Daehwan Kim
Daehwan Kim
Michael L. Rosenberg Assistant Professor of Bioinformatics at the University of Texas Southwestern
Verified email at UTSouthwestern.edu - Homepage
Title
Cited by
Cited by
Year
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), 1-13, 2013
107272013
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), 562-578, 2012
104002012
HISAT: a fast spliced aligner with low memory requirements
D Kim, B Langmead, SL Salzberg
Nature methods 12 (4), 357-360, 2015
81642015
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), 1650-1667, 2016
22792016
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
14662019
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
D Kim, SL Salzberg
Genome biology 12 (8), 1-15, 2011
7222011
Centrifuge: rapid and sensitive classification of metagenomic sequences
D Kim, L Song, FP Breitwieser, SL Salzberg
Genome research 26 (12), 1721-1729, 2016
6312016
HISAT2: graph-based alignment of next-generation sequencing reads to a population of genomes
D Kim, B Langmead, S Salzberg
172017
Hisat-genotype: Next generation genomic analysis platform on a personal computer
D Kim, JM Paggi, S Salzberg
BioRxiv, 266197, 2018
132018
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
82018
HISAT: hierarchical indexing for spliced alignment of transcripts
D Kim, B Langmead, SL Salzberg
BioRxiv, 012591, 2014
82014
Salzberg 753 SL, Rinn JL, and Pachter L
C Trapnell, A Roberts, L Goff, G Pertea, D Kim, DR Kelley, H Pimentel
Differential gene and transcript expression analysis of RNA-seq 752, 562-578, 0
7
H. 568 Pimentel, SL Salzberg, JL Rinn, and L. Pachter. 2012. Differential gene 569 and transcript expression analysis of RNA-seq experiments with TopHat and 570 Cufflinks
C Trapnell, A Roberts, L Goff, G Pertea, D Kim, DR Kelley
Nature Protocols 7, 562-578, 0
7
Pachter
C Trapnell, A Roberts, L Goff, G Pertea, D Kim, DR Kelley, H Pimentel, ...
L. and Salzberg, SL TopHat: discovering splice junctions with RNA-seq …, 2009
52009
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
Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N
Y Zhang, C Park, C Bennett, M Thornton, D Kim
Genome Research, gr. 275193.120, 2021
22021
HISAT-3N: a rapid and accurate three-nucleotide sequence aligner
Y Zhang, C Park, C Bennett, M Thornton, D Kim
bioRxiv, 2020.12. 15.422906, 2021
12021
SeqWho: Reliable, rapid determination of sequence file identity using k-mer frequencies
C Bennett, M Thornton, C Park, G Henry, Y Zhang, VS Malladi, D Kim
bioRxiv, 2021
2021
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 Lizée, E Geffard, ...
Assises de génétique humaine et médicale 2018, 2018
2018
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