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Daehwan Kim
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HISAT: a fast spliced aligner with low memory requirements
D Kim, B Langmead, SL Salzberg
Nature methods 12 (4), 357-360, 2015
172892015
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, 1-13, 2013
132912013
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
129182012
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
77062019
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
49642016
Centrifuge: rapid and sensitive classification of metagenomic sequences
D Kim, L Song, FP Breitwieser, SL Salzberg
Genome research 26 (12), 1721-1729, 2016
12172016
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
D Kim, SL Salzberg
Genome biology 12, 1-15, 2011
8872011
Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N
Y Zhang, C Park, C Bennett, M Thornton, D Kim
Genome Research 31 (7), 1290-1295, 2021
1482021
HISAT2: graph-based alignment of next-generation sequencing reads to a population of genomes
D Kim, B Langmead, S Salzberg
242017
Hisat-genotype: Next generation genomic analysis platform on a personal computer
D Kim, JM Paggi, S Salzberg
BioRxiv, 266197, 2018
222018
BNT162b2-induced neutralizing and non-neutralizing antibody functions against SARS-CoV-2 diminish with age
TA Bates, P Lu, YJ Kang, D Schoen, M Thornton, SK McBride, C Park, ...
Cell Reports 41 (4), 2022
212022
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
112018
HISAT: hierarchical indexing for spliced alignment of transcripts
D Kim, B Langmead, SL Salzberg
BioRxiv, 012591, 2014
112014
Automated classification of cytogenetic abnormalities in hematolymphoid neoplasms
A Cox, C Park, P Koduru, K Wilson, O Weinberg, W Chen, R García, ...
Bioinformatics 38 (5), 1420-1426, 2022
72022
Graph-based 683 genome alignment and genotyping with HISAT2 and HISAT-genotype
D Kim, JM Paggi, C Park, C Bennett, SL Salzberg
Nat. 684 Biotechnol 37 (907-915), 685, 2019
72019
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
52017
SeqWho: reliable, rapid determination of sequence file identity using k-mer frequencies in Random Forest classifiers
C Bennett, M Thornton, C Park, G Henry, Y Zhang, V Malladi, D Kim
Bioinformatics 38 (7), 1830-1837, 2022
32022
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, 2020
32020
MultiQC: summarize analysis results for multiple tools and samples in a single report
D Kim, JM Paggi, C Park, C Bennett, SL Salzberg
Nat Biotechnol 37, 907-15, 2019
32019
TReNCo: Topologically associating domain (TAD) aware regulatory network construction
VM Christopher Bennett, Viren Amin, Daehwan Kim, Murat Cobanoglu
F1000Research 11 (426), 2022
2022
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Articles 1–20