nature Biotechnology
  ↗ 16,401
• FLASH: fast length adjustment of short reads to improve genome assemblies

  Tanja Magoč, Steven L. Salzberg·2011·Bioinformatics
  ↗ 15,538OA
• Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

  Daehwan Kim, Joseph M. Paggi, Chanhee Park, et al.·2019·Nature Biotechnology
  ↗ 15,279OA
• StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

  Mihaela Pertea, Geo Pertea, Corina Antonescu, et al.·2015·Nature Biotechnology
  ↗ 15,171OA
• The Sequence of the Human Genome

  J. Craig Venter, Mark D. Adams, Eugene W. Myers, et al.·2001·Science
  ↗ 13,633
• TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

  Daehwan Kim, Geo Pertea, Cole Trapnell, et al.·2013·Genome biology
  ↗ 13,611OA
• Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

  Cole Trapnell, Adam Roberts, Loyal A. Goff, et al.·2012·Nature Protocols
  ↗ 12,837OA
• TopHat: discovering splice junctions with RNA-Seq

  Cole Trapnell, Lior Pachter, Steven L. Salzberg·2009·Bioinformatics
  ↗ 12,112OA
• Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

  Mihaela Pertea, Daehwan Kim, Geo Pertea, et al.·2016·Nature Protocols
  ↗ 7,507