User profiles for "author:Daehwan Kim"

Daehwan Kim

- Verified email at UTSouthwestern.edu - Cited by 55826

Daehwan Kim

- Verified email at hood.edu - Cited by 977

Daehwan Kim

- Verified email at pknu.ac.kr - Cited by 848

[HTML][HTML] Physico-chemical conversion of lignocellulose: inhibitor effects and detoxification strategies: a mini review

D Kim - Molecules, 2018 - mdpi.com
A pretreatment of lignocellulosic biomass to produce biofuels, polymers, and other
chemicals plays a vital role in the biochemical conversion process toward disrupting the …

HISAT: a fast spliced aligner with low memory requirements

D Kim, B Langmead, SL Salzberg - Nature methods, 2015 - nature.com
HISAT (hierarchical indexing for spliced alignment of transcripts) is a highly efficient system
for aligning reads from RNA sequencing experiments. HISAT uses an indexing scheme …

[HTML][HTML] TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

D Kim, G Pertea, C Trapnell, H Pimentel, R Kelley… - Genome biology, 2013 - Springer
TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this
paper, we describe TopHat2, which incorporates many significant enhancements to TopHat …

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

D Kim, JM Paggi, C Park, C Bennett… - Nature biotechnology, 2019 - nature.com
The human reference genome represents only a small number of individuals, which limits its
usefulness for genotyping. We present a method named HISAT2 (hierarchical indexing for …

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

C Trapnell, A Roberts, L Goff, G Pertea, D Kim… - Nature protocols, 2012 - nature.com
Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes
and splice variants and quantify expression genome-wide in a single assay. The volume …

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, 2016 - nature.com
High-throughput sequencing of mRNA (RNA-seq) has become the standard method for
measuring and comparing the levels of gene expression in a wide variety of species and …

[HTML][HTML] Beneficial Effects of Monascus sp. KCCM 10093 Pigments and Derivatives: A Mini Review

D Kim, S Ku - Molecules, 2018 - mdpi.com
The production of Monascus pigments and related byproducts, via microbial fermentation,
has been broadly utilized as coloring by traditional food industries and as a natural textile …

Centrifuge: rapid and sensitive classification of metagenomic sequences

D Kim, L Song, FP Breitwieser, SL Salzberg - Genome research, 2016 - genome.cshlp.org
Centrifuge is a novel microbial classification engine that enables rapid, accurate, and
sensitive labeling of reads and quantification of species on desktop computers. The system …

[HTML][HTML] TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

D Kim, SL Salzberg - Genome biology, 2011 - Springer
TopHat-Fusion is an algorithm designed to discover transcripts representing fusion gene
products, which result from the breakage and re-joining of two different chromosomes, or …

Biomaterials to model and measure epithelial cancers

P Beri, BF Matte, L Fattet, D Kim, J Yang… - Nature Reviews …, 2018 - nature.com
The use of biomaterials has substantially contributed to both our understanding of
tumorigenesis and our ability to identify and capture tumour cells in vitro and in vivo. Natural …