Publications

Selected Publications

Google Scholar

• Graph-Based Genome Alignment and Genotyping with HISAT2 and HISAT-genotype. (Cited >2.4K times)
  Daehwan Kim, Joseph M. Paggi, Chanhee Park, Christopher Bennett, and Steven L. Salzberg.
  Nature Biotechnology 37, 907-915 (2019).
  PDF: paper

• Centrifuge: rapid and accurate classification of metagenomic sequences. (Cited >0.7K times)
  Daehwan Kim, Li Song, Florian Breitwieser, and Steven L. Salzberg.
  Genome Research 2016. 26: 1721-1729
  PDF: paper

• Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie, and Ballgown. (Cited >2.8K times)
  Mihaela Pertea, Daehwan Kim, Geo Pertea, Jeffrey T. Leek, and Steven L. Salzberg.
  Nature Protocols 11, 1650–1667 (2016).
  PDF: paper

• HISAT: a fast spliced aligner with low memory requirements. (Cited >10K times)
  Daehwan Kim, Ben Langmead, and Steven L. Salzberg.
  Nature Methods 12 (4), 357-360 (2015).
  PDFs: paper suppl.

• TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. (Cited >11K times)
  Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, and Steven L. Salzberg.
  Genome Biology 2013, 14:R36.
  PDFs: paper suppl.

• Differential Gene and Transcript Expression Analysis of RNA-Seq Experiments with TopHat and Cufflinks. (Cited >10K times)
  Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim, David R. Kelley, Harold Pimentel, Steven L. Salzberg, John L. Rinn, Lior Pachter.
  Nature Protocols 7, 562–578 (2012).
  PDF: paper

• TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. (Cited >0.7K times)
  Daehwan Kim and Steven L. Salzberg.
  Genome Biology 2011, 12:R72.
  PDF: paper