Javni dostop

HISAT: a fast spliced aligner with low memory requirements

D Kim, B Langmead, SL Salzberg

Nature methods 12 (4), 357-360, 2015

Zahteve: US National Institutes of Health

[HTML] springer.com

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

Zahteve: US National Institutes of Health

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

Zahteve: US National Institutes of Health

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

Zahteve: US National Institutes of Health, Cancer Prevention Research Institute of …

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

Zahteve: US National Science Foundation, US National Institutes of Health

[PDF] cshlp.org

Centrifuge: rapid and sensitive classification of metagenomic sequences

D Kim, L Song, FP Breitwieser, SL Salzberg

Genome research 26 (12), 1721-1729, 2016

Zahteve: US National Science Foundation, US National Institutes of Health

[PDF] springer.com

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

D Kim, SL Salzberg

Genome biology 12, 1-15, 2011

Zahteve: US National Institutes of Health

[HTML] cshlp.org

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

Zahteve: US National Institutes of Health, Cancer Prevention Research Institute of …

[HTML] cell.com

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

Zahteve: US National Institutes of Health

Hisat-genotype: Next generation genomic analysis platform on a personal computer

D Kim, JM Paggi, S Salzberg

BioRxiv, 266197, 2018

Zahteve: US National Institutes of Health

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

Zahteve: US National Institutes of Health

HISAT: hierarchical indexing for spliced alignment of transcripts

D Kim, B Langmead, SL Salzberg

BioRxiv, 012591, 2014

Zahteve: US National Institutes of Health

[PDF] google.com

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

Zahteve: Cancer Prevention Research Institute of Texas, USA

[PDF] wiley.com

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

Zahteve: US National Institutes of Health

[PDF] google.com

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

Zahteve: US National Institutes of Health, Cancer Prevention Research Institute of …

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

Zahteve: US National Institutes of Health, Cancer Prevention Research Institute of …