Daehwan Kim, Ph.D.
Assistant Professor
Endowed Title Michael L. Rosenberg Scholar in Medical Research
Department Lyda Hill Department of Bioinformatics
Graduate Programs Biomedical Engineering, Cancer Biology
Biography
Dr. Daehwan Kim has been an assistant professor in the Lyda Hill Department of Bioinformatics since September 2017. He is a member of the Cecil H. and Ida Green Center for Systems Biology. He is also a Michael L. Rosenberg Scholar in Medical Research and a Scholar of the Cancer Prevention and Research Institute of Texas (CPRIT).
Education
- Undergraduate
- (2017), Computer Sciences
- Graduate School
- (2017), Computer Sciences
Research Interest
- Life Design Platform development: L++ (a computer programming language), LCC (a compiler), simulation, and visualization
- Next-generation sequence alignment, and graph alignment of genomes and genotyping
- Personalized medicine with a focus on cancer diagnosis
Publications
Featured Publications
- Graph-Based Genome Alignment and Genotyping with HISAT2 and HISAT-genotype
- Kim D, Paggi JM, Park C, Bennett C, and Salzberg SL Nature Biotechnology 2019 37 8 907-915
- HISAT: a fast spliced aligner with low memory requirements.
- Kim D, Langmead B, Salzberg SL Nat. Methods 2015 Apr 12 4 357-60
- TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
- Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL Genome Biol. 2013 Apr 14 4 R36
- Centrifuge: rapid and sensitive classification of metagenomic sequences.
- Kim D, Song L, Breitwieser FP, Salzberg SL Genome Res. 2016 Dec 26 12 1721-1729
- Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.
- Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL Nat Protoc 2016 Sep 11 9 1650-67
- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
- Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L Nat Protoc 2012 Mar 7 3 562-78
- TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.
- Kim D, Salzberg SL Genome Biol. 2011 Aug 12 8 R72
- * See Google Scholar webpage for more publications
- Since 2011
Professional Associations/Affiliations
- Department of Bioinformatics (2017)