Daehwan Kim
Daehwan Kim
Michael L. Rosenberg Assistant professor of Bioinformatics at the University of Texas Southwestern
Verified email at UTSouthwestern.edu - Homepage
TitleCited byYear
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
D Kim, G Pertea, C Trapnell, H Pimentel, R Kelley, SL Salzberg
Genome biology 14 (4), R36, 2013
73732013
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
C Trapnell, A Roberts, L Goff, G Pertea, D Kim, DR Kelley, H Pimentel, ...
Nature protocols 7 (3), 562, 2012
73652012
HISAT: a fast spliced aligner with low memory requirements
D Kim, B Langmead, SL Salzberg
Nature methods 12 (4), 357, 2015
29722015
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
M Pertea, D Kim, GM Pertea, JT Leek, SL Salzberg
Nature protocols 11 (9), 1650, 2016
7372016
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
D Kim, SL Salzberg
Genome biology 12 (8), R72, 2011
5582011
Centrifuge: rapid and sensitive classification of metagenomic sequences
D Kim, L Song, FP Breitwieser, SL Salzberg
Genome research 26 (12), 1721-1729, 2016
2202016
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
D Kim, JM Paggi, C Park, C Bennett, SL Salzberg
Nature biotechnology 37 (8), 907-915, 2019
102019
Hisat-genotype: Next generation genomic analysis platform on a personal computer
D Kim, JM Paggi, S Salzberg
BioRxiv, 266197, 2018
62018
HISAT2: graph-based alignment of next-generation sequencing reads to a population of genomes
D Kim, B Langmead, S Salzberg
62017
Genomic characterization of chromosome translocations in patients with T/myeloid mixed-phenotype acute leukemia
A Pallavajjala, D Kim, T Li, G Ghiaur, RJ Jones, KH Burns, SL Salzberg, ...
Leukemia & lymphoma 59 (5), 1231-1238, 2018
52018
The novel fusion transcript NR5A2‐KLHL29FT is generated by an insertion at the KLHL29 locus
Z Sun, X Ke, SL Salzberg, D Kim, V Antonescu, Y Cheng, B Huang, ...
Cancer 123 (9), 1507-1515, 2017
32017
HLA-DRB1* 09: 01 IS ASSOCIATED WITH A SEVERE ASTHMA OUTCOME IN THE CONSORTIUM ON ASTHMA AMONG AFRICAN-ANCESTRY POPULATIONS IN THE AMERICAS (CAAPA)
N Vince, S Limou, M Daya, N Rafaels, J Hollenbach, A Lizee, E Geffard, ...
HLA 91 (5), 351-351, 2018
2018
HLA and asthma in the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA)
N Vince, S Limou, M Daya, N Rafaels, J Hollenbach, A Lize, E Geffard, ...
2018
Fast and Sensitive Metagenomic Sequence Assignment with Centrifuge
F Breitwieser, D Kim, L Song, S Salzberg
HUMAN HEREDITY 81 (2), 52-52, 2016
2016
HISAT2 source code
D Kim
Github, 2015
2015
HISAT: Hierarchical Indexing for Spliced Alignment of Transcripts
D Kim, B Langmead, S Salzberg
bioRxiv, 012591, 2014
2014
Reconstruction and Estimation of Fusion Transcripts from RNA‐Sequencing reads
D Kim, SL Salzberg
Cold Spring Harbor Laboratory Meeting on the Biology of Genomes, 2013
2013
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Articles 1–17